WorldWideScience

Sample records for inbred line mapping

  1. Variability among inbred lines and RFLP mapping of sunflower isozymes

    Directory of Open Access Journals (Sweden)

    Carrera Alicia D.

    2002-01-01

    Full Text Available Eight isozyme systems were used in this study: acid phosphatase (ACP, alcohol dehydrogenase (ADH, esterase (EST, glutamate dehydrogenase (GDH, malate dehydrogenase (MDH, phosphoglucoisomerase (PGI, 6-phosphogluconate dehydrogenase (PGD, and phosphoglucomutase (PGM. The polymorphism of these enzyme systems was studied in 25 elite inbred lines. A total of 19 loci were identified, but only eight of them were polymorphic in the germplasm tested. The polymorphic index for the eight informative markers ranged from 0.08 to 0.57, with a mean value of 0.36. Five isozyme loci were mapped in F2:3 populations with existing RFLP data. Est-1, Gdh-2 and Pgi-2 were mapped to linkage groups 3, 14 and 9, respectively. As in previous reports, an ACP locus and a PGD locus were found to be linked, both located in linkage group 2 of the public sunflower map.

  2. Quantitative Trait Loci in Inbred Lines

    NARCIS (Netherlands)

    Jansen, R.C.

    2001-01-01

    Quantitative traits result from the influence of multiple genes (quantitative trait loci) and environmental factors. Detecting and mapping the individual genes underlying such 'complex' traits is a difficult task. Fortunately, populations obtained from crosses between inbred lines are relatively

  3. QTL analysis of seed dormancy in Arabidopsis using recombinant inbred lines and MQM mapping

    NARCIS (Netherlands)

    Schaar, Wybe van der; Alonso-Blanco, Carlos; Léon-Kloosterziel, Karen M.; Jansen, Ritsert C.; Ooijen, Johan W. van; Koornneef, Maarten

    1997-01-01

    The genetic differences for seed germination between two commonly used Arabidopsis thaliana ecotypes Ler and Col, both showing a low level of seed dormancy, were investigated. The analysis was performed with 98 recombinant inbred lines (RILs) derived from the cross between the two ecotypes, and

  4. QTL mapping of fruit rot resistance to the plant pathogen Phytophthora capsici in a recombinant inbred line Capsicum annuum population.

    Science.gov (United States)

    Naegele, R P; Ashrafi, H; Hill, T A; Chin-Wo, S Reyes; Van Deynze, A E; Hausbeck, M K

    2014-05-01

    Phytophthora capsici is an important pepper (Capsicum annuum) pathogen causing fruit and root rot, and foliar blight in field and greenhouse production. Previously, an F6 recombinant inbred line population was evaluated for fruit rot susceptibility. Continuous variation among lines and partial and isolate-specific resistance were found. In this study, Phytophthora fruit rot resistance was mapped in the same F6 population between Criollo del Morelos 334 (CM334), a landrace from Mexico, and 'Early Jalapeno' using a high-density genetic map. Isolate-specific resistance was mapped independently in 63 of the lines evaluated and the two parents. Heritability of the resistance for each isolate at 3 and 5 days postinoculation (dpi) was high (h(2) = 0.63 to 0.68 and 0.74 to 0.83, respectively). Significant additive and epistatic quantitative trait loci (QTL) were identified for resistance to isolates OP97 and 13709 (3 and 5 dpi) and 12889 (3 dpi only). Mapping of fruit traits showed potential linkage with few disease resistance QTL. The partial fruit rot resistance from CM334 suggests that this may not be an ideal source for fruit rot resistance in pepper.

  5. Cluster Analysis of Maize Inbred Lines

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    Jiban Shrestha

    2016-12-01

    Full Text Available The determination of diversity among inbred lines is important for heterosis breeding. Sixty maize inbred lines were evaluated for their eight agro morphological traits during winter season of 2011 to analyze their genetic diversity. Clustering was done by average linkage method. The inbred lines were grouped into six clusters. Inbred lines grouped into Clusters II had taller plants with maximum number of leaves. The cluster III was characterized with shorter plants with minimum number of leaves. The inbred lines categorized into cluster V had early flowering whereas the group into cluster VI had late flowering time. The inbred lines grouped into the cluster III were characterized by higher value of anthesis silking interval (ASI and those of cluster VI had lower value of ASI. These results showed that the inbred lines having widely divergent clusters can be utilized in hybrid breeding programme.

  6. Genetic mapping of QTLs associated with seed macronutrients accumulation in 'MD96-5722' by 'Spencer' recombinant inbred lines of soybean

    Science.gov (United States)

    Research of genetic mapping of QTLs for macronutrient accumulation in soybean seed is limited. Therefore, the objective of this research was to identify QTLs related to macronutrients (N, C, S, P, K, Ca, and Mg) in seeds in 92 F5:7 recombinant inbred lines developed from a cross between MD 96-5722 (...

  7. Genetic dissection of maize plant architecture with an ultra-high density bin map based on recombinant inbred lines.

    Science.gov (United States)

    Zhou, Zhiqiang; Zhang, Chaoshu; Zhou, Yu; Hao, Zhuanfang; Wang, Zhenhua; Zeng, Xing; Di, Hong; Li, Mingshun; Zhang, Degui; Yong, Hongjun; Zhang, Shihuang; Weng, Jianfeng; Li, Xinhai

    2016-03-03

    Plant architecture attributes, such as plant height, ear height, and internode number, have played an important role in the historical increases in grain yield, lodging resistance, and biomass in maize (Zea mays L.). Analyzing the genetic basis of variation in plant architecture using high density QTL mapping will be of benefit for the breeding of maize for many traits. However, the low density of molecular markers in existing genetic maps has limited the efficiency and accuracy of QTL mapping. Genotyping by sequencing (GBS) is an improved strategy for addressing a complex genome via next-generation sequencing technology. GBS has been a powerful tool for SNP discovery and high-density genetic map construction. The creation of ultra-high density genetic maps using large populations of advanced recombinant inbred lines (RILs) is an efficient way to identify QTL for complex agronomic traits. A set of 314 RILs derived from inbreds Ye478 and Qi319 were generated and subjected to GBS. A total of 137,699,000 reads with an average of 357,376 reads per individual RIL were generated, which is equivalent to approximately 0.07-fold coverage of the maize B73 RefGen_V3 genome for each individual RIL. A high-density genetic map was constructed using 4183 bin markers (100-Kb intervals with no recombination events). The total genetic distance covered by the linkage map was 1545.65 cM and the average distance between adjacent markers was 0.37 cM with a physical distance of about 0.51 Mb. Our results demonstrated a relatively high degree of collinearity between the genetic map and the B73 reference genome. The quality and accuracy of the bin map for QTL detection was verified by the mapping of a known gene, pericarp color 1 (P1), which controls the color of the cob, with a high LOD value of 80.78 on chromosome 1. Using this high-density bin map, 35 QTL affecting plant architecture, including 14 for plant height, 14 for ear height, and seven for internode number were detected

  8. Genetic loci mapping for ear axis weight using recombinant inbred line

    African Journals Online (AJOL)

    Jane

    2011-08-08

    Aug 8, 2011 ... mays L.) ear-related traits were concentrated on yield per ... but the studies on using different N environments to map. QTL for .... ANOVA of the RIL population on EAW under two N regimes. ... (2007), but our study was different from theirs in many ... Mapping QTLs for grain yield and yield components under.

  9. QTL Mapping of Agronomic Waterlogging Tolerance Using Recombinant Inbred Lines Derived from Tropical Maize (Zea mays L) Germplasm

    Science.gov (United States)

    Zaidi, Pervez Haider; Rashid, Zerka; Vinayan, Madhumal Thayil; Almeida, Gustavo Dias; Phagna, Ramesh Kumar; Babu, Raman

    2015-01-01

    Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate

  10. Morphological variation in maize inbred lines

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    Jiban Shrestha

    2014-05-01

    Full Text Available In order to identify morphological variation in maize inbred lines, one hundred five inbred lines were planted under randomized complete block design with two replications at research field of National Maize Research Program, Rampur, Chitwan, Nepal during summer season (March to June, 2010. Descriptive statistics and cluster analysis were done. The results revealed a wide range of morphological variation among the tested inbred lines. The inbred lines grouped in cluster 4 namely PUTU-13, L-9, RL-105, RL-197, RL-103, RML-9, RML-41, RL-165, RL-36, RL-76, RL-125, RL-30-3, L-6, RL-107, RL-174, RL-41, L-13, RML-76 and L-5 had 0.833 days anthesis-silking interval and earlier in flowering (tasseling in 54.50 days and silking in 55.33 days. Moreover they consisted of 1.16 plant aspect, 1.25 ear aspect, 33.08 cm tassel length and 13.5 tassel branch number. Among tested lines, the above inbred lines had better morphological traits, so it was concluded that they were good candidates for development of hybrids and synthetic varieties. DOI: http://dx.doi.org/10.3126/ije.v3i2.10521 International Journal of the Environment Vol.3(2 2014: 98-107

  11. QTL mapping of combining ability and heterosis of agronomic traits in rice backcross recombinant inbred lines and hybrid crosses.

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    Zhen Qu

    Full Text Available BACKGROUND: Combining ability effects are very effective genetic parameters in deciding the next phase of breeding programs. Although some breeding strategies on the basis of evaluating combining ability have been utilized extensively in hybrid breeding, little is known about the genetic basis of combining ability. Combining ability is a complex trait that is controlled by polygenes. With the advent and development of molecular markers, it is feasible to evaluate the genetic bases of combining ability and heterosis of elite rice hybrids through QTL analysis. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we first developed a QTL-mapping method for dissecting combining ability and heterosis of agronomic traits. With three testcross populations and a BCRIL population in rice, biometric and QTL analyses were conducted for ten agronomic traits. The significance of general combining ability and special combining ability for most of the traits indicated the importance of both additive and non-additive effects on expression levels. A large number of additive effect QTLs associated with performance per se of BCRIL and general combining ability, and dominant effect QTLs associated with special combining ability and heterosis were identified for the ten traits. CONCLUSIONS/SIGNIFICANCE: The combining ability of agronomic traits could be analyzed by the QTL mapping method. The characteristics revealed by the QTLs for combining ability of agronomic traits were similar with those by multitudinous QTLs for agronomic traits with performance per se of BCRIL. Several QTLs (1-6 in this study were identified for each trait for combining ability. It demonstrated that some of the QTLs were pleiotropic or linked tightly with each other. The identification of QTLs responsible for combining ability and heterosis in the present study provides valuable information for dissecting genetic basis of combining ability.

  12. recombinant inbred lines intercropped with oat

    African Journals Online (AJOL)

    ADMIN

    The QTLs identified are stable for these characters and are located on ... number of seeds per ear, with better thousand kernel weight and grain yield ... to determine environmentally friendly way of barley lines to withstand oat .... The analysis of variance (ANOVA) was done .... yield components, multiple QTL mapping or.

  13. Registration of Wyandot × PI 567301B soybean recombinant inbred line population

    Science.gov (United States)

    A soybean [Glycine max (L.) Merr] mapping population (Reg. No., SNL MAP) consisting of 357 F7-derived recombinant inbred lines (RILs) was jointly developed by the USDA-Agricultural Research Service and the Ohio Agricultural Research and Development Center (OARDC) in Wooster, OH. The population was ...

  14. Studies on maize inbred lines susceptibility to herbicides

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    Stefanović Lidija

    2010-01-01

    Full Text Available This paper presents the analysis of results obtained during long- term studies on the response of maize inbred lines to herbicides. Under the agroecological conditions of Zemun Polje the response (reaction of maize inbred lines to herbicides of different classes was investigated. Biological tests were performed and some agronomic, morphological, physiological and biochemical parameters were determined when the response of maize inbred lines to herbicides was estimated. The use of active ingredients of herbicides from triazine, acetanilide, thiocarbamate to new chemical groups (sulfonylurea etc., have been resulted in changes in weed suppression and susceptibility of inbred lines. Obtained results show that effects of herbicides on susceptible maize genotypes can be different: they can slowdown the growth and development and affect the plant height; they can also affect the stages of the tassel and ear development and at the end they can reduced grain yield of the tested inbreds. Numerous studies confirmed the existence of differences in susceptibility level of maize genotypes in relation to herbicides. According to gained results the recommendations for growers are made on the possibility of the application of new herbicides in the hybrid seed production.

  15. Regeneration of Sudanese maize inbred lines and open pollinated ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-06-03

    Jun 3, 2008 ... Callus induction capacity was highest in inbred lines IL3, IL15 and IL1. The. Varieties Hudiba-2 and ... Maize plant regeneration can take place through two avenues, that is ..... regenerants were tussel ear formation and dwarfism. These abnormalities are typical of tissue-cultured cells, plants derived from ...

  16. Screening of recombinant inbred lines for salinity tolerance in bread ...

    African Journals Online (AJOL)

    Screening a large number of plants for salinity tolerance is not easy, therefore this investigation was performed to evaluate and screen 186 F8 recombinant inbred lines (RILs) derived from a cross between Superhead#2 (Super Seri) and Roshan wheat varieties for salinity tolerance. All the individuals were evaluated under ...

  17. Assessment of genetic variability of maize inbred lines and their ...

    African Journals Online (AJOL)

    Assessment of genetic variability of maize inbred lines and their hybrids under normal and drought conditions. ... Nigeria Agricultural Journal ... Analysis of variance revealed significant differences for most of the characters under study which indicates the presence of sufficient amount of variability offering ample scope for ...

  18. Genetic Analysis of Recombinant Inbred Lines for Sorghum bicolor ? Sorghum propinquum

    OpenAIRE

    Kong, Wenqian; Jin, Huizhe; Franks, Cleve D.; Kim, Changsoo; Bandopadhyay, Rajib; Rana, Mukesh K.; Auckland, Susan A.; Goff, Valorie H.; Rainville, Lisa K.; Burow, Gloria B.; Woodfin, Charles; Burke, John J.; Paterson, Andrew H.

    2013-01-01

    We describe a recombinant inbred line (RIL) population of 161 F5 genotypes for the widest euploid cross that can be made to cultivated sorghum (Sorghum bicolor) using conventional techniques, S. bicolor ? Sorghum propinquum, that segregates for many traits related to plant architecture, growth and development, reproduction, and life history. The genetic map of the S. bicolor ? S. propinquum RILs contains 141 loci on 10 linkage groups collectively spanning 773.1 cM. Although the genetic map ha...

  19. Evaluation of Drought Tolerance of Bread Wheat Recombinant Inbred Lines

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    N Zafar Naderi

    2014-10-01

    Full Text Available To evaluateresponse of bread wheat recombinant inbred lines to water deficit, a split plot experiment arranged in randomized complete block design (CRBD was conducted using eight recombinant inbred lines and their parental cultivars (Roshan and Super Head with three replications under three irrigation levels (80, 120 and 160 mm evaporation from class A pan at the Agriculture Research Station of Islamic Azad University, Tabriz Branch during 2009. The results of analysis of variance data collected revealed significant difference among lines and irrigation levels for grain yield. While line × irrigation level interaction was non significant for grain yield. Based on SSI and TOL, drought tolerance indices lines number 1, 7, 41 and Roshan cultivar under 120 mm evaporation, and lines number 7 and 19 under 160 mm evaporation were the tolerant lines. Under both stress conditions according to STI, MP and GMP indices, lines number 37, 38 and Roshan cultivar were recognized as the tolerant lines to water deficiet. Cluster analyses based on grain yield and drought tolerance indices recognized the lines number 1, 30, 32, 37, 38, 41 and Roshan cultivar under 120 mm and lines number 30, 37 and 38 and Roshan under 160 mm evaporation as the most drought tolerants and higher producers.

  20. Array-based genotyping and genetic dissimilarity analysis of a set of maize inbred lines belonging to different heterotic groups

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    Jambrović Antun

    2014-01-01

    Full Text Available Here we describe the results of the detailed array-based genotyping obtained by using the Illumina MaizeSNP50 BeadChip of eleven inbred lines belonging to different heterotic groups relevant for maize breeding in Southeast Europe - European Corn Belt. The objectives of this study were to assess the utility of the MaizeSNP50 BeadChip platform by determining its descriptive power and to assess genetic dissimilarity of the inbred lines. The distribution of the SNPs was found not completely uniform among chromosomes, but average call rate was very high (97.9% and number of polymorphic loci was 33200 out of 50074 SNPs with known mapping position indicating descriptive power of the MaizeSNP50 BeadChip. The dendrogram obtained from UPGMA cluster analysis as well as principal component analysis (PCA confirmed pedigree information, undoubtedly distinguishing lines according to their background in two population varieties of Reid Yellow Dent and Lancaster Sure Crop. Dissimilarity analysis showed that all of the inbred lines could be distinguished from each other. Whereas cluster analysis did not definitely differentiate Mo17 and Ohio inbred lines, PCA revealed clear genetic differences between them. The studied inbred lines were confirmed to be genetically diverse, representing a large proportion of the genetic variation occurring in two maize heterotic groups.

  1. Evaluation of Spring Wheat Recombinant Inbred Lines under Drought Stress

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    M. Moghaddaszadeh-Ahrabi

    2012-07-01

    Full Text Available Iran is one of arid and semi-arid regions of the world. Wheat as a strategic agricultural products faces water deficiency in most areas of the country. Therefore, identification of the resistant varieties to drought stress is one of main aims for breeders. To assess effect of drought stress at heading on 72 spring wheat recombinant inbred lines derived from American Yecora Rojo (high yielder, dwarf and early maturity as paternal parent and Iranian No. 49 line (tall and late maturiting as maternal parent cross were studied. The experiment was conducted at the Research Station of the University of Tabriz using a randomized complete block design with two replications during 2009 growing season. Based on the results from combined analysis of variance significant difference was observed among lines for all of traits studied, except for harvest index, grain number per spike and days to heading. There was significant difference between normal and drought stress conditions. Since the interaction between line and conditions was insignificant for all traits, it does therefore, provide the possibility of comparing the lines without regard to irrigation levels. Based on the means of, the traits it was found that the lines 96, 122, 123 and 155 were superior. MP, GMP and STI indices were recognized to be suitable indices to identify superior lines. With respect to these indices, lines 96, 122, 123, 138, 149 and 155 were found superior as compared with remaining lines. Based on stepwise regression analysis of grain yield with other traits, respectively grain number per spike, number of spikes/m2 and 1000 kernel weight were inserted into final model as effective variables on grain yield, which made 81/9 percent of the grain yield variation. Path analysis of grain yield and related traits, based on stepwise regression, demonstrated the significant positive direct effect for grain number per spike, number of spikes/m2 and 1000 kernel weight on grain yield

  2. Effective selection criteria for screening drought tolerant recombinant inbred lines of sunflower

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    Abdi Nishtman

    2013-01-01

    Full Text Available In this study, seventy two sunflower recombinant inbred lines were tested for their yielding ability under both water-stressed and well-watered states. The inbred lines were evaluated in a rectangular 8´9 lattice design with two replications in both well-watered and water-stressed conditions, separately. Eight drought tolerance indices including stability tolerance index (STI, mean productivity (MP, geometric mean productivity (GMP, harmonic mean (HM, stress susceptibility index (SSI, tolerance index (TOL, yield index (YI and yield stability index (YSI were calculated based on grain yield for every genotype. Results showed the highest values of mean productivity (MP index, geometric mean productivity (GMP, yield index (YI, harmonic mean (HM and stress tolerance index (STI indices for ‘C134a’ inbred line and least values of stress susceptibility index (SSI and tolerance (TOL for C61 inbred line. According to correlation of indices with yield performance under both drought stress and non-stress states and principle component analysis, indices including HM, MP, GMP and STI could properly distinguish drought tolerant sunflower inbred lines with high yield performance under both states. Cluster analysis of inbred lines using Ys, Yp and eight indices, categorized them into four groups including 19, 6, 26 and 19 inbred lines.

  3. A new set of BXD recombinant inbred lines from advanced intercross populations in mice

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    Gu Jing

    2004-04-01

    Full Text Available Abstract Background Recombinant inbred (RI strains are an important resource for mapping complex traits in many species. While large RI panels are available for Arabidopsis, maize, C. elegans, and Drosophila, mouse RI panels typically consist of fewer than 30 lines. This is a severe constraint on the power and precision of mapping efforts and greatly hampers analysis of epistatic interactions. Results In order to address these limitations and to provide the community with a more effective collaborative RI mapping panel we generated new BXD RI strains from two independent advanced intercrosses (AI between C57BL/6J (B6 and DBA/2J (D2 progenitor strains. Progeny were intercrossed for 9 to 14 generations before initiating inbreeding, which is still ongoing for some strains. Since this AI base population is highly recombinant, the 46 advanced recombinant inbred (ARI strains incorporate approximately twice as many recombinations as standard RI strains, a fraction of which are inevitably shared by descent. When combined with the existing BXD RI strains, the merged BXD strain set triples the number of previously available unique recombinations and quadruples the total number of recombinations in the BXD background. Conclusion The combined BXD strain set is the largest mouse RI mapping panel. It is a powerful tool for collaborative analysis of quantitative traits and gene function that will be especially useful to study variation in transcriptome and proteome data sets under multiple environments. Additional strains also extend the value of the extensive phenotypic characterization of the previously available strains. A final advantage of expanding the BXD strain set is that both progenitors have been sequenced, and approximately 1.8 million SNPs have been characterized. This provides unprecedented power in screening candidate genes and can reduce the effective length of QTL intervals. It also makes it possible to reverse standard mapping strategies and

  4. Inbreeding depression in maize populations and its effects on the obtention of promising inbred lines

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    Deoclecio Domingos Garbuglio

    2017-10-01

    Full Text Available Inbreeding can potentially be used for the development of inbred lines containing alleles of interest, but the genetic causes that control inbreeding depression are not completely known, and there are few studies found in the literature. The present study aimed to obtain estimates of inbreeding depression for eight traits in seven tropical maize populations, analyze the effects of inbreeding over generations and environments, and predict the behavior of inbred lines in future generation S? through linear regression methods. It was found that regardless of the base population used, prediction values could vary when the model was based on only 2 generations of inbreeding due to the environmental component. The influence of the environment in this type of study could be reduced when considering 3 generations of inbreeding, allowing greater precision in predicting the phenotypes of inbred lines. The use of linear regression was effective for inbred line prediction for the different agronomic traits evaluated. The use of 3 levels of inbreeding minimizes the effects of the environmental component in inbred line prediction for grain yield. GO-S was the most promising population for inbred line extraction.

  5. QTLs for agronomic traits in the Mediterranean environment identified in recombinant inbred lines of the cross 'Arta' × ¤H. spontaneum¤ 41-1

    DEFF Research Database (Denmark)

    Baum, M.; Grando, S.; Backes, G.

    2003-01-01

    A genetic linkage map has been developed for recombinant inbred lines (RILs) of the cross 'Arta' x Hordeum spontaneum 41-1. One hundred and ninety four RILs, randomly chosen from a population of 494 RILs, were mapped with 189 markers including one morphological trait (btr = brittle rachis locus...

  6. Forward Genetics by Sequencing EMS Variation-Induced Inbred Lines

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    Charles Addo-Quaye

    2017-02-01

    Full Text Available In order to leverage novel sequencing techniques for cloning genes in eukaryotic organisms with complex genomes, the false positive rate of variant discovery must be controlled for by experimental design and informatics. We sequenced five lines from three pedigrees of ethyl methanesulfonate (EMS-mutagenized Sorghum bicolor, including a pedigree segregating a recessive dwarf mutant. Comparing the sequences of the lines, we were able to identify and eliminate error-prone positions. One genomic region contained EMS mutant alleles in dwarfs that were homozygous reference sequences in wild-type siblings and heterozygous in segregating families. This region contained a single nonsynonymous change that cosegregated with dwarfism in a validation population and caused a premature stop codon in the Sorghum ortholog encoding the gibberellic acid (GA biosynthetic enzyme ent-kaurene oxidase. Application of exogenous GA rescued the mutant phenotype. Our method for mapping did not require outcrossing and introduced no segregation variance. This enables work when line crossing is complicated by life history, permitting gene discovery outside of genetic models. This inverts the historical approach of first using recombination to define a locus and then sequencing genes. Our formally identical approach first sequences all the genes and then seeks cosegregation with the trait. Mutagenized lines lacking obvious phenotypic alterations are available for an extension of this approach: mapping with a known marker set in a line that is phenotypically identical to starting material for EMS mutant generation.

  7. Caenorhabditis briggsae recombinant inbred line genotypes reveal inter-strain incompatibility and the evolution of recombination.

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    Joseph A Ross

    2011-07-01

    Full Text Available The nematode Caenorhabditis briggsae is an emerging model organism that allows evolutionary comparisons with C. elegans and exploration of its own unique biological attributes. To produce a high-resolution C. briggsae recombination map, recombinant inbred lines were generated from reciprocal crosses between two strains and genotyped at over 1,000 loci. A second set of recombinant inbred lines involving a third strain was also genotyped at lower resolution. The resulting recombination maps exhibit discrete domains of high and low recombination, as in C. elegans, indicating these are a general feature of Caenorhabditis species. The proportion of a chromosome's physical size occupied by the central, low-recombination domain is highly correlated between species. However, the C. briggsae intra-species comparison reveals striking variation in the distribution of recombination between domains. Hybrid lines made with the more divergent pair of strains also exhibit pervasive marker transmission ratio distortion, evidence of selection acting on hybrid genotypes. The strongest effect, on chromosome III, is explained by a developmental delay phenotype exhibited by some hybrid F2 animals. In addition, on chromosomes IV and V, cross direction-specific biases towards one parental genotype suggest the existence of cytonuclear epistatic interactions. These interactions are discussed in relation to surprising mitochondrial genome polymorphism in C. briggsae, evidence that the two strains diverged in allopatry, the potential for local adaptation, and the evolution of Dobzhansky-Muller incompatibilities. The genetic and genomic resources resulting from this work will support future efforts to understand inter-strain divergence as well as facilitate studies of gene function, natural variation, and the evolution of recombination in Caenorhabditis nematodes.

  8. The Genetic Basis of Plant Architecture in 10 Maize Recombinant Inbred Line Populations.

    Science.gov (United States)

    Pan, Qingchun; Xu, Yuancheng; Li, Kun; Peng, Yong; Zhan, Wei; Li, Wenqiang; Li, Lin; Yan, Jianbing

    2017-10-01

    Plant architecture is a key factor affecting planting density and grain yield in maize ( Zea mays ). However, the genetic mechanisms underlying plant architecture in diverse genetic backgrounds have not been fully addressed. Here, we performed a large-scale phenotyping of 10 plant architecture-related traits and dissected the genetic loci controlling these traits in 10 recombinant inbred line populations derived from 14 diverse genetic backgrounds. Nearly 800 quantitative trait loci (QTLs) with major and minor effects were identified as contributing to the phenotypic variation of plant architecture-related traits. Ninety-two percent of these QTLs were detected in only one population, confirming the diverse genetic backgrounds of the mapping populations and the prevalence of rare alleles in maize. The numbers and effects of QTLs are positively associated with the phenotypic variation in the population, which, in turn, correlates positively with parental phenotypic and genetic variations. A large proportion (38.5%) of QTLs was associated with at least two traits, suggestive of the frequent occurrence of pleiotropic loci or closely linked loci. Key developmental genes, which previously were shown to affect plant architecture in mutant studies, were found to colocalize with many QTLs. Five QTLs were further validated using the segregating populations developed from residual heterozygous lines present in the recombinant inbred line populations. Additionally, one new plant height QTL, qPH3 , has been fine-mapped to a 600-kb genomic region where three candidate genes are located. These results provide insights into the genetic mechanisms controlling plant architecture and will benefit the selection of ideal plant architecture in maize breeding. © 2017 American Society of Plant Biologists. All Rights Reserved.

  9. Analysis of genetic diversity among the maize inbred lines (Zea mays L. under heat stress condition

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    Manoj Kandel

    2017-12-01

    Full Text Available High temperature adversely affects the plant physiological processes: limits plant growth and reduction in grain yield. Heat stress is often encountered to spring sowing of maize in spring season. Twenty maize inbred lines were studied for days to 50 % anthesis and silking, anthesis–silking interval, leaf firing, tassel blast, SPAD reading and leaf senescence, plant and ear height, leaf area index, ear per plant, cob length and diameter, number of kernel/ear, number of kernel row/ear, number of kernel row, silk receptivity, shelling percentage, thousand kernel weight and grain yield in alpha lattice design at National Maize Research Program at Rampur, Chitwan,Nepal with the objective to identify superior heat stress tolerant lines. Analysis of variance showed significant difference for all the traits. Result of multivariable analysis revealed that twenty inbred lines formed four clusters. The resistance inbred lines and susceptible inbred lines formed different clusters. The members of cluster 4 were found to be tolerant to heat stress due to they had lowest value of tassel blast, leaf firing, and leaf area index with highest value of cob diameter and length, ear per plant, number of kernel row/ear, number of kernel/ear, number of kernel row, shelling percentage, silk receptivity and grain yield whereas as members of cluster 1were found most susceptible due to they had longer anthesis silking interval, with maximum tassel blast and leaf firing along with no grain yield under heat stress condition. From this study inbred lines RL-140, RML-76, RML-91 and RML-40 were found most tolerant to heat stress. These inbred lines belonging to superior cluster could be considered very useful in developing heat tolerant variety and other breeding activities.

  10. Estimation of genetic variability level in inbred CF1 mouse lines ...

    Indian Academy of Sciences (India)

    To estimate the genetic variability levels maintained by inbred lines selected for body weight and to compare them with a nonselected population from which the lines were derived, we calculated the per cent polymorphic loci (P) and marker diversity (MD) index from data on 43 putative loci of inter simple sequence repeats ...

  11. Identification of Single Nucleotide Polymorphisms and analysis of Linkage Disequilibrium in sunflower elite inbred lines using the candidate gene approach

    Directory of Open Access Journals (Sweden)

    Heinz Ruth A

    2008-01-01

    Full Text Available Abstract Background Association analysis is a powerful tool to identify gene loci that may contribute to phenotypic variation. This includes the estimation of nucleotide diversity, the assessment of linkage disequilibrium structure (LD and the evaluation of selection processes. Trait mapping by allele association requires a high-density map, which could be obtained by the addition of Single Nucleotide Polymorphisms (SNPs and short insertion and/or deletions (indels to SSR and AFLP genetic maps. Nucleotide diversity analysis of randomly selected candidate regions is a promising approach for the success of association analysis and fine mapping in the sunflower genome. Moreover, knowledge of the distance over which LD persists, in agronomically meaningful sunflower accessions, is important to establish the density of markers and the experimental design for association analysis. Results A set of 28 candidate genes related to biotic and abiotic stresses were studied in 19 sunflower inbred lines. A total of 14,348 bp of sequence alignment was analyzed per individual. In average, 1 SNP was found per 69 nucleotides and 38 indels were identified in the complete data set. The mean nucleotide polymorphism was moderate (θ = 0.0056, as expected for inbred materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88. Model-based population structure analysis allowed detection of admixed individuals within the set of accessions examined. Two putative gene pools were identified (G1 and G2, with a large proportion of the inbred lines being assigned to one of them (G1. Consistent with the absence of population sub-structuring, LD for G1 decayed more rapidly (r2 = 0.48 at 643 bp; trend line, pooled data than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance. Conclusion Knowledge about the patterns of diversity and the genetic relationships between breeding materials could be an invaluable aid in crop

  12. [Systematically induced effects of Tetranychus cinnabarinus infestation on chemical defense in Zea mays inbred lines].

    Science.gov (United States)

    Zhu, Yu-xi; Yang, Qun-fang; Huang, Yu-bi; Li, Qing

    2015-09-01

    In the present study, we investigated the systematically induced production of defense-related compounds, including DIMBOA, total phenol, trypsin inhibitors (TI) and chymotrypsin inhibitor (CI), by Tetranychus cinnabarinus infestation in Zea mays. The first leaves of two corn in-bred line seedlings, the mite-tolerant line ' H1014168' and the mite-sensitive line 'H1014591', were sucked by T. cinnabarinus adult female for seven days, and then the contents of DIMBOA, total phenol, TI and CI were measured in the second leaf and in the roots, respectively. Results showed that as compared to the unsucked control, all contents of DIMBOA, total phenol, TI and CI induced by T. cinnabarinus sucking were significantly higher in the second leaf of both inbred lines as well as in the roots of the mite-tolerant 'H1014168'. However, in the roots of 'H1014591', these defense compounds had different trends, where there was a higher induction of TI and a lower level of total phenol than that of the healthy control, while had almost no difference in DIMBOA and CI. These findings suggested that the infestation of T. cinnabarinus could systematically induce accumulation of defense-related compounds, and this effect was stronger in the mite-tolerant inbred line than in the mite-sensitive inbred line.

  13. Determination of the Heterotic groups of Maize inbred lines and the ...

    African Journals Online (AJOL)

    Maize weevil (Sitophilus zeamais Motschulsky) is a major maize (Zea mays L) storage insect pest in the tropics. Fifty-two inbred lines developed for weevil resistance were crossed to two testers, A and B, to determine their heterotic groups and inheritance of resistance to maize weevil. For 10 testcrosses selected for ...

  14. Genetic Analysis of Health-Related Secondary Metabolites in a Brassica rapa Recombinant Inbred Line Population

    NARCIS (Netherlands)

    Bagheri, H.; Soda, El M.; Kim, H.K.; Fritsche, S.; Jung, C.; Aarts, M.G.M.

    2013-01-01

    The genetic basis of the wide variation for nutritional traits in Brassica rapa is largely unknown. A new Recombinant Inbred Line (RIL) population was profiled using High Performance Liquid Chromatography (HPLC) and Nuclear Magnetic Resonance (NMR) analysis to detect quantitative trait loci (QTLs)

  15. The Combining Ability of Maize Inbred Lines for Grain Yield and ...

    African Journals Online (AJOL)

    The Combining Ability of Maize Inbred Lines for Grain Yield and Reaction to Grey ... East African Journal of Sciences ... (GLS) to maize production, the national maize research program of Ethiopia ... The information from this study will be useful for the development of high-yielding and GLS disease-resistant maize varieties.

  16. Identification of resistance to Maize rayado fino virus in maize inbred lines

    Science.gov (United States)

    Maize rayado fino virus (MRFV) is one of the most important virus diseases of maize in America. Severe yield losses, ranging from 10 to 50% in landraces to nearly 100% in contemporary cultivars, have been reported. Resistance has been reported in populations, but few inbred lines have been identifie...

  17. Analysis of the genetic diversity of super sweet corn inbred lines using SSR and SSAP markers.

    Science.gov (United States)

    Ko, W R; Sa, K J; Roy, N S; Choi, H-J; Lee, J K

    2016-01-22

    In this study, we compared the efficiency of simple sequence repeat (SSR) and sequence specific amplified polymorphism (SSAP) markers for analyzing genetic diversity, genetic relationships, and population structure of 87 super sweet corn inbred lines from different origins. SSR markers showed higher average gene diversity and Shannon's information index than SSAP markers. To assess genetic relationships and characterize inbred lines using SSR and SSAP markers, genetic similarity (GS) matrices were constructed. The dendrogram using SSR marker data showed a complex pattern with nine clusters and a GS of 53.0%. For SSAP markers, three clusters were observed with a GS of 50.8%. Results of combined marker data showed six clusters with 53.5% GS. To analyze the genetic population structure of SSR and SSAP marker data, the 87 inbred lines were divided into groups I, II, and admixed based on the membership probability threshold of 0.8. Using combined marker data, the population structure was K = 3 and was divided into groups I, II, III, and admixed. This study represents a comparative analysis of SSR and SSAP marker data for the study of genetic diversity and genetic relationships in super sweet corn inbred lines. Our results would be useful for maize-breeding programs in Korea.

  18. Demarcation of informative chromosomes in tropical sweet corn inbred lines using microsatellite DNA markers

    Directory of Open Access Journals (Sweden)

    Pedram Kashiani

    2012-01-01

    Full Text Available A study of genetic variation among 10 pairs of chromosomes extracted from 13 tropical sweet corn inbred lines, using 99 microsatellite markers, revealed a wide range of genetic diversity. Allelic richness and the number of effective alleles per chromosome ranged from 2.78 to 4.33 and 1.96 to 3.47, respectively, with respective mean values of 3.62 and 2.73. According to the Shannon's information index (I and Nei's gene diversity coefficient (Nei, Chromosome 10 was the most informative chromosome (I = 1.311 and Nei = 0.703, while Chromosome 2 possessed the least (I = 0.762 and Nei = 0.456. Based on linkage disequilibrium (LD measurements for loci less than 50 cM apart on the same chromosome, all loci on Chromosomes 1, 6 and 7 were in equilibrium. Even so, there was a high proportion of genetic variation in Chromosomes 4, 5, 8, 9 and 10, thereby revealing their appropriateness for use in the genetic diversity investigations among tropical sweet corn lines. Chromosome 4, with the highest number of loci in linkage disequilibrium, was considered the best for marker-phenotype association and QTL mapping, followed by Chromosomes 5, 8, 9 and 10.

  19. Genetic analysis of recombinant inbred lines for Sorghum bicolor × Sorghum propinquum.

    Science.gov (United States)

    Kong, Wenqian; Jin, Huizhe; Franks, Cleve D; Kim, Changsoo; Bandopadhyay, Rajib; Rana, Mukesh K; Auckland, Susan A; Goff, Valorie H; Rainville, Lisa K; Burow, Gloria B; Woodfin, Charles; Burke, John J; Paterson, Andrew H

    2013-01-01

    We describe a recombinant inbred line (RIL) population of 161 F5 genotypes for the widest euploid cross that can be made to cultivated sorghum (Sorghum bicolor) using conventional techniques, S. bicolor × Sorghum propinquum, that segregates for many traits related to plant architecture, growth and development, reproduction, and life history. The genetic map of the S. bicolor × S. propinquum RILs contains 141 loci on 10 linkage groups collectively spanning 773.1 cM. Although the genetic map has DNA marker density well-suited to quantitative trait loci mapping and samples most of the genome, our previous observations that sorghum pericentromeric heterochromatin is recalcitrant to recombination is highlighted by the finding that the vast majority of recombination in sorghum is concentrated in small regions of euchromatin that are distal to most chromosomes. The advancement of the RIL population in an environment to which the S. bicolor parent was well adapted (indeed bred for) but the S. propinquum parent was not largely eliminated an allele for short-day flowering that confounded many other traits, for example, permitting us to map new quantitative trait loci for flowering that previously eluded detection. Additional recombination that has accrued in the development of this RIL population also may have improved resolution of apices of heterozygote excess, accounting for their greater abundance in the F5 than the F2 generation. The S. bicolor × S. propinquum RIL population offers advantages over early-generation populations that will shed new light on genetic, environmental, and physiological/biochemical factors that regulate plant growth and development.

  20. Resistance Evaluation of Radish (Raphanus sativus L. Inbred Lines against Turnip mosaic virus

    Directory of Open Access Journals (Sweden)

    Ju-Yeon Yoon

    2017-03-01

    Full Text Available Leaves of twenties radish (Raphanus sativus L. inbred lines were mechanically inoculated with Turnip mosaic virus (TuMV strain HY to evaluate TuMV resistance of the radish inbred lines. The inoculated radish plants were incubated at 22°C±3°C and resistance assessment was examined using symptom development for 4 weeks. Based on the reactions of differential radish inbred lines, 16 radish lines were produced mild mosaic, mottling, mosaic and severe mosaic symptoms by TuMV infection. These results were confirmed by RT-PCR analysis of TuMV coat protein gene, suggesting that TuMV is responsible for the disease symptoms. Four resistant radish lines did not induce systemic mosaic symptoms on upper leaves and chlorosis in stem tissues for 4 weeks, showing they were symptomless by 8 weeks. Further examination of TuMV infection in the 4 radish lines showed no TuMV infection in all systemic leaves. These results suggest that the 4 radish lines are highly resistant to TuMV.

  1. Characterization and performance of 16 new inbred lines of lettuce

    Science.gov (United States)

    The Agricultural Research Service, U.S. Department of Agriculture announces the release of sixteen breeding lines of lettuce (Lactuca sativa L.). Five (SM13-I1, SM13-I2, SM13-I3, SM13-I4, and SM13-I5) of the six iceberg breeding lines can be used for whole head or salad blend production; the sixth i...

  2. Screening of inbred popcorn lines for tolerance to low phosphorus.

    Science.gov (United States)

    Santos, O J A P; Gonçalves, L S A; Scapim, C A; S M de Sousa, de; Castro, C R; Y Baba, V; de Oliveira, A L M

    2016-05-06

    Increasing phosphorus use efficiency in agriculture is essential for sustainable food production. Thus, the aims of this study were: i) to identify phosphorus use efficiency (PUE) in popcorn lines during the early plant stages, ii) to study the relationship between traits correlated with PUE, and iii) to analyze genetic diversity among lines. To accomplish this, 35 popcorn lines from Universidade Estadual de Maringá breeding program were studied. The experiment was conducted in a growth chamber using a nutrient solution containing two concentrations of phosphorus (P): 2.5 μM or low P (LP) and 250 μM or high P (HP). After 13 days in the nutrient solution, root morphology traits, shoot and root dry weight, and P content of the maize seedlings were measured. A deviance analysis showed there was a high level of genetic variability. An unweighted pair group method with arithmetic mean (UPGMA) clustering analysis identified three groups for the LP treatment (efficient, intermediate, and inefficient) and three groups for the HP treatment (responsive, moderately responsive, and unresponsive). The results of a principal component analysis and selection index were consistent with the UPGMA analysis, and lines 1, 2, 13, 17, 26, and 31 were classified as PUE.

  3. The application of protein markers in conversion of maize inbred lines to the cytoplasmic male sterility basis

    Directory of Open Access Journals (Sweden)

    Stevanovic Milan

    2016-01-01

    Full Text Available A total of seven maize inbred lines of different origin and maturity group were used in the trial set up according to the split-plot randomized complete block design in five environments. Each inbred was observed in five variants: original inbred (N; cytoplasmic male sterile C-type (CMS-C; restorer for CMS-C (RfC; cytoplasmic male sterile S-type (CMS-S and restorer for CMS-S (RfS. The objective was to compare grain yield of original inbreds and their CMS and Rf variants and to apply Isoelectric focusing (IEF to determine whether the conversion of original inbreds to their CMS and Rf counterparts have been done completely. Protein markers have shown that conversion of almost all inbreds was done good and completely. Only original inbreds ZPL2 and ZPL5 did not concur on banding patterns with their RfC variants. The type of cytoplasm had a very significant impact on grain yield. Namely, CMS-C counterparts significantly out yielded their CMS-S versions, while the inbreds with C and S cytoplasm over yielded inbreds with N cytoplasm, as well as their RfC and RfS versions.

  4. Maize forage aptitude: Combining ability of inbred lines and stability of hybrids

    Directory of Open Access Journals (Sweden)

    Luis Máximo Bertoia

    2014-12-01

    Full Text Available Breeding of forage maize should combine improvement achieved for grain with the specific needs of forage hybrids. Production stability is important when maize is used for silage if the planting area is not in the ideal agronomic environment. The objectives of the present research were: (i to quantify environmental and genetic and their interaction effects on maize silage traits; (ii to identify possible heterotic groups for forage aptitude and suggest the formation of potential heterotic patterns, and (iii to identify suitable inbred line combinations for producing hybrids with forage aptitude. Forty-five hybrids derived from diallelic crosses (without reciprocals among ten inbred lines of maize were evaluated in this study. Combined ANOVA over environments showed differences between genotypes (G, environments (E, and their interactions (GEI. Heritability (H2, and genotypic and phenotypic correlations were estimated to evaluate the variation in and relationships between forage traits. Postdictive and predictive AMMI models were fitted to determine the importance of each source of variation, G, E, and GEI, and to select genotypes simultaneously on yield, quality and stability. A predominance of additive effects was found in the evaluated traits. The heterotic pattern Reid-BSSS × Argentine flint was confirmed for ear yield (EY and harvest index (HI. High and broad genetic variation was found for stover and whole plant traits. Some inbred lines had genes with differential breeding aptitude for ear and stover. Stover and ear yield should be the main breeding objectives in maize forage breeding.

  5. Agronomic and molecular evaluation of maize inbred lines for drought tolerance

    International Nuclear Information System (INIS)

    Mikić, S.; Zorić, M.; Stanisavljević, D.; Kondić-Špika, A.; Brbaklić, L.; Kobiljski, B.; Nastasić, A.; Mitrović, B.; Šurlan-Momirović, G.

    2016-01-01

    Drought is a severe threat to maize yield stability in Serbia and other temperate Southeast European countries occurring occasionally but with significant yield losses. The development of resilient genotypes that perform well under drought is one of the main focuses of maize breeding programmes. To test the tolerance of newly developed elite maize inbred lines to drought stress, field trials for grain yield performance and anthesis silk interval (ASI) were set in drought stressed environments in 2011 and 2012. Inbred lines performing well under drought, clustered into a group with short ASI and a smaller group with long ASI, were considered as a potential source for tolerance. The former contained inbreds from different heterotic groups and with a proportion of local germplasm. The latter consisted of genotypes with mixed exotic and Lancaster germplasm, which performed better in more drought-affected environments. Three inbreds were selected for their potential drought tolerance, showing an above-average yield and small ASI in all environments. Association analysis indicated significant correlations between ASI and grain yield and three microsatellites (bnlg1525, bnlg238 and umc1025). Eight alleles were selected for their favourable concurrent effect on yield increase and ASI decrease. The proportion of phenotypic variation explained by the markers varied across environments from 5.7% to 22.4% and from 4.6% to 8.1% for ASI and yield, respectively. The alleles with strongest effect on performance of particular genotypes and their interactions in specific environments were identified by the mean of partial least square interactions analysis indicating potential suitability of the makers for tolerant genotype selection.

  6. Agronomic and molecular evaluation of maize inbred lines for drought tolerance

    Energy Technology Data Exchange (ETDEWEB)

    Mikić, S.; Zorić, M.; Stanisavljević, D.; Kondić-Špika, A.; Brbaklić, L.; Kobiljski, B.; Nastasić, A.; Mitrović, B.; Šurlan-Momirović, G.

    2016-07-01

    Drought is a severe threat to maize yield stability in Serbia and other temperate Southeast European countries occurring occasionally but with significant yield losses. The development of resilient genotypes that perform well under drought is one of the main focuses of maize breeding programmes. To test the tolerance of newly developed elite maize inbred lines to drought stress, field trials for grain yield performance and anthesis silk interval (ASI) were set in drought stressed environments in 2011 and 2012. Inbred lines performing well under drought, clustered into a group with short ASI and a smaller group with long ASI, were considered as a potential source for tolerance. The former contained inbreds from different heterotic groups and with a proportion of local germplasm. The latter consisted of genotypes with mixed exotic and Lancaster germplasm, which performed better in more drought-affected environments. Three inbreds were selected for their potential drought tolerance, showing an above-average yield and small ASI in all environments. Association analysis indicated significant correlations between ASI and grain yield and three microsatellites (bnlg1525, bnlg238 and umc1025). Eight alleles were selected for their favourable concurrent effect on yield increase and ASI decrease. The proportion of phenotypic variation explained by the markers varied across environments from 5.7% to 22.4% and from 4.6% to 8.1% for ASI and yield, respectively. The alleles with strongest effect on performance of particular genotypes and their interactions in specific environments were identified by the mean of partial least square interactions analysis indicating potential suitability of the makers for tolerant genotype selection.

  7. Nucleotide polymorphisms and haplotype diversity of RTCS gene in China elite maize inbred lines.

    Directory of Open Access Journals (Sweden)

    Enying Zhang

    Full Text Available The maize RTCS gene, encoding a LOB domain transcription factor, plays important roles in the initiation of embryonic seminal and postembryonic shoot-borne root. In this study, the genomic sequences of this gene in 73 China elite inbred lines, including 63 lines from 5 temperate heteroric groups and 10 tropic germplasms, were obtained, and the nucleotide polymorphisms and haplotype diversity were detected. A total of 63 sequence variants, including 44 SNPs and 19 indels, were identified at this locus, and most of them were found to be located in the regions of UTR and intron. The coding region of this gene in all tested inbred lines carried 14 haplotypes, which encoding 7 deferring RTCS proteins. Analysis of the polymorphism sites revealed that at least 6 recombination events have occurred. Among all 6 groups tested, only the P heterotic group had a much lower nucleotide diversity than the whole set, and selection analysis also revealed that only this group was under strong negative selection. However, the set of Huangzaosi and its derived lines possessed a higher nucleotide diversity than the whole set, and no selection signal were identified.

  8. Field screening of experimental corn hybrids and inbred lines for multiple ear-feeding insect resistance.

    Science.gov (United States)

    Ni, Xinzhi; Xu, Wenwei; Krakowsky, Matthew D; Buntin, G David; Brown, Steve L; Lee, R Dewey; Coy, Anton E

    2007-10-01

    Identifying and using native insect resistance genes is the core of integrated pest management. In this study, 10 experimental corn, Zea mays L., hybrids and 10 inbred lines were screened for resistance to major ear-feeding insects in the southeastern Coastal Plain region of the United States during 2004 and 2005. Ear-feeding insect damage was assessed at harvest by visual damage rating for the corn earworm, Helicoverpa zea (Boddie), and by the percentage of kernels damaged by the maize weevil, Sitophilus zeamais Motschulsky, and stink bugs [combination of Euschistus servus (Say) and southern green stink bug, Nezara viridula (L.)]. Among the eight inbred lines and two control populations examined, C3S1B73-5b was resistant to corn earworm, maize weevil, and stink bugs. In contrast, C3S1B73-4 was resistant to corn earworm and stink bugs, but not to maize weevil. In a similar manner, the corn hybrid S1W*CML343 was resistant to all three ear-feeding insects, whereas hybrid C3S1B73-3*Tx205 was resistant to corn earworm and maize weevil in both growing seasons, but susceptible to stink bugs in 2005. The silk-feeding bioassay showed that corn earworm developed better on corn silk than did fall armyworm. Among all phenotypic traits examined (i.e., corn ear size, husk extension, and husk tightness), only corn ear size was negatively correlated to corn earworm damage in the inbred lines examined, whereas only husk extension (i.e., coverage) was negatively correlated to both corn earworm and maize weevil damage on the experimental hybrids examined. Such information could be used to establish a baseline for developing agronomically elite corn germplasm that confers multiple ear-feeding insect resistance.

  9. Bike Map Lines

    Data.gov (United States)

    Town of Chapel Hill, North Carolina — Chapel Hill Bike Map Lines from KMZ file.This data came from the wiki comment board for the public, not an “official map” showing the Town of Chapel Hill's plans or...

  10. Salt-induced root protein profile changes in seedlings of maize inbred lines with differing salt tolerances

    Directory of Open Access Journals (Sweden)

    Yujing Cheng

    2014-12-01

    Full Text Available Salt stress is one of the severest growth limited-factors to agriculture production. To gain in-depth knowledge of salt-stress response mechanisms, the proteomics analysis from two maize (Zea mays L. inbred lines was carried out using two-dimensional gel electrophoresis (2-DGE and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF-MS. There were 57 salt-regulated proteins identified, 21 and 36 proteins were differentially regulated in inbred lines 'Nongda 1145' (salt-resistant and 'D340' (salt-sensitive, respectively. The identified proteins were distributed in 11 biological processes and seven molecular functions. Under salt stress, proteins related to antioxidation and lignin synthesis were increased in both inbred lines. The relative abundance of proteins involved in translation initiation, elongation, and protein proteolysis increased in 'Nongda 1145' and decreased in 'D340'. In addition, the abundance of proteins involved in carbohydrate metabolism, protein refolding, ATP synthase and transcription differed between the two inbred lines. Our results suggest that the enhanced ability of salt-tolerant inbred line 'Nongda 1145' to combat salt stress occurs via regulation of transcription factors promoting increased antioxidation and lignin biosynthesis, enhanced energy production, and acceleration of protein translation and protein proteolysis.

  11. Correlation and path analysis on main agronomic traits of progeny from space mutation maize inbred lines

    International Nuclear Information System (INIS)

    Zhang Caibo; Wu Zhangdong; Xu Wei; Rong Tingzhao; Cao Moju

    2013-01-01

    In order to discover and utilize the valuable resources from spaceflight mutagenesis maize offspring effectively, cross combinations derived from the offspring of three different maize inbred lines induced by space flight were made to investigate the yield and related agronomic traits under different environmental conditions. Correlation and path analysis indicated that the factors affecting the yield of combinations varied with different mutagenic materials and environmental effects with larger effect coming from environment. Therefore, different selection strategies should be chosen for different induced maize. For the 08-641 mutagenic material, the 100-kernel weight should be first considered to select while taking into account the number of rows per ear and kernels per row. For the RP125 mutagenic material, the kernels per row should be first selected, and then to select the 100-kernels weight and the number of rows per ear traits. For 18-599 mutagenic material, the 100-seed weight should be first selected, then the plant height, ear diameter, ear height, kernels rate and other traits should be selected in different environments. Combined with field resistance, plant types and other traits, excellent maize inbred lines with high yield potential from space mutagenesis offspring were selected. Thus study has obtained some breeding materials useful for further breeding purpose, and provide a reference method as how to use the spaceflight induced materials for for maize breeding. (authors)

  12. Comparative Cytotoxicity of the Herbicide Atrazine to Four Inbred Maize Lines (Zea mays L.)

    International Nuclear Information System (INIS)

    Shehata, Afaf I; AlGhethar, Haila A; AlHomaidan, Ali A; Arif, Ibrahim A

    2008-01-01

    Atrazine is one of the most widely used herbicides in the world. Recent reports have indicated that it has adverse impacts on the endocrine systems and on the early developments of wild animals and it has been banned in many European countries including Switzerland, the home of the manufacturing company. The genotoxic effects of Atrazine on four inbred lines of maize (Zea mays L.) were investigated. The herbicide showed mitoinhibition and clastogenic effects on the mitotic index of maize lines and they were proportional to the concentrations and time. The frequency of abnormality, chromosomal breakage, stickiness, lagging, C-metaphase and C-anaphase were observed at different stages of mitosis in treated cells. The harmful effect of this environmental pollutant proved that it may act as a strong mutagen. (author)

  13. Genetic analysis of morphological traits in a new, versatile, rapid-cycling Brassica rapa recombinant inbred line population

    Directory of Open Access Journals (Sweden)

    Hedayat eBagheri

    2012-08-01

    Full Text Available A recombinant inbred line (RIL population was produced based on a wide cross between the rapid-cycling and self-compatible genotypes L58, a Caixin vegetable type, and R-o-18, a yellow sarson oil type. A linkage map based on 160 F7 lines was constructed using 100 SNP, 130 AFLP®, 27 InDel and 13 publicly available SSR markers. The map covers a total length of 1150 cM with an average resolution of 4.3 cM/marker. To demonstrate the versatility of this new population, 17 traits, related to plant architecture and seed characteristics, were subjected to QTL analysis. A total of 47 QTLs were detected, each explaining between 6 to 54% of the total phenotypic variance for the concerned trait. The genetic analysis shows that this population is a useful new tool for analyzing genetic variation for interesting traits in B. rapa, and for further exploitation of the recent availability of the B. rapa whole genome sequence for gene cloning and gene function analysis.

  14. Evaluation of ear rot (Fusarium verticillioides resistance and fumonisin accumulation in Italian maize inbred lines

    Directory of Open Access Journals (Sweden)

    Carlotta BALCONI

    2014-05-01

    Full Text Available Mycotoxin contamination of maize (Zea mays L. grain is a global threat to the safety of both human food and animal feed. Hence, the development of maize genotypes with reduced mycotoxin accumulation in grain is of major importance. In order to find maize germplasm sources of resistance to Fusarium ear rot, 34 Italian and six public inbred lines were evaluated by means of artificial inoculation in field experiments during 2009 and 2010. Relationships between ear rot and fumonisin concentration in the ears were investigated. Primary ears were challenged with a mixture of two Fusarium verticillioides isolates from Northern Italy, through kernel inoculation, and ear rot severity was assessed.The average number of visibly infected kernels per ear, after inoculation, ranged from 2 to 68 in 2009 and from 0 to 120 in 2010. Fumonisin concentrations in the inoculated ears were greater than in the experimental controls for both years. Variability was found between the inbred lines: fumonisin accumulation ranged from 0.56 to 240.83 mg kg-1 in 2009 and from 1.09 to 190.60 mg kg-1 in 2010. In both years, six inbred lines showed high fumonisin content (≥100 mg kg-1, while the other genotypes were almost equally split into two groups, low (≤10 mg kg-1 and medium (from 11 to 100 mg kg-1 fumonisin content. The number of infected kernels after artificial inoculation correlated with fumonisin concentration both in 2009 (r = 0.94; P≤0.01 and 2010 (r = 0.67; P≤0.01. Additionally, the percentage of internally infected kernels correlated positively with fumonisin concentration (r = 0.37; P≤0.01 and with the number of infected kernels (r = 0.29; P≤0.05. This research has demonstrated that Italian maize germplasm is a valid source of resistance to Fusarium ear rot. Furthermore, there is a strong association of visible Fusarium symptoms with fumonisin concentration, suggesting that selection in maize for reduced visible moulds should reduce the risk of

  15. Artificial induction of third-stage dispersal juveniles of Bursaphelenchus xylophilus using newly established inbred lines.

    Directory of Open Access Journals (Sweden)

    Suguru E Tanaka

    Full Text Available The pine wood nematode, Bursaphelenchus xylophilus, is the causal agent of pine wilt disease. This nematode has two developmental forms in its life cycle; i.e., the propagative and dispersal forms. The former is the form that builds up its population inside the host pine. The latter is specialized for transport by the vector. This form is separated into two dispersal stages (third and fourth; the third-stage dispersal juvenile (JIII is specialized for survival under unfavorable conditions, whereas the fourth-stage juvenile (JIV, which is induced by a chemical signal from the carrier Monochamus beetle, is transported to new host pines and invades them. Because of its importance in the disease cycle, molecular and chemical aspects of the JIV have been investigated, while the mechanism of JIII induction has not been sufficiently investigated. In an effort to clarify the JIII induction process, we established inbred lines of B. xylophilus and compared their biological features. We found that the total number of nematodes (propagation proportion was negatively correlated with the JIII emergence proportion, likely because nematode development was arrested at JIII; i.e., they could not develop to adults via the reproductive stage. In addition, JIII induction seemed to be regulated by a small number of genes because the JIII induction proportion varied among inbred lines despite the high homozygosity of the parental line. We also demonstrated that JIII can be artificially induced by the nematode's secreted substances. This is the first report of artificial induction of JIII in B. xylophilus. The dauer (dispersal juvenile of the model organism Caenorhabditis elegans corresponds functionally to JIII of B. xylophilus, and this stage is known to be induced by a chemical signal referred to as daumone, derived from the nematodes' secretion. The artificial induction of JIII suggests the presence of daumone-like material in B. xylophilus.

  16. Carotenoid accumulation and carotenogenic gene expression during fruit development in novel interspecific inbred squash lines and their parents.

    Science.gov (United States)

    Nakkanong, Korakot; Yang, Jing Hua; Zhang, Ming Fang

    2012-06-13

    Carotenoid levels and composition during squash fruit development were compared in Cucurbita moschata , Cucurbita maxima , and two lines of their interspecific inbred lines, namely, Maxchata1 and Maxchata2. Eight genes associated with carotenoid biosynthesis were analyzed by quantitative RT-PCR. The two squash species and their interspecific inbred lines exhibited different qualitative and quantitative carotenoid profiles and regulatory mechanisms. C. moschata had the lowest total carotenoid content and mainly accumulated α-carotene and β-carotene, as expected in a fruit with pale-orange flesh. Low carotenoid content in this species was probably due to the comparatively low expression of all genes investigated, especially PSY1 gene, compared to the other squashes. The predominant carotenoids in C. maxima were violaxanthin and lutein, which produced a corresponding yellow flesh color in mature fruit. The relationship between the expression of the CHYB and ZEP genes may result in almost equal concentrations of violaxanthin and lutein in C. maxima at fruit ripening. In contrast, their interspecific inbred lines principally accumulated lutein and β-carotene, leading to orange flesh color. The PSY1 gene exhibited higher expression levels at earlier stages of fruit development in the Maxchata lines, potentially triggering the increased carotenoid accumulation seen in these fruits. Likewise, the higher transcription level of CHYB gene observed in the two interspecific inbred lines might be correlated with high lutein in these hybrids. However, this study could not explain the observed β-carotene accumulation on the basis of gene expression.

  17. Preliminary study on mutagenic effects of heavy ions irradiation on maize inbred lines

    International Nuclear Information System (INIS)

    Yu Lixia; Li Wenjian; Xie Hongmei; Chen Xuejun; Chen Jing

    2010-01-01

    In order to study mutagenic effects of different heavy ions irradiation on maize inbred lines,corn seeds of Zheng58, Lu9801, Jinxiang4C-1, CSR24001, 308 and 478 were irradiated with 12 C 6+ and 36 Ar 18+ ions. The experimental results showed that the germination rate and planting percent were different after irradiation. The wettish seeds had higher sensibility to heavy ion irradiation. The leaf type of the plant appeared visible changes in M 1 generation. In M 2 generation, great changes had taken place in economic traits, many of which are beneficial mutation. Some beneficia1 mutation could be stably inherited in M 3 generation. From the above, it can be predicted that heavy ions irradiation is an effective means of genetic improvement of maize. (authors)

  18. Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines

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    Antonio A. F. Garcia

    2004-01-01

    Full Text Available In order to compare their relative efficiencies as markers and to find the most suitable marker for maize diversity studies we evaluated 18 inbred tropical maize lines using a number of different loci as markers. The loci used were: 774 amplified fragment length polymorphisms (AFLPs; 262 random amplified polymorphic DNAs (RAPDs; 185 restriction fragment length polymorphisms (RFLPs; and 68 simple sequence repeats (SSR. For estimating genetic distance the AFLP and RFLP markers gave the most correlated results, with a correlation coefficient of r = 0.87. Bootstrap analysis were used to evaluate the number of loci for the markers and the coefficients of variation (CV revealed a skewed distribution. The dominant markers (AFLP and RAPD had small CV values indicating a skewed distribution while the codominant markers gave high CV values. The use of maximum values of genetic distance CVs within each sample size was efficient in determining the number of loci needed to obtain a maximum CV of 10%. The number of RFLP and AFLP loci used was enough to give CV values of below 5%, while the SSRs and RAPD loci gave higher CV values. Except for the RAPD markers, all the markers correlated genetic distance with single cross performance and heterosis which showed that they could be useful in predicting single cross performance and heterosis in intrapopulation crosses for broad-based populations. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationships among tropical maize inbred lines with high accuracy.

  19. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines

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    Smith Oscar

    2002-10-01

    Full Text Available Abstract Background Recent studies of ancestral maize populations indicate that linkage disequilibrium tends to dissipate rapidly, sometimes within 100 bp. We set out to examine the linkage disequilibrium and diversity in maize elite inbred lines, which have been subject to population bottlenecks and intense selection by breeders. Such population events are expected to increase the amount of linkage disequilibrium, but reduce diversity. The results of this study will inform the design of genetic association studies. Results We examined the frequency and distribution of DNA polymorphisms at 18 maize genes in 36 maize inbreds, chosen to represent most of the genetic diversity in U.S. elite maize breeding pool. The frequency of nucleotide changes is high, on average one polymorphism per 31 bp in non-coding regions and 1 polymorphism per 124 bp in coding regions. Insertions and deletions are frequent in non-coding regions (1 per 85 bp, but rare in coding regions. A small number (2–8 of distinct and highly diverse haplotypes can be distinguished at all loci examined. Within genes, SNP loci comprising the haplotypes are in linkage disequilibrium with each other. Conclusions No decline of linkage disequilibrium within a few hundred base pairs was found in the elite maize germplasm. This finding, as well as the small number of haplotypes, relative to neutral expectation, is consistent with the effects of breeding-induced bottlenecks and selection on the elite germplasm pool. The genetic distance between haplotypes is large, indicative of an ancient gene pool and of possible interspecific hybridization events in maize ancestry.

  20. Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains.

    Science.gov (United States)

    Zych, Konrad; Li, Yang; van der Velde, Joeri K; Joosen, Ronny V L; Ligterink, Wilco; Jansen, Ritsert C; Arends, Danny

    2015-02-19

    Genetic markers and maps are instrumental in quantitative trait locus (QTL) mapping in segregating populations. The resolution of QTL localization depends on the number of informative recombinations in the population and how well they are tagged by markers. Larger populations and denser marker maps are better for detecting and locating QTLs. Marker maps that are initially too sparse can be saturated or derived de novo from high-throughput omics data, (e.g. gene expression, protein or metabolite abundance). If these molecular phenotypes are affected by genetic variation due to a major QTL they will show a clear multimodal distribution. Using this information, phenotypes can be converted into genetic markers. The Pheno2Geno tool uses mixture modeling to select phenotypes and transform them into genetic markers suitable for construction and/or saturation of a genetic map. Pheno2Geno excludes candidate genetic markers that show evidence for multiple possibly epistatically interacting QTL and/or interaction with the environment, in order to provide a set of robust markers for follow-up QTL mapping. We demonstrate the use of Pheno2Geno on gene expression data of 370,000 probes in 148 A. thaliana recombinant inbred lines. Pheno2Geno is able to saturate the existing genetic map, decreasing the average distance between markers from 7.1 cM to 0.89 cM, close to the theoretical limit of 0.68 cM (with 148 individuals we expect a recombination every 100/148=0.68 cM); this pinpointed almost all of the informative recombinations in the population. The Pheno2Geno package makes use of genome-wide molecular profiling and provides a tool for high-throughput de novo map construction and saturation of existing genetic maps. Processing of the showcase dataset takes less than 30 minutes on an average desktop PC. Pheno2Geno improves QTL mapping results at no additional laboratory cost and with minimum computational effort. Its results are formatted for direct use in R/qtl, the leading R

  1. Functional Coding Variation in Recombinant Inbred Mouse Lines Reveals Novel Serotonin Transporter-Associated Phenotypes

    Energy Technology Data Exchange (ETDEWEB)

    Carneiro, Ana [Vanderbilt University; Airey, David [University of Tennessee Health Science Center, Memphis; Thompson, Brent [Vanderbilt University; Zhu, C [Vanderbilt University; Rinchik, Eugene M [ORNL; Lu, Lu [University of Tennessee Health Science Center, Memphis; Chesler, Elissa J [ORNL; Erikson, Keith [University of North Carolina; Blakely, Randy [Vanderbilt University

    2009-01-01

    The human serotonin (5-hydroxytryptamine, 5-HT) transporter (hSERT, SLC6A4) figures prominently in the etiology or treatment of many prevalent neurobehavioral disorders including anxiety, alcoholism, depression, autism and obsessive-compulsive disorder (OCD). Here we utilize naturally occurring polymorphisms in recombinant inbred (RI) lines to identify novel phenotypes associated with altered SERT function. The widely used mouse strain C57BL/6J, harbors a SERT haplotype defined by two nonsynonymous coding variants (Gly39 and Lys152 (GK)). At these positions, many other mouse lines, including DBA/2J, encode Glu39 and Arg152 (ER haplotype), assignments found also in hSERT. Synaptosomal 5-HT transport studies revealed reduced uptake associated with the GK variant. Heterologous expression studies confirmed a reduced SERT turnover rate for the GK variant. Experimental and in silico approaches using RI lines (C57Bl/6J X DBA/2J=BXD) identifies multiple anatomical, biochemical and behavioral phenotypes specifically impacted by GK/ER variation. Among our findings are multiple traits associated with anxiety and alcohol consumption, as well as of the control of dopamine (DA) signaling. Further bioinformatic analysis of BXD phenotypes, combined with biochemical evaluation of SERT knockout mice, nominates SERT-dependent 5-HT signaling as a major determinant of midbrain iron homeostasis that, in turn, dictates ironregulated DA phenotypes. Our studies provide a novel example of the power of coordinated in vitro, in vivo and in silico approaches using murine RI lines to elucidate and quantify the system-level impact of gene variation.

  2. Expression Profiling of Glucosinolate Biosynthetic Genes in Brassica oleracea L. var. capitata Inbred Lines Reveals Their Association with Glucosinolate Content

    Directory of Open Access Journals (Sweden)

    Arif Hasan Khan Robin

    2016-06-01

    Full Text Available Glucosinolates are the biochemical compounds that provide defense to plants against pathogens and herbivores. In this study, the relative expression level of 48 glucosinolate biosynthesis genes was explored in four morphologically-different cabbage inbred lines by qPCR analysis. The content of aliphatic and indolic glucosinolate molecules present in those cabbage lines was also estimated by HPLC analysis. The possible association between glucosinolate accumulation and related gene expression level was explored by principal component analysis (PCA. The genotype-dependent variation in the relative expression level of different aliphatic and indolic glucosinolate biosynthesis genes is the novel result of this study. A total of eight different types of glucosinolates, including five aliphatic and three indolic glucosinolates, was detected in four cabbage lines. Three inbred lines BN3383, BN4059 and BN4072 had no glucoraphanin, sinigrin and gluconapin detected, but the inbred line BN3273 had these three aliphatic glucosinolate compounds. PCA revealed that a higher expression level of ST5b genes and lower expression of GSL-OH was associated with the accumulation of these three aliphatic glucosinolate compounds. PCA further revealed that comparatively higher accumulation of neoglucobrassicin in the inbred line, BN4072, was associated with a high level of expression of MYB34 (Bol017062 and CYP81F1 genes. The Dof1 and IQD1 genes probably trans-activated the genes related to biosynthesis of glucoerucin and methoxyglucobrassicin for their comparatively higher accumulation in the BN4059 and BN4072 lines compared to the other two lines, BN3273 and BN3383. A comparatively higher progoitrin level in BN3273 was probably associated with the higher expression level of the GSL-OH gene. The cabbage inbred line BN3383 accounted for the significantly higher relative expression level for the 12 genes out of 48, but this line had comparatively lower total

  3. Strain screen and haplotype association mapping of wheel running in inbred mouse strains.

    Science.gov (United States)

    Lightfoot, J Timothy; Leamy, Larry; Pomp, Daniel; Turner, Michael J; Fodor, Anthony A; Knab, Amy; Bowen, Robert S; Ferguson, David; Moore-Harrison, Trudy; Hamilton, Alicia

    2010-09-01

    Previous genetic association studies of physical activity, in both animal and human models, have been limited in number of subjects and genetically homozygous strains used as well as number of genomic markers available for analysis. Expansion of the available mouse physical activity strain screens and the recently published dense single-nucleotide polymorphism (SNP) map of the mouse genome (approximately 8.3 million SNPs) and associated statistical methods allowed us to construct a more generalizable map of the quantitative trait loci (QTL) associated with physical activity. Specifically, we measured wheel running activity in male and female mice (average age 9 wk) in 41 inbred strains and used activity data from 38 of these strains in a haplotype association mapping analysis to determine QTL associated with activity. As seen previously, there was a large range of activity patterns among the strains, with the highest and lowest strains differing significantly in daily distance run (27.4-fold), duration of activity (23.6-fold), and speed (2.9-fold). On a daily basis, female mice ran further (24%), longer (13%), and faster (11%). Twelve QTL were identified, with three (on Chr. 12, 18, and 19) in both male and female mice, five specific to males, and four specific to females. Eight of the 12 QTL, including the 3 general QTL found for both sexes, fell into intergenic areas. The results of this study further support the findings of a moderate to high heritability of physical activity and add general genomic areas applicable to a large number of mouse strains that can be further mined for candidate genes associated with regulation of physical activity. Additionally, results suggest that potential genetic mechanisms arising from traditional noncoding regions of the genome may be involved in regulation of physical activity.

  4. Mapping genetic variants associated with beta-adrenergic responses in inbred mice.

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    Micha Hersch

    Full Text Available β-blockers and β-agonists are primarily used to treat cardiovascular diseases. Inter-individual variability in response to both drug classes is well recognized, yet the identity and relative contribution of the genetic players involved are poorly understood. This work is the first genome-wide association study (GWAS addressing the values and susceptibility of cardiovascular-related traits to a selective β(1-blocker, Atenolol (ate, and a β-agonist, Isoproterenol (iso. The phenotypic dataset consisted of 27 highly heritable traits, each measured across 22 inbred mouse strains and four pharmacological conditions. The genotypic panel comprised 79922 informative SNPs of the mouse HapMap resource. Associations were mapped by Efficient Mixed Model Association (EMMA, a method that corrects for the population structure and genetic relatedness of the various strains. A total of 205 separate genome-wide scans were analyzed. The most significant hits include three candidate loci related to cardiac and body weight, three loci for electrocardiographic (ECG values, two loci for the susceptibility of atrial weight index to iso, four loci for the susceptibility of systolic blood pressure (SBP to perturbations of the β-adrenergic system, and one locus for the responsiveness of QTc (p<10(-8. An additional 60 loci were suggestive for one or the other of the 27 traits, while 46 others were suggestive for one or the other drug effects (p<10(-6. Most hits tagged unexpected regions, yet at least two loci for the susceptibility of SBP to β-adrenergic drugs pointed at members of the hypothalamic-pituitary-thyroid axis. Loci for cardiac-related traits were preferentially enriched in genes expressed in the heart, while 23% of the testable loci were replicated with datasets of the Mouse Phenome Database (MPD. Altogether these data and validation tests indicate that the mapped loci are relevant to the traits and responses studied.

  5. Large-scale in silico mapping of complex quantitative traits in inbred mice.

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    Pengyuan Liu

    2007-07-01

    Full Text Available Understanding the genetic basis of common disease and disease-related quantitative traits will aid in the development of diagnostics and therapeutics. The processs of gene discovery can be sped up by rapid and effective integration of well-defined mouse genome and phenome data resources. We describe here an in silico gene-discovery strategy through genome-wide association (GWA scans in inbred mice with a wide range of genetic variation. We identified 937 quantitative trait loci (QTLs from a survey of 173 mouse phenotypes, which include models of human disease (atherosclerosis, cardiovascular disease, cancer and obesity as well as behavioral, hematological, immunological, metabolic, and neurological traits. 67% of QTLs were refined into genomic regions <0.5 Mb with approximately 40-fold increase in mapping precision as compared with classical linkage analysis. This makes for more efficient identification of the genes that underlie disease. We have identified two QTL genes, Adam12 and Cdh2, as causal genetic variants for atherogenic diet-induced obesity. Our findings demonstrate that GWA analysis in mice has the potential to resolve multiple tightly linked QTLs and achieve single-gene resolution. These high-resolution QTL data can serve as a primary resource for positional cloning and gene identification in the research community.

  6. Photosynthetic properties of erect leaf maize inbred lines as the efficient photo-model in breeding and seed production

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    Radenović Čedomir N.

    2003-01-01

    Full Text Available The initial idea of this study was a hypothesis that erect leaf maize inbred lines were characterized by properties of an efficient photo-model and that as such were very desirable in increasing the number of plants per area unit (plant density in the process of contemporary selection and seed production. The application of a non-invasive bioluminescence-photosynthetic method, suitable for the efficiency estimation of the photo-model, verified the hypothesis. Obtained photosynthetic properties of observed erect leaf maize inbred lines were based on the effects and characteristics of thermal processes of delayed chlorophyll fluorescence occurring in their thylakoid membranes. The temperature dependence of the delayed chlorophyll fluorescence intensity phase transitions (critical temperatures in the thylakoid membranes and activation energy are the principal parameters of the thermal processes. Based on obtained photosynthetic properties it is possible to select erect leaf maize inbred lines that are resistant and tolerant to high and very high temperatures, as well as, to drought. They could be good and efficient photo-models wherewith.

  7. Quantitative trait loci underlying resistance to sudden death syndrome (SDS) in MD96-5722 by 'Spencer' recombinant inbred line population of soybean.

    Science.gov (United States)

    Anderson, J; Akond, M; Kassem, M A; Meksem, K; Kantartzi, S K

    2015-04-01

    The best way to protect yield loss of soybean [Glycine max (L.) Merr.] due to sudden death syndrome (SDS), caused by Fusarium virguliforme (Aoki, O'Donnel, Homma & Lattanzi), is the development and use of resistant lines. Mapping quantitative trait loci (QTL) linked to SDS help developing resistant soybean germplasm through molecular marker-assisted selection strategy. QTL for SDS presented herein are from a high-density SNP-based genetic linkage map of MD 96-5722 (a.k.a 'Monocacy') by 'Spencer' recombinant inbred line using SoySNP6K Illumina Infinium BeadChip genotyping array. Ninety-four F 5:7 lines were evaluated for 2 years (2010 and 2011) at two locations (Carbondale and Valmeyer) in southern Illinois, USA to identify QTL controlling SDS resistance using disease index (DX). Composite interval mapping identified 19 SDS controlling QTL which were mapped on 11 separate linkage group (LG) or chromosomes (Chr) out of 20 LG or Chr of soybean genome. Many of these significant QTL identified in one environment/year were confirmed in another year or environment, which suggests a common genetic effects and modes of the pathogen. These new QTL are useful sources for SDS resistance studies in soybean breeding, complementing previously reported loci.

  8. Characterization of opaque2 modifier QTLs and candidate genes in recombinant inbred lines derived from the K0326Y quality protein maize inbred

    KAUST Repository

    Holding, David R.

    2010-11-13

    Quality protein maize (QPM) is a high lysine-containing corn that is based on genetic modification of the opaque2 (o2) mutant. In QPM, modifier genes convert the starchy endosperm of o2 to the vitreous phenotype of wild type maize. There are multiple, unlinked o2 modifier loci (Opm) in QPM and their nature and mode of action are unknown. We previously identified seven Opm QTLs and characterized 16 genes that are differentially up-regulated at a significant level in K0326Y QPM, compared to the starchy endosperm mutant W64Ao2. In order to further characterize these Opm QTLs and the genes up-regulated in K0326Y QPM, we created a population of 314 recombinant inbred lines (RILs) from a cross between K0326Y QPM and W64Ao2. The RILs were characterized for three traits associated with endosperm texture: vitreousness, density and hardness. Genetic linkage analysis of the RIL population confirmed three of the previously identified QTLs associated with o2 endosperm modification in K0326Y QPM. Many of the genes up-regulated in K0326Y QPM showed substantially higher levels of expression in vitreous compared with opaque RILs. These included genes associated with the upstream regulation of the ethylene response pathway, and a gene encoding a regulatory subunit of pyrophosphate-dependent fructose-6-phosphate 1-phosphotransferase, an adaptive enzyme of the glycolytic pathway. © 2010 Springer-Verlag.

  9. Study of Yield and Effective Traits in Bread Wheat Recombinant Inbred Lines (Triticum aestivum L. under Water Deficit Condition

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    S. Mohammad zadeh

    2013-11-01

    Full Text Available The effects some traits on seed yield of recombinant inbred lines of wheat under water deficit stress was studied. This research was done at the Agricultural Research Stations, Islamic Azad University, Tabriz Branch in 2010- 2011. 28 recombinant inbred lines of wheat bread with two parents (Norstar and Zagros in split plot experiment based on a randomized complete block design with three replications at two irrigation levels (70 and 140 mm evaporation from pan class A were studied. Analysis of variance indicated a significant genetic differences in all traits under study among the lines. Lines No. 32, 163 and 182 produced highest yield under both irrigation levels. Number of spikes, grains per spike and harvest index had the highest positive correlation with grain yield. Path analysis based on stepwise regression showed that under the normal irrigation conditions, number spike (0.556, number of grains per spike (0.278, weight of 1000 grain (0.259 and the drought stress number spike (0.430, straw yield (0.276 and peduncle length (0.323 had the most direct and positive effect on yield respectively.

  10. Sequence and ionomic analysis of divergent strains of maize inbred line B73 with an altered growth phenotype.

    Science.gov (United States)

    Mascher, Martin; Gerlach, Nina; Gahrtz, Manfred; Bucher, Marcel; Scholz, Uwe; Dresselhaus, Thomas

    2014-01-01

    Maize (Zea mays) is the most widely grown crop species in the world and a classical model organism for plant research. The completion of a high-quality reference genome sequence and the advent of high-throughput sequencing have greatly empowered re-sequencing studies in maize. In this study, plants of maize inbred line B73 descended from two different sets of seed material grown for several generations either in the field or in the greenhouse were found to show a different growth phenotype and ionome under phosphate starvation conditions and moreover a different responsiveness towards mycorrhizal fungi of the species Glomus intraradices (syn: Rhizophagus irregularis). Whole genome re-sequencing of individuals from both sets and comparison to the B73 reference sequence revealed three cryptic introgressions on chromosomes 1, 5 and 10 in the line grown in the greenhouse summing up to a total of 5,257 single-nucleotide polymorphisms (SNPs). Transcriptome sequencing of three individuals from each set lent further support to the location of the introgression intervals and confirmed them to be fixed in all sequenced individuals. Moreover, we identified >120 genes differentially expressed between the two B73 lines. We thus have found a nearly-isogenic line (NIL) of maize inbred line B73 that is characterized by an altered growth phenotype under phosphate starvation conditions and an improved responsiveness towards symbiosis with mycorrhizal fungi. Through next-generation sequencing of the genomes and transcriptomes we were able to delineate exact introgression intervals. Putative de novo mutations appeared approximately uniformly distributed along the ten maize chromosomes mainly representing G:C -> A:T transitions. The plant material described in this study will be a valuable tool both for functional studies of genes differentially expressed in both B73 lines and for research on growth behavior especially in response to symbiosis between maize and mycorrhizal fungi.

  11. Sequence and ionomic analysis of divergent strains of maize inbred line B73 with an altered growth phenotype.

    Directory of Open Access Journals (Sweden)

    Martin Mascher

    Full Text Available Maize (Zea mays is the most widely grown crop species in the world and a classical model organism for plant research. The completion of a high-quality reference genome sequence and the advent of high-throughput sequencing have greatly empowered re-sequencing studies in maize. In this study, plants of maize inbred line B73 descended from two different sets of seed material grown for several generations either in the field or in the greenhouse were found to show a different growth phenotype and ionome under phosphate starvation conditions and moreover a different responsiveness towards mycorrhizal fungi of the species Glomus intraradices (syn: Rhizophagus irregularis. Whole genome re-sequencing of individuals from both sets and comparison to the B73 reference sequence revealed three cryptic introgressions on chromosomes 1, 5 and 10 in the line grown in the greenhouse summing up to a total of 5,257 single-nucleotide polymorphisms (SNPs. Transcriptome sequencing of three individuals from each set lent further support to the location of the introgression intervals and confirmed them to be fixed in all sequenced individuals. Moreover, we identified >120 genes differentially expressed between the two B73 lines. We thus have found a nearly-isogenic line (NIL of maize inbred line B73 that is characterized by an altered growth phenotype under phosphate starvation conditions and an improved responsiveness towards symbiosis with mycorrhizal fungi. Through next-generation sequencing of the genomes and transcriptomes we were able to delineate exact introgression intervals. Putative de novo mutations appeared approximately uniformly distributed along the ten maize chromosomes mainly representing G:C -> A:T transitions. The plant material described in this study will be a valuable tool both for functional studies of genes differentially expressed in both B73 lines and for research on growth behavior especially in response to symbiosis between maize and

  12. Differential performance and parasitism of caterpillars on maize inbred lines with distinctly different herbivore-induced volatile emissions.

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    Thomas Degen

    Full Text Available Plant volatiles induced by insect feeding are known to attract natural enemies of the herbivores. Six maize inbred lines that showed distinctly different patterns of volatile emission in laboratory assays were planted in randomized plots in the Central Mexican Highlands to test their ability to recruit parasitic wasps under field conditions. The plants were artificially infested with neonate larvae of the fall armyworm Spodoptera frugiperda, and two of its main endoparasitoids, Campoletis sonorensis and Cotesia marginiventris, were released in the plots. Volatiles were collected from equally treated reference plants in the neighbourhood of the experimental field. The cumulative amount of 36 quantified volatile compounds determined for each line was in good accordance with findings from the laboratory; there was an almost 15-fold difference in total emission between the two extreme lines. We found significant differences among the lines with respect to the numbers of armyworms recovered from the plants, their average weight gain and parasitism rates. Average weight of the caterpillars was negatively correlated with the average total amount of volatiles released by the six inbred lines. However, neither total volatile emission nor any specific single compound within the blend could explain the differential parasitism rates among the lines, with the possible exception of (E-2-hexenal for Campoletis sonorensis and methyl salicylate for Cotesia marginiventris. Herbivore-induced plant volatiles and/or correlates thereof contribute to reducing insect damage of maize plants through direct plant defence and enhanced attraction of parasitoids, alleged indirect defence. The potential to exploit these volatiles for pest control deserves to be further evaluated.

  13. Evaluation of maize inbred lines for resistance to pre-harvest aflatoxin and fumonisin contamination in the field

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    Baozhu Guo

    2017-06-01

    Full Text Available Two important mycotoxins, aflatoxin and fumonisin, are among the most potent naturally occurring carcinogens, contaminating maize (Zea mays and affecting crop yield and quality. Resistance of maize to pre-harvest mycotoxin contamination, specifically aflatoxin produced by Aspergillus flavus and fumonisin produced by Fusarium verticillioides, is a goal in breeding programs that screen for these important traits with the aim of developing resistant commercial hybrids. We conducted two years of field evaluations on 87 inbred lines originating primarily in China and Mexico and not previously screened for resistance. The objectives of our study were to identify resistant germplasm for breeding purposes and to examine possible relationships between resistances to the two mycotoxins. Aflatoxin and fumonisin were present in samples harvested from all lines in both years. Concentrations of total aflatoxin ranged from 52.00 ± 20.00 to 1524.00 ± 396.00 μg kg−1, while those of fumonisin ranged from 0.60 ± 0.06 to 124.00 ± 19.50 mg kg−1. The inbred lines TUN15, TUN61, TUN37, CY2, and TUN49 showed the lowest aflatoxin accumulation and CN1, GT601, TUN09, TUN61, and MP717 the lowest fumonisin accumulation. TUN61 showed the lowest accumulation of both mycotoxins. This study confirmed previous observations that high levels of aflatoxin can coexist with fumonisin, with 55 maize lines showing a positive correlation coefficient between the concentrations of aflatoxin and fumonisin and 32 lines showing a negative correlation coefficient. These selected lines, particularly TUN61, may provide sources of resistance to mycotoxin contamination in breeding programs. However, the mechanism of resistance in this germplasm remains to be identified. Future research should also address factors that influence the fungus–plant interaction, such as herbivory and environmental stress.

  14. Identification of flowering-related genes responsible for differences in bolting time between two radish inbred lines

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    Hye Sun Cho

    2016-12-01

    Full Text Available Late bolting after cold exposure is an economically important characteristic of radish (Raphanus sativus L., an important Brassicaceae root vegetable crop. However, little information is available regarding the genes and pathways that govern flowering time in this species. We performed high-throughput RNA sequencing analysis to elucidate the molecular mechanisms that determine the differences in flowering times between two radish lines, NH-JS1 (late bolting and NH-JS2 (early bolting. In total, 71,188 unigenes were identified by reference-guided assembly, of which 309, 788, and 980 genes were differentially expressed between the two inbred lines after 0, 15, and 35 days of vernalization, respectively. Among these genes, 218 homologs of Arabidopsis flowering-time (Ft genes were identified in the radish, and 49 of these genes were differentially expressed between the two radish lines in the presence or absence of vernalization treatment. Most of the Ft genes up-regulated in NH-JS1 vs NH-JS2 were repressors of flowering, such as RsFLC, consistent with the late-bolting phenotype of NH-JS1. Although the functions of genes down-regulated in NH-JS1 were less consistent with late-bolting characteristics than the up-regulated Ft genes, several Ft enhancer genes, including RsSOC1, a key floral integrator, showed an appropriate expression to the late-bolting phenotype. In addition, the patterns of gene expression related to the vernalization pathway closely corresponded with the different bolting times of the two inbred lines. These results suggest that the vernalization pathway is conserved between radish and Arabidopsis.

  15. [Effect of selenium deficiency on the F344 inbred line offspring rats' neuro-behavior, ability of learning and memory].

    Science.gov (United States)

    Hong, Liang-Li; Tian, Dong-Ping; Su, Min; Shen, Xiu-Na; Gao, Yuxia

    2006-01-01

    To establish the selenium (Se) deficient animal model on F344 inbred line rats and observe the effects of a long-term Se-deficiency on the offspring's neuro-behavior, abilities of learning and memory. Feeding F344 inbred line rats on Se-deficient diet to establish Se-deficient animal model. For the offspring, the body weight, physiological indexes nervous reflections for growth and development were monitored during the early postnatal period. The Se-deficient diet contained less than 0.01 mg/kg and the glutathione peroxidase (GSH-Px) activity in blood of the Se-deficient group rats is lower than the Se-normal group after feeding on Se-deficient diet for 4 weeks. For the offspring, the birth weight and the body weight of Se-deficient group were obviously lower than the Se-normal group before weaning. Se-deficient offspring rats differed from Se-normal controls in lower scores in surface righting reflex (RR) test at postnatal 4th day after delivery, cliff avoidance test at postnatal 7th day and auditory acuity trial at postnatal 10th day respectively. But these differences disappear after a few days in the same tests. In addition, no significant differences between two groups in suspending test and walking ability test at postnatal 12th and 14th day. In open field test, Se-deficient male offspring stayed less time in the middle grid and moved less. In Morris water maze test, the Se-deficient offspring spent more time to find the hidden platform at the 6th and 9th training tests in the place navigation trial. Furthermore, the Se-deficient group spent less time in target quadrant when giving the spatial probe trial. A Se-deficient animal model have been established on F344 inbred line rats successfully. A long-term Se deficiency could retard the development of the offspring in uterus and after delivery. Se deficiency also decreased the offspring's abilities of spatial learning and memory in Morris water maze test and resulted in the male offspring's nervousness to new

  16. Effects of the time of application and the form of nitrogen on two maize inbred lines seed yield

    Directory of Open Access Journals (Sweden)

    Hojka Zdravko

    2005-01-01

    Full Text Available The study was carried out in the experimental filed of the Maize Research Institute, Zemun Polje, on calcareous chernozem in the period 2001-2003. The traits of two maize inbred lines (L1-FAO 400 and L2-FAO 600 were observed in dependence on the time of the nitrogen application (No-control without fertilizing; Nautumn - 60 kg P2O5 ha-1 and 60 kg K2O ha-1 applied in autumn (const + 100 kg N ha-1 (applied in autumn; Nspring - PK (const + 100 kg N ha-1 (applied in spring; N1/2 - PK (const + 100 kg N ha-1 (half of which was applied in autumn and the other half in spring; N1/2-PK (const 100 kg N ha-1 (1/3 of which was applied in autumn, 1/3 in spring and 1/3 through soil dressing; Nmin - PK (const + fertilizing in spring on the basis of the Nmin method, and forms of applied nitrogen: Urea (amide form KAN (ammonium-nitrate form and (NH42SO4 (ammonium form. The highest average yield was obtained by the use of Nmin method (3,486 kg ha-1, as well as, 100 kg N ha-1 applied in sprig (Nspring (3,337 kg ha-1, 100 kg N ha-1 applied in autumn and spring (N1/2 (3,020 kgha-1 and 100 kg N ha-1 applied in autumn, spring and soil dressing (N1/3 (3,005 kg ha-1 in the ammonium-nitrate form (KAN. The highest average seed yield of observed maize inbred lines (3,264 kg ha-1 was obtained by the application of ammonium-sulphate in the primary tillage (Nautumn. The use of the Nmin method (N ranging from 17 to 35 kg ha-1, in dependence on the soil mineral nitrogen content, especially in years with lower precipitation sums resulted in the highest increase in seed yield (39.2% of observed maize inbred lines in relation to the control.

  17. Identification and validation of quantitative trait loci for seed yield, oil and protein contents in two recombinant inbred line populations of soybean.

    Science.gov (United States)

    Wang, Xianzhi; Jiang, Guo-Liang; Green, Marci; Scott, Roy A; Song, Qijian; Hyten, David L; Cregan, Perry B

    2014-10-01

    Soybean seeds contain high levels of oil and protein, and are the important sources of vegetable oil and plant protein for human consumption and livestock feed. Increased seed yield, oil and protein contents are the main objectives of soybean breeding. The objectives of this study were to identify and validate quantitative trait loci (QTLs) associated with seed yield, oil and protein contents in two recombinant inbred line populations, and to evaluate the consistency of QTLs across different environments, studies and genetic backgrounds. Both the mapping population (SD02-4-59 × A02-381100) and validation population (SD02-911 × SD00-1501) were phenotyped for the three traits in multiple environments. Genetic analysis indicated that oil and protein contents showed high heritabilities while yield exhibited a lower heritability in both populations. Based on a linkage map constructed previously with the mapping population and using composite interval mapping and/or interval mapping analysis, 12 QTLs for seed yield, 16 QTLs for oil content and 11 QTLs for protein content were consistently detected in multiple environments and/or the average data over all environments. Of the QTLs detected in the mapping population, five QTLs for seed yield, eight QTLs for oil content and five QTLs for protein content were confirmed in the validation population by single marker analysis in at least one environment and the average data and by ANOVA over all environments. Eight of these validated QTLs were newly identified. Compared with the other studies, seven QTLs for seed yield, eight QTLs for oil content and nine QTLs for protein content further verified the previously reported QTLs. These QTLs will be useful for breeding higher yield and better quality cultivars, and help effectively and efficiently improve yield potential and nutritional quality in soybean.

  18. [Expression and distribution of xenoantigen alpha-Gal in intervertebral disk of Chinese banna minipig inbred line].

    Science.gov (United States)

    Shou, Jian-guo; Mi, Jian-hong; Ying, Da-jun

    2002-09-01

    To investigate the expression and distribution of xenoantigen in intervertebral disk of Chinese banna minipig inbred line, and to study the availability of xenograft transplantation of intervertebral disk. Samples of intervertebral disk were collected from six Banna pigs of 8 to 11-month-old. The fixation, embedment and slice were performed. alpha-Gal specific binding lection (BSI-B4) were used as affinity reagents and affinity-immunohistochemistry assays (SABC methods and DAB stain) were conducted to detect the expression and distribution of xenoantigen (alpha-Gal). alpha-Gal was found in chondrocyte cell and chondrocyte-like cell in intervertebral disk which have the positive yellow-stained particulate aggradation. There was no stain in the matrix, elastic fiber and collagen fiber. The distribution of xenoantigen is locally in the tissue of intervertebral disk and its expression is weak. This suggests that the intervertebral disk of Banna pig may be alternative donor for xenotransplantation.

  19. Identification of candidate genes associated with cell wall digestibility and eQTL (expression quantitative trait loci analysis in a Flint × Flint maize recombinant inbred line population

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    Wenzel Gerhard

    2007-01-01

    Full Text Available Abstract Background Cell-wall digestibility is the major target for improving the feeding value of forage maize. An understanding of the molecular basis for cell-wall digestibility is crucial towards breeding of highly digestible maize. Results 865 candidate ESTs for cell-wall digestibility were selected according to the analysis of expression profiles in 1 three sets of brown-midrib isogenic lines in the genetic background of inbreds 1332 (1332 and 1332 bm3, 5361 (5361 and 5361 bm3, and F2 (F2, F2 bm1, F2 bm2, and F2 bm3, 2 the contrasting extreme lines of FD (Flint × Dent, AS08 × AS 06, DD1 (Dent × Dent, AS11 × AS09, and DD2 (Dent × Dent, AS29 × AS30 mapping populations, and 3 two contrasting isogenic inbreds, AS20 and AS21. Out of those, 439 ESTs were assembled on our "Forage Quality Array", a small microarray specific for cell wall digestibility related experiments. Transcript profiles of 40 lines of a Flint × Flint population were monitored using the Forage Quality Array, which were contrasting for cell wall digestibility. Using t-tests (p Conclusion 102 candidate genes for cell-wall digestibility were validated by genetical genomics approach. Although the cDNA array highlights gene types (the tested gene and any close family members, trans-acting factors or metabolic bottlenecks seem to play the major role in controlling heritable variation of gene expression related to cell-wall digestibility, since no in silico mapped ESTs were in the same location as their own eQTL. Transcriptional variation was generally found to be oligogenic rather than monogenic inherited due to only 26% ESTs detected a single eQTL in the present study. One eQTL hotspot was co-localized with cell wall digestibility related QTL cluster on bins 3.05, implying that in this case the gene(s underlying QTL and eQTL are identical. As the field of genetical genomics develops, it is expected to significantly improve our knowledge about complex traits, such as cell

  20. An inbred line of the diploid strawberry Fragaria vesca f. semperflorens for genomic and molecular genetic studies in the Rosaceae.

    Science.gov (United States)

    Slovin, Janet P; Schmitt, Kyle; Folta, Kevin M

    2009-10-31

    The diploid woodland strawberry (Fragaria vesca) is an attractive system for functional genomics studies. Its small stature, fast regeneration time, efficient transformability and small genome size, together with substantial EST and genomic sequence resources make it an ideal reference plant for Fragaria and other herbaceous perennials. Most importantly, this species shares gene sequence similarity and genomic microcolinearity with other members of the Rosaceae family, including large-statured tree crops (such as apple, peach and cherry), and brambles and roses as well as with the cultivated octoploid strawberry, F. xananassa. F. vesca may be used to quickly address questions of gene function relevant to these valuable crop species. Although some F. vesca lines have been shown to be substantially homozygous, in our hands plants in purportedly homozygous populations exhibited a range of morphological and physiological variation, confounding phenotypic analyses. We also found the genotype of a named variety, thought to be well-characterized and even sold commercially, to be in question. An easy to grow, standardized, inbred diploid Fragaria line with documented genotype that is available to all members of the research community will facilitate comparison of results among laboratories and provide the research community with a necessary tool for functionally testing the large amount of sequence data that will soon be available for peach, apple, and strawberry. A highly inbred line, YW5AF7, of a diploid strawberry Fragaria vesca f. semperflorens line called "Yellow Wonder" (Y2) was developed and examined. Botanical descriptors were assessed for morphological characterization of this genotype. The plant line was found to be rapidly transformable using established techniques and media formulations. The development of the documented YW5AF7 line provides an important tool for Rosaceae functional genomic analyses. These day-neutral plants have a small genome, a seed to seed

  1. An inbred line of the diploid strawberry Fragaria vesca f. semperflorens for genomic and molecular genetic studies in the Rosaceae

    Directory of Open Access Journals (Sweden)

    Folta Kevin M

    2009-10-01

    Full Text Available Abstract Background The diploid woodland strawberry (Fragaria vesca is an attractive system for functional genomics studies. Its small stature, fast regeneration time, efficient transformability and small genome size, together with substantial EST and genomic sequence resources make it an ideal reference plant for Fragaria and other herbaceous perennials. Most importantly, this species shares gene sequence similarity and genomic microcolinearity with other members of the Rosaceae family, including large-statured tree crops (such as apple, peach and cherry, and brambles and roses as well as with the cultivated octoploid strawberry, F. ×ananassa. F. vesca may be used to quickly address questions of gene function relevant to these valuable crop species. Although some F. vesca lines have been shown to be substantially homozygous, in our hands plants in purportedly homozygous populations exhibited a range of morphological and physiological variation, confounding phenotypic analyses. We also found the genotype of a named variety, thought to be well-characterized and even sold commercially, to be in question. An easy to grow, standardized, inbred diploid Fragaria line with documented genotype that is available to all members of the research community will facilitate comparison of results among laboratories and provide the research community with a necessary tool for functionally testing the large amount of sequence data that will soon be available for peach, apple, and strawberry. Results A highly inbred line, YW5AF7, of a diploid strawberry Fragaria vesca f. semperflorens line called "Yellow Wonder" (Y2 was developed and examined. Botanical descriptors were assessed for morphological characterization of this genotype. The plant line was found to be rapidly transformable using established techniques and media formulations. Conclusion The development of the documented YW5AF7 line provides an important tool for Rosaceae functional genomic analyses

  2. Identification of multiple ear-colonizing insect and disease resistance in CIMMYT maize inbred lines with varying levels of silk maysin.

    Science.gov (United States)

    Ni, Xinzhi; Krakowsky, Matthew D; Buntin, G David; Rector, Brian G; Guo, Baozhu; Snook, Maurice E

    2008-08-01

    Ninety four corn inbred lines selected from International Center for the Improvement of Maize and Wheat (CIMMYT) in Mexico were evaluated for levels of silk maysin in 2001 and 2002. Damage by major ear-feeding insects [i.e., corn earworm, Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae); maize weevil, Sitophilus zeamais (Motschulsky) (Coleoptera: Curculionidae); brown stink bug, Euschistus servus (Say); southern green stink bugs, Nezara viridula (L.) (Heteroptera: Pentatomidae)], and common smut [Ustilago maydis DC (Corda)] infection on these inbred lines were evaluated in 2005 and 2006 under subtropical conditions at Tifton, GA. Ten inbred lines possessing good agronomic traits were also resistant to the corn earworm. The correlation between ear-feeding insect damage or smut infection and three phenotypic traits (silk maysin level, husk extension, and husk tightness of corn ears) was also examined. Corn earworm and stink bug damage was negatively correlated to husk extension, but not to either silk maysin levels or husk tightness. In combination with the best agronomic trait ratings that show the least corn earworm and stink bug damage, lowest smut infection rate, and good insect-resistant phenotypic traits (i.e., high maysin and good husk coverage and husk tightness), 10 best inbred lines (CML90, CML92, CML94, CML99, CML104, CML108, CML114, CML128, CML137, and CML373) were identified from the 94 lines examined. These selected inbred lines will be used for further examination of their resistance mechanisms and development of new corn germplasm that confers multiple ear-colonizing pest resistance.

  3. Identification of quantitative trait Loci for resistance to southern leaf blight and days to anthesis in a maize recombinant inbred line population.

    Science.gov (United States)

    Balint-Kurti, P J; Krakowsky, M D; Jines, M P; Robertson, L A; Molnár, T L; Goodman, M M; Holl, J B

    2006-10-01

    ABSTRACT A recombinant inbred line population derived from a cross between the maize lines NC300 (resistant) and B104 (susceptible) was evaluated for resistance to southern leaf blight (SLB) disease caused by Cochliobolus heterostrophus race O and for days to anthesis in four environments (Clayton, NC, and Tifton, GA, in both 2004 and 2005). Entry mean and average genetic correlations between disease ratings in different environments were high (0.78 to 0.89 and 0.9, respectively) and the overall entry mean heritability for SLB resistance was 0.89. When weighted mean disease ratings were fitted to a model using multiple interval mapping, seven potential quantitative trait loci (QTL) were identified, the two strongest being on chromosomes 3 (bin 3.04) and 9 (bin 9.03-9.04). These QTL explained a combined 80% of the phenotypic variation for SLB resistance. Some time-point-specific SLB resistance QTL were also identified. There was no significant correlation between disease resistance and days to anthesis. Six putative QTL for time to anthesis were identified, none of which coincided with any SLB resistance QTL.

  4. Genetic determination of the biological radiation response in inbred mice lines; Genetische Determination der biologischen Strahlenantwort in Mausinzuchtstaemmen

    Energy Technology Data Exchange (ETDEWEB)

    Gomolka, M.; Hornhardt, S.; Jung, T. [Bundesamt fuer Strahlenschutz Oberschleissheim (Germany). Institut fuer Strahlenhygiene

    2000-07-01

    Variation in radiation sensitivity and radiation resistance is influenced by the genetic constitution of an individual. Loss of function of genes involved in DNA repair, cell cycle or controlled cell death can have serious consequences on individual radiation sensitivity. For example, individuals suffering on the clinical syndrome of Ataxia telangiectasia exhibit radiation sensitivity in the order of 2-3 magnitudes higher than other cancer patients. For radiation protection it is important to clarify the role of genetic predisposition for radiation sensitivity in clinical healthy people. Therefore, data were collected from the literature describing the genetic variation (heritability) of radiation sensitivity in the mouse model. A heritability of 30-50% was calculated for 27 inbred mice lines by Roderick (1963) based on days of survival after a daily dose of 1 Gy {gamma}-irradiation. The following inbred lines were described in the literature as radiation sensitive (phenotypical markers were e.g., time of survival, mortality, reduction in fertility post exposure): SWR, RIII, NC, K, HLG, DBA, CBA, BALB/c, A, AKR. Radiation resistance was demonstrated in SJL, SEC, RF, MA, C58, C57BR, BDP and 129. Parameter of longevity, some physiological, biochemical and immunological parameters as given in the data bank of the Jackson Laboratory, U.S.A., were compared between radiation sensitive and radiation resistant inbred strains. No correlation was seen for the most of the parameters except for the development of breast cancer. In 6 out of 10 radiosensitive inbred strains breast cancer is described while only 1 of 8 strains exhibits breast cancer. The higher heritability of 30-50% in spite of a very complex phenotype like survival and the correlation between radiosensitivity and tumour incidence show that individual genetic susceptibility is important on the biological radiation reaction. (orig.) [German] Die phaenotypische Variation der Strahlensensitivitaet und

  5. Comparison of whole-genome prediction models for traits with contrasting genetic architecture in a diversity panel of maize inbred lines

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    Riedelsheimer Christian

    2012-09-01

    Full Text Available Abstract Background There is increasing empirical evidence that whole-genome prediction (WGP is a powerful tool for predicting line and hybrid performance in maize. However, there is a lack of knowledge about the sensitivity of WGP models towards the genetic architecture of the trait. Whereas previous studies exclusively focused on highly polygenic traits, important agronomic traits such as disease resistances, nutrifunctional or climate adaptational traits have a genetic architecture which is either much less complex or unknown. For such cases, information about model robustness and guidelines for model selection are lacking. Here, we compared five WGP models with different assumptions about the distribution of the underlying genetic effects. As contrasting model traits, we chose three highly polygenic agronomic traits and three metabolites each with a major QTL explaining 22 to 30% of the genetic variance in a panel of 289 diverse maize inbred lines genotyped with 56,110 SNPs. Results We found the five WGP models to be remarkable robust towards trait architecture with the largest differences in prediction accuracies ranging between 0.05 and 0.14 for the same trait, most likely as the result of the high level of linkage disequilibrium prevailing in elite maize germplasm. Whereas RR-BLUP performed best for the agronomic traits, it was inferior to LASSO or elastic net for the three metabolites. We found the approach of genome partitioning of genetic variance, first applied in human genetics, as useful in guiding the breeder which model to choose, if prior knowledge of the trait architecture is lacking. Conclusions Our results suggest that in diverse germplasm of elite maize inbred lines with a high level of LD, WGP models differ only slightly in their accuracies, irrespective of the number and effects of QTL found in previous linkage or association mapping studies. However, small gains in prediction accuracies can be achieved if the WGP model is

  6. Impacts of irrigation and genotype on yield, protein, starch and oil contents in grain of maize inbred lines

    Directory of Open Access Journals (Sweden)

    Josipovic Marko

    2014-01-01

    Full Text Available Four inbred lines of maize (Os 438-95 = C1, Os 30-8 = C2, Os 6 = C3 and Os 1-44 =C4 were grown for 4-year period (2006-2009 in the stationary field experiment on Osijek eutric cambisol. Impact of irrigation, nitrogen fertilization and genotype were tested. Soil moisture was maintained by two irrigation rates from 60-100% and 80-100% of the field water capacity. Two steps of N (0, 100 and 200 kg N ha-1 were applied, while P and K fertilization was equal (500 kg/ha NPK 0:30:20. Eight maize genotypes (four inbred lines and four hybrids were grown on each basic plot of fertilization. The experiment was duplicated for maize - soybean rotation. The experiment was set by split-split plot method according to randomized block design in three replicates. The basic plot areas were 617.2 m2 (irrigation, 313.6 m2 (fertilization and 39.2 m2 (genotype. Selection of N non-fertilized treatment and four inbred lines were made for this study with aim of testing year (A irrigation (B and genotype (C effects under natural N-soil conditions. Average grain yield in level 1809 kg ha-1without N fertilization is indication of very high fertility of the soil. Differences of yield among the years were from 823 (2007 to 2450 (2006 kg ha-1. Excessive drought and high air-temperature stress is responsible for the low maize yield in 2007. Irrigation considerable affected on maize yields (4-year averages: 1500, 1809 and 2118 kg ha-1, for B1, B2 and B3, respectively. Differences of the 4-year average yields among the genotypes were from 1259 (C3 to 2765 (C1 kg ha-1. Differences of yield among the genotypes in the different years were also considerable because the lowest yield was for 71% (A1, 23% (A2, 63% (A3 and 40% (A4 lower in comparison to the highest yield. The genotype effects under different water supplies were less influencing factor because the high-yielding C1 had for 128%, 129% and 106% the higher yield compared to the low-yielding C3, for B1, B2 and B3, respectively

  7. Evaluation of Grain Quality in Bread Wheat Recombinant Inbred Lines Under Drought Stress Conditions

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    H. Shahbazi

    2014-04-01

    Full Text Available To study drought stress effect on grain quality properties of wheat, an experiment was conductedusing 169 recombinant inbreed lines (RILS under water stress and non-stress condition and with two separated lattice designs. Grain yield, protein yield, protein content, volume of Zeleny sediment, grain hardness, water absorption, grain moisture content and grain dry matter were evaluated. Analysis of variance showed that there were significant differences among the lines for all traits. Moreover, comparison between two lines in two environmental conditions showed, the quality in bread wheat under drought stress conditions due to increment of protein yield is improved. Protein yield in both irrigation regimes has a significant and negative correlation with grain moisture and in the other hand, significant and positive correlation with the grain hardiness dry matter, Zeleny sedimentation and water intake in both conditions. The results showed that the identification of favorable quality characteristics in optimum and stressed conditions were possible and the lines with high grain quality can be used in breeding programs for improving of baking quality. Although some drought sensitive genotypes possessed a favorable baking quality but their grain yield was low.

  8. M6: A diploid potato inbred line for use in breeding and genetics research

    Science.gov (United States)

    M6 is a vigorous, homozygous breeding line derived by self-pollinating the diploid wild potato relative Solanum chacoense for seven generations. While most wild Solanum species are self-incompatible, this clone is homozygous for the dominant self-incompatibility inhibitor gene Sli. It is homozygous ...

  9. Comparative miRNAs analysis of Two contrasting broccoli inbred lines with divergent head-forming capacity under temperature stress.

    Science.gov (United States)

    Chen, Chi-Chien; Fu, Shih-Feng; Norikazu, Monma; Yang, Yau-Wen; Liu, Yu-Ju; Ikeo, Kazuho; Gojobori, Takashi; Huang, Hao-Jen

    2015-12-01

    MicroRNAs (miRNAs) play a vital role in growth, development, and stress response at the post-transcriptional level. Broccoli (Brassica oleracea L. var italic) is an important vegetable crop, and the yield and quality of broccoli are decreased by heat stress. The broccoli inbred lines that are capable of producing head at high temperature in summer are unique varieties in Taiwan. However, knowledge of miRNAomes during the broccoli head formation under heat stress is limited. In this study, molecular characterization of two nearly isogenic lines with contrasting head-forming capacity was investigated. Head-forming capacity was better for heat-tolerant (HT) than heat-sensitive (HS) broccoli under heat stress. By deep sequencing and computational analysis, 20 known miRNAs showed significant differential expression between HT and HS genotypes. According to the criteria for annotation of new miRNAs, 24 novel miRNA sequences with differential expression between the two genotypes were identified. To gain insight into functional significance, 213 unique potential targets of these 44 differentially expressed miRNAs were predicted. These targets were implicated in shoot apical development, phase change, response to temperature stimulus, hormone and energy metabolism. The head-forming capacity of the unique HT line was related to autonomous regulation of Bo-FT genes and less expression level of heat shock protein genes as compared to HS. For the genotypic comparison, a set of miRNAs and their targets had consistent expression patterns in various HT genotypes. This large-scale characterization of broccoli miRNAs and their potential targets is to unravel the regulatory roles of miRNAs underlying heat-tolerant head-forming capacity.

  10. Effect of x-ray irradiation on maize inbred line B73 tissue cultures and regenerated plants

    International Nuclear Information System (INIS)

    Wang, A.S.; Cheng, D.S.K.; Milcic, J.B.; Yang, T.C.

    1988-01-01

    In order to enhance variation induced by the tissue culture process and to obtain agronomically desirable mutants, friable embryogenic tissue cultures of maize (Zea mays L.) inbred line B73 were x-ray irradiated with 11 doses [0-8.4 kilorads (kR)]. Reductions in callus growth rate and embryogenic callus formation occurred with increasing x-ray doses 20 d and 3 months after irradiation. Callus irradiated with 0.8 kR showed a significant increase in growth rate and a 20% increase in embryogenic callus 9 months after irradiation. A total of 230 R 0 plants were regenerated for evaluation. Pollen fertility and seed set of R 0 plants decreased with increasing x-ray dosage. Days to anthesis and plant height of R 0 plants varied among x-ray treatments but were generally reduced with higher dosages. The number of chromosomal aberrations increased with x-ray dosage. The R 1 seeds taken from R 0 plants were also grown and tested for mutant segregation. Plants regenerated from irradiated calli had a two- to 10-fold increase in mutations over plants regenerated from unirradiated control callus. Germination frequency of seeds from R 0 plants decreased with increasing x-ray dosage. Although chlorophyll mutants were most frequently observed, a number of vigorous plants with earlier anthesis date were also recovered

  11. Bursal transcriptome profiling of different inbred chicken lines reveals key differentially expressed genes at 3 days post-infection with very virulent infectious bursal disease virus.

    Science.gov (United States)

    Farhanah, Mohd Isa; Yasmin, Abd Rahaman; Mat Isa, Nurulfiza; Hair-Bejo, Mohd; Ideris, Aini; Powers, Claire; Oladapo, Omobolanle; Nair, Venugopal; Khoo, Jia-Shiun; Ghazali, Ahmad-Kamal; Yee, Wai-Yan; Omar, Abdul Rahman

    2018-01-01

    Infectious bursal disease is a highly contagious disease in the poultry industry and causes immunosuppression in chickens. Genome-wide regulations of immune response genes of inbred chickens with different genetic backgrounds, following very virulent infectious bursal disease virus (vvIBDV) infection are poorly characterized. Therefore, this study aims to analyse the bursal tissue transcriptome of six inbred chicken lines 6, 7, 15, N, O and P following infection with vvIBDV strain UK661 using strand-specific next-generation sequencing, by highlighting important genes and pathways involved in the infected chicken during peak infection at 3 days post-infection. All infected chickens succumbed to the infection without major variations among the different lines. However, based on the viral loads and bursal lesion scoring, lines P and 6 can be considered as the most susceptible lines, while lines 15 and N were regarded as the least affected lines. Transcriptome profiling of the bursa identified 4588 genes to be differentially expressed, with 2985 upregulated and 1642 downregulated genes, in which these genes were commonly or uniquely detected in all or several infected lines. Genes that were upregulated are primarily pro-inflammatory cytokines, chemokines and IFN-related. Various genes that are associated with B-cell functions and genes related to apoptosis were downregulated, together with the genes involved in p53 signalling. In conclusion, bursal transcriptome profiles of different inbred lines showed differential expressions of pro-inflammatory cytokines and chemokines, Th1 cytokines, JAK-STAT signalling genes, MAPK signalling genes, and their related pathways following vvIBDV infection.

  12. Proteomic Mapping of Dental Enamel Matrix from Inbred Mouse Strains: Unraveling Potential New Players in Enamel.

    Science.gov (United States)

    Lima Leite, Aline; Silva Fernandes, Mileni; Charone, Senda; Whitford, Gary Milton; Everett, Eric T; Buzalaf, Marília Afonso Rabelo

    2018-01-01

    Enamel formation is a complex 2-step process by which proteins are secreted to form an extracellular matrix, followed by massive protein degradation and subsequent mineralization. Excessive systemic exposure to fluoride can disrupt this process and lead to a condition known as dental fluorosis. The genetic background influences the responses of mineralized tissues to fluoride, such as dental fluorosis, observed in A/J and 129P3/J mice. The aim of the present study was to map the protein profile of enamel matrix from A/J and 129P3/J strains. Enamel matrix samples were obtained from A/J and 129P3/J mice and analyzed by 2-dimensional electrophoresis and liquid chromatography coupled with mass spectrometry. A total of 120 proteins were identified, and 7 of them were classified as putative uncharacterized proteins and analyzed in silico for structural and functional characterization. An interesting finding was the possibility of the uncharacterized sequence Q8BIS2 being an enzyme involved in the degradation of matrix proteins. Thus, the results provide a comprehensive view of the structure and function for putative uncharacterized proteins found in the enamel matrix that could help to elucidate the mechanisms involved in enamel biomineralization and genetic susceptibility to dental fluorosis. © 2018 S. Karger AG, Basel.

  13. Agrobacterium-mediated high-frequency transformation of an elite commercial maize (Zea mays L.) inbred line.

    Science.gov (United States)

    Cho, Myeong-Je; Wu, Emily; Kwan, Jackie; Yu, Maryanne; Banh, Jenny; Linn, Wutt; Anand, Ajith; Li, Zhi; TeRonde, Susan; Register, James C; Jones, Todd J; Zhao, Zuo-Yu

    2014-10-01

    An improved Agrobacterium -mediated transformation protocol is described for a recalcitrant commercial maize elite inbred with optimized media modifications and AGL1. These improvements can be applied to other commercial inbreds. This study describes a significantly improved Agrobacterium-mediated transformation protocol in a recalcitrant commercial maize elite inbred, PHR03, using optimal co-cultivation, resting and selection media. The use of green regenerative tissue medium components, high copper and 6-benzylaminopurine, in resting and selection media dramatically increased the transformation frequency. The use of glucose in resting medium further increased transformation frequency by improving the tissue induction rate, tissue survival and tissue proliferation from immature embryos. Consequently, an optimal combination of glucose, copper and cytokinin in the co-cultivation, resting and selection media resulted in significant improvement from 2.6 % up to tenfold at the T0 plant level using Agrobacterium strain LBA4404 in transformation of PHR03. Furthermore, we evaluated four different Agrobacterium strains, LBA4404, AGL1, EHA105, and GV3101 for transformation frequency and event quality. AGL1 had the highest transformation frequency with up to 57.1 % at the T0 plant level. However, AGL1 resulted in lower quality events (defined as single copy for transgenes without Agrobacterium T-DNA backbone) when compared to LBA4404 (30.1 vs 25.6 %). We propose that these improvements can be applied to other recalcitrant commercial maize inbreds.

  14. Avaliação de linhagens de melão Evaluation of melon inbred lines for plant and fruit characteristics

    Directory of Open Access Journals (Sweden)

    Waldelice Oliveira de Paiva

    2000-07-01

    Full Text Available Com o objetivo de produzir híbridos de melão adaptados à região Nordeste do Brasil, foi avaliado, em Pacajús-CE o comportamento de 29 linhagens, sendo 23 do grupo cantalupensis, cinco do inodorus e uma do grupo momordica. Para efeito de comparação, foram utilizadas cultivares comerciais: o híbrido Hy-mark e a cultivar Eldorado-300. Na avaliação da precocidade a maturação das linhagens do grupo cantalupensis levaram em média 35,1 dias, as do grupo inodorus 30,6 dias e as do grupo momordica 24,4 dias. A concentração da produção, estimada aos 70 dias, foi mais elevada (75,8% numa linhagem que não produz frutos comerciais. A produção das linhagens variou de 16,2 t/ha a 65,1 t/ha, enquanto a média das testemunhas comerciais foi de 28,4 t/ha. Três linhagens do grupo cantalupensis e todas do grupo inodorus mostraram-se mais produtivas que as testemunhas. O teor de sólidos solúveis entre linhagens e testemunhas foi semelhante (8,6%, sendo que uma das linhagens, M46-00 se destacou pelos altos teores (Brix=12,2%. Em geral, os frutos das linhagens tardias mostraram elevado teor de sólidos solúveis.In order to obtain melon hybrids adapted for growing in the Northeast of Brazil, 29 inbred lines (23 belonging to the cantaloupensis group, 5 to the inodorus and 1 to the momordica group were evaluated in Pacajus, in the state of Ceará. Two commercial varieties, the hybrid Hy-mark and the cultivar Eldorado-300, were used as checks. It was observed that the average period for fruit ripening was 35.1 days for the cantalupensis group, 30.6 days for the inodorus group and 24.4 days for the momordica group. The highest yield concentration (75.8%, evaluated 70 days after sowing, was attained in a inbred line that does not produce commercial fruits. The yield of the lines ranged from 16.2 t/ha up to 65.1 t/ha, whereas the two commercial varieties produced 28.0 t/ha. Three of the cantalupensis group and all inbred lines of the inodorus group

  15. Line Generalization and AutoCAD Map

    Directory of Open Access Journals (Sweden)

    Nada Vučetić

    2001-01-01

    Full Text Available The paper offers the results of original research made on the application of AutoCAD Map in line generalisation. The differences and similarities have been found out between the Douglas-Peucker method and the method of line simplification that is incorporated in AutoCAD Map. There have been also the inaccuracies found out in AutoCAD Map manual relating to the issues of buffer width and tolerance, and the line width before and after simplification. The paper gives recommendations about pseudo nodes dissolving. It has been noticed that AutoCAD Map simplification method is not independent of the order of points. The application of the method is illustrated by an example of coastal line of Istria.

  16. Combing Ability Analysis ofamong Early Generation Maize Inbred ...

    African Journals Online (AJOL)

    dagne.cimdom

    estimate combining ability effects of locally developed and introduced early generation maize inbred lines for grain yield, yield .... mass selection followed by self-pollination for generating inbred lines. The inbred lines ... for the experiment was an alpha (0, 1) lattice (Patterson and Williams, 1996) with two replications at each ...

  17. Evaluation of the Morpho-physiology characteristics of maize inbred lines introduced from CIMMYT to identify the best candidates for planting in acidic soil in Jasinga, Indonesia

    Science.gov (United States)

    Lubis, K.; Sutjahjo, S. H.; Syukur, M.; Trikoesoemaningtyas

    2016-08-01

    Technological developments and climate change have affected crop planting strategies. For example, maize production has expanded to sub-optimal lands, including acidic soil common in areas like Indonesia. Breeding programs have created inbred lines of maize introduced from CIMMYT; they were tested locally in acidic soils to determine their adaptability and tolerance mechanisms. Breeds CLA 46 and NEI 9008 were found to be excellent candidates for acidic soil due to their ASI, high number of grains per year, and suitable dry seed weight.

  18. SSR marker analysis on genetic variation of M3 from maize inbred lines 48-2 and R08 after irradiation inducement

    International Nuclear Information System (INIS)

    Li Qi; Shi Haichun; Ke Yongpei; Yuan Jichao; Yu Xuejie

    2011-01-01

    Analyzing the biological effects and the genetic variations of maize mutagenic progenies is important to facilitate effective selections and utilization of the mutants. In this study, the genetic variation of 103 mutagenic progenies of M 3 lines of inbred lines 48-2 and R08 with 60 Co γ-rays inducement were evaluated with SSR molecular markers. The results indicated that, the amplitude of polymorphism information content (PIC) of the 48-2 and R08 M 3 lines ranged 0.307 ∼ 0.948 and 0.108 ∼ 0.955, with an average of 0.762 and 0.701, respectively. The amplitude of genetic diversity indexes (H') ranged 0.552 ∼ 2.830 and 0.254 ∼ 3.309, with an average of 1.830 and 1.777, respectively. The average value of genetic similarity coefficient of the 49 M 3 lines of 48-2 with its check (M673) was 0.8194. However, the average value of genetic similarity coefficient of the M 3 lines of R08 with its check (M487) was 0.8373. Based on the genetic similarity coefficient, inbred lines 48-2, R08 and their 101 M 3 lines were clustered in 7 and 5 populations respectively. This phenomenon indicated that massive genetic variation could appear in progenies due to irradiation. The strengthen of selection and utilization of mutants based on the breeding objectives and in accordance with the feature and regularity on genetic variations of main characteristics of mutant lines in various populations could be enhanced in breeding program, to some extent, which can increase the breeding efficiency of irradiation induced mutation in maize. (authors)

  19. Expression Analysis of Stress-Related Genes in Kernels of Different Maize (Zea mays L.) Inbred Lines with Different Resistance to Aflatoxin Contamination

    Science.gov (United States)

    Jiang, Tingbo; Zhou, Boru; Luo, Meng; Abbas, Hamed K.; Kemerait, Robert; Lee, Robert Dewey; Scully, Brian T.; Guo, Baozhu

    2011-01-01

    This research examined the expression patterns of 94 stress-related genes in seven maize inbred lines with differential expressions of resistance to aflatoxin contamination. The objective was to develop a set of genes/probes associated with resistance to A. flavus and/or aflatoxin contamination. Ninety four genes were selected from previous gene expression studies with abiotic stress to test the differential expression in maize lines, A638, B73, Lo964, Lo1016, Mo17, Mp313E, and Tex6, using real-time RT-PCR. Based on the relative-expression levels, the seven maize inbred lines clustered into two different groups. One group included B73, Lo1016 and Mo17, which had higher levels of aflatoxin contamination and lower levels of overall gene expression. The second group which included Tex6, Mp313E, Lo964 and A638 had lower levels of aflatoxin contamination and higher overall levels of gene expressions. A total of six “cross-talking” genes were identified between the two groups, which are highly expressed in the resistant Group 2 but down-regulated in susceptible Group 1. When further subjected to drought stress, Tex6 expressed more genes up-regulated and B73 has fewer genes up-regulated. The transcript patterns and interactions measured in these experiments indicate that the resistant mechanism is an interconnected process involving many gene products and transcriptional regulators, as well as various host interactions with environmental factors, particularly, drought and high temperature. PMID:22069724

  20. Shelf life determinants and enzyme activities of pearl millet: a comparison of changes in stored flour of hybrids, CMS lines, inbreds and composites.

    Science.gov (United States)

    Goyal, Preeti; Chugh, L K

    2017-09-01

    Shelf life of pearl millet flour is very short because of rapid development of rancidity. This investigation was carried out in view of generating breeding material for development of low rancid pearl millet hybrids/varieties. Flour of twenty-one genotypes; seven hybrids, seven CMS lines, five inbreds and two composites stored in covered aluminium boxes at 37 °C for 30 days along with respective fresh flour was analysed for shelf life indicators/determinants. Crude fat content and fat acidity (FA) of fresh flour of the genotypes varied from 3.8 to 7.2% and 11 to 75 mg KOH/100 g d.m., respectively. FA in stored flour ranged between 180 and 330 mg KOH/100 g d.m. After storage, magnitude of decrease in pH of water extract of flour of the genotypes varied from 0.15 to 0.44. Activity of peroxidase (POX) varied from 378 to 588 units in control flour and irrespective of the genotypes decreased upon storage. Increase in FA (difference between FA of fresh and stored flour) rather total build up of FA was positively associated with crude fat content (r = 0.440*) indicated comparatively more prominent role of lipolytic enzymes. Chemical changes taking place in water soluble fraction of flour were independent of fat content as no correlation was discerned between fat content and decrease in pH. Among the hybrids, HHB 197 had lowest crude fat content (4.7%), lowest total build up FA (212 mg KOH/100 g d.m.), slowest increase in FA (191 mg KOH/100 g d.m.), least decrease in pH (0.31) of water soluble fraction flour during storage and lowest activity of POX in fresh flour (377 units/g d.m). Among all the tested CMS lines, inbreds and composites, HBL 11 showed pattern of quantitative changes in FA, pH and POX activity similar to the hybrid HHB 197 and was identified a promising inbred for developing low-rancid pearl millet variety or hybrid.

  1. Estimates of Combining Ability and Heterosis for Yield and Its Related Traits in Pearl Millet Inbred Lines under Downy Mildew Prevalent Areas of Senegal

    Directory of Open Access Journals (Sweden)

    Ghislain Kanfany

    2018-01-01

    Full Text Available Pearl millet is an important cereal crop for smallholder farmers’ food security in West and Central Africa. However, its production has stagnated due to several factors such as the continuous use of local populations. A set of 17 inbred lines was crossed with Sosat C 88 and Souna 3 following a line × tester mating design. The F1 hybrids, their parents, and a check were evaluated in Bambey and Nioro research stations during the rainy season of 2017. Data on downy mildew incidence, plant height, flowering time, panicle length and diameter, productive tillers, thousand-grain weight, panicle, and grain yield were recorded. GCA and SCA mean squares were significant for most of the traits indicating that both additive and nonadditive gene effects were involved in the control of the inheritance of these traits. However, the contribution of GCA to total mean squares was higher than that of SCA for all the traits, providing that additive gene action was more important in their inheritance. The top-cross hybrid IBL155-2-1 × Sosat C 88 exhibited negative and significant SCA effects for downy mildew incidence, flowering time, and plant height. Lines IBL003-B-1, IBL091-1-1, IBL095-4-1, IBL110-B-1, and IBL 206-1-1 had positive GCA effects for grain yield and negative GCA effects for downy mildew, flowering time, and plant height. These lines can be used as parents to create synthetic varieties or hybrids.

  2. Potencial de híbridos simples de milho para extração de linhagens Potential of maize single hybrids to generate inbred lines

    Directory of Open Access Journals (Sweden)

    Odair Bison

    2003-04-01

    Full Text Available A utilização de híbridos simples comerciais de milho é uma das opções de populações para a extração de linhagens, porque são adaptados e provavelmente concentram alta freqüência de alelos favoráveis já fixados. Mesmo nos locos que estão segregando, a freqüência de alelos favoráveis é 0,5. Assim, a identificação de populações promissoras, derivadas de híbridos simples superiores, é uma boa estratégia para aumentar a eficiência dos programas de melhoramento. As populações derivadas dos híbridos simples comerciais AG9012 e C333 foram avaliadas com o objetivo de verificar o potencial dessas para extração de linhagens superiores, por meio das estimativas de parâmetros genéticos e fenotípicos, da estimativa de m+a e a metodologia proposta por Jinks & Pooni (1976. Foram avaliadas 169 famílias S1 de cada população, durante a safra agrícola de 1999/2000, na área experimental do Departamento de Biologia da UFLA, em Lavras - MG, em látice simples 13x13, sendo as parcelas constituídas por uma linha de 3 m. As características analisadas foram incidência de Phaeosphaeria maydis em duas épocas, altura de plantas, altura de espigas e produtividade de espigas despalhadas. Foi constatado que há possibilidade de se obterem linhagens com bom desempenho per se, sendo a população derivada do C333 a mais promissora, por associar resistência a Phaeosphaeria maydis e possuir média mais alta e maior probabilidade de obtenção de linhagens superiores. A metodologia proposta por Jinks & Pooni (1976 mostrou-se mais informativa do que a estimativa de m+a para a escolha de populações, mas, quando possível, as duas podem ser utilizadas simultaneamente para auxiliar na decisão dos melhoristas.Populations derived from commercial single hybrids are one of the breeder options for inbred line extraction because of their adaptation and probable high frequency of loci with fixed favorable alleles. Even the segregating loci carry

  3. Reconstruction of multiple line source attenuation maps

    International Nuclear Information System (INIS)

    Celler, A.; Sitek, A.; Harrop, R.

    1996-01-01

    A simple configuration for a transmission source for the single photon emission computed tomography (SPECT) was proposed, which utilizes a series of collimated line sources parallel to the axis of rotation of a camera. The detector is equipped with a standard parallel hole collimator. We have demonstrated that this type of source configuration can be used to generate sufficient data for the reconstruction of the attenuation map when using 8-10 line sources spaced by 3.5-4.5 cm for a 30 x 40cm detector at 65cm distance from the sources. Transmission data for a nonuniform thorax phantom was simulated, then binned and reconstructed using filtered backprojection (FBP) and iterative methods. The optimum maps are obtained with data binned into 2-3 bins and FBP reconstruction. The activity in the source was investigated for uniform and exponential activity distributions, as well as the effect of gaps and overlaps of the neighboring fan beams. A prototype of the line source has been built and the experimental verification of the technique has started

  4. Effectiveness of the Ty-3 Introgression for Conferring Resistance in Recombinant Inbred Lines of Tomato to Bipartite Begomoviruses in Guatemala

    Science.gov (United States)

    Management of begomovirus-incited diseases on tomatoes in Guatemala continues to be a challenge and there continues to be a need to better understand the genetics of resistance to begomoviruses. In this study, the resistant line, Gh13, was crossed with the susceptible line, HUJ-VF, that lacked the ...

  5. Quantification of glucosinolates, anthocyanins, free amino acids, and vitamin C in inbred lines of cabbage (Brassica oleracea L.).

    Science.gov (United States)

    Park, Suhyoung; Valan Arasu, Mariadhas; Lee, Min-Ki; Chun, Jin-Hyuk; Seo, Jeong Min; Lee, Sang-Won; Al-Dhabi, Naif Abdullah; Kim, Sun-Ju

    2014-02-15

    We profiled and quantified glucosinolates (GSLs), anthocyanins, free amino acids, and vitamin C metabolites in forty-five lines of green and red cabbages. Analysis of these distinct cabbages revealed the presence of 11 GSLs, 13 anthocyanins, 22 free amino acids, and vitamin C. GSL contents were varied amongst the different lines of cabbage. The total GSL content was mean 10.6 μmol/g DW, and sinigrin was the predominant GSL accounted mean 4.0 μmol/g DW (37.7% of the total) followed by glucoraphanin (1.9) and glucobrassicin (2.4). Amongst the 13 anthocyanins, cyanidin 3-(sinapoyl) diglucoside-5-glucoside levels were the highest. The amounts of total free amino acids in green cabbage lines ranged 365.9 mg/100g fresh weight (FW) to 1089.1mg/100g FW. Vitamin C levels were much higher in red cabbage line (129.9 mg/100g FW). Thus, the amounts of GSLs, anthocyanins, free amino acids, and vitamin C varied widely, and the variations in these compounds between the lines of cabbage were significant. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Nitrogen-15 uptake by whole plants and root callus cultures of inbred maize lines and their F1 hybrids

    International Nuclear Information System (INIS)

    Mladenova, Y.; Karadimova, M.

    1981-01-01

    The uptake of nitrogen-15 by 3 maize genotypes was investigated. Comparative analysis of N15 assimilation and distribution in the organs of intact plants of two self-pollinated lines and their F1 hybrid and also in a callus tissue of roots of the same genotypes was made. From the results the conclusion is drawn that the N-use efficiency of the female line is higher than that of the male line both in intact plants and callus tissues from roots. This fact indicates that the N-use efficiency is determined not only by the functions of the cells in the shoots, suggesting the participation of the photosynthetic carboxylases but also by the functions of cells without a photosynthesizing apparatus. The N-use efficiency in the F1 hybrid manifests ''heterosis'', in spite of the intact plants or root callus tissues are being studied. (author)

  7. Use of molecular markers aids in the development of diverse inbred backcross lines in Beit Alpha cucumber (Cucumis sativus L.)

    Science.gov (United States)

    Beit Alpha cucumber (Cucumis sativus L.) is a Mediterranean fresh-market type with a relatively narrow genetic base. To broaden its base for plant improvement, 42 diverse accessions were compared employing a previously defined standard marker array to choose wide-based parental lines for use in bac...

  8. Global transcriptome analysis of the maize (Zea mays L.) inbred line 08LF during leaf senescence initiated by pollination-prevention.

    Science.gov (United States)

    Wu, Liancheng; Li, Mingna; Tian, Lei; Wang, Shunxi; Wu, Liuji; Ku, Lixia; Zhang, Jun; Song, Xiaoheng; Liu, Haiping; Chen, Yanhui

    2017-01-01

    In maize (Zea mays), leaf senescence acts as a nutrient recycling process involved in proteins, lipids, and nucleic acids degradation and transport to the developing sink. However, the molecular mechanisms of pre-maturation associated with pollination-prevention remain unclear in maize. To explore global gene expression changes during the onset and progression of senescence in maize, the inbred line 08LF, with severe early senescence caused by pollination prevention, was selected. Phenotypic observation showed that the onset of leaf senescence of 08LF plants occurred approximately 14 days after silking (DAS) by pollination prevention. Transcriptional profiling analysis of the leaf at six developmental stages during induced senescence revealed that a total of 5,432 differentially expressed genes (DEGs) were identified, including 2314 up-regulated genes and 1925 down-regulated genes. Functional annotation showed that the up-regulated genes were mainly enriched in multi-organism process and nitrogen compound transport, whereas down-regulated genes were involved in photosynthesis. Expression patterns and pathway enrichment analyses of early-senescence related genes indicated that these DEGs are involved in complex regulatory networks, especially in the jasmonic acid pathway. In addition, transcription factors from several families were detected, particularly the CO-like, NAC, ERF, GRAS, WRKY and ZF-HD families, suggesting that these transcription factors might play important roles in driving leaf senescence in maize as a result of pollination-prevention.

  9. Assessment and genetic analysis of heavy metal content in rice grain using an Oryza sativa × O. rufipogon backcross inbred line population.

    Science.gov (United States)

    Huang, De-Run; Fan, Ye-Yang; Hu, Biao-Lin; Xiao, Ye-Qing; Chen, Da-Zhou; Zhuang, Jie-Yun

    2018-03-01

    Heavy metal accumulation in rice is a growing concern for public health. Backcross inbred lines derived from an interspecific cross of Oryza sativa × O. rufipogon were grown in two distinct ecological locations (Hangzhou and Lingshui, China). The objective of this study was to characterise the contents of heavy metal in rice grains, and to identify quantitative trait loci (QTLs) for heavy metal contents. The contents of Ni, As, Pb, Cr and Hg in milled rice showed a significant decline as compared with those in brown rice, whereas the content of Cd showed little change. The concentration of heavy metal in rice grain varied greatly between the two environments. A total of 24 QTLs responsible for heavy metal contents were detected, including two for both the brown and milled rice, 13 for brown rice only, and nine for milled rice only. All the QTLs except two had the enhancing alleles derived from O. rufipogon. Sixteen QTLs were clustered in six chromosomal regions. Environmental variation plays an important role in the heavy metal contents in rice grain. QTLs detected in this study might be useful for breeding rice varieties with low heavy metal content. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  10. Genome wide analysis of inbred mouse lines identifies a locus containing Ppar-gamma as contributing to enhanced malaria survival.

    Directory of Open Access Journals (Sweden)

    Selina E R Bopp

    2010-05-01

    Full Text Available The genetic background of a patient determines in part if a person develops a mild form of malaria and recovers, or develops a severe form and dies. We have used a mouse model to detect genes involved in the resistance or susceptibility to Plasmodium berghei malaria infection. To this end we first characterized 32 different mouse strains infected with P. berghei and identified survival as the best trait to discriminate between the strains. We found a locus on chromosome 6 by linking the survival phenotypes of the mouse strains to their genetic variations using genome wide analyses such as haplotype associated mapping and the efficient mixed-model for association. This new locus involved in malaria resistance contains only two genes and confirms the importance of Ppar-gamma in malaria infection.

  11. Protein Profiles Reveal Diverse Responsive Signaling Pathways in Kernels of Two Maize Inbred Lines with Contrasting Drought Sensitivity

    Directory of Open Access Journals (Sweden)

    Liming Yang

    2014-10-01

    Full Text Available Drought stress is a major factor that contributes to disease susceptibility and yield loss in agricultural crops. To identify drought responsive proteins and explore metabolic pathways involved in maize tolerance to drought stress, two maize lines (B73 and Lo964 with contrasting drought sensitivity were examined. The treatments of drought and well water were applied at 14 days after pollination (DAP, and protein profiles were investigated in developing kernels (35 DAP using iTRAQ (isobaric tags for relative and absolute quantitation. Proteomic analysis showed that 70 and 36 proteins were significantly altered in their expression under drought treatments in B73 and Lo964, respectively. The numbers and levels of differentially expressed proteins were generally higher in the sensitive genotype, B73, implying an increased sensitivity to drought given the function of the observed differentially expressed proteins, such as redox homeostasis, cell rescue/defense, hormone regulation and protein biosynthesis and degradation. Lo964 possessed a more stable status with fewer differentially expressed proteins. However, B73 seems to rapidly initiate signaling pathways in response to drought through adjusting diverse defense pathways. These changes in protein expression allow for the production of a drought stress-responsive network in maize kernels.

  12. Metabolic profiling of two maize (Zea mays L.) inbred lines inoculated with the nitrogen fixing plant-interacting bacteria Herbaspirillum seropedicae and Azospirillum brasilense

    Science.gov (United States)

    Brusamarello-Santos, Liziane Cristina; Gilard, Françoise; Brulé, Lenaïg; Quilleré, Isabelle; Gourion, Benjamin; Ratet, Pascal; Maltempi de Souza, Emanuel; Lea, Peter J.; Hirel, Bertrand

    2017-01-01

    Maize roots can be colonized by free-living atmospheric nitrogen (N2)-fixing bacteria (diazotrophs). However, the agronomic potential of non-symbiotic N2-fixation in such an economically important species as maize, has still not been fully exploited. A preliminary approach to improve our understanding of the mechanisms controlling the establishment of such N2-fixing associations has been developed, using two maize inbred lines exhibiting different physiological characteristics. The bacterial-plant interaction has been characterized by means of a metabolomic approach. Two established model strains of Nif+ diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense and their Nif- couterparts defficient in nitrogenase activity, were used to evaluate the impact of the bacterial inoculation and of N2 fixation on the root and leaf metabolic profiles. The two N2-fixing bacteria have been used to inoculate two genetically distant maize lines (FV252 and FV2), already characterized for their contrasting physiological properties. Using a well-controlled gnotobiotic experimental system that allows inoculation of maize plants with the two diazotrophs in a N-free medium, we demonstrated that both maize lines were efficiently colonized by the two bacterial species. We also showed that in the early stages of plant development, both bacterial strains were able to reduce acetylene, suggesting that they contain functional nitrogenase activity and are able to efficiently fix atmospheric N2 (Fix+). The metabolomic approach allowed the identification of metabolites in the two maize lines that were representative of the N2 fixing plant-bacterial interaction, these included mannitol and to a lesser extend trehalose and isocitrate. Whilst other metabolites such as asparagine, although only exhibiting a small increase in maize roots following bacterial infection, were specific for the two Fix+ bacterial strains, in comparison to their Fix- counterparts. Moreover, a number

  13. Metabolic profiling of two maize (Zea mays L. inbred lines inoculated with the nitrogen fixing plant-interacting bacteria Herbaspirillum seropedicae and Azospirillum brasilense.

    Directory of Open Access Journals (Sweden)

    Liziane Cristina Brusamarello-Santos

    Full Text Available Maize roots can be colonized by free-living atmospheric nitrogen (N2-fixing bacteria (diazotrophs. However, the agronomic potential of non-symbiotic N2-fixation in such an economically important species as maize, has still not been fully exploited. A preliminary approach to improve our understanding of the mechanisms controlling the establishment of such N2-fixing associations has been developed, using two maize inbred lines exhibiting different physiological characteristics. The bacterial-plant interaction has been characterized by means of a metabolomic approach. Two established model strains of Nif+ diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense and their Nif- couterparts defficient in nitrogenase activity, were used to evaluate the impact of the bacterial inoculation and of N2 fixation on the root and leaf metabolic profiles. The two N2-fixing bacteria have been used to inoculate two genetically distant maize lines (FV252 and FV2, already characterized for their contrasting physiological properties. Using a well-controlled gnotobiotic experimental system that allows inoculation of maize plants with the two diazotrophs in a N-free medium, we demonstrated that both maize lines were efficiently colonized by the two bacterial species. We also showed that in the early stages of plant development, both bacterial strains were able to reduce acetylene, suggesting that they contain functional nitrogenase activity and are able to efficiently fix atmospheric N2 (Fix+. The metabolomic approach allowed the identification of metabolites in the two maize lines that were representative of the N2 fixing plant-bacterial interaction, these included mannitol and to a lesser extend trehalose and isocitrate. Whilst other metabolites such as asparagine, although only exhibiting a small increase in maize roots following bacterial infection, were specific for the two Fix+ bacterial strains, in comparison to their Fix- counterparts

  14. Metabolic profiling of two maize (Zea mays L.) inbred lines inoculated with the nitrogen fixing plant-interacting bacteria Herbaspirillum seropedicae and Azospirillum brasilense.

    Science.gov (United States)

    Brusamarello-Santos, Liziane Cristina; Gilard, Françoise; Brulé, Lenaïg; Quilleré, Isabelle; Gourion, Benjamin; Ratet, Pascal; Maltempi de Souza, Emanuel; Lea, Peter J; Hirel, Bertrand

    2017-01-01

    Maize roots can be colonized by free-living atmospheric nitrogen (N2)-fixing bacteria (diazotrophs). However, the agronomic potential of non-symbiotic N2-fixation in such an economically important species as maize, has still not been fully exploited. A preliminary approach to improve our understanding of the mechanisms controlling the establishment of such N2-fixing associations has been developed, using two maize inbred lines exhibiting different physiological characteristics. The bacterial-plant interaction has been characterized by means of a metabolomic approach. Two established model strains of Nif+ diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense and their Nif- couterparts defficient in nitrogenase activity, were used to evaluate the impact of the bacterial inoculation and of N2 fixation on the root and leaf metabolic profiles. The two N2-fixing bacteria have been used to inoculate two genetically distant maize lines (FV252 and FV2), already characterized for their contrasting physiological properties. Using a well-controlled gnotobiotic experimental system that allows inoculation of maize plants with the two diazotrophs in a N-free medium, we demonstrated that both maize lines were efficiently colonized by the two bacterial species. We also showed that in the early stages of plant development, both bacterial strains were able to reduce acetylene, suggesting that they contain functional nitrogenase activity and are able to efficiently fix atmospheric N2 (Fix+). The metabolomic approach allowed the identification of metabolites in the two maize lines that were representative of the N2 fixing plant-bacterial interaction, these included mannitol and to a lesser extend trehalose and isocitrate. Whilst other metabolites such as asparagine, although only exhibiting a small increase in maize roots following bacterial infection, were specific for the two Fix+ bacterial strains, in comparison to their Fix- counterparts. Moreover, a number

  15. Identification of quantitative trait loci controlling root and shoot traits associated with drought tolerance in a lentil (Lens culinaris Medik. recombinant inbred line population

    Directory of Open Access Journals (Sweden)

    Omar Idrissi

    2016-08-01

    Full Text Available Drought is one of the major abiotic stresses limiting lentil productivity in rainfed production systems. Specific rooting patterns can be associated with drought avoidance mechanisms that can be used in lentil breeding programs. In all, 252 co-dominant and dominant markers were used for Quantitative Trait Loci (QTL analysis on 132 lentil recombinant inbred lines based on greenhouse experiments for root and shoot traits during two seasons under progressive drought-stressed conditions. Eighteen QTLs controlling a total of 14 root and shoot traits were identified. A QTL-hotspot genomic region related to a number of root and shoot characteristics associated with drought tolerance such as dry root biomass, root surface area, lateral root number, dry shoot biomass and shoot length was identified. Interestingly, a QTL related to root-shoot ratio, an important trait for drought avoidance, explaining the highest phenotypic variance of 27.6 % and 28.9 % for the two consecutive seasons, respectively, was detected. This QTL was closed to the co-dominant SNP marker TP6337 and also flanked by the two SNP TP518 and TP1280. An important QTL related to lateral root number was found close to TP3371 and flanked by TP5093 and TP6072 SNP markers. Also, a QTL associated with specific root length was identified close to TP1873 and flanked by F7XEM6b SRAP marker and TP1035 SNP marker. These two QTLs were detected in both seasons. Our results could be used for marker-assisted selection in lentil breeding programs targeting root and shoot characteristics conferring drought avoidance as an efficient alternative to slow and labour-intensive conventional breeding methods.

  16. Towards mouse models of perseveration: a heritable component in extinction of operant behavior in fourteen standard and recombinant inbred mouse lines.

    NARCIS (Netherlands)

    Malkki, H.A.I.; Donga, L.A.B.; de Groot, S.E.; Brussaard, A.B.; Borst, J.G.G.; Elgersma, J.W.; Galjart, N.; van der Horst, G.T.; Levelt, C.N.; Pennartz, C.M.A.; Smit, A.B.; Spruijt, B.M.; Verhage, M.; de Zeeuw, C.I.; Battaglia, F.P.

    2011-01-01

    Extinction of instrumental responses is an essential skill for adaptive behavior such as foraging. So far, only few studies have focused on extinction following appetitive conditioning in mice. We studied extinction of appetitive operant lever-press behavior in six standard inbred mouse strains

  17. Grouping and clustering of maize Lancaster germplasm inbreds according to the results of SNP-analysis

    Directory of Open Access Journals (Sweden)

    K. V. Derkach

    2017-08-01

    Full Text Available The objective of this article is the grouping and clustering of maize inbred lines based on the results of SNP-genotyping for the verification of a separate cluster of Lancaster germplasm inbred lines. As material for the study, we used 91 maize (Zea mays L. inbred lines, including 31 Lancaster germplasm lines and 60 inbred lines of other germplasms (23 Iodent inbreds, 15 Reid inbreds, 7 Lacon inbreds, 12 Mix inbreds and 3 exotic inbreds. The majority of the given inbred lines are included in the Dnipro breeding programme. The SNP-genotyping of these inbred lines was conducted using BDI-III panel of 384 SNP-markers developed by BioDiagnostics, Inc. (USA on the base of Illumina VeraCode Bead Plate. The SNP-markers of this panel are biallelic and are located on all 10 maize chromosomes. Their range of conductivity was >0.6. The SNP-analysis was made in completely automated regime on Illumina BeadStation equipment at BioDiagnostics, Inc. (USA. A principal component analysis was applied to group a general set of 91 inbreds according to allelic states of SNP-markers and to identify a cluster of Lancaster inbreds. The clustering and determining hierarchy in 31 Lancaster germplasm inbreds used quantitative cluster analysis. The share of monomorphic markers in the studied set of 91 inbred lines equaled 0.7%, and the share of dimorphic markers equaled 99.3%. Minor allele frequency (MAF > 0.2 was observed for 80.6% of dimorphic markers, the average index of shift of gene diversity equaled 0.2984, PIC on average reached 0.3144. The index of gene diversity of markers varied from 0.1701 to 0.1901, pairwise genetic distances between inbred lines ranged from 0.0316–0.8000, the frequencies of major alleles of SNP-markers were within 0.5085–0.9821, and the frequencies of minor alleles were within 0.0179–0.4915. The average homozygosity of inbred lines was 98.8%. The principal component analysis of SNP-distances confirmed the isolation of the Lancaster

  18. Absorção de nutrientes e resposta à adubação em linhagens de tomateiro Nutrient uptake and response to fertilization of tomato inbred lines

    Directory of Open Access Journals (Sweden)

    Antônio Régis de Oliveira

    2009-12-01

    Full Text Available Vinte e nove linhagens de tomateiro rasteiro foram avaliadas quanto à eficiência de absorção de nutrientes e resposta à adubação, em dois ensaios, no ano de 2006, na Embrapa Hortaliças. No primeiro ensaio aplicou-se 1/3 da dosagem de fertilizante utilizada no segundo. O delineamento experimental foi inteiramente casualizado, com três repetições. As linhagens foram classificadas quanto à eficiência na absorção de nutrientes e reposta à adubação baseando-se nos incrementos de índice DRIS e nos incrementos de produtividade. Os valores críticos para eficiência na absorção e resposta à adubação foram as médias de incremento de índice DRIS e produtividade, respectivamente. As linhagens diferenciaram-se quanto à eficiência na absorção dos nutrientes e quanto à resposta à adubação. Foram consideradas responsivas à adubação e eficientes na absorção de nutrientes as linhagens 03, 04, 05, 09 e 22, para o N; 03, 04, 09, 13, 15 e 29, para o P; 03, 05, 10, 21, 22, 25 e 27, para o K; 05, 10, 21, 22, 25, 27 e 29, para o Ca; 04, 13, 15, 27 e 29, para o S e B; e 03, 05, 09, 10 e 27, para o Cu. As linhagens com os melhores desempenhos foram a 27, na absorção dos nutrientes, e 03, 04, 05 e 29, na responsividade à adubação.Twenty nine processing tomato inbred lines were evaluated for their efficiency in nutrient uptake and in their response to fertilization. Two field assays were carried out at Embrapa Hortaliças, Brazil, with distinct fertilization dosages in 2006. In the first assay 1/3 of the total fertilization was applied when compared with the second assay. The experiments were conducted using a completely randomized design with three replications. The criteria to rank the inbred lines in both assays were the DRIS (Diagnosis and Recommendation Integrated System index value and fruit yield. The critical values in order to distinguish efficient versus non-efficient as well as responsive versus non-responsive inbred

  19. Selection of Common Bean Lines, Recombinant Inbred Lines and Commercial Genotypes Tolerant to Low Phosphorus Availability in an Acrisol Soil on the Basis of Root Traits and Grain Yield

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, A.; Gomez, L. A.; Morales, A. [Instituto de Suelos, MINAG (Cuba); others, and

    2013-11-15

    Common bean (Phaseolus vulgaris L.) is the most important food legume for human consumption worldwide and especially in Latin America and Africa, but low soil phosphorus (P) availability limits grain production in these areas. For these reason eighty five recombinant inbred lines (RILs) of BAT 477 x DOR 364 and twenty commercial bean genotypes were sown in plots in an Acrisol soil with low P availability to evaluate nine root traits and grain yield. The study was carried out in Pinar del Rio province in Cuba between November 2006 and February 2009. The plots received basal fertilization (N and K) and P fertilization between 15 and 90 kg P{sub 2}O{sub 5} ha{sup -1}. Ten plants were sampled from each plot at R{sub 6} pod fill to evaluate root traits and shoot biomass, and at R{sub 9} physiological maturity to estimate grain yield. The 85 RILs showed great variability for root traits, grain yield and P stress tolerance calculated as relative grain yield. The commercial bean lines also showed large diversity in yield parameters. Principal Component Analysis showed that there were high and significant correlations between root traits (basal root number, primary root depth, adventitious root length and adventitious root number) and grain yield parameters (grain yield at 15 P level and relative grain yields). Adventitious root traits showed the greatest correlation with yield under low P. Promising RILs included 75.1.1, 60.1.1, 38.1.1, 14.1.1 and 38.1.1 and promising commercial bean lines included ICA Pijao, BAT 482, ICA 23, BAT 24 and BAT 832. (author)

  20. Estimation of Initial Position Using Line Segment Matching in Maps

    Directory of Open Access Journals (Sweden)

    Chongyang Wei

    2016-06-01

    Full Text Available While navigating in a typical traffic scene, with a drastic drift or sudden jump in its Global Positioning System (GPS position, the localization based on such an initial position is unable to extract precise overlapping data from the prior map in order to match the current data, thus rendering the localization as unfeasible. In this paper, we first propose a new method to estimate an initial position by matching the infrared reflectivity maps. The maps consist of a highly precise prior map, built with the offline simultaneous localization and mapping (SLAM technique, and a smooth current map, built with the integral over velocities. Considering the attributes of the maps, we first propose to exploit the stable, rich line segments to match the lidar maps. To evaluate the consistency of the candidate line pairs in both maps, we propose to adopt the local appearance, pairwise geometric attribute and structural likelihood to construct an affinity graph, as well as employ a spectral algorithm to solve the graph efficiently. The initial position is obtained according to the relationship between the vehicle's current position and matched lines. Experiments on the campus with a GPS error of dozens of metres show that our algorithm can provide an accurate initial value with average longitudinal and lateral errors being 1.68m and 1.04m, respectively.

  1. Molecular mapping and improvement of leaf rust resistance in wheat breeding lines.

    Science.gov (United States)

    Tsilo, Toi J; Kolmer, James A; Anderson, James A

    2014-08-01

    Leaf rust, caused by Puccinia triticina, is the most common and widespread disease of wheat (Triticum aestivum) worldwide. Deployment of host-plant resistance is one of the strategies to reduce losses due to leaf rust disease. The objective of this study was to map genes for adult-plant resistance to leaf rust in a recombinant inbred line (RIL) population originating from MN98550-5/MN99394-1. The mapping population of 139 RILs and five checks were evaluated in 2005, 2009, and 2010 in five environments. Natural infection occurred in the 2005 trials and trials in 2009 and 2010 were inoculated with leaf rust. Four quantitative trait loci (QTL) on chromosomes 2BS, 2DS, 7AL, and 7DS were detected. The QTL on 2BS explained up to 33.6% of the phenotypic variation in leaf rust response, whereas the QTL on 2DS, 7AL, and 7DS explained up to 15.7, 8.1, and 34.2%, respectively. Seedling infection type tests conducted with P. triticina races BBBD and SBDG confirmed that the QTL on 2BS and 2DS were Lr16 and Lr2a, respectively, and these genes were expressed in the seedling and field plot tests. The Lr2a gene mapped at the same location as Sr6. The QTL on 7DS was Lr34. The QTL on 7AL is a new QTL for leaf rust resistance. The joint effects of all four QTL explained 74% of the total phenotypic variation in leaf rust severity. Analysis of different combinations of QTL showed that the RILs containing all four or three of the QTL had the lowest average leaf rust severity in all five environments. Deployment of these QTL in combination or with other effective genes will lead to successful control of leaf rust.

  2. Triticale: avaliação de linhagens em diferentes regiões paulistas Triticale: evaluation on inbred lines in different regions of the state of São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    Carlos Eduardo de Oliveira Camargo

    1989-01-01

    Full Text Available Compararam-se entre si vinte e quatro linhagens de triticale e o cultivar de trigo IAC-21, através de ensaios em diferentes localidades do Estado de São Paulo, nos anos de 1986 e 1987, analisando-se os seguintes parâmetros: rendimento de grãos, altura de plantas, ciclo em dias da emergência ao florescimento, porcentagem de plantas acamadas, peso de cem grãos e resistência à ferrugem-da-folha e às manchas-foliares em condições de campo. A linhagem de triticale Nutria 7272 foi a mais produtiva (3.098kg/ha, diferindo do 'IAC-21' (2.241 kg/ha e das demais linhagens de triticale, com exceção da Merino"S" - JLO"S" (T-20 e 21, Nutria 440 e Juanillo 159, com 2.891, 2.870, 2.805 e 2.645kg/ha respectivamente. As linhagens de triticale exibiram maior resistência à ferrugem-da-folha com relação ao 'IAC-21'. A Panche 7287 mostrou-se moderadamente resistente às manchas-foliares e, as demais, suscetíveis. As linhagens M2A-KLA"S" x MA (T-6, Faro"S" e Panche 7287 apresentaram ciclo da emergência ao florescimento significativamente maior que o 'IAC-21', e M2A-CML 360 x M2A (T-2, Turk DWF-V 127 x 6TA 204/IA 146, M2A-CML x IA, TCEP 77138, BGL "S"-IGA x PND"S" e BCM"S"-Addax"S" exibiram plantas significativamente mais baixas. A Juanillo 159 apresentou o maior peso de cem grãos, diferindo do 'IAC-21' e das demais linhagens, com exceção da Nutria 7272 e Merino"S" - JLO"S" (T-21.Twenty four triticale inbred lines and the wheat cultivar IAC-21 were evaluated in field experiments carried out at different locations of the State of São Paulo, Brazil, during the years of 1986 and 1987. Grain yield, plant height, number of days from emergence to flowering, percentage of layed plants, weight of 100 grains, resistance to leaf rust (Puccinia graminis sp. tritici and to leaf spots (Helminthosporium sp. and Septoria sp. were evaluated under field conditions. The triticale inbred line Nutria 7272 pre-sented the best grain yield (3,098 kg/ha, showing

  3. Draft genome sequence of an inbred line of Chenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties.

    Science.gov (United States)

    Yasui, Yasuo; Hirakawa, Hideki; Oikawa, Tetsuo; Toyoshima, Masami; Matsuzaki, Chiaki; Ueno, Mariko; Mizuno, Nobuyuki; Nagatoshi, Yukari; Imamura, Tomohiro; Miyago, Manami; Tanaka, Kojiro; Mise, Kazuyuki; Tanaka, Tsutomu; Mizukoshi, Hiroharu; Mori, Masashi; Fujita, Yasunari

    2016-12-01

    Chenopodium quinoa Willd. (quinoa) originated from the Andean region of South America, and is a pseudocereal crop of the Amaranthaceae family. Quinoa is emerging as an important crop with the potential to contribute to food security worldwide and is considered to be an optimal food source for astronauts, due to its outstanding nutritional profile and ability to tolerate stressful environments. Furthermore, plant pathologists use quinoa as a representative diagnostic host to identify virus species. However, molecular analysis of quinoa is limited by its genetic heterogeneity due to outcrossing and its genome complexity derived from allotetraploidy. To overcome these obstacles, we established the inbred and standard quinoa accession Kd that enables rigorous molecular analysis, and presented the draft genome sequence of Kd, using an optimized combination of high-throughput next generation sequencing on the Illumina Hiseq 2500 and PacBio RS II sequencers. The de novo genome assembly contained 25 k scaffolds consisting of 1 Gbp with N50 length of 86 kbp. Based on these data, we constructed the free-access Quinoa Genome DataBase (QGDB). Thus, these findings provide insights into the mechanisms underlying agronomically important traits of quinoa and the effect of allotetraploidy on genome evolution. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  4. Field line mapping results in the CNT stellarator

    International Nuclear Information System (INIS)

    Sarasola, X.; Pedersen, T. Sunn; Kremer, J.P.; Lefrancois, R.G.; Marksteiner, Q.; Ahmad, N.

    2005-01-01

    The Columbia Non-neutral Torus (CNT), located at Columbia University, is a toroidal, ultra-high vacuum stellarator designed to confine pure electron and other non-neutral plasmas. Its coil configuration is the simplest of any stellarator constructed, since it consists only of two pairs of circular planar copper coils. CNT started operation in November 2004. During its first months of operation a detailed mapping of the nested magnetic surfaces has been developed using the fluorescent method. An electron beam was emitted along a field line by a small moveable electron gun. Different beam energies (ranging from 50 to 200 eV) were used to perform the field line mapping. The e- beam emitted by the electron gun followed the field lines around the torus and hit two moveable ZnO coated aluminum rods that emit visible light when struck by the e-beam. For each position of the e- gun, the phosphor rods scanned the cross-section of the torus allowing a standard digital camera to record a single magnetic surface in a five second exposure. Multiple photos were taken and then manipulated and superposed using IDL software to create composite images of the nested magnetic surfaces. Detailed mapping of the magnetic flux surfaces was completed at a variety of magnetic configurations and at pressures in the 10 -8 Torr range. The experimental results were compared with numerical calculations demonstrating that the obtained measurements agree very well with numerical predictions. In particular, the current configuration has an ultralow aspect ratio (A≤ 1.9) and excellent magnetic surface quality with no detectable island structures or stochastic regions, except at the edge of the plasma where a predicted island chain is present. These experimental results will be presented along with details of the field line mapping system. (author)

  5. Reverberation Mapping of Optical Emission Lines in Five Active Galaxies

    Energy Technology Data Exchange (ETDEWEB)

    Fausnaugh, M. M.; Denney, K. D.; Peterson, B. M.; Kochanek, C. S.; Pogge, R. W.; Brown, Jonathan S.; Coker, C. T. [Department of Astronomy, The Ohio State University, 140 W. 18th Avenue, Columbus, OH 43210 (United States); Grier, C. J.; Beatty, Thomas G. [Department of Astronomy and Astrophysics, The Pennsylvania State University, 525 Davey Laboratory, University Park, PA 16802 (United States); Bentz, M. C. [Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303 (United States); Rosa, G. De [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Adams, S. M. [Cahill Center for Astrophysics, California Institute of Technology, Pasadena, CA 91125 (United States); Barth, A. J. [Department of Physics and Astronomy, 4129 Frederick Reines Hall, University of California, Irvine, CA 92697 (United States); Bhattacharjee, A.; Brotherton, M. S. [Department of Physics and Astronomy, University of Wyoming, 1000 E. University Avenue, Laramie, WY (United States); Borman, G. A. [Crimean Astrophysical Observatory, P/O Nauchny, Crimea 298409 (Russian Federation); Boroson, T. A. [Las Cumbres Global Telescope Network, 6740 Cortona Drive, Suite 102, Santa Barbara, CA 93117 (United States); Bottorff, M. C. [Fountainwood Observatory, Department of Physics FJS 149, Southwestern University, 1011 E. University Avenue, Georgetown, TX 78626 (United States); Brown, Jacob E. [Department of Physics and Astronomy, University of Missouri, Columbia (United States); Crawford, S. M. [South African Astronomical Observatory, P.O. Box 9, Observatory 7935, Cape Town (South Africa); and others

    2017-05-10

    We present the first results from an optical reverberation mapping campaign executed in 2014 targeting the active galactic nuclei (AGNs) MCG+08-11-011, NGC 2617, NGC 4051, 3C 382, and Mrk 374. Our targets have diverse and interesting observational properties, including a “changing look” AGN and a broad-line radio galaxy. Based on continuum-H β lags, we measure black hole masses for all five targets. We also obtain H γ and He ii λ 4686 lags for all objects except 3C 382. The He ii λ 4686 lags indicate radial stratification of the BLR, and the masses derived from different emission lines are in general agreement. The relative responsivities of these lines are also in qualitative agreement with photoionization models. These spectra have extremely high signal-to-noise ratios (100–300 per pixel) and there are excellent prospects for obtaining velocity-resolved reverberation signatures.

  6. Reverberation Mapping of Optical Emission Lines in Five Active Galaxies

    International Nuclear Information System (INIS)

    Fausnaugh, M. M.; Denney, K. D.; Peterson, B. M.; Kochanek, C. S.; Pogge, R. W.; Brown, Jonathan S.; Coker, C. T.; Grier, C. J.; Beatty, Thomas G.; Bentz, M. C.; Rosa, G. De; Adams, S. M.; Barth, A. J.; Bhattacharjee, A.; Brotherton, M. S.; Borman, G. A.; Boroson, T. A.; Bottorff, M. C.; Brown, Jacob E.; Crawford, S. M.

    2017-01-01

    We present the first results from an optical reverberation mapping campaign executed in 2014 targeting the active galactic nuclei (AGNs) MCG+08-11-011, NGC 2617, NGC 4051, 3C 382, and Mrk 374. Our targets have diverse and interesting observational properties, including a “changing look” AGN and a broad-line radio galaxy. Based on continuum-H β lags, we measure black hole masses for all five targets. We also obtain H γ and He ii λ 4686 lags for all objects except 3C 382. The He ii λ 4686 lags indicate radial stratification of the BLR, and the masses derived from different emission lines are in general agreement. The relative responsivities of these lines are also in qualitative agreement with photoionization models. These spectra have extremely high signal-to-noise ratios (100–300 per pixel) and there are excellent prospects for obtaining velocity-resolved reverberation signatures.

  7. Genetic Analysis of Fusarium Head Blight Resistance in CIMMYT Bread Wheat Line C615 Using Traditional and Conditional QTL Mapping.

    Science.gov (United States)

    Yi, Xin; Cheng, Jingye; Jiang, Zhengning; Hu, Wenjing; Bie, Tongde; Gao, Derong; Li, Dongsheng; Wu, Ronglin; Li, Yuling; Chen, Shulin; Cheng, Xiaoming; Liu, Jian; Zhang, Yong; Cheng, Shunhe

    2018-01-01

    Fusarium head blight (FHB) is a destructive wheat disease present throughout the world, and host resistance is an effective and economical strategy used to control FHB. Lack of adequate resistance resource is still a main bottleneck for FHB genetics and wheat breeding research. The synthetic-derived bread wheat line C615, which does not carry the Fhb1 gene, is a promising source of FHB resistance for breeding. A population of 198 recombinant inbred lines (RILs) produced by crossing C615 with the susceptible cultivar Yangmai 13 was evaluated for FHB response using point and spray inoculations. As the disease phenotype is frequently complicated by other agronomic traits, we used both traditional and multivariate conditional QTL mapping approaches to investigate the genetic relationships (at the individual QTL level) between FHB resistance and plant height (PH), spike compactness (SC), and days to flowering (FD). A linkage map was constructed from 3,901 polymorphic SNP markers, which covered 2,549.2 cM. Traditional and conditional QTL mapping analyses found 13 and 22 QTL for FHB, respectively; 10 were identified by both methods. Among these 10, three QTL from C615 were detected in multiple years; these QTL were located on chromosomes 2AL, 2DS, and 2DL. Conditional QTL mapping analysis indicated that, at the QTL level, SC strongly influenced FHB in point inoculation; whereas PH and SC contributed more to FHB than did FD in spray inoculation. The three stable QTL ( QFhbs-jaas.2AL, QFhbp-jaas.2DS , and QFhbp-jaas.2DL ) for FHB were partly affected by or were independent of the three agronomic traits. The QTL detected in this study improve our understanding of the genetic relationships between FHB response and related traits at the QTL level and provide useful information for marker-assisted selection for the improvement of FHB resistance in breeding.

  8. Genetic Analysis of Fusarium Head Blight Resistance in CIMMYT Bread Wheat Line C615 Using Traditional and Conditional QTL Mapping

    Science.gov (United States)

    Yi, Xin; Cheng, Jingye; Jiang, Zhengning; Hu, Wenjing; Bie, Tongde; Gao, Derong; Li, Dongsheng; Wu, Ronglin; Li, Yuling; Chen, Shulin; Cheng, Xiaoming; Liu, Jian; Zhang, Yong; Cheng, Shunhe

    2018-01-01

    Fusarium head blight (FHB) is a destructive wheat disease present throughout the world, and host resistance is an effective and economical strategy used to control FHB. Lack of adequate resistance resource is still a main bottleneck for FHB genetics and wheat breeding research. The synthetic-derived bread wheat line C615, which does not carry the Fhb1 gene, is a promising source of FHB resistance for breeding. A population of 198 recombinant inbred lines (RILs) produced by crossing C615 with the susceptible cultivar Yangmai 13 was evaluated for FHB response using point and spray inoculations. As the disease phenotype is frequently complicated by other agronomic traits, we used both traditional and multivariate conditional QTL mapping approaches to investigate the genetic relationships (at the individual QTL level) between FHB resistance and plant height (PH), spike compactness (SC), and days to flowering (FD). A linkage map was constructed from 3,901 polymorphic SNP markers, which covered 2,549.2 cM. Traditional and conditional QTL mapping analyses found 13 and 22 QTL for FHB, respectively; 10 were identified by both methods. Among these 10, three QTL from C615 were detected in multiple years; these QTL were located on chromosomes 2AL, 2DS, and 2DL. Conditional QTL mapping analysis indicated that, at the QTL level, SC strongly influenced FHB in point inoculation; whereas PH and SC contributed more to FHB than did FD in spray inoculation. The three stable QTL (QFhbs-jaas.2AL, QFhbp-jaas.2DS, and QFhbp-jaas.2DL) for FHB were partly affected by or were independent of the three agronomic traits. The QTL detected in this study improve our understanding of the genetic relationships between FHB response and related traits at the QTL level and provide useful information for marker-assisted selection for the improvement of FHB resistance in breeding. PMID:29780395

  9. Tolerância à toxicidade de alumínio de linhagens e híbridos de milho em solução nutritiva Aluminium toxicity tolerance of maize inbred lines and hybrids evaluated in nutrient solution

    Directory of Open Access Journals (Sweden)

    Maria Elisa Ayres Guidetti Zagatto Paterniani

    2002-04-01

    Full Text Available Avaliaram-se dez linhagens de milho do programa de melhoramento do Instituto Agronômico (IAC, em cruzamentos dialélicos e os 45 híbridos resultantes quanto à tolerância à toxicidade de alumínio em laboratório. Estimou-se a tolerância pelo comprimento líquido da radícula (CLR de plântulas em solução nutritiva contendo 4,5 mg.L-1 de alumínio, em ensaio sob delineamento experimental de blocos casualizados com quatro repetições, utilizando-se como padrões linhagens sensível e tolerante de IAC Taiúba. Apresentam-se, ainda, resultados da produtividade desses cruzamentos em ensaios de campo. Identificaram-se linhagens que constituem fontes de tolerância (L 06 e L 09 e híbridos tolerantes à toxicidade de alumínio com elevada produtividade em solos corrigidos. Na análise dialélica, o desdobramento dos efeitos de tratamentos, em capacidade geral (CGC e específica (CEC de combinação, indicou a predominância de efeitos aditivos na manifestação da tolerância ao alumínio tóxico. Obtiveram-se elevados valores de heterose, indicando a existência de interações não alélicas na manifestação do CLR. O híbrido HS 10X11 (denominado IAC 21 aliou alta produtividade e tolerância ao alumínio, apresentando a maior estimativa da CEC para CLR.Ten inbred lines and the resulting forty-five hybrids from the maize IAC breeding program were evaluated for Al tolerance by the nutrient solution technique. Net radicle lengths (CLR of plants grown with 4.5 mg.L-1 were used to estimate Al tolerance. The experimental design was randomized complete block with four replications, and it was used two divergent inbred lines IAC Taiuba as control for Al tolerance and sensitivity, respectively. In addition to these data, it is shown also the grain yield of the same materials from field plots. It was identified two inbred lines (L 06 and L 09 as Al tolerance sources and hybrids potentially adapted to acid soil conditions (tolerant to Al toxicity

  10. Analysis of natural allelic variation of Arabidopsis seed germination and seed longevity traits between the accessions Landberg erecta and Shakdara, using a new recombinant inbred line population

    NARCIS (Netherlands)

    Clerkx, E.J.M.; El-Lithy, M.E.M.; Vierling, E.; Ruijs, G.J.; Vries, de M.H.C.; Groot, S.P.C.; Vreugdenhil, D.; Koornneef, M.

    2004-01-01

    Quantitative trait loci (QTL) mapping was used to identify loci controlling various aspects of seed longevity during storage and germination. Similar locations for QTLs controlling different traits might be an indication for a common genetic control of such traits. For this analysis we used a new

  11. Índice baseado em RFLPs para seleção de linhagens visando sintéticos de milho RFLP marker index for selection of inbred lines aimed at synthetic maize populations

    Directory of Open Access Journals (Sweden)

    Glauce Cristina Ricardo Rumin

    2001-06-01

    Full Text Available Marcadores moleculares têm sido sugeridos como ferramentas úteis em programas de melhoramento de plantas. Assim, este trabalho teve como objetivo propor um índice de seleção de linhagens visando a geração de populações sintéticas de milho, baseado em marcadores moleculares e dados de campo. Para tanto foram utilizados valores fenotípicos e genotípicos, oriundos de experimentos convencionais de campo e através da genotipagem das plantas-mãe das linhagens por marcadores RFLP, respectivamente. O índice foi examinado quanto à sua capacidade de originar sintéticos com alta freqüência de alelos favoráveis, em comparação com os obtidos baseando-se na seleção convencional. Utilizaram-se inicialmente 157 locos marcadores com distância média de 15,30 cM entre eles. Sessenta e oito linhagens S2, provenientes da geração F2 do cruzamento entre duas linhagens homozigóticas foram cruzadas em topcross e avaliadas em quatro locais de Iowa, EUA, em 1996. Dos 157 locos foram selecionados 18 que explicaram 74,70% da variância genética entre progênies, na média dos locais. O índice proposto leva em conta o comportamento próprio (per se das linhagens e a complementaridade genotípica entre elas, o que não é conseguido utilizando-se apenas dados dos topcrosses. O uso do índice proposto permite obter homólogo de tabela dialélica tendo-se apenas dados de médias de topcrosses. O índice levou à seleção de sintéticos com propriedades superiores às esperadas pela seleção baseada apenas nas médias das progênies topcross. Essa conclusão, no entanto, só é válida para os QTL's abrangidos pelas marcas. A metodologia proposta permite monitoramento muito adequado e útil das propriedades genéticas dos sintéticos a serem obtidos.Molecular markers have been suggested as useful tools in breeding programmes. The purpose of this work was to propose and apply an index for inbred line selection to be used for generating synthetic

  12. Resistance to Fusarium verticillioides and fumonisin accumulation in maize inbred lines involves an earlier and enhanced expression of lipoxygenase (LOX) genes.

    Science.gov (United States)

    Maschietto, Valentina; Marocco, Adriano; Malachova, Alexandra; Lanubile, Alessandra

    2015-09-01

    Fusarium verticillioides causes ear rot in maize and contaminates the kernels with the fumonisin mycotoxins. It is known that plant lipoxygenase (LOX)-derived oxylipins regulate defence against pathogens and that the host-pathogen lipid cross-talk influences the pathogenesis. The expression profiles of fifteen genes of the LOX pathway were studied in kernels of resistant and susceptible maize lines, grown in field condition, at 3, 7 and 14 days post inoculation (dpi) with F. verticillioides. Plant defence responses were correlated with the pathogen growth, the expression profiles of fungal FUM genes for fumonisin biosynthesis and fumonisin content in the kernels. The resistant genotype limited fungal growth and fumonisin accumulation between 7 and 14 dpi. Pathogen growth became exponential in the susceptible line after 7 dpi, in correspondence with massive transcription of FUM genes and fumonisins augmented exponentially at 14 dpi. LOX pathway genes resulted strongly induced after pathogen inoculation in the resistant line at 3 and 7 dpi, whilst in the susceptible line the induction was reduced or delayed at 14 dpi. In addition, all genes resulted overexpressed before infection in kernels of the resistant genotype already at 3 dpi. The results suggest that resistance in maize may depend on an earlier activation of LOX genes and genes for jasmonic acid biosynthesis. Copyright © 2015 Elsevier GmbH. All rights reserved.

  13. A protein interaction map of the kalimantacin biosynthesis assembly line

    Directory of Open Access Journals (Sweden)

    Birgit Uytterhoeven

    2016-11-01

    Full Text Available The antimicrobial secondary metabolite kalimantacin is produced by a hybrid polyketide/ non-ribosomal peptide system in Pseudomonas fluorescens BCCM_ID9359. In this study, the kalimantacin biosynthesis gene cluster is analyzed by yeast two-hybrid analysis, creating a protein-protein interaction map of the entire assembly line. In total, 28 potential interactions were identified, of which 13 could be confirmed further. These interactions include the dimerization of ketosynthase domains, a link between assembly line modules 9 and 10, and a specific interaction between the trans-acting enoyl reductase BatK and the carrier proteins of modules 8 and 10. These interactions reveal fundamental insight into the biosynthesis of secondary metabolites.This study is the first to reveal interactions in a complete biosynthetic pathway. Similar future studies could build a strong basis for engineering strategies in such clusters.

  14. Capacidade de combinação entre linhagens de milho visando à produção de milho verde Combining ability of inbred lines of sweet corn

    Directory of Open Access Journals (Sweden)

    Fabricio Rodrigues

    2009-01-01

    specific combining ability (SCA in vegetable corn production. Eight inbred lines and 28 hybrids derived from them were evaluated in 2004/2005 season in two environments, in Lavras and Ijaci, State of Minas Gerais. A randomized complete block design with two replications per environment were used, and seven traits of agronomic and commercial interest for vegetable corn production were studied. The quadratic component of specific of combining ability (SCA was greater than the general combining ability (GCA for all the traits assessed. Non-additive genetic effects were more important than additive effects for genotypes variation, indicating that heterosis is important for hybrid selection for vegetable corn production. The inbred line L55 showed higher concentration of favorable alleles to the increase of traits PEC, PEE, MASSA, COR e COMP, being more suitable for the formation of new hybrid and the hybrids HS27, HS48 and HS24 accumulated a larger number of traits with SCA positive effect, significant and of high magnitude, indicating that those combinations presented better performance for all the traits, simultaneously, and can be recommended to the market for vegetable corn.

  15. Antioxidant enzymatic activities and gene expression associated with heat tolerance in the stems and roots of two cucurbit species ("Cucurbita maxima" and "Cucurbita moschata") and their interspecific inbred line "Maxchata".

    Science.gov (United States)

    Ara, Neelam; Nakkanong, Korakot; Lv, Wenhui; Yang, Jinghua; Hu, Zhongyuan; Zhang, Mingfang

    2013-12-10

    The elucidation of heat tolerance mechanisms is required to combat the challenges of global warming. This study aimed to determine the antioxidant enzyme responses to heat stress, at the enzymatic activity and gene expression levels, and to investigate the antioxidative alterations associated with heat tolerance in the stems and roots of squashes using three genotypes differing in heat tolerance. Plants of heat-tolerant "C. moschata", thermolabile "C. maxima" and moderately heat-tolerant interspecific inbred line "Maxchata" genotypes were exposed to moderate (37 °C) and severe (42 °C) heat shocks. "C. moschata" exhibited comparatively little oxidative damage, with the lowest hydrogen peroxide (H2O2), superoxide (O2(-)) and malondialdehyde (MDA) contents in the roots compared to stems, followed by "Maxchata". The enzyme activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), catalase (CAT) and peroxidase (POD) were found to be increased with heat stress in tolerant genotypes. The significant inductions of FeSOD, MnSOD, APX2, CAT1 and CAT3 isoforms in tolerant genotypes suggested their participation in heat tolerance. The differential isoform patterns of SOD, APX and CAT between stems and roots also indicated their tissue specificity. Furthermore, despite the sequence similarity of the studied antioxidant genes among "C. maxima" and "Maxchata", most of these genes were highly induced under heat stress in "Maxchata", which contributed to its heat tolerance. This phenomenon also indicated the involvement of other unknown genetic and/or epigenetic factors in controlling the expression of these antioxidant genes in squashes, which demands further exploration.

  16. Antioxidant Enzymatic Activities and Gene Expression Associated with Heat Tolerance in the Stems and Roots of Two Cucurbit Species (“Cucurbita maxima” and “Cucurbita moschata”) and Their Interspecific Inbred Line “Maxchata”

    Science.gov (United States)

    Ara, Neelam; Nakkanong, Korakot; Lv, Wenhui; Yang, Jinghua; Hu, Zhongyuan; Zhang, Mingfang

    2013-01-01

    The elucidation of heat tolerance mechanisms is required to combat the challenges of global warming. This study aimed to determine the antioxidant enzyme responses to heat stress, at the enzymatic activity and gene expression levels, and to investigate the antioxidative alterations associated with heat tolerance in the stems and roots of squashes using three genotypes differing in heat tolerance. Plants of heat-tolerant “C. moschata”, thermolabile “C. maxima” and moderately heat-tolerant interspecific inbred line “Maxchata” genotypes were exposed to moderate (37 °C) and severe (42 °C) heat shocks. “C. moschata” exhibited comparatively little oxidative damage, with the lowest hydrogen peroxide (H2O2), superoxide (O2−) and malondialdehyde (MDA) contents in the roots compared to stems, followed by “Maxchata”. The enzyme activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), catalase (CAT) and peroxidase (POD) were found to be increased with heat stress in tolerant genotypes. The significant inductions of FeSOD, MnSOD, APX2, CAT1 and CAT3 isoforms in tolerant genotypes suggested their participation in heat tolerance. The differential isoform patterns of SOD, APX and CAT between stems and roots also indicated their tissue specificity. Furthermore, despite the sequence similarity of the studied antioxidant genes among “C. maxima” and “Maxchata”, most of these genes were highly induced under heat stress in “Maxchata”, which contributed to its heat tolerance. This phenomenon also indicated the involvement of other unknown genetic and/or epigenetic factors in controlling the expression of these antioxidant genes in squashes, which demands further exploration. PMID:24336062

  17. Antioxidant Enzymatic Activities and Gene Expression Associated with Heat Tolerance in the Stems and Roots of Two Cucurbit Species (“Cucurbita maxima” and “Cucurbita moschata” and Their Interspecific Inbred Line “Maxchata”

    Directory of Open Access Journals (Sweden)

    Neelam Ara

    2013-12-01

    Full Text Available The elucidation of heat tolerance mechanisms is required to combat the challenges of global warming. This study aimed to determine the antioxidant enzyme responses to heat stress, at the enzymatic activity and gene expression levels, and to investigate the antioxidative alterations associated with heat tolerance in the stems and roots of squashes using three genotypes differing in heat tolerance. Plants of heat-tolerant “C. moschata”, thermolabile “C. maxima” and moderately heat-tolerant interspecific inbred line “Maxchata” genotypes were exposed to moderate (37 °C and severe (42 °C heat shocks. “C. moschata” exhibited comparatively little oxidative damage, with the lowest hydrogen peroxide (H2O2, superoxide (O2− and malondialdehyde (MDA contents in the roots compared to stems, followed by “Maxchata”. The enzyme activities of superoxide dismutase (SOD, ascorbate peroxidase (APX, catalase (CAT and peroxidase (POD were found to be increased with heat stress in tolerant genotypes. The significant inductions of FeSOD, MnSOD, APX2, CAT1 and CAT3 isoforms in tolerant genotypes suggested their participation in heat tolerance. The differential isoform patterns of SOD, APX and CAT between stems and roots also indicated their tissue specificity. Furthermore, despite the sequence similarity of the studied antioxidant genes among “C. maxima” and “Maxchata”, most of these genes were highly induced under heat stress in “Maxchata”, which contributed to its heat tolerance. This phenomenon also indicated the involvement of other unknown genetic and/or epigenetic factors in controlling the expression of these antioxidant genes in squashes, which demands further exploration.

  18. Combing Ability Analysis ofamong Early Generation Maize Inbred ...

    African Journals Online (AJOL)

    dagne.cimdom

    estimate combining ability effects of locally developed and introduced early generation maize inbred lines for grain ... variance revealed significant difference among the hybrids for all studied traits. General ... Guto LMS5, L15 x SC22 and L20 x TSC22) gave significantly higher grain yield advantage over the two standard ...

  19. Induced cytomictic diversity in maize (Zea mays L.) inbred.

    Science.gov (United States)

    Rai, Prashant Kumar; Kumar, Girjesh; Tripathi, Avinash

    2010-01-01

    Mutation breeding has been used for improving oligogenic and polygenic characters, disease resistance and quantitative characters including yielding ability. The cytological stability of maize inbred lines is an important consideration in view of their extensive use in genetics and plant breeding research. Investigation in Zea mays L. confirms that the migration of chromosomes is a real event that cannot be misunderstood as an artifact produced by fixation or mechanical injuries. During present investigation, we found that out of six inbred lines of Zea mays L. viz. CM-135, CM-136, CM-137, CM-138, CM-142 and CM-213 at various treatment doses of gamma irradiations viz. 200, 400 and 600 Gy, some of the plants of inbred line CM- 138 at 200 Gy dose displayed characteristic cytoplasmic connections during all the stages of meiosis. Four plants from this treatment set were found to be engaged in a rare phenomenon reported as "Cytomixis". It elucidates that in inbred of Zea mays L., induced cytomixis through gamma rays treatment may be considered to be a possible source of production of aneuploid and polyploid gametes. This phenomenon may have several applications in Zea mays L. improvement in the sense of diversity and ever yield potential.

  20. Selection of common bean inbred lines with tolerance to high moisture at harvest Seleção de linhagens de feijão com tolerância a alta umidade no momento da colheita

    Directory of Open Access Journals (Sweden)

    Lidiane Kely de Lima

    2013-04-01

    Full Text Available The occurrence of precipitation / rain in harvest bean causes damage to the product and reduces the yield. The main alternative to mitigate this problem is to obtain cultivars presenting low germination of beans in the pods under conditions of high moisture. The purpose of this study was to verify if there is genetic variability among the common bean inbred lines that are in the phase of recommendation for the South of Minas Gerais, Brazil in regard to tolerance to moisture after harvest, and identify traits that may be routinely used in selection of tolerant lines to these conditions. Ninety-five lines in the phase of recommendation by the Genetic Breeding Program from UFLA were used. After harvest, a sample of plants from each plot was removed for assessments of seed germination in the pods in a moist chamber and water absorption by pod and seed. Eight days after harvest, another sample was removed to assess seed appearance using a scoring scale. The data were submitted to analysis of variance and estimates of the Pearson phenotypic correlations were obtained among traits. Lines differ in relation to tolerance to moisture at the time of harvest, with those of higher tolerance having lighter colored seeds. The main difficulty in selection of common bean lines for tolerance to high moisture at harvest is the repeatability of the environmental conditions among crop seasons. The alternative is assessing the amount of water absorbed by pods.A ocorrência de precipitação / chuva na colheita do feijão comum provoca danos ao produto e reduz o rendimento. A principal alternativa para mitigar este problema é a obtenção de cultivares com baixa germinação de grãos nas vagens em condições de alta umidade. Neste trabalho, objetivou-se vrificar se há variabilidade genética entre as linhagens do feijoeiro que estão em fase de recomendação para o Sul de Minas Gerais quanto à tolerância à umidade após a colheita e identificar caracteres que

  1. Crescimento diferencial de linhagens de milho em solução nutritiva com baixo nível de potássio Differential growth of corn inbred lines in low potassium nutrient solutions

    Directory of Open Access Journals (Sweden)

    Angela Maria Cangiani Furlani

    1986-01-01

    Full Text Available Dois ensaios foram conduzidos no Centro Experimental de Campinas, no período agosto-outubro de 1983, em condições de casa de vegetação, para avaliar e selecionar linhagens de milho (Zea mays L. quanto à eficiência na absorção e utilização de potássio em solução nutritiva. No primeiro ensaio, seis linhagens foram cultivadas com 20, 40, 60, 80 e 100 mg/litro de K até aos 34 dias de idade, com o objetivo de determinar o nível adequado para diferenciação das plantas. No segundo, 37 linhagens de milho foram selecionadas com 20 mg/litro de K até aos 25 dias de idade. As soluções nutritivas foram continuamente arejadas e não renovadas e as plantas, deixadas crescer até aparecerem sintomas de deficiência de potássio nas folhas inferiores. As variações observadas nos pesos de matéria seca das raízes (CV das médias = 38,9% foram maiores que aquelas da parte aérea (CV das médias = 28,5%. As linhagens foram classificadas de acordo com a produção de matéria seca total, em grupos eficientes, ineficientes e medianamente eficientes, utilizando-se de um intervalo de confiança para a média geral. A absorção de K pelas linhagens, avaliada pelo seu conteúdo total, variou (CV das médias = 9% acompanhando a variação observada nos pesos de matéria seca total (r = 0,92. Entretanto, a relação de eficiência das linhagens apresentou variação maior (CV das médias = 23% e também acompanhou a variação no crescimento das plantas (r = 0,99. Isso é uma indicação de que o mecanismo de utilização de K pelas plantas foi o fator que mais contribuiu para a diferenciação entre os genótipos.Two experiments were conducted in the Experimental Station of Campinas, Instituto Agronômico, State of São Paulo, Brazil, in 1983, under greenhouse conditions, in order to evaluate and select efficient corn (Zea mays L. inbred lines in the uptake and use of potassium in nutrient solution. In a first trial, six lines were grow n with 20

  2. Melhoramento do trigo: XVIII. Comportamento de linhagens em cinco regiões paulistas Wheat breeding. XVIII: evaluation on inbred lines for the State of São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    Carlos Eduardo de Oliveira Camargo

    1988-01-01

    Full Text Available Avaliaram-se vinte e duas linhagens e três cultivares de trigo em ensaios instalados em cinco regiões paulistas, em 1984-86, analisando-se os seguintes parâmetros: rendimento de grãos, altura de plantas, ciclo, em dias, da emergência ao florescimento e da emergência à maturação, porcentagem de plantas acamadas, comprimento da espiga, número de grãos por espiga e por espigueta, número de espiguetas por espiga, peso de cem grãos, resistência à ferrugem-do-colmo e da-folha em condições de campo e de casa de vegetação, resistência à helmintosporiose e ao oídio em condições de campo. Em laboratório, foram realizados estudos da tolerância ao alumínio, em soluções nutritivas. Em sequeiro, nos ensaios conduzidos em Capão Bonito e no Vale do Paranapanema (Maracaí e Cruzália, destacaram-se, quanto à produção de grãos, respectivamente, o cultivar BH-1146 e a linhagem 12. As linhagens 4, 9 e 13, em Campinas, e a 8, em Tatuí, evidenciaram alta produção de grãos em condição de irrigação por aspersão. Na média de nove experimentos, destacaram-se em produção de grãos, por ordem decrescente, o cultivar BH-1146 e as linhagens 13, 20 e 14. As linhagens 2, 7, 8, 17 e 18 e o 'Alondra-S-46' mostraram plantas significativamente mais baixas que o 'BH-1146' e 'IAC-5'. As linhagens 7 e 8 e o cultivar Alondra-S-46 mostraram resistência às seis raças e as linhagens 17 e 18 a cinco raças testadas do agente causal de ferrugem-do-colmo em estádio de plântula, em casa de vegetação. Em campo, no estádio de planta adulta, apresentaram menor área infectada por essa doença as linhagens 1, 2, 7, 8, 12 e 17 e o cultivar Alondra-S-46. Nas mesmas condições, as linhagens 1, 5, 8 e 18 exibiram menor área infectada por ferrugem-da-folha. As linhagens 11, 12, 13, 19, 20 e 21 e o cultivar BH-1146 mostraram tolerância à presença de 10mg/litro de Al3+ na solução nutritiva.Twenty two inbred lines from the wheat breeding

  3. Combined linkage and association mapping of flowering time in Sunflower (Helianthus annuus L.).

    Science.gov (United States)

    Cadic, Elena; Coque, Marie; Vear, Felicity; Grezes-Besset, Bruno; Pauquet, Jerôme; Piquemal, Joël; Lippi, Yannick; Blanchard, Philippe; Romestant, Michel; Pouilly, Nicolas; Rengel, David; Gouzy, Jerôme; Langlade, Nicolas; Mangin, Brigitte; Vincourt, Patrick

    2013-05-01

    Association mapping and linkage mapping were used to identify quantitative trait loci (QTL) and/or causative mutations involved in the control of flowering time in cultivated sunflower Helianthus annuus. A panel of 384 inbred lines was phenotyped through testcrosses with two tester inbred lines across 15 location × year combinations. A recombinant inbred line (RIL) population comprising 273 lines was phenotyped both per se and through testcrosses with one or two testers in 16 location × year combinations. In the association mapping approach, kinship estimation using 5,923 single nucleotide polymorphisms was found to be the best covariate to correct for effects of panel structure. Linkage disequilibrium decay ranged from 0.08 to 0.26 cM for a threshold of 0.20, after correcting for structure effects, depending on the linkage group (LG) and the ancestry of inbred lines. A possible hitchhiking effect is hypothesized for LG10 and LG08. A total of 11 regions across 10 LGs were found to be associated with flowering time, and QTLs were mapped on 11 LGs in the RIL population. Whereas eight regions were demonstrated to be common between the two approaches, the linkage disequilibrium approach did not detect a documented QTL that was confirmed using the linkage mapping approach.

  4. Melhoramento do trigo: XII. Comportamento de novas linhagens e cultivares no Estado de São Paulo Wheat breeding: XII. Evaluation of new inbred lines for the State of São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    Carlos Eduardo de Oliveira Camargo

    1985-01-01

    -18',foram tolerantes à presença de 10mg/litro de Al3+ na solução nutritiva.Twenty one inbred lines obtained at the Instituto Agronômico from the wheat breeding program plus the cultivars BH-1146, IAC-18, IAC-17, and Alondra-S-46 were evaluated in field experiments carried out at Campinas Experiment Center and Capão Bonito Experiment Station, during the years of 1982 and 1983, at Tietê Experiment Station, in 1982 and at Floresta Negra Farm, Maracaí, in 1983. Grain yield, plant height, number of days from emergence to flowering and from emergente to maturation, percentage of layed plants, head length, number of grain per spike and per spikelet, number of spikelets, weight of 100 grains, and resistance to stem and leaf rusts were evaluated under field conditions and tests of resistance to stem and leal rusts and to aluminum were also made, respectively, in greenhouse and in laboratory. Considering the trials planted under sprinkler irrigation, at Campinas, the lines IAC-60 and IAC-67 showed good performance regarding to grain yield. In Capão Bonito, represented by acid soils, the lnes IAC-66, IAC-60 and IAC-69 showed high grain yield. The lines IAC-64, IAC-68, IAC-71 and IAC-60 presented good productivity at Tietê Experiment Station and IAC-67, IAC-63 and IAC-64 were more adapted to high soil fertility showing the best grain yields at Maracaí. The lines IAC-52, IAC-53, IAC-54, IAC-55, IAC-56, IAC-57, IAC-58, IAC-60, IAC-64, IAC-65, IAC-67, IAC-71 and the cultivar Alondra-S-46 exhibited semi-dwarf type when compared to the tall cultivar BH-1146. In relation to stem rust, the lines IAC-62 and IAC-65 and the cultivar Alondra-S-46 showed very good resistance presenting at seedling stage, resistance to seven rates under both greenhouse and field conditions. The line IAC-64 was resistant to four and IAC-52 and IAC-55 to three races of leaf rust in the seedling stage under greenhouse condition. The lines IAC-51, IAC-56, IAC-61, IAC-62, IAC-63 and IAC-67 presented

  5. Long-distance pulse propagation on high-frequency dissipative nonlinear transmission lines/resonant tunneling diode line cascaded maps

    International Nuclear Information System (INIS)

    Klofai, Yerima; Essimbi, B Z; Jaeger, D

    2011-01-01

    Pulse propagation on high-frequency dissipative nonlinear transmission lines (NLTLs)/resonant tunneling diode line cascaded maps is investigated for long-distance propagation of short pulses. Applying perturbative analysis, we show that the dynamics of each line is reduced to an expanded Korteweg-de Vries-Burgers equation. Moreover, it is found by computer experiments that the soliton developed in NLTLs experiences an exponential amplitude decay on the one hand and an exponential amplitude growth on the other. As a result, the behavior of a pulse in special electrical networks made of concatenated pieces of lines is closely similar to the transmission of information in optical/electrical communication systems.

  6. Long-distance pulse propagation on high-frequency dissipative nonlinear transmission lines/resonant tunneling diode line cascaded maps

    Energy Technology Data Exchange (ETDEWEB)

    Klofai, Yerima [Department of Physics, Higher Teacher Training College, University of Maroua, PO Box 46 Maroua (Cameroon); Essimbi, B Z [Department of Physics, Faculty of Science, University of Yaounde 1, PO Box 812 Yaounde (Cameroon); Jaeger, D, E-mail: bessimb@yahoo.fr [ZHO, Optoelectronik, Universitaet Duisburg-Essen, D-47048 Duisburg (Germany)

    2011-10-15

    Pulse propagation on high-frequency dissipative nonlinear transmission lines (NLTLs)/resonant tunneling diode line cascaded maps is investigated for long-distance propagation of short pulses. Applying perturbative analysis, we show that the dynamics of each line is reduced to an expanded Korteweg-de Vries-Burgers equation. Moreover, it is found by computer experiments that the soliton developed in NLTLs experiences an exponential amplitude decay on the one hand and an exponential amplitude growth on the other. As a result, the behavior of a pulse in special electrical networks made of concatenated pieces of lines is closely similar to the transmission of information in optical/electrical communication systems.

  7. Mapping of stripe rust resistance gene in an Aegilops caudate introgression line in wheat and its genetic association with leaf rust resistance.

    Science.gov (United States)

    Toor, Puneet Inder; Kaur, Satinder; Bansal, Mitaly; Yadav, Bharat; Chhuneja, Parveen

    2016-12-01

    A pair of stripe rust and leaf rust resistance genes was introgressed from Aegilops caudata, a nonprogenitor diploid species with the CC genome, to cultivated wheat. Inheritance and genetic mapping of stripe rust resistance gene in backcrossrecombinant inbred line (BC-RIL) population derived from the cross of a wheat-Ae. caudata introgression line (IL) T291- 2(pau16060) with wheat cv. PBW343 is reported here. Segregation of BC-RILs for stripe rust resistance depicted a single major gene conditioning adult plant resistance (APR) with stripe rust reaction varying from TR-20MS in resistant RILs signifying the presence of some minor genes as well. Genetic association with leaf rust resistance revealed that two genes are located at a recombination distance of 13%. IL T291-2 had earlier been reported to carry introgressions on wheat chromosomes 2D, 3D, 4D, 5D, 6D and 7D. Genetic mapping indicated the introgression of stripe rust resistance gene on wheat chromosome 5DS in the region carrying leaf rust resistance gene LrAc, but as an independent introgression. Simple sequence repeat (SSR) and sequence-tagged site (STS) markers designed from the survey sequence data of 5DS enriched the target region harbouring stripe and leaf rust resistance genes. Stripe rust resistance locus, temporarily designated as YrAc, mapped at the distal most end of 5DS linked with a group of four colocated SSRs and two resistance gene analogue (RGA)-STS markers at a distance of 5.3 cM. LrAc mapped at a distance of 9.0 cM from the YrAc and at 2.8 cM from RGA-STS marker Ta5DS_2737450, YrAc and LrAc appear to be the candidate genes for marker-assisted enrichment of the wheat gene pool for rust resistance.

  8. Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line.

    Science.gov (United States)

    Teo, Audrey S M; Verzotto, Davide; Yao, Fei; Nagarajan, Niranjan; Hillmer, Axel M

    2015-01-01

    Next-generation sequencing (NGS) technologies have changed our understanding of the variability of the human genome. However, the identification of genome structural variations based on NGS approaches with read lengths of 35-300 bases remains a challenge. Single-molecule optical mapping technologies allow the analysis of DNA molecules of up to 2 Mb and as such are suitable for the identification of large-scale genome structural variations, and for de novo genome assemblies when combined with short-read NGS data. Here we present optical mapping data for two human genomes: the HapMap cell line GM12878 and the colorectal cancer cell line HCT116. High molecular weight DNA was obtained by embedding GM12878 and HCT116 cells, respectively, in agarose plugs, followed by DNA extraction under mild conditions. Genomic DNA was digested with KpnI and 310,000 and 296,000 DNA molecules (≥ 150 kb and 10 restriction fragments), respectively, were analyzed per cell line using the Argus optical mapping system. Maps were aligned to the human reference by OPTIMA, a new glocal alignment method. Genome coverage of 6.8× and 5.7× was obtained, respectively; 2.9× and 1.7× more than the coverage obtained with previously available software. Optical mapping allows the resolution of large-scale structural variations of the genome, and the scaffold extension of NGS-based de novo assemblies. OPTIMA is an efficient new alignment method; our optical mapping data provide a resource for genome structure analyses of the human HapMap reference cell line GM12878, and the colorectal cancer cell line HCT116.

  9. Desempenho agronômico de linhas endogâmicas recombinadas de pimenta em dois sistemas de cultivo Agronomic performance of recombinant chili pepper inbred lines in two cultivation systems

    Directory of Open Access Journals (Sweden)

    Sarah Ola Moreira

    2009-08-01

    .Climate and management diversity play an important role in crop production, since these characteristics are related to genotype and cultivation environment. The aim of this study was to evaluate the effects of genotype, environment and genotype-environmental interaction (GE in 12 recombinant inbred lines of C. annuum. These lines were originated from crosses between the following accessions: a sweet pepper cultivar (susceptible to bacterial spot and a chili pepper (resistant to bacterial spot. Two tests were conducted, the first in a conventional agriculture system, under field conditions and the second in ecological or organic system, under greenhouse conditions. The field experiment was carried out in Campos dos Goytacazes, RJ. The greenhouse experiment was conducted in Seropédica, RJ. Both experiments were performed using a randomized block design with three replications. The measured variables were total fruit number (TFN; total fruit weight (TFW; mean fruit weight (MFW; fruit length (FL; fruit diameter (FD; length/diameter fruit ratio (FL/FD and capsaicin presence (CAPS. Data obtained for each experimental condition were submitted to variance analysis, joint variance analysis, and partitioning of genotype environment interaction. Genotype and GE quadratic components, genotypic determination coefficient, genetic variation coefficient and variation index were determined. The GE interaction was significant for TFN, TFW, MFN, FD, and FL/FD. Cultivation under greenhouse conditions was responsible for the highest mean performance for every trait studied but FL. Values observed for genetic variation were greater than values obtained for environmental variation. For field conditions, the high yield ability observed for line 2 (pungent is suggestive of a potential to be used as a commercial genotype. For greenhouse conditions, line 8 (pungent, had higher fruit number yield. Line 1 (non-pungent also seems promising for commercial cultivation under both conditions.

  10. The Multiplication Map for Global Sections of Line Bundles and ...

    Indian Academy of Sciences (India)

    Let be an integral projective curve and ∈ Pic(), ∈ Pic() with ℎ1(, ) = ℎ1(, ) = 0 and , general. Here we study the rank of the multiplication map ,:0(, ) ⊗ 0(, ) → 0(, ⊗ ). We also study the same problem when and are rank 1 torsion free sheaves on . Most of our results are for  ...

  11. Melhoramento do trigo: XVII. comportamento de linhagens de origem mexicana no estado de São Paulo Wheat breeding: XVII. evaluation of mexican inbred lines for the State of São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    Carlos Eduardo de Oliveira Camargo

    1988-01-01

    Full Text Available Em ensaios instalados nas Estações Experimentais de Monte Alegre do Sul e Tatuí e no município de Maracaí, de 1984 a 1986, estudaram-se 23 linhagens de trigo introduzidas do Centro Internacional de Melhoramento de Milho e Trigo (CIMMYT, México, juntamente com os cultivares IAC-24 e Anahuac. Analisaram-se os seguintes parâmetros: rendimento de grãos, altura de plantas, ciclo em dias da emergência ao florescimento e da emergência à maturação, porcentagem de plantas acamadas, comprimento da espiga, número de grãos por espiga e por espigueta e de espiguetas por espiga, resistência às ferrugens do colmo e da folha em condições de campo e de casa de vegetação, tolerância à toxicidade de Al3+ empregando-se soluções nutritivas, em laboratório. As linhas mexicanas, nominadas como IAC-215, IAC-216, IAC-217 e IAC-219, destacaram-se quanto à produção de grãos, porém não diferiram do cultivar controle IAC-24. As linhagens Festiguay-Tecolote 363.30.6.1 x Ciguena e [4777² x (Frontana/Kenya 58//Newthatch] Gabo/Pavon-76 mostraram-se resistentes às nove raças do agente causal da ferrugem-do-colmo e às seis raças do agente causal da ferrugem-da-folha. Os resultados evidenciaram que são fontes genéticas de grande valor para o programa de melhoramento do trigo no Instituto Agronômico os genótipos seguintes: IAC-215, IAC-216, Yaco"S", IAC-218, Dougga-Bluejay (T-4, Buckbuck"S" - Bulbul"S", com ciclo precoce; IAC-215, Yaco"S" e Jupateco 73-Bluejay, com porte baixo, Bonanza-Yecora F-70/Florence 35.70, com espigas compridas e maior número de espiguetas e de grãos por espiga; Jupateco 73-Bluejay, com grande fertilidade de espigas; [(IAS-58-IAS-55 x Alondra"S"/IAC-5 Alondra"S" - IAS-58 103A x Alondra"S"] e IAC-215, IAC-216, IAC-219 e IAC-24, com tolerância a 10 mg/litro de Al3+.Twenty three Mexican inbred lines and the cultivars IAC-24 and Anahuac were evaluated in field experiments carried out at Monte Alegre do Sul and Tatu

  12. Mapping and validation of a new QTL for adult-plant resistance to powdery mildew in Chinese elite bread wheat line Zhou8425B.

    Science.gov (United States)

    Jia, Aolin; Ren, Yan; Gao, Fengmei; Yin, Guihong; Liu, Jindong; Guo, Lu; Zheng, Jizhou; He, Zhonghu; Xia, Xianchun

    2018-05-01

    Four QTLs for adult-plant resistance to powdery mildew were mapped in the Zhou8425B/Chinese Spring population, and a new QTL on chromosome 3B was validated in 103 wheat cultivars derived from Zhou8425B. Zhou8425B is an elite wheat (Triticum aestivum L.) line widely used as a parent in Chinese wheat breeding programs. Identification of genes for adult-plant resistance (APR) to powdery mildew in Zhou8425B is of high importance for continued controlling the disease. In the current study, the high-density Illumina iSelect 90K single-nucleotide polymorphism (SNP) array was used to map quantitative trait loci (QTL) for APR to powdery mildew in 244 recombinant inbred lines derived from the cross Zhou8425B/Chinese Spring. Inclusive composite interval mapping identified QTL on chromosomes 1B, 3B, 4B, and 7D, designated as QPm.caas-1BL.1, QPm.caas-3BS, QPm.caas-4BL.2, and QPm.caas-7DS, respectively. Resistance alleles at the QPm.caas-1BL.1, QPm.caas-3BS, and QPm.caas-4BL.2 loci were contributed by Zhou8425B, whereas that at QPm.caas-7DS was from Chinese Spring. QPm.caas-3BS, likely to be a new APR gene for powdery mildew resistance, was detected in all four environments. One SNP marker closely linked to QPm.caas-3BS was transferred into a semi-thermal asymmetric reverse PCR (STARP) marker and tested on 103 commercial wheat cultivars derived from Zhou8425B. Cultivars with the resistance allele at the QPm.caas-3BS locus had averaged maximum disease severity reduced by 5.3%. This STARP marker can be used for marker-assisted selection in improvement of the level of powdery mildew resistance in wheat breeding.

  13. Characterization and Mapping of Leaf Rust and Stripe Rust Resistance Loci in Hexaploid Wheat Lines UC1110 and PI610750 under Mexican Environments.

    Science.gov (United States)

    Lan, Caixia; Hale, Iago L; Herrera-Foessel, Sybil A; Basnet, Bhoja R; Randhawa, Mandeep S; Huerta-Espino, Julio; Dubcovsky, Jorge; Singh, Ravi P

    2017-01-01

    Growing resistant wheat varieties is a key method of minimizing the extent of yield losses caused by the globally important wheat leaf rust (LR) and stripe rust (YR) diseases. In this study, a population of 186 F 8 recombinant inbred lines (RILs) derived from a cross between a synthetic wheat derivative (PI610750) and an adapted common wheat line (cv. "UC1110") were phenotyped for LR and YR response at both seedling and adult plant stages over multiple seasons. Using a genetic linkage map consisting of single sequence repeats and diversity arrays technology markers, in combination with inclusive composite interval mapping analysis, we detected a new LR adult plant resistance (APR) locus, QLr.cim-2DS , contributed by UC1110. One co-located resistance locus to both rusts, QLr.cim-3DC/QYr.cim-3DC , and the known seedling resistance gene Lr26 were also mapped. QLr.cim-2DS and QLr.cim-3DC showed a marginally significant interaction for LR resistance in the adult plant stage. In addition, two previously reported YR APR loci, QYr.ucw-3BS and Yr48 , were found to exhibit stable performances in rust environments in both Mexico and the United States and showed a highly significant interaction in the field. Yr48 was also observed to confer intermediate seedling resistance against Mexican YR races, thus suggesting it should be re-classified as an all-stage resistance gene. We also identified 5 and 2 RILs that possessed all detected YR and LR resistance loci, respectively. With the closely linked molecular markers reported here, these RILs could be used as donors for multiple resistance loci to both rusts in wheat breeding programs.

  14. On Line Segment Length and Mapping 4-regular Grid Structures in Network Infrastructures

    DEFF Research Database (Denmark)

    Riaz, Muhammad Tahir; Nielsen, Rasmus Hjorth; Pedersen, Jens Myrup

    2006-01-01

    The paper focuses on mapping the road network into 4-regular grid structures. A mapping algorithm is proposed. To model the road network GIS data have been used. The Geographic Information System (GIS) data for the road network are composed with different size of line segment lengths...

  15. Crop characteristics and weed Interactions of diverse Rrecurrent Inbred Lines (RILs) from a weed-suppressive x non-suppressive rice mapping population

    Science.gov (United States)

    ndica rice genotypes with enhanced weed suppression traits have been previously identified as potentially useful in supplementing weed control efforts in drill-seeded systems in the southern USA. A particularly weed-suppressive indica genotype (PI 312777) that was also high tillering and high yield...

  16. Procedimento para escolha de populações de milho promissoras para extração de linhagens Procedure to select superior maize populations for inbred line extraction

    Directory of Open Access Journals (Sweden)

    MAX WENDEL PAULA LIMA

    2000-01-01

    Full Text Available O sucesso de um programa de melhoramento de milho visando à obtenção de híbridos está intimamente ligado à identificação da população mais promissora para a extração de linhagens. O presente trabalho objetivou identificar procedimentos para a escolha dessas populações. Para isso, foram obtidas populações segregantes S0, S1 e 196 famílias S0:1 de cada um dos quatro materiais comerciais avaliados: híbridos simples (C 333B e Z 8392, duplo (AG 1051 e variedade (BR-105. Os experimentos foram conduzidos na safra agrícola 98/99 em duas localidades na região sul do Estado de Minas Gerais: Lavras e Ijaci. Na avaliação das 196 famílias S0:1 de cada população foi empregado o delineamento látice simples 14 x 14. Adicionalmente foi instalado um experimento em blocos casualizados, com 4 repetições, para avaliação simultânea das gerações F1, S0 e S1 A partir dos dados de produtividade de espigas despalhadas (kg por parcela das gerações F1, S0 e S1, foram obtidas as estimativas da contribuição dos locos em homozigose (m + a e em heterozigose (d. Foram também foram estimados os parâmetros genéticos e fenotípicos com os experimentos das famílias S0:1. Constatou-se que houve boa associação (r = 0,81 entre a estimativa de (m + a e a média das famílias S0:1 e que população com maior potencial para a extração de linhagens, maior (m + a, foi a AG 1051. A correlação entre as estimativas de (d e h² foi baixa, indicando que a estimativa da contribuição dos locos em heterozigose não foi bom indicador da variabilidade potencial da população.The identification of the population with greatest potential for inbred line extraction is directly linked to the success of a maize hybrid breeding program. This study was carried out to identify procedures for selecting these populations. Segregant S0, S1 populations and 196 S0:1 families were obtained from each of four commercial cultivars assessed: single hybrids (C 333B and

  17. Solar monochromatic images in magneto-sensitive spectral lines and maps of vector magnetic fields

    Science.gov (United States)

    Shihui, Y.; Jiehai, J.; Minhan, J.

    1985-01-01

    A new method which allows by use of the monochromatic images in some magneto-sensitive spectra line to derive both the magnetic field strength as well as the angle between magnetic field lines and line of sight for various places in solar active regions is described. In this way two dimensional maps of vector magnetic fields may be constructed. This method was applied to some observational material and reasonable results were obtained. In addition, a project for constructing the three dimensional maps of vector magnetic fields was worked out.

  18. Complex genetic architecture of cardiac disease in a wild type inbred strain of Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Zhi Zhang

    Full Text Available Natural populations of the fruit fly, Drosophila melanogaster, segregate genetic variation that leads to cardiac disease phenotypes. One nearly isogenic line from a North Carolina peach orchard, WE70, is shown to harbor two genetically distinct heart phenotypes: elevated incidence of arrhythmias, and a dramatically constricted heart diameter in both diastole and systole, with resemblance to restrictive cardiomyopathy in humans. Assuming the source to be rare variants of large effect, we performed Bulked Segregant Analysis using genomic DNA hybridization to Affymetrix chips to detect single feature polymorphisms, but found that the mutant phenotypes are more likely to have a polygenic basis. Further mapping efforts revealed a complex architecture wherein the constricted cardiomyopathy phenotype was observed in individual whole chromosome substitution lines, implying that variants on both major autosomes are sufficient to produce the phenotype. A panel of 170 Recombinant Inbred Lines (RIL was generated, and a small subset of mutant lines selected, but these each complemented both whole chromosome substitutions, implying a non-additive (epistatic contribution to the "disease" phenotype. Low coverage whole genome sequencing was also used to attempt to map chromosomal regions contributing to both the cardiomyopathy and arrhythmia, but a polygenic architecture had to be again inferred to be most likely. These results show that an apparently simple rare phenotype can have a complex genetic basis that would be refractory to mapping by deep sequencing in pedigrees. We present this as a cautionary tale regarding assumptions related to attempts to map new disease mutations on the assumption that probands carry a single causal mutation.

  19. Regional analysis assessment of landslide hazard and zoning map for transmission line route selection using GIS

    International Nuclear Information System (INIS)

    Baharuddin, I N Z; Omar, R C; Usman, F; Mejan, M A; Halim, M K Abd; Zainol, M A; Zulkarnain, M S

    2013-01-01

    The stability of ground as foundation for infrastructure development is always associated with geology and geomorphology aspects. Failure to carefully analyze these aspects may induce ground instability such subsidence and landslide which eventually can cause catastrophe to the infrastructure i.e. instability of transmission tower. However, in some cases such as the study area this is unavoidable. A GIS system for analysis of route was favoured to perform optimal route predictions based selection by incorporating multiple influence factors into its analysis by incorporating the Landslide Hazard Map (LHM) that was produced on basis of slope map, aspect map, land use map and geological map with the help of ArcGIS using weighted overlay method. Based on LHM it is safe to conclude that the proposed route for Ulu Jelai- Neggiri-Lebir-LILO transmission line has very low risk in term of landslides.

  20. Ultrasound line-by-line scanning method of spatial-temporal active cavitation mapping for high-intensity focused ultrasound.

    Science.gov (United States)

    Ding, Ting; Zhang, Siyuan; Fu, Quanyou; Xu, Zhian; Wan, Mingxi

    2014-01-01

    This paper presented an ultrasound line-by-line scanning method of spatial-temporal active cavitation mapping applicable in a liquid or liquid filled tissue cavities exposed by high-intensity focused ultrasound (HIFU). Scattered signals from cavitation bubbles were obtained in a scan line immediately after one HIFU exposure, and then there was a waiting time of 2 s long enough to make the liquid back to the original state. As this pattern extended, an image was built up by sequentially measuring a series of such lines. The acquisition of the beamformed radiofrequency (RF) signals for a scan line was synchronized with HIFU exposure. The duration of HIFU exposure, as well as the delay of the interrogating pulse relative to the moment while HIFU was turned off, could vary from microseconds to seconds. The feasibility of this method was demonstrated in tap-water and a tap-water filled cavity in the tissue-mimicking gelatin-agar phantom as capable of observing temporal evolutions of cavitation bubble cloud with temporal resolution of several microseconds, lateral and axial resolution of 0.50 mm and 0.29 mm respectively. The dissolution process of cavitation bubble cloud and spatial distribution affected by cavitation previously generated were also investigated. Although the application is limited by the requirement for a gassy fluid (e.g. tap water, etc.) that allows replenishment of nuclei between HIFU exposures, the technique may be a useful tool in spatial-temporal cavitation mapping for HIFU with high precision and resolution, providing a reference for clinical therapy. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Aerial image geolocalization by matching its line structure with route map

    Science.gov (United States)

    Kunina, I. A.; Terekhin, A. P.; Khanipov, T. M.; Kuznetsova, E. G.; Nikolaev, D. P.

    2017-03-01

    The classic way of aerial photographs geolocation is to bind their local coordinates to a geographic coordinate system using GPS and IMU data. At the same time the possibility of geolocation in a jammed navigation field is also of interest for practical purposes. In this paper we consider one approach to visual localization relatively to a vector road map without GPS. We suggest a geolocalization algorithm which detects image line segments and looks for a geometrical transformation which provides the best mapping between the obtained segments set and line segments in the road map. We consider IMU and altimeter data still known which allows to work with orthorectified images. The problem is hence reduced to a search for a transformation which contains an arbitrary shift and bounded rotation and scaling relatively to the vector map. These parameters are estimated using RANSAC by matching straight line segments from the image to vector map segments. We also investigate how the proposed algorithm's stability is influenced by segment coordinates (two spatial and one angular).

  2. On Line Neutron Flux Mapping in Fuel Coolant Channels of a Research Reactor

    International Nuclear Information System (INIS)

    Barbot, Loic; Domergue, Christophe; Villard, Jean-Francois; Destouches, Christophe; Braoudakis, George; Wassink, David; Sinclair, Bradley; Osborn, John-C.; Wu, Huayou; Blandin, C.; Thevenin, Mathieu; Corre, Gwenole; Normand, Stephane

    2013-06-01

    This work deals with the on-line neutron flux mapping of the OPAL research reactor. A specific irradiation device has been set up to investigate fuel coolant channels using subminiature fission chambers to get thermal neutron flux profiles. Experimental results are compared to first neutronic calculations and show good agreement (C/E ∼0.97). (authors)

  3. The SAURON project - VI. Line strength maps of 48 elliptical and lenticular galaxies

    NARCIS (Netherlands)

    Kuntschner, Harald; Emsellem, Eric; Bacon, R.; Bureau, M.; Cappellari, Michele; Davies, Roger L.; de Zeeuw, P. T.; Falcon-Barroso, Jesus; Krajnovic, Davor; McDermid, Richard M.; Peletier, Reynier F.; Sarzi, Marc

    2006-01-01

    We present absorption line strength maps of 48 representative elliptical and lenticular galaxies obtained as part of a survey of nearby galaxies using our custom-built integral-field spectrograph, SAURON, operating on the William Herschel Telescope. Using high-quality spectra, spatially binned to a

  4. Spitzer spectral line mapping of the HH211 outflow

    DEFF Research Database (Denmark)

    Dionatos, Odyssefs; Nisini, Brunella; Cabrit, Sylvie

    2010-01-01

    of emission line diagnostics and an existing grid of molecular shock models. The physical properties of the warm gas are compared against other molecular jet tracers and to the results of a similar study towards the L1448-C outflow. Results: We have detected and mapped the v=0-0 S(0) - S(7) H2 lines and fine...... compared to solar abundances by a factor ~10-50. Conclusions: Spitzer spectral mapping observations reveal for the first time a cool H$_2$ component towards the CO jet of HH211 consistent with the CO material being fully molecular and warm at ~ 300 K. The maps also reveal for the first time the existence...... uncertainties on jet speed and shock conditions are too large for a definite conclusion....

  5. On Estimation of Contamination from Hydrogen Cyanide in Carbon Monoxide Line-intensity Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Dongwoo T.; Li, Tony Y.; Viero, Marco P.; Church, Sarah E.; Wechsler, Risa H., E-mail: dongwooc@stanford.edu [Kavli Institute for Particle Astrophysics and Cosmology, Physics Department, Stanford University, Stanford, CA 94305 (United States)

    2017-09-01

    Line-intensity mapping surveys probe large-scale structure through spatial variations in molecular line emission from a population of unresolved cosmological sources. Future such surveys of carbon monoxide line emission, specifically the CO(1-0) line, face potential contamination from a disjointed population of sources emitting in a hydrogen cyanide emission line, HCN(1-0). This paper explores the potential range of the strength of HCN emission and its effect on the CO auto power spectrum, using simulations with an empirical model of the CO/HCN–halo connection. We find that effects on the observed CO power spectrum depend on modeling assumptions but are very small for our fiducial model, which is based on current understanding of the galaxy–halo connection. Given the fiducial model, we expect the bias in overall CO detection significance due to HCN to be less than 1%.

  6. Mapping of a rice thermosensitive genic male sterility gene from a TGMS mutant line

    Energy Technology Data Exchange (ETDEWEB)

    Vu Duc Quang; Nguyen Van Dong; Pham Ngoc Luong; Tran Duy Quy [Argicultural Genetics Institute, Hanoi (Viet Nam); Nguyen, Henry T. [Texas Tech Univ., Department of Plant and Soil Science, Lubbock TX (United States)

    2001-03-01

    At the Agricultural Genetics Institute (AGI), Hanoi, Vietnam, a number of thermo-sensitive genic male sterility (TGMS) homozygous rice lines have been developed by means of experimental mutagenesis followed by anther culture techniques. One of them (TGMS-1 indica mutant line) was used in this research. The critical temperature (at the period from pollen mother cell formation to the beginning of meiotic division) for TGMS-1 sterility was 24-25degC, below which the plants were fertile and above which the plants became sterile. Segregation analysis showed that the TGMS trait of the TGMS-1 mutant line was controlled by a single recessive gene. An F{sub 2} mapping population from a cross between TGMS-1 mutant line and CH1 (a fertile indica line) was developed for tagging and mapping the TGMS gene. From survey of 200 AFLP primer combinations in a bulked segregant analysis, 4 AFLP markers (E2/M5-200, E3/M16-400, E5/M12-600 and E5/M12-200) linked to TGMS-1 gene were identified and cloned. All except E2/M5-200 were found to be low-copy number sequences. The marker E5/M12-600 showed polymorphism in RFLP analysis and was closely linked to the TGMS gene at a distance of 3.3cM. This marker was subsequently mapped on chromosome 2 using doubled-haploid mapping populations derived from the crosses IR64xAzucena and CT9993xIR62666. Linkage of microsatellite marker RM27 with the TGMS gene further confirmed its location on chromosome 2. The closest marker, E5/M12-600, was sequenced so that a PCR marker can be developed for the use in marker-assisted breeding. The application of TGMS genes to the commercial two-line hybrid rice breeding system was discussed. (author)

  7. Mapping of a rice thermosensitive genic male sterility gene from a TGMS mutant line

    International Nuclear Information System (INIS)

    Vu Duc Quang; Nguyen Van Dong; Pham Ngoc Luong; Tran Duy Quy; Nguyen, Henry T.

    2001-01-01

    At the Agricultural Genetics Institute (AGI), Hanoi, Vietnam, a number of thermo-sensitive genic male sterility (TGMS) homozygous rice lines have been developed by means of experimental mutagenesis followed by anther culture techniques. One of them (TGMS-1 indica mutant line) was used in this research. The critical temperature (at the period from pollen mother cell formation to the beginning of meiotic division) for TGMS-1 sterility was 24-25degC, below which the plants were fertile and above which the plants became sterile. Segregation analysis showed that the TGMS trait of the TGMS-1 mutant line was controlled by a single recessive gene. An F 2 mapping population from a cross between TGMS-1 mutant line and CH1 (a fertile indica line) was developed for tagging and mapping the TGMS gene. From survey of 200 AFLP primer combinations in a bulked segregant analysis, 4 AFLP markers (E2/M5-200, E3/M16-400, E5/M12-600 and E5/M12-200) linked to TGMS-1 gene were identified and cloned. All except E2/M5-200 were found to be low-copy number sequences. The marker E5/M12-600 showed polymorphism in RFLP analysis and was closely linked to the TGMS gene at a distance of 3.3cM. This marker was subsequently mapped on chromosome 2 using doubled-haploid mapping populations derived from the crosses IR64xAzucena and CT9993xIR62666. Linkage of microsatellite marker RM27 with the TGMS gene further confirmed its location on chromosome 2. The closest marker, E5/M12-600, was sequenced so that a PCR marker can be developed for the use in marker-assisted breeding. The application of TGMS genes to the commercial two-line hybrid rice breeding system was discussed. (author)

  8. Identification of QTLs for grain yield and grain-related traits of maize (Zea mays L.) using an AFLP-map, different testers, and cofactor analysis

    NARCIS (Netherlands)

    Ajimone Marsan, P.; Gorni, C.; Chitto, A.; Redaelli, R.; Vijk, van R.; Stam, P.; Motto, M.

    2001-01-01

    Abstract We exploited the AFLP?1(AFLP? is a registered trademark of Keygene, N.V.) technique to map and characterise quantitative trait loci (QTLs) for grain yield and two grain-related traits of a maize segregating population. Two maize elite inbred lines were crossed to produce 229 F2 individuals

  9. A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues

    NARCIS (Netherlands)

    Marcel, T.C.; Varshney, R.K.; Barbieri, M.; Jafary, H.; Kock, de M.J.D.; Graner, A.; Niks, R.E.

    2007-01-01

    A consensus map of barley was constructed based on three reference doubled haploid (DH) populations and three recombinant inbred line (RIL) populations. Several sets of microsatellites were used as bridge markers in the integration of those populations previously genotyped with RFLP or with AFLP

  10. Developmental and Architectural Principles of the Lateral-line Neural Map

    Directory of Open Access Journals (Sweden)

    Hernan eLopez-Schier

    2013-03-01

    Full Text Available The transmission and central representation of sensory cues through the accurate construction of neural maps is essential for animals to react to environmental stimuli. Structural diversity of sensorineural maps along a continuum between discrete- and continuous-map architectures can influence behavior. The mechanosensory lateral line of fishes and amphibians, for example, detects complex hydrodynamics occurring around the animal body. It. It triggers innate fast escape reactions but also modulates complex navigation behaviors that require constant knowledge about the environment. The aim of this article is to summarize recent work in the zebrafish that has shed light on the development and structure of the lateralis neural map, which is helping to understand how individual sensory modalities generate appropriate behavioral responses to the sensory context.

  11. Seleção de linhagens com tolerância ao calor em germoplasma de tomateiro coletado na região Norte do Brasil Selection of heat tolerant tomato inbred lines from landraces adapted for cultivation in the North Region of Brazil

    Directory of Open Access Journals (Sweden)

    Leonardo de B. Giordano

    2005-03-01

    Full Text Available As altas temperaturas nas regiões tropicais e equatoriais induzem uma série de distúrbios morfológicos e/ou fisiológicos em estruturas florais do tomateiro, resultando em menor produtividade devido a maiores taxas de abortamento e má formação de frutos. Neste trabalho foram avaliadas linhagens de tomateiro oriundas de duas populações que vêm sendo cultivadas em Roraima, região Norte do Brasil. Doze linhagens foram obtidas após um ciclo prévio de seleção (em Brasília-DF em condições de temperatura elevada. A avaliação destas doze linhagens e duas cultivares testemunhas ('Viradoro' e 'Santa Clara' foi conduzida em casa de vegetação com temperaturas média das mínimas de 15ºC e média das máximas de 46,2ºC. Foram observadas diferenças significativas para número de frutos abortados, número de frutos maduros, peso de frutos maduros, teores de sólidos solúveis, firmeza e coloração de frutos. As linhagens (como um grupo apresentaram melhor desempenho do que as testemunhas 'Viradoro' e 'Santa Clara' para os parâmetros número de frutos abortados, peso, número e coloração de frutos maduros. A metodologia adotada no presente trabalho, permite a identificação de genótipos superiores adaptados ao cultivo em regiões tropicais e equatoriais com elevadas temperaturas.Heat tolerance is a major trait for tomato breeding programs targeted for lowland wet climates in equatorial and tropical areas of the world. High temperatures might cause several disturbances to morphological and physiological characteristics of the tomato flowers leading to yield constraints due to reduction in fruit setting. In the present work, an experiment was conducted to evaluate tomato breeding lines, derived from two tomato landrace populations cultivated by farmers in Roraima State (North Region of Brazil. Twelve inbred lines were obtained from these populations after one cycle of selection in a plastic house with high temperatures. These 12

  12. Characterization of phenylpropanoid pathway genes within European maize (Zea mays L.) inbreds

    DEFF Research Database (Denmark)

    Andersen, Jeppe Reitan; Zein, Imad; Wenzel, Gerhard

    2008-01-01

    genomic fragments of six putative phenylpropanoid pathway genes in a panel of elite European inbred lines of maize (Zea mays L.) contrasting in forage quality traits. Six loci, encoding C4H, 4CL1, 4CL2, C3H, F5H, and CAD, displayed different levels of nucleotide diversity and linkage disequilibrium (LD...

  13. The Mapping of On-Line Learning to Flipped Classroom: Small Private Online Course

    Directory of Open Access Journals (Sweden)

    Muqiang Zheng

    2018-03-01

    Full Text Available This study uses an integrated pedagogical tool for knowledge learning as an on-line tool for flipped classroom activities and as an off-line capability training tool. Theoretically, the Experiential Learning Cycle (ELC plays a critical role in promoting students learning effectiveness and performance. However, a dearth of research has applied M-learning and flipped classroom in combination with the ELC stages such as concrete experience, reflective observation, abstract conceptualization, and active experimentation to examine the knowledge and ability learning outcomes for students. This study integrates the On line to Off line (O2O classroom development and usage derived from the four stages of ELC based on on-line knowledge learning and off-line ability training in Microeconomics courses. The results revealed significant improvements in students learning outcomes after O2O mode was implemented. In comparison with traditional teaching methods, not only does O2O teaching significantly improve the students’ learning result of professional knowledge, but O2O teaching also significantly enhanced the capabilities of the students. Furthermore, this study reports the findings from major activities of each ELC stage in O2O classroom practice along with the mapping of on-line learning and off-line training included in the aforementioned stages. Finally, the study provides pedagogical implications and future research directions.

  14. Off-line mapping of multi-rate dependent task sets to many-core platforms

    DEFF Research Database (Denmark)

    Puffitsch, Wolfgang; Noulard, Eric; Pagetti, Claire

    2015-01-01

    This paper presents an approach to execute safety-critical applications on multi- and many-core processors in a predictable manner. We investigate three concrete platforms: the Intel Single-chip Cloud Computer, the Texas Instruments TMS320C6678 and the Tilera TILEmpower-Gx36. We define an execution...... model to safely execute dependent periodic task sets on these platforms. The four rules of the execution model entail that an off-line mapping of the application to the platform must be computed. The paper details our approach to automatically compute a valid mapping. Furthermore, we evaluate our...

  15. Emission-line maps with OSIRIS-TF: The case of M101

    Science.gov (United States)

    Méndez-Abreu, J.

    2013-05-01

    We investigate the suitability of GTC/OSIRIS Tunable Filters (TFs) for obtaining emission-line maps of extended objects. We developed a technique to reconstruct an emission-line image from a set of images taken at consecutive central wavelengths. We demonstrate the feasibility of the reconstruction method by generating a flux calibrated Hα image of the well-known spiral galaxy M101. We tested our emission-line fluxes and ratios by using data present in the literature. We found that the differences in both Hα fluxes and N II/Hα line ratios are ~15% and ~50%, respectively. These results are fully in agreement with the expected values for our observational setup. The proposed methodology will allow us to use OSIRIS/GTC to perform accurate spectrophotometric studies of extended galaxies in the local Universe.

  16. Rhumb lines and map wars a social history of the Mercator projection

    CERN Document Server

    Monmonier, Mark

    2010-01-01

    In Rhumb Lines and Map Wars, Mark Monmonier offers an insightful, richly illustrated account of the controversies surrounding Flemish cartographer Gerard Mercator's legacy. He takes us back to 1569, when Mercator announced a clever method of portraying the earth on a flat surface, creating the first projection to take into account the earth's roundness. As Monmonier shows, mariners benefited most from Mercator's projection, which allowed for easy navigation of the high seas with rhumb lines-clear-cut routes with a constant compass bearing-for true direction. But the projection's popularity amo

  17. The symmetric quartic map for trajectories of magnetic field lines in elongated divertor tokamak plasmas

    Science.gov (United States)

    Jones, Morgin; Wadi, Hasina; Ali, Halima; Punjabi, Alkesh

    2009-04-01

    The coordinates of the area-preserving map equations for integration of magnetic field line trajectories in divertor tokamaks can be any coordinates for which a transformation to (ψt,θ,φ) coordinates exists [A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys. Lett. A 364, 140 (2007)]. ψt is toroidal magnetic flux, θ is poloidal angle, and φ is toroidal angle. This freedom is exploited to construct the symmetric quartic map such that the only parameter that determines magnetic geometry is the elongation of the separatrix surface. The poloidal flux inside the separatrix, the safety factor as a function of normalized minor radius, and the magnetic perturbation from the symplectic discretization are all held constant, and only the elongation is κ varied. The width of stochastic layer, the area, and the fractal dimension of the magnetic footprint and the average radial diffusion coefficient of magnetic field lines from the stochastic layer; and how these quantities scale with κ is calculated. The symmetric quartic map gives the correct scalings which are consistent with the scalings of coordinates with κ. The effects of m =1, n =±1 internal perturbation with the amplitude that is expected to occur in tokamaks are calculated by adding a term [H. Ali, A. Punjabi, A. H. Boozer, and T. Evans, Phys. Plasmas 11, 1908 (2004)] to the symmetric quartic map. In this case, the width of stochastic layer scales as 0.35 power of κ. The area of the footprint is roughly constant. The average radial diffusion coefficient of field lines near the X-point scales linearly with κ. The low mn perturbation changes the quasisymmetric structure of the footprint, and reorganizes it into a single, large scale, asymmetric structure. The symmetric quartic map is combined with the dipole map [A. Punjabi, H. Ali, and A. H. Boozer, Phys. Plasmas 10, 3992 (2003)] to calculate the effects of magnetic perturbation from a current carrying coil. The coil position and coil current coil are

  18. The symmetric quartic map for trajectories of magnetic field lines in elongated divertor tokamak plasmas

    International Nuclear Information System (INIS)

    Jones, Morgin; Wadi, Hasina; Ali, Halima; Punjabi, Alkesh

    2009-01-01

    The coordinates of the area-preserving map equations for integration of magnetic field line trajectories in divertor tokamaks can be any coordinates for which a transformation to (ψ t ,θ,φ) coordinates exists [A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys. Lett. A 364, 140 (2007)]. ψ t is toroidal magnetic flux, θ is poloidal angle, and φ is toroidal angle. This freedom is exploited to construct the symmetric quartic map such that the only parameter that determines magnetic geometry is the elongation of the separatrix surface. The poloidal flux inside the separatrix, the safety factor as a function of normalized minor radius, and the magnetic perturbation from the symplectic discretization are all held constant, and only the elongation is κ varied. The width of stochastic layer, the area, and the fractal dimension of the magnetic footprint and the average radial diffusion coefficient of magnetic field lines from the stochastic layer; and how these quantities scale with κ is calculated. The symmetric quartic map gives the correct scalings which are consistent with the scalings of coordinates with κ. The effects of m=1, n=±1 internal perturbation with the amplitude that is expected to occur in tokamaks are calculated by adding a term [H. Ali, A. Punjabi, A. H. Boozer, and T. Evans, Phys. Plasmas 11, 1908 (2004)] to the symmetric quartic map. In this case, the width of stochastic layer scales as 0.35 power of κ. The area of the footprint is roughly constant. The average radial diffusion coefficient of field lines near the X-point scales linearly with κ. The low mn perturbation changes the quasisymmetric structure of the footprint, and reorganizes it into a single, large scale, asymmetric structure. The symmetric quartic map is combined with the dipole map [A. Punjabi, H. Ali, and A. H. Boozer, Phys. Plasmas 10, 3992 (2003)] to calculate the effects of magnetic perturbation from a current carrying coil. The coil position and coil current coil are

  19. GRILLIX. A 3D turbulence code for magnetic fusion devices based on a field line map

    International Nuclear Information System (INIS)

    Stegmeir, Andreas Korbinian

    2015-01-01

    The complex geometry in the scrape-off layer of tokamaks poses problems to existing turbulence codes. The usually employed field aligned coordinates become ill defined at the separatrix. Therefore the parallel code GRILLIX was developed, which is based on a field line map. This allows simulations in additional complex geometries, especially across the separatrix. A new discretisation, based on the support operator method, for the highly anisotropic diffusion was developed and applied to a simple turbulence model (Hasegawa-Wakatani).

  20. Melhoramento do trigo: XXX. Avaliação de linhagens com tolerância a toxicidade de alumínio, manganês e ferro em condições de campo Wheat breeding: XXX. Evaluation of inbred lines tolerant to aluminum, manganese and iron toxicities under field conditions

    Directory of Open Access Journals (Sweden)

    Carlos Eduardo de Oliveira Camargo

    1995-01-01

    Full Text Available Compararam-se 23 linhagens tolerantes, ao mesmo tempo, à toxicidade de Al3+ Mn2+ e Fe2+, provindas do cruzamento entre 'BH-1146' (tolerante à toxicidade de A1(3+ e sensível à de Mn2+ e Fe2+ e 'Siete Cerros' (sensível à toxicidade de A1(3+ e tolerante à de Mn2+ e Fe2+ e os dois cultivares utilizados como pais em quatro ensaios instalados nas Estações Experimentais de Itararé (1990-92 e de Capão Bonito (1992, em solos ácidos, e em cinco ensaios realizados no Centro Experimental de Campinas (1990-92 e na Fazenda Santa Lúcia (1990-91, município de Cruzália, em solos corrigidos, analisando os seguintes parâmetros: rendimento de grãos, características agronômicas e resistência às doenças. Em solos ácidos, vinte linhagens e o 'BH-1146' mostraram maior rendimento de grãos em relação ao 'Siete Cerros' indicando que a toxicidade de alumínio foi um dos principais fatores limitantes à produção. Em solos corrigidos, não se verificaram diferenças significativas entre os genótipos estudados quanto ao rendimento de grãos, mostrando não haver urna associação entre baixa produtividade e tolerância ao A1(3+ nessas condições. A linhagem 21 foi moderadamente resistente ao agente causal de oídio em condições naturais de infecção. Todos os genótipos avaliados revelaram suscetibilidade aos agentes causais das manchas foliares. O 'Siete Cerros' e as linhagens 3 a 12 apresentaram porte baixo associado à menor porcentagem de acamamento; as 13, 14 e 23 mostraram espigas compridas; a 12, maior número de espiguetas e grãos por espiga, e a 17, grãos mais pesados, representando fontes genéticas de valor para essas características.Twenty three inbred lines showing at the same time tolerance to A1(3+, Mn2+ and Fe2+ toxicities, originated from the cross between 'BH-1146' (tolerant to Al3+ toxicity and sensitive to Mn2+ and Fe2+ toxicities and 'Siete Cerros' (sensitive to Al3+ and tolerant to Mn2+ and Fe2+ toxicities, and the two

  1. MAPPING THE LINEARLY POLARIZED SPECTRAL LINE EMISSION AROUND THE EVOLVED STAR IRC+10216

    Energy Technology Data Exchange (ETDEWEB)

    Girart, J. M. [Institut de Ciencies de l' Espai, (CSIC-IEEC), Campus UAB, Facultat de Ciencies, C5p 2, 08193 Bellaterra, Catalunya (Spain); Patel, N. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Vlemmings, W. H. T. [Department of Earth and Space Sciences, Chalmers University of Technology, Onsala Space Observatory, SE-439 92 Onsala (Sweden); Rao, Ramprasad, E-mail: girart@ice.cat [Submillimeter Array, Academia Sinica Institute of Astronomy and Astrophysics, 645 N. Aohoku Place, Hilo, HI 96720 (United States)

    2012-05-20

    We present spectro-polarimetric observations of several molecular lines obtained with the Submillimeter Array toward the carbon-rich asymptotic giant branch star IRC+10216. We have detected and mapped the linear polarization of the CO 3-2, SiS 19-18, and CS 7-6 lines. The polarization arises at a distance of {approx_equal} 450 AU from the star and is blueshifted with respect to the Stokes I. The SiS 19-18 polarization pattern appears to be consistent with a locally radial magnetic field configuration. However, the CO 3-2 and CS 7-6 line polarization suggests an overall complex magnetic field morphology within the envelope. This work demonstrates the feasibility of using spectro-polarimetric observations to carry out tomographic imaging of the magnetic field in circumstellar envelopes.

  2. Mapping the Antarctic grounding line with CryoSat-2 radar altimetry

    Science.gov (United States)

    Bamber, J. L.; Dawson, G. J.

    2017-12-01

    The grounding line, where grounded ice begins to float, is the boundary at which the ocean has the greatest influence on the ice-sheet. Its position and dynamics are critical in assessing the stability of the ice-sheet, for mass budget calculations and as an input into numerical models. The most reliable approaches to map the grounding line remotely are to measure the limit of tidal flexure of the ice shelf using differential synthetic aperture radar interferometry (DInSAR) or ICESat repeat-track measurements. However, these methods are yet to provide satisfactory spatial and temporal coverage of the whole of the Antarctic grounding zone. It has not been possible to use conventional radar altimetry to map the limit of tidal flexure of the ice shelf because it performs poorly near breaks in slope, commonly associated with the grounding zone. The synthetic aperture radar interferometric (SARin) mode of CryoSat-2, performs better over steeper margins of the ice sheet and allows us to achieve this. The SARin mode combines "delay Doppler" processing with a cross-track interferometer, and enables us to use elevations based on the first return (point of closest approach or POCA) and "swath processed" elevations derived from the time-delayed waveform beyond the first return, to significantly improve coverage. Here, we present a new method to map the limit of tidal motion from a combination of POCA and swath data. We test this new method on the Siple Coast region of the Ross Ice Shelf, and the mapped grounding line is in good agreement with previous observations from DinSAR and ICESat measurements. There is, however, an approximately constant seaward offset between these methods and ours, which we believe is due to the poorer precision of CryoSat-2. This new method has improved the coverage of the grounding zone across the Siple Coast, and can be applied to the rest of Antarctica.

  3. THE APPLICATION OF DIGITAL LINE GRAPHS AND MAP IN THE NETWORK ENVIRONMENT

    Directory of Open Access Journals (Sweden)

    X. Guo

    2012-07-01

    Full Text Available WebGIS is an important research field in GIS. W3C organization established SVG standard, which laid a foundation for WebGIS based on vector data. In China, Digital Line Graphs(DLG is a significant GIS product and it has been used in many medium and large WebGIS system. Geographic information-portrayal is the common method of DLG visualization. However, the inherent characteristics of Geographic information-portrayal may lead to a relatively higher data production input, still, the visualization effect is not ideal. We put forward a new product named Digital Line Graphs and Map(DLGM, which consists of DLG and DLG's cartographic presentation data. It provides visualization data based on the cartographic standards. Due to the manufacture and management of DLGM data that are independent from software and platform, its data can be used in many fields. Network application is one of them. This paper is to use DLGM in the network applications. First it reveals the connotation and characteristics of DLGM then analyses the model that DLGM organizes, manages DLG and map symbol data. After that, combined with SVG standards, we put forward DLGM’s SVG encoding method without any information loss. Finally we provide a web map system based on local area network by using 1:10000 DLGM data of a certain area. Based on this study, we conclude that DLGM can be used in the network environment providing high quality DLG and cartographic data for WebGIS.

  4. Inbred decorated crickets exhibit higher measures of macroparasitic immunity than outbred individuals.

    Science.gov (United States)

    Gershman, S N; Barnett, C A; Pettinger, A M; Weddle, C B; Hunt, J; Sakaluk, S K

    2010-09-01

    Inbreeding is assumed to have negative effects on fitness, including the reduced ability to withstand immune challenges. We examined the immunological consequences of inbreeding in decorated crickets, Gryllodes sigillatus, by comparing lytic activity, phenoloxidase (PO) activity, and encapsulation ability of crickets from eight inbred lines with that of crickets from the outbred founder population. Surprisingly, crickets from inbred lines had a greater encapsulation ability compared with crickets from the outbred population. We suggest that because inbred crickets have reduced reproductive effort, they may, therefore, have the option of devoting more resources to this form of immunity than outbred individuals. We also found that both inbred and outbred females had higher immunity than males in PO activity and implant darkness. This result supports the hypothesis that females should devote more effort to somatic maintenance and immunity than males. PO activity and implant darkness were heritable in both males and females, but lytic activity was only heritable in females. Males and females differed in the heritability of, and genetic correlations among, immune traits, suggesting that differences in selective pressures on males and females may have resulted in a sexual conflict over optimal immune trait values.

  5. LINES

    Directory of Open Access Journals (Sweden)

    Minas Bakalchev

    2015-10-01

    Full Text Available The perception of elements in a system often creates their interdependence, interconditionality, and suppression. The lines from a basic geometrical element have become the model of a reductive world based on isolation according to certain criteria such as function, structure, and social organization. Their traces are experienced in the contemporary world as fragments or ruins of a system of domination of an assumed hierarchical unity. How can one release oneself from such dependence or determinism? How can the lines become less “systematic” and forms more autonomous, and less reductive? How is a form released from modernistic determinism on the new controversial ground? How can these elements or forms of representation become forms of action in the present complex world? In this paper, the meaning of lines through the ideas of Le Corbusier, Leonidov, Picasso, and Hitchcock is presented. Spatial research was made through a series of examples arising from the projects of the architectural studio “Residential Transformations”, which was a backbone for mapping the possibilities ranging from playfulness to exactness, as tactics of transformation in the different contexts of the contemporary world.

  6. POTENTIAL OF COMMERCIAL MAIZE HYBRIDS TO GENERATE INBRED LINES IN BREEDING PROGRAMS POTENCIAL DE HÍBRIDOS COMERCIAIS DE MILHO PARA OBTENÇÃO DE LINHAGENS EM PROGRAMAS DE MELHORAMENTO

    Directory of Open Access Journals (Sweden)

    Maria Elisa Ayres Guidetti Zagatto Paterniani

    2010-08-01

    Full Text Available

    line-height: 120%; text-decoration: none;" lang="pt-BR" align="JUSTIFY">With the objective of identifying the best commercial hybrids to extract maize lines, a top cross scheme of 49 endogamic partial lines (S3 was carried out with the IA33 tester. The resultant hybrids were evaluated for grain yield, in Campinas, Mococa, and Palmital (São Paulo State, Brazil, in two agricultural years (2005/2006 and 2006/2007, in a randomized block design, with three replications, in two experiments (TC1 and TC2. Individual and group variance analysis and a grouped analysis of the experiments with common treatments were carried out, for each place. The top cross hybrids were grouped according to the line origins. Afterwards, orthogonal contrasts were carried out by using the Student’s t test, in order to compare the hybrid groups. It was verified that the use of commercial hybrids to extract lines is an interesting strategy. In general, it was also verified that the top cross hybrid groups, whose lines originated from the AG1051, Master, and XL357 hybrids, obtained high yield, with a higher potential for lines extraction.

    line-height: 120%; text-decoration: none;" lang="en-US" align="JUSTIFY">KEY-WORDS: Zea mays L.; top cross hybrids; partially endogamic lines (S3.

    line-height: 120%; text-decoration: none;" lang="pt-BR" align="JUSTIFY">O presente trabalho teve por objetivo identificar os melhores híbridos comerciais para extração de linhagens de milho. Para isto, foram

  7. Construction of a genetic linkage map in Lilium using a RIL mapping population based on SRAP marker

    Directory of Open Access Journals (Sweden)

    Chen Li-Jing

    2015-01-01

    Full Text Available A genetic linkage map of lily was constructed using RILs (recombinant inbred lines population of 180 individuals. This mapping population was developed by crossing Raizan No.1 (Formolongo and Gelria (Longiflomm cultivars through single-seed descent (SSD. SRAPs were generated by using restriction enzymes EcoRI in combination with either MseI. The resulting products were separated by electrophoresis on 6% denaturing polyacrylamide gel and visualized by silver staining. The segregation of each marker and linkage analysis was done using the program Mapmaker3.0. With 50 primer pairs, a total of 189 parental polymorphic bands were detected and 78 were used for mapping. The total map length was 2,135.5 cM consisted of 16 linkage groups. The number of markers in the linkage groups varied from 1 to 12. The length of linkage groups was range from 11.2 cM to 425.9 cM and mean marker interval distance range from 9.4 cM to 345.4 cM individually. The mean marker interval distance between markers was 27.4 cM. The map developed in the present study was the first sequence-related amplified polymorphism markers map of lily constructed with recombinant inbred lines, it could be used for genetic mapping and molecular marker assisted breeding and quantitative trait locus mapping of Lilium.

  8. A symplectic map for trajectories of magnetic field lines in double-null divertor tokamaks

    Science.gov (United States)

    Crank, Willie; Ali, Halima; Punjabi, Alkesh

    2009-11-01

    The coordinates of the area-preserving map equations for integration of magnetic field line trajectories in tokamaks can be any coordinates for which a transformation to (ψ,θ,φ) coordinates exists [A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys. Lett. A 364, 140 (2007)]. ψ is toroidal magnetic flux, θ is poloidal angle, and φ is toroidal angle. This freedom is exploited to construct a map that represents the magnetic topology of double-null divertor tokamaks. For this purpose, the generating function of the simple map [A. Punjabi, A. Verma, and A. Boozer, Phys. Rev. Lett. 69, 3322 (1992)] is slightly modified. The resulting map equations for the double-null divertor tokamaks are: x1=x0-ky0(1-y0^2 ), y1=y0+kx1. k is the map parameter. It represents the generic topological effects of toroidal asymmetries. The O-point is at (0.0). The X-points are at (0,±1). The equilibrium magnetic surfaces are calculated. These surfaces are symmetric about the x- and y- axes. The widths of stochastic layer near the X-points in the principal plane, and the fractal dimensions of the magnetic footprints on the inboard and outboard side of upper and lower X-points are calculated from the map. This work is supported by US Department of Energy grants DE-FG02-07ER54937, DE-FG02-01ER54624 and DE-FG02-04ER54793.

  9. On a Hopping-Points SVD and Hough Transform-Based Line Detection Algorithm for Robot Localization and Mapping

    Directory of Open Access Journals (Sweden)

    Abhijeet Ravankar

    2016-05-01

    Full Text Available Line detection is an important problem in computer vision, graphics and autonomous robot navigation. Lines detected using a laser range sensor (LRS mounted on a robot can be used as features to build a map of the environment, and later to localize the robot in the map, in a process known as Simultaneous Localization and Mapping (SLAM. We propose an efficient algorithm for line detection from LRS data using a novel hopping-points Singular Value Decomposition (SVD and Hough transform-based algorithm, in which SVD is applied to intermittent LRS points to accelerate the algorithm. A reverse-hop mechanism ensures that the end points of the line segments are accurately extracted. Line segments extracted from the proposed algorithm are used to form a map and, subsequently, LRS data points are matched with the line segments to localize the robot. The proposed algorithm eliminates the drawbacks of point-based matching algorithms like the Iterative Closest Points (ICP algorithm, the performance of which degrades with an increasing number of points. We tested the proposed algorithm for mapping and localization in both simulated and real environments, and found it to detect lines accurately and build maps with good self-localization.

  10. Mapping low- and high-density clouds in astrophysical nebulae by imaging forbidden line emission

    Science.gov (United States)

    Steiner, J. E.; Menezes, R. B.; Ricci, T. V.; Oliveira, A. S.

    2009-06-01

    Emission line ratios have been essential for determining physical parameters such as gas temperature and density in astrophysical gaseous nebulae. With the advent of panoramic spectroscopic devices, images of regions with emission lines related to these physical parameters can, in principle, also be produced. We show that, with observations from modern instruments, it is possible to transform images taken from density-sensitive forbidden lines into images of emission from high- and low-density clouds by applying a transformation matrix. In order to achieve this, images of the pairs of density-sensitive lines as well as the adjacent continuum have to be observed and combined. We have computed the critical densities for a series of pairs of lines in the infrared, optical, ultraviolet and X-rays bands, and calculated the pair line intensity ratios in the high- and low-density limit using a four- and five-level atom approximation. In order to illustrate the method, we applied it to Gemini Multi-Object Spectrograph (GMOS) Integral Field Unit (GMOS-IFU) data of two galactic nuclei. We conclude that this method provides new information of astrophysical interest, especially for mapping low- and high-density clouds; for this reason, we call it `the ld/hd imaging method'. Based on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the National Science Foundation on behalf of the Gemini partnership: the National Science Foundation (United States); the Science and Technology Facilities Council (United Kingdom); the National Research Council (Canada), CONICYT (Chile); the Australian Research Council (Australia); Ministério da Ciência e Tecnologia (Brazil) and Secretaria de Ciencia y Tecnologia (Argentina). E-mail: steiner@astro.iag.usp.br

  11. Híbridos pré-comerciais resistentes a Tuta absoluta obtidos de linhagem de tomateiro rica em acilaçúcares Pre-commercial hybrids obtained from an acylsugar-rich tomato inbred line, resistant to Tuta absoluta

    Directory of Open Access Journals (Sweden)

    Gabriel M Maciel

    2011-06-01

    Full Text Available O trabalho foi realizado com o objetivo de avaliar o potencial agronômico de híbridos de tomateiro a partir da linhagem TOM-687, rica em acilaçúcares e de resistência comprovada a pragas. O experimento foi instalado na HortiAgro, município de Ijaci, MG. Foi constituído de 30 genótipos (5 híbridos comerciais, 1 linhagem pré-comercial (TOM-687, e 24 híbridos nos quais TOM-687 foi utilizada como um dos pais, os quais foram conduzidos em tutoramento com haste dupla, no espaçamento de 1,30 x 0,50 m, totalizando 15.385 plantas por hectare. Foram realizadas nove colheitas, entre as datas de 01/11/08 a 28/11/08. Foram avaliadas as características de massa média por fruto (g fruto-1 e produção por hectare (t ha-1. Os 24 híbridos que tiveram TOM-687 como um dos pais apresentaram potencial produtivo similar ao das testemunhas comerciais Débora Max, Bravo, Bônus, Kombat e Atyna. Dos 24 híbridos experimentais, quatro (TEX-298, TEX-310, TEX-315 e TEX-316 foram avaliados quanto à resistência à traça-do-tomateiro (Tuta absoluta e mostraram-se mais resistentes do que as testemunhas comerciais.This experiment was designed to assess the agronomic potential of tomato hybrids obtained from the tomato line TOM-687, an acylsugar-rich line with confirmed resistance to an array of tomato pests. The experiment was carried out at the HortiAgro Sementes research station, in Ijaci, Minas Gerais State, Brazil. The treatments comprised 30 genotypes (5 commercial hybrid checks, 1 high acylsugar line (TOM-687, and 24 hybrids in which TOM-687 was one of the parents. Plants were trained to two stems, in a spacing of 1.30 m between rows x 0.50 m between plants within a row, totaling 15,385 plants per hectare. Nine harvests were performed between November 1st, 2008 and November 28th,2008. Traits assessed were mean fruit weight (g fruit-1 and total yield (t ha-1. All 24 hybrids with TOM-687 as a parent showed yields similar to those of the commercial check

  12. IDENTIFICATION AND MAPPING OF A GENE FOR RICE SLENDER KERNEL USING Oryza glumaepatula INTROGRESSION LINES

    Directory of Open Access Journals (Sweden)

    Sobrizal Sobrizal

    2016-10-01

    Full Text Available World demand for superior rice grain quality tends to increase. One of the  criteria of appearance quality of rice grain is grain shape. Rice consumers  exhibit wide preferences for grain shape, but most Indonesian rice consumers prefer long and slender grain. The objectives of this study were to identify and map a gene for rice slender kernel trait using Oryza  glumaepatula introgression lines with O. sativa cv. Taichung 65 genetic background. A segregation analysis of BC4F2 population derived from backcrosses of a donor parent O. glumaepatula into a recurrent parent Taichung 65 showed that the slender kernel was controlled by a single recessive gene. This new identified gene was designated as sk1 (slender kernel 1. Moreover, based on the RFLP analyses using 14 RFLP markers located on chromosomes 2, 8, 9, and 10 in which the O. glumaepatula chromosomal segments were retained in BC4F2 population, the sk1 was located between RFLP markers C679 and C560 on the long arm of chromosome 2, with map distances of 2.8 and 1.5 cM, respectively. The wild rice O. glumaepatula carried a recessive allele for slender kernel. This allele may be useful in breeding of rice with slender kernel types. In addition, the development of plant materials and RFLP map associated with slender kernel in this study is the preliminary works in the effort to isolate this important grain shape gene.

  13. CD4+ T-cell lines used to evaluate a Mycobacterium avium subsp. paratuberculosis (MAP) peptide vaccine

    DEFF Research Database (Denmark)

    Lybeck, Kari; Sjurseth, Siri K.; Al-Touama, Zainab

    The aim of the study was to establish a protocol for generation of MAP-specific T-cell lines and to use these lines for evaluation of a peptide vaccine. A protocol for culturing T-cell lines from peripheral blood of goats naturally infected with MAP was established. CD4+ T cells were positively...... selected using an anti CD4 mAb and Dynabeads. Sorted CD4+ cells were cultivated with purified protein derivative from MAP (PPDj) or E. coli sonicate, IL-2, and IL-15. After two cultivation cycles, T cells were tested for recall responses in a proliferative T-cell assay. T-cell line responses were...... in average 92 % for PPDj, and -3 % for E. coli sonicate. CD4+ T-cell lines stimulated with PPDj showed a 6 fold increase in IFN- γ production compared to controls. These results indicated that the T-cell lines were MAP-specific. The protocol was subsequently used to evaluate MAP-specific peptides as vaccine...

  14. ActionMap: A web-based software that automates loci assignments to framework maps.

    Science.gov (United States)

    Albini, Guillaume; Falque, Matthieu; Joets, Johann

    2003-07-01

    Genetic linkage computation may be a repetitive and time consuming task, especially when numerous loci are assigned to a framework map. We thus developed ActionMap, a web-based software that automates genetic mapping on a fixed framework map without adding the new markers to the map. Using this tool, hundreds of loci may be automatically assigned to the framework in a single process. ActionMap was initially developed to map numerous ESTs with a small plant mapping population and is limited to inbred lines and backcrosses. ActionMap is highly configurable and consists of Perl and PHP scripts that automate command steps for the MapMaker program. A set of web forms were designed for data import and mapping settings. Results of automatic mapping can be displayed as tables or drawings of maps and may be exported. The user may create personal access-restricted projects to store raw data, settings and mapping results. All data may be edited, updated or deleted. ActionMap may be used either online or downloaded for free (http://moulon.inra.fr/~bioinfo/).

  15. NeuroLines: A Subway Map Metaphor for Visualizing Nanoscale Neuronal Connectivity

    KAUST Repository

    Al-Awami, Ali K.

    2014-12-31

    We present NeuroLines, a novel visualization technique designed for scalable detailed analysis of neuronal connectivity at the nanoscale level. The topology of 3D brain tissue data is abstracted into a multi-scale, relative distance-preserving subway map visualization that allows domain scientists to conduct an interactive analysis of neurons and their connectivity. Nanoscale connectomics aims at reverse-engineering the wiring of the brain. Reconstructing and analyzing the detailed connectivity of neurons and neurites (axons, dendrites) will be crucial for understanding the brain and its development and diseases. However, the enormous scale and complexity of nanoscale neuronal connectivity pose big challenges to existing visualization techniques in terms of scalability. NeuroLines offers a scalable visualization framework that can interactively render thousands of neurites, and that supports the detailed analysis of neuronal structures and their connectivity. We describe and analyze the design of NeuroLines based on two real-world use-cases of our collaborators in developmental neuroscience, and investigate its scalability to large-scale neuronal connectivity data.

  16. NeuroLines: A Subway Map Metaphor for Visualizing Nanoscale Neuronal Connectivity

    KAUST Repository

    Al-Awami, Ali K.; Beyer, Johanna; Strobelt, Hendrik; Kasthuri, Narayanan; Lichtman, Jeff W.; Pfister, Hanspeter; Hadwiger, Markus

    2014-01-01

    We present NeuroLines, a novel visualization technique designed for scalable detailed analysis of neuronal connectivity at the nanoscale level. The topology of 3D brain tissue data is abstracted into a multi-scale, relative distance-preserving subway map visualization that allows domain scientists to conduct an interactive analysis of neurons and their connectivity. Nanoscale connectomics aims at reverse-engineering the wiring of the brain. Reconstructing and analyzing the detailed connectivity of neurons and neurites (axons, dendrites) will be crucial for understanding the brain and its development and diseases. However, the enormous scale and complexity of nanoscale neuronal connectivity pose big challenges to existing visualization techniques in terms of scalability. NeuroLines offers a scalable visualization framework that can interactively render thousands of neurites, and that supports the detailed analysis of neuronal structures and their connectivity. We describe and analyze the design of NeuroLines based on two real-world use-cases of our collaborators in developmental neuroscience, and investigate its scalability to large-scale neuronal connectivity data.

  17. THE SLOAN DIGITAL SKY SURVEY REVERBERATION MAPPING PROJECT: RAPID C iv BROAD ABSORPTION LINE VARIABILITY

    International Nuclear Information System (INIS)

    Grier, C. J.; Brandt, W. N.; Trump, J. R.; Schneider, D. P.; Hall, P. B.; Shen, Yue; Vivek, M.; Dawson, K. S.; Ak, N. Filiz; Chen, Yuguang; Denney, K. D.; Kochanek, C. S.; Peterson, B. M.; Green, Paul J.; Jiang, Linhua; McGreer, Ian D.; Pâris, I.; Tao, Charling; Wood-Vasey, W. M.; Bizyaev, Dmitry

    2015-01-01

    We report the discovery of rapid variations of a high-velocity C iv broad absorption line trough in the quasar SDSS J141007.74+541203.3. This object was intensively observed in 2014 as a part of the Sloan Digital Sky Survey Reverberation Mapping Project, during which 32 epochs of spectroscopy were obtained with the Baryon Oscillation Spectroscopic Survey spectrograph. We observe significant (>4σ) variability in the equivalent width (EW) of the broad (∼4000 km s −1 wide) C iv trough on rest-frame timescales as short as 1.20 days (∼29 hr), the shortest broad absorption line variability timescale yet reported. The EW varied by ∼10% on these short timescales, and by about a factor of two over the duration of the campaign. We evaluate several potential causes of the variability, concluding that the most likely cause is a rapid response to changes in the incident ionizing continuum. If the outflow is at a radius where the recombination rate is higher than the ionization rate, the timescale of variability places a lower limit on the density of the absorbing gas of n e ≳ 3.9 × 10 5 cm −3 . The broad absorption line variability characteristics of this quasar are consistent with those observed in previous studies of quasars, indicating that such short-term variability may in fact be common and thus can be used to learn about outflow characteristics and contributions to quasar/host-galaxy feedback scenarios

  18. NeuroLines: A Subway Map Metaphor for Visualizing Nanoscale Neuronal Connectivity.

    Science.gov (United States)

    Al-Awami, Ali K; Beyer, Johanna; Strobelt, Hendrik; Kasthuri, Narayanan; Lichtman, Jeff W; Pfister, Hanspeter; Hadwiger, Markus

    2014-12-01

    We present NeuroLines, a novel visualization technique designed for scalable detailed analysis of neuronal connectivity at the nanoscale level. The topology of 3D brain tissue data is abstracted into a multi-scale, relative distance-preserving subway map visualization that allows domain scientists to conduct an interactive analysis of neurons and their connectivity. Nanoscale connectomics aims at reverse-engineering the wiring of the brain. Reconstructing and analyzing the detailed connectivity of neurons and neurites (axons, dendrites) will be crucial for understanding the brain and its development and diseases. However, the enormous scale and complexity of nanoscale neuronal connectivity pose big challenges to existing visualization techniques in terms of scalability. NeuroLines offers a scalable visualization framework that can interactively render thousands of neurites, and that supports the detailed analysis of neuronal structures and their connectivity. We describe and analyze the design of NeuroLines based on two real-world use-cases of our collaborators in developmental neuroscience, and investigate its scalability to large-scale neuronal connectivity data.

  19. Line-Based Registration of Panoramic Images and LiDAR Point Clouds for Mobile Mapping

    Directory of Open Access Journals (Sweden)

    Tingting Cui

    2016-12-01

    Full Text Available For multi-sensor integrated systems, such as the mobile mapping system (MMS, data fusion at sensor-level, i.e., the 2D-3D registration between an optical camera and LiDAR, is a prerequisite for higher level fusion and further applications. This paper proposes a line-based registration method for panoramic images and a LiDAR point cloud collected by a MMS. We first introduce the system configuration and specification, including the coordinate systems of the MMS, the 3D LiDAR scanners, and the two panoramic camera models. We then establish the line-based transformation model for the panoramic camera. Finally, the proposed registration method is evaluated for two types of camera models by visual inspection and quantitative comparison. The results demonstrate that the line-based registration method can significantly improve the alignment of the panoramic image and the LiDAR datasets under either the ideal spherical or the rigorous panoramic camera model, with the latter being more reliable.

  20. Genome characterization of the selected long- and short-sleep mouse lines.

    Science.gov (United States)

    Dowell, Robin; Odell, Aaron; Richmond, Phillip; Malmer, Daniel; Halper-Stromberg, Eitan; Bennett, Beth; Larson, Colin; Leach, Sonia; Radcliffe, Richard A

    2016-12-01

    The Inbred Long- and Short-Sleep (ILS, ISS) mouse lines were selected for differences in acute ethanol sensitivity using the loss of righting response (LORR) as the selection trait. The lines show an over tenfold difference in LORR and, along with a recombinant inbred panel derived from them (the LXS), have been widely used to dissect the genetic underpinnings of acute ethanol sensitivity. Here we have sequenced the genomes of the ILS and ISS to investigate the DNA variants that contribute to their sensitivity difference. We identified ~2.7 million high-confidence SNPs and small indels and ~7000 structural variants between the lines; variants were found to occur in 6382 annotated genes. Using a hidden Markov model, we were able to reconstruct the genome-wide ancestry patterns of the eight inbred progenitor strains from which the ILS and ISS were derived, and found that quantitative trait loci that have been mapped for LORR were slightly enriched for DNA variants. Finally, by mapping and quantifying RNA-seq reads from the ILS and ISS to their strain-specific genomes rather than to the reference genome, we found a substantial improvement in a differential expression analysis between the lines. This work will help in identifying and characterizing the DNA sequence variants that contribute to the difference in ethanol sensitivity between the ILS and ISS and will also aid in accurate quantification of RNA-seq data generated from the LXS RIs.

  1. THE STRUCTURE OF THE BROAD-LINE REGION IN ACTIVE GALACTIC NUCLEI. I. RECONSTRUCTED VELOCITY-DELAY MAPS

    International Nuclear Information System (INIS)

    Grier, C. J.; Peterson, B. M.; Pogge, R. W.; De Rosa, G.; Martini, Paul; Kochanek, C. S.; Zu, Y.; Shappee, B.; Beatty, T. G.; Salvo, C. Araya; Bird, J. C.; Horne, Keith; Bentz, M. C.; Denney, K. D.; Siverd, R.; Sergeev, S. G.; Borman, G. A.; Kaspi, S.; Bord, D. J.; Che, X.

    2013-01-01

    We present velocity-resolved reverberation results for five active galactic nuclei. We recovered velocity-delay maps using the maximum entropy method for four objects: Mrk 335, Mrk 1501, 3C 120, and PG 2130+099. For the fifth, Mrk 6, we were only able to measure mean time delays in different velocity bins of the Hβ emission line. The four velocity-delay maps show unique dynamical signatures for each object. For 3C 120, the Balmer lines show kinematic signatures consistent with both an inclined disk and infalling gas, but the He II λ4686 emission line is suggestive only of inflow. The Balmer lines in Mrk 335, Mrk 1501, and PG 2130+099 show signs of infalling gas, but the He II emission in Mrk 335 is consistent with an inclined disk. We also see tentative evidence of combined virial motion and infalling gas from the velocity-binned analysis of Mrk 6. The maps for 3C 120 and Mrk 335 are two of the most clearly defined velocity-delay maps to date. These maps constitute a large increase in the number of objects for which we have resolved velocity-delay maps and provide evidence supporting the reliability of reverberation-based black hole mass measurements.

  2. THE STRUCTURE OF THE BROAD-LINE REGION IN ACTIVE GALACTIC NUCLEI. I. RECONSTRUCTED VELOCITY-DELAY MAPS

    Energy Technology Data Exchange (ETDEWEB)

    Grier, C. J.; Peterson, B. M.; Pogge, R. W.; De Rosa, G.; Martini, Paul; Kochanek, C. S.; Zu, Y.; Shappee, B.; Beatty, T. G.; Salvo, C. Araya; Bird, J. C. [Department of Astronomy, The Ohio State University, 140 W 18th Ave, Columbus, OH 43210 (United States); Horne, Keith [SUPA Physics and Astronomy, University of St. Andrews, Fife, KY16 9SS Scotland (United Kingdom); Bentz, M. C. [Department of Physics and Astronomy, Georgia State University, Astronomy Offices, One Park Place South SE, Suite 700, Atlanta, GA 30303 (United States); Denney, K. D. [Marie Curie Fellow at the Dark Cosmology Centre, Niels Bohr Institute, University of Copenhagen, Juliane Maries Vej 30, DK-2100 Copenhagen (Denmark); Siverd, R. [Department of Physics and Astronomy, Vanderbilt University, 5301 Stevenson Center, Nashville, TN 37235 (United States); Sergeev, S. G.; Borman, G. A. [Crimean Astrophysical Observatory, P/O Nauchny Crimea 98409 (Ukraine); Kaspi, S. [School of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 (Israel); Bord, D. J. [Department of Natural Sciences, The University of Michigan - Dearborn, 4901 Evergreen Rd, Dearborn, MI 48128 (United States); Che, X. [Department of Astronomy, University of Michigan, 500 Church Street, Ann Arbor, MI 41809 (United States); and others

    2013-02-10

    We present velocity-resolved reverberation results for five active galactic nuclei. We recovered velocity-delay maps using the maximum entropy method for four objects: Mrk 335, Mrk 1501, 3C 120, and PG 2130+099. For the fifth, Mrk 6, we were only able to measure mean time delays in different velocity bins of the H{beta} emission line. The four velocity-delay maps show unique dynamical signatures for each object. For 3C 120, the Balmer lines show kinematic signatures consistent with both an inclined disk and infalling gas, but the He II {lambda}4686 emission line is suggestive only of inflow. The Balmer lines in Mrk 335, Mrk 1501, and PG 2130+099 show signs of infalling gas, but the He II emission in Mrk 335 is consistent with an inclined disk. We also see tentative evidence of combined virial motion and infalling gas from the velocity-binned analysis of Mrk 6. The maps for 3C 120 and Mrk 335 are two of the most clearly defined velocity-delay maps to date. These maps constitute a large increase in the number of objects for which we have resolved velocity-delay maps and provide evidence supporting the reliability of reverberation-based black hole mass measurements.

  3. Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

    Science.gov (United States)

    Paschold, Anja; Jia, Yi; Marcon, Caroline; Lund, Steve; Larson, Nick B.; Yeh, Cheng-Ting; Ossowski, Stephan; Lanz, Christa; Nettleton, Dan; Schnable, Patrick S.; Hochholdinger, Frank

    2012-01-01

    Typically, F1-hybrids are more vigorous than their homozygous, genetically distinct parents, a phenomenon known as heterosis. In the present study, the transcriptomes of the reciprocal maize (Zea mays L.) hybrids B73×Mo17 and Mo17×B73 and their parental inbred lines B73 and Mo17 were surveyed in primary roots, early in the developmental manifestation of heterotic root traits. The application of statistical methods and a suitable experimental design established that 34,233 (i.e., 86%) of all high-confidence maize genes were expressed in at least one genotype. Nearly 70% of all expressed genes were differentially expressed between the two parents and 42%–55% of expressed genes were differentially expressed between one of the parents and one of the hybrids. In both hybrids, ∼10% of expressed genes exhibited nonadditive gene expression. Consistent with the dominance model (i.e., complementation) for heterosis, 1124 genes that were expressed in the hybrids were expressed in only one of the two parents. For 65 genes, it could be shown that this was a consequence of complementation of genomic presence/absence variation. For dozens of other genes, alleles from the inactive inbred were activated in the hybrid, presumably via interactions with regulatory factors from the active inbred. As a consequence of these types of complementation, both hybrids expressed more genes than did either parental inbred. Finally, in hybrids, ∼14% of expressed genes exhibited allele-specific expression (ASE) levels that differed significantly from the parental-inbred expression ratios, providing further evidence for interactions of regulatory factors from one parental genome with target genes from the other parental genome. PMID:23086286

  4. Physiological and photosynthesis response of popcorn inbred seedings to waterlogging stress

    International Nuclear Information System (INIS)

    Zhu, M.; Wang, J.; Li, F.; Shi, Z.

    2015-01-01

    Waterlogging is one of the most severe global problems, which affects crop growth and yield worldwide, especially in the low-lying rainfed areas, and irrigated and heavy rainfall environment. Our objective was to study the physiological and photosynthetic characteristics of two popcorn genotypes under waterlogging conditions. The experiment was carried out in pots with two contrasting inbred lines differing in waterlogging tolerance: Q5 (tolerant) and Q10 (sensitive). Leaf gas exchange, oxidative stress, and chlorophyll (Chl) fluorescence were measured at 0, 2, 4, and 6d in the control and waterlogged plants. A decrease in net photosynthesis, stomatal conductance, and transpiration was observed in both genotypes. The waterlogging-sensitive plants showed reduced chlorophyll fluorescence, chlorophyll content and increased activity of peroxidase and polyphenol oxidase. Response curves for the relationship between photosynthetically active radiation (PAR) and net photosynthetic rate (P /subN/ ) for waterlogged plants were similar in both genotypes. The different physiological and photosynthetic response in the two popcorn inbred lines might be responsible for higher tolerance of Q5 than Q10. These results suggest that Q5 popcorn inbred lines are a source of genetic diversity for important traits such as P /subN/ and WUE. (author)

  5. Climate Signals: An On-Line Digital Platform for Mapping Climate Change Impacts in Real Time

    Science.gov (United States)

    Cutting, H.

    2016-12-01

    Climate Signals is an on-line digital platform for cataloging and mapping the impacts of climate change. The CS platform specifies and details the chains of connections between greenhouse gas emissions and individual climate events. Currently in open-beta release, the platform is designed to to engage and serve the general public, news media, and policy-makers, particularly in real-time during extreme climate events. Climate Signals consists of a curated relational database of events and their links to climate change, a mapping engine, and a gallery of climate change monitors offering real-time data. For each event in the database, an infographic engine provides a custom attribution "tree" that illustrates the connections to climate change. In addition, links to key contextual resources are aggregated and curated for each event. All event records are fully annotated with detailed source citations and corresponding hyper links. The system of attribution used to link events to climate change in real-time is detailed here. This open-beta release is offered for public user testing and engagement. Launched in May 2016, the operation of this platform offers lessons for public engagement in climate change impacts.

  6. Desempenho agronômico de linhas endogâmicas ecombinadas de Capsicum annuum L. em sistema orgânico sob cultivo protegido Agronomic performance of recombinant inbred of Capsicum annuum L. lines cultivated under organic system and greenhouse conditions

    Directory of Open Access Journals (Sweden)

    Sarah Ola Moreira

    2010-08-01

    of this work was to study the agronomic performance of 12 recombinant inbred chili pepper (Capsicum annuum L. lines, from crosses between UENF 1421 and UENF 1381 accessions, under greenhouse conditions and using an organic system. The experiment was carried out at Seropédica Experimental Station of PESAGRO-RIO, in randomized block design, with four replications. The following variables were evaluated: total number of fruits (TNF; total fruit weight (TFW; average weight of fruits (MWF; fruit length (FL; fruit diameter (FD; length and diameter fruit ratio (LDFR, and capsaicin presence (CAPS. Genotypic, phenotypic and environmental variances, as well as genotypic determination coefficient and variation index were estimated. There was highly significant difference for all traits unless TFW. The lines produced a high number of fruits, with low weight and with variability in shape among lines. Absence of capsaicin was observed only in two lines and other three lines segregated for capsaicin presence. High values of genotypic variance and genotypic determination coefficient were estimated for all traits, indicating that the results were due to genetic causes. The data pointed to a preliminary indication of lines 5 and 8 for cultivation in an organic system under greenhouse conditions.

  7. Screening of recombinant inbred lines for salinity tolerance in bread ...

    African Journals Online (AJOL)

    Jane

    2011-10-05

    Oct 5, 2011 ... 2Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran ... indexes for screening bread wheat genotypes for salinity tolerance. ... published on screening methods in salinity tolerance in.

  8. Regenerability of elite tropical maize (Zea mays L.) inbred lines ...

    African Journals Online (AJOL)

    Yomi

    2012-01-10

    Jan 10, 2012 ... maize production (Evenson and Gollin, 2003) due to high heterotic ... the culture media used in the process (Armstrong and. Green, 1985). This calls .... a temperature of 27 ± 1°C. After two weeks of culture on the EMM, embryogenic .... al., 2008). This could be due to blockage of cell division and inactivation ...

  9. Regeneration of Sudanese maize inbred lines and open pollinated ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-06-03

    Jun 3, 2008 ... Keywords: Sudanese maize genotypes, embryogenic callus, regeneration, and tissue culture. INTRODUCTION. Maize is an important food and forage crop in the North- ern and Southern regions of ... Skoog, 1965) containing 60 g l-1 sucrose and lacking 2,4-D (referred to as maturation or RI medium) and ...

  10. Haldane, Waddington and recombinant inbred lines: extension of ...

    Indian Academy of Sciences (India)

    Areejit Samal

    2017-11-24

    Nov 24, 2017 ... advantage for genetic research (Crow 2007). RILs are typically ... quencies to consider which by symmetry can be reduced to 5. ... coined two decades after the work of of Haldane and. Waddington ... and short cut for 3 loci.

  11. Highly efficient generation of GGTA1 biallelic knockout inbred mini-pigs with TALENs.

    Directory of Open Access Journals (Sweden)

    Jige Xin

    Full Text Available Inbred mini-pigs are ideal organ donors for future human xenotransplantations because of their clear genetic background, high homozygosity, and high inbreeding endurance. In this study, we chose fibroblast cells from a highly inbred pig line called Banna mini-pig inbred line (BMI as donor nuclei for nuclear transfer, combining with transcription activator-like effector nucleases (TALENs and successfully generated α-1,3-galactosyltransferase (GGTA1 gene biallelic knockout (KO pigs. To validate the efficiency of TALEN vectors, in vitro-transcribed TALEN mRNAs were microinjected into one-cell stage parthenogenetically activated porcine embryos. The efficiency of indel mutations at the GGTA1-targeting loci was as high as 73.1% (19/26 among the parthenogenetic blastocysts. TALENs were co-transfected into porcine fetal fibroblasts of BMI with a plasmid containing neomycin gene. The targeting efficiency reached 89.5% (187/209 among the survived cell clones after a 10 d selection. More remarkably 27.8% (58/209 of colonies were biallelic KO. Five fibroblast cell lines with biallelic KO were chosen as nuclear donors for somatic cell nuclear transfer (SCNT. Three miniature piglets with biallelic mutations of the GGTA1 gene were achieved. Gal epitopes on the surface of cells from all the three biallelic KO piglets were completely absent. The fibroblasts from the GGTA1 null piglets were more resistant to lysis by pooled complement-preserved normal human serum than those from wild-type pigs. These results indicate that a combination of TALENs technology with SCNT can generate biallelic KO pigs directly with high efficiency. The GGTA1 null piglets with inbred features created in this study can provide a new organ source for xenotransplantation research.

  12. THE SLOAN DIGITAL SKY SURVEY REVERBERATION MAPPING PROJECT: RAPID C iv BROAD ABSORPTION LINE VARIABILITY

    Energy Technology Data Exchange (ETDEWEB)

    Grier, C. J.; Brandt, W. N.; Trump, J. R.; Schneider, D. P. [Department of Astronomy and Astrophysics and Institute for Gravitation and the Cosmos, The Pennsylvania State University, 525 Davey Laboratory, University Park, PA 16802 (United States); Hall, P. B. [Department of Physics and Astronomy, York University, Toronto, ON M3J 1P3 (Canada); Shen, Yue [Carnegie Observatories, 813 Santa Barbara Street, Pasadena, CA 91101 (United States); Vivek, M.; Dawson, K. S. [Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112 (United States); Ak, N. Filiz [Faculty of Sciences, Department of Astronomy and Space Sciences, Erciyes University, 38039 Kayseri (Turkey); Chen, Yuguang [Department of Astronomy, School of Physics, Peking University, Beijing 100871 (China); Denney, K. D.; Kochanek, C. S.; Peterson, B. M. [Department of Astronomy, The Ohio State University, 140 West 18th Avenue, Columbus, OH 43210 (United States); Green, Paul J. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Jiang, Linhua [Kavli Institute for Astronomy and Astrophysics, Peking University, Beijing 100871 (China); McGreer, Ian D. [Steward Observatory, The University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721-0065 (United States); Pâris, I. [INAF-Osservatorio Astronomico di Trieste, Via G. B. Tiepolo 11, I-34131 Trieste (Italy); Tao, Charling [Centre de Physique des Particules de Marseille, Aix-Marseille Universite, CNRS /IN2P3, 163, avenue de Luminy, Case 902, F-13288 Marseille Cedex 09 (France); Wood-Vasey, W. M. [PITT PACC, Department of Physics and Astronomy, University of Pittsburgh, 3941 O’Hara Street, Pittsburgh, PA 15260 (United States); Bizyaev, Dmitry, E-mail: grier@psu.edu [Apache Point Observatory and New Mexico State University, P.O. Box 59, Sunspot, NM, 88349-0059 (United States); and others

    2015-06-10

    We report the discovery of rapid variations of a high-velocity C iv broad absorption line trough in the quasar SDSS J141007.74+541203.3. This object was intensively observed in 2014 as a part of the Sloan Digital Sky Survey Reverberation Mapping Project, during which 32 epochs of spectroscopy were obtained with the Baryon Oscillation Spectroscopic Survey spectrograph. We observe significant (>4σ) variability in the equivalent width (EW) of the broad (∼4000 km s{sup −1} wide) C iv trough on rest-frame timescales as short as 1.20 days (∼29 hr), the shortest broad absorption line variability timescale yet reported. The EW varied by ∼10% on these short timescales, and by about a factor of two over the duration of the campaign. We evaluate several potential causes of the variability, concluding that the most likely cause is a rapid response to changes in the incident ionizing continuum. If the outflow is at a radius where the recombination rate is higher than the ionization rate, the timescale of variability places a lower limit on the density of the absorbing gas of n{sub e} ≳ 3.9 × 10{sup 5} cm{sup −3}. The broad absorption line variability characteristics of this quasar are consistent with those observed in previous studies of quasars, indicating that such short-term variability may in fact be common and thus can be used to learn about outflow characteristics and contributions to quasar/host-galaxy feedback scenarios.

  13. Development of a sensor platform for roadway mapping : part b - mapping the road fog lines : final report.

    Science.gov (United States)

    2015-04-01

    Our objective is the development and evaluation of a low-cost, vehicle-mounted sensor suite capable of generating : map data with lane and road boundary information accurate to the 10 cm (4 in) level. Such a map could be used for : a number of differ...

  14. The SAURON project - XI. Stellar populations from absorption-line strength maps of 24 early-type spirals

    NARCIS (Netherlands)

    Peletier, Reynier F.; Falcon-Barroso, Jesus; Bacon, Roland; Cappellari, Michele; Davies, Roger L.; de Zeeuw, P. T.; Emsellem, Eric; Ganda, Katia; Krajnovic, Davor; Kuntschner, Harald; McDermid, Richard M.; Sarzi, Marc; van de Ven, Glenn

    2007-01-01

    We present absorption-line strength maps of a sample of 24 representative early-type spiral galaxies, mostly of type Sa, obtained as part of the SAURON (Spectrographic Areal Unit for Research on Optical Nebulae) survey of nearby galaxies using our custom-built integral-field spectrograph. Using

  15. Pipeline mapping and strain assessment using ILI (In-line Inspection) tolls

    Energy Technology Data Exchange (ETDEWEB)

    Purvis, Brian [GE PII Pipeline Solutions, Rio de Janeiro, RJ (Brazil); Huewener, Thomas [E.ON Ruhrgas AG, Essen (Germany)

    2009-07-01

    GE PII IMU Mapping inspection system measures pipeline location coordinates (x, y, z) and provides data for determining pipeline curvature and consequential pipeline bending strain. The changes in strain can be used in the application of structural analyses and integrity evaluation of pipeline systems. This paper reviews the Inertia Measuring Unit (IMU) system and field investigation works performed on a high-pressure gas pipeline for E.ON Ruhrgas AG. The Inertial Measuring Unit of the pipeline inspection tool provides continuous measurement of the pipeline centreline coordinates. More than one inspection run was performed which allowed a more accurate strain comparison to be made. Repeatability is important to establish the reasons for increasing strain values detected at specific pipeline sections through in-line inspection surveys conducted in regular intervals over many years. Moreover, the flexibility resulting from a combination of different sensor technologies, makes it possible to provide a more complete picture of the overall situation. This paper reviews the work involved in detecting, locating and determining the magnitude and type of strain corresponding to the pipeline movement in field. (author)

  16. Construction of a genome-anchored, high-density genetic map for melon (Cucumis melo L.) and identification of Fusarium oxysporum f. sp. melonis race 1 resistance QTL.

    Science.gov (United States)

    Branham, Sandra E; Levi, Amnon; Katawczik, Melanie; Fei, Zhangjun; Wechter, W Patrick

    2018-04-01

    Four QTLs and an epistatic interaction were associated with disease severity in response to inoculation with Fusarium oxysporum f. sp. melonis race 1 in a recombinant inbred line population of melon. The USDA Cucumis melo inbred line, MR-1, harbors a wealth of alleles associated with resistance to several major diseases of melon, including powdery mildew, downy mildew, Alternaria leaf blight, and Fusarium wilt. MR-1 was crossed to an Israeli cultivar, Ananas Yok'neam, which is susceptible to all of these diseases, to generate a recombinant inbred line (RIL) population of 172 lines. In this study, the RIL population was genotyped to construct an ultra-dense genetic linkage map with 5663 binned SNPs anchored to the C. melo genome and exhibits the overall high quality of the assembly. The utility of the densely genotyped population was demonstrated through QTL mapping of a well-studied trait, resistance to Fusarium wilt caused by Fusarium oxysporum f. sp. melonis (Fom) race 1. A major QTL co-located with the previously validated resistance gene Fom-2. In addition, three minor QTLs and an epistatic interaction contributing to Fom race 1 resistance were identified. The MR-1 × AY RIL population provides a valuable resource for future QTL mapping studies and marker-assisted selection of disease resistance in melon.

  17. A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification

    Directory of Open Access Journals (Sweden)

    Daniel Fulop

    2016-10-01

    Full Text Available Quantitative Trait Loci (QTL mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum and its more distant interfertile relatives typically follow a near isogenic line (NIL design, such as the S. pennellii Introgression Line (IL population, with a single wild introgression per line in an otherwise domesticated genetic background. Here, we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennellii. This so-called Backcrossed Inbred Line (BIL population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs, we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous hidden Markov model for genotyping the lines, and by using state-of-the-art sparse regression techniques for QTL mapping.

  18. Analysis of aneuploid lines of bread wheat to map chromosomal locations of genes controlling root hair length.

    Science.gov (United States)

    Liu, Miao; Rathjen, Tina; Weligama, Kumara; Forrest, Kerrie; Hayden, Matthew; Delhaize, Emmanuel

    2017-06-01

    Long root hairs enable the efficient uptake of poorly mobile nutrients such as phosphorus. Mapping the chromosomal locations of genes that control root hair length can help exploit the natural variation within crops to develop improved cultivars. Genetic stocks of the wheat cultivar 'Chinese Spring' were used to map genes that control root hair length. Aneuploid stocks of 'Chinese Spring' were screened using a rapid method based on rhizosheath size and then selected lines were assayed for root hair length to identify chromosomes harbouring genes controlling root hair length. A series of lines with various fractional deletions of candidate chromosomes were then screened to map the root hair loci more accurately. A line with a deletion in chromosome 5A was analysed with a 90 000 single nucleotide polymorphism (SNP) array. The phosphorus acquisition efficiency (PAE) of one deletion line was compared with that of euploid 'Chinese Spring' by growing the seedlings in pots at low and luxury phosphorus supplies. Chromosomes 1A, 1D and 5A were found to harbour genes controlling root hair length. The 90 000 SNP array identified two candidate genes controlling root hair length located on chromosome 5A. The line with a deletion in chromosome 5A had root hairs that were approx. 20 % shorter than euploid 'Chinese Spring', but this was insufficient to reduce its PAE. A rapid screen for rhizosheath size enabled chromosomal regions controlling root hair length to be mapped in the wheat cultivar 'Chinese Spring' and subsequent analysis with an SNP array identified candidate genes controlling root hair length. The difference in root hair length between euploid 'Chinese Spring' and a deletion line identified in the rapid screen was still apparent, albeit attenuated, when the seedlings were grown on a fully fertilized soil. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  19. FEDERAL USERS CONFERENCE PRODUCT LINE TOOL SET (PLTS) MAP PRODUCTION SYSTEM (MPS) ATLAS CUSTOM GRIDS [Rev 0 was draft

    Energy Technology Data Exchange (ETDEWEB)

    HAYENGA, J.L.

    2006-12-19

    Maps, and more importantly Atlases, are assisting the user community in managing a large land area with complex issues, the most complex of which is the management of nuclear waste. The techniques and experiences discussed herein were gained while developing several atlases for use at the US Department of Energy's Hanford Site. The user community requires the ability to locate not only waste sites, but other features as well. Finding a specific waste site on a map and in the field is a difficult task at a site the size of Hanford. To find a specific waste site, the user begins by locating the item or object in an index, then locating the feature on the corresponding map within an atlas. Locating features requires a method for indexing them. The location index and how to place it on a map or atlas is the central theme presented in this article. The user requirements for atlases forced the design team to develop new and innovative solutions for requirements that Product Line Tool Set (PLTS) Map Production System (MPS)-Atlas was not designed to handle. The layout of the most complex atlases includes custom reference grids, multiple data frames, multiple map series, and up to 250 maps. All of these functional requirements are at the extreme edge of the capabilities of PLTS MPS-Atlas. This document outlines the setup of an atlas using PLTS MPS-Atlas to meet these requirements.

  20. FEDERAL USERS CONFERENCE PRODUCT LINE TOOL SET (PLTS) MAP PRODUCTION SYSTEM (MPS) ATLAS CUSTOM GRIDS [Rev 0 was draft

    International Nuclear Information System (INIS)

    HAYENGA, J.L.

    2006-01-01

    Maps, and more importantly Atlases, are assisting the user community in managing a large land area with complex issues, the most complex of which is the management of nuclear waste. The techniques and experiences discussed herein were gained while developing several atlases for use at the US Department of Energy's Hanford Site. The user community requires the ability to locate not only waste sites, but other features as well. Finding a specific waste site on a map and in the field is a difficult task at a site the size of Hanford. To find a specific waste site, the user begins by locating the item or object in an index, then locating the feature on the corresponding map within an atlas. Locating features requires a method for indexing them. The location index and how to place it on a map or atlas is the central theme presented in this article. The user requirements for atlases forced the design team to develop new and innovative solutions for requirements that Product Line Tool Set (PLTS) Map Production System (MPS)-Atlas was not designed to handle. The layout of the most complex atlases includes custom reference grids, multiple data frames, multiple map series, and up to 250 maps. All of these functional requirements are at the extreme edge of the capabilities of PLTS MPS-Atlas. This document outlines the setup of an atlas using PLTS MPS-Atlas to meet these requirements

  1. A simple highly accurate field-line mapping technique for three-dimensional Monte Carlo modeling of plasma edge transport

    International Nuclear Information System (INIS)

    Feng, Y.; Sardei, F.; Kisslinger, J.

    2005-01-01

    The paper presents a new simple and accurate numerical field-line mapping technique providing a high-quality representation of field lines as required by a Monte Carlo modeling of plasma edge transport in the complex magnetic boundaries of three-dimensional (3D) toroidal fusion devices. Using a toroidal sequence of precomputed 3D finite flux-tube meshes, the method advances field lines through a simple bilinear, forward/backward symmetric interpolation at the interfaces between two adjacent flux tubes. It is a reversible field-line mapping (RFLM) algorithm ensuring a continuous and unique reconstruction of field lines at any point of the 3D boundary. The reversibility property has a strong impact on the efficiency of modeling the highly anisotropic plasma edge transport in general closed or open configurations of arbitrary ergodicity as it avoids artificial cross-field diffusion of the fast parallel transport. For stellarator-symmetric magnetic configurations, which are the standard case for stellarators, the reversibility additionally provides an average cancellation of the radial interpolation errors of field lines circulating around closed magnetic flux surfaces. The RFLM technique has been implemented in the 3D edge transport code EMC3-EIRENE and is used routinely for plasma transport modeling in the boundaries of several low-shear and high-shear stellarators as well as in the boundary of a tokamak with 3D magnetic edge perturbations

  2. Optimization of particle bombardment parameters for the genetic transformation of Brazilian maize inbred lines Otimização dos parâmetros de bombardeamento de partículas para a transformação genética de linhagens brasileiras de milho

    Directory of Open Access Journals (Sweden)

    Caroline Pereira Petrillo

    2008-03-01

    Full Text Available The objective of this work was to develop a genetic transformation system for tropical maize genotypes via particle bombardment of immature zygotic embryos. Particle bombardment was carried out using a genetic construct with bar and uidA genes under control of CaMV35S promoter. The best conditions to transform maize tropical inbred lines L3 and L1345 were obtained when immature embryos were cultivated, prior to the bombardment, in higher osmolarity during 4 hours and bombarded at an acceleration helium gas pressure of 1,100 psi, two shots per plate, and a microcarrier flying distance of 6.6 cm. Transformation frequencies obtained using these conditions ranged from 0.9 to 2.31%. Integration of foreign genes into the genome of maize plants was confirmed by Southern blot analysis as well as bar and uidA gene expressions. The maize genetic transformation protocol developed in this work will possibly improve the efficiency to produce new transgenic tropical maize lines expressing desirable agronomic characteristics.O objetivo deste trabalho foi desenvolver um sistema de transformação genética para genótipos tropicais de milho pelo bombardeamento de embriões imaturos com micropartículas. O bombardeamento com partículas foi realizado utilizando-se uma construção gênica contendo os genes bar e uidA sob o controle do promotor CaMV35S. As melhores condições para transformação das linhagens de milho tropical L3 e L1345 foram obtidas após o cultivo de embriões imaturos durante 4 horas, antes do bombardeamento, em alta osmolaridade, e bombardeados com a pressão de 1.100 psi de gás hélio, dois tiros por placa e uma distância de vôo da micropartícula de 6,6 cm. As freqüências de transformação obtidas variaram entre 0,9 e 2,31%. A integração dos genes heterólogos no genoma das plantas transgênicas de milho foi confirmada por análises de Southern blot e expressão dos genes bar e uidA. O protocolo de transformação genética de

  3. Heterogeneous stock rat: a unique animal model for mapping genes influencing bone fragility.

    Science.gov (United States)

    Alam, Imranul; Koller, Daniel L; Sun, Qiwei; Roeder, Ryan K; Cañete, Toni; Blázquez, Gloria; López-Aumatell, Regina; Martínez-Membrives, Esther; Vicens-Costa, Elia; Mont, Carme; Díaz, Sira; Tobeña, Adolf; Fernández-Teruel, Alberto; Whitley, Adam; Strid, Pernilla; Diez, Margarita; Johannesson, Martina; Flint, Jonathan; Econs, Michael J; Turner, Charles H; Foroud, Tatiana

    2011-05-01

    Previously, we demonstrated that skeletal mass, structure and biomechanical properties vary considerably among 11 different inbred rat strains. Subsequently, we performed quantitative trait loci (QTL) analysis in four inbred rat strains (F344, LEW, COP and DA) for different bone phenotypes and identified several candidate genes influencing various bone traits. The standard approach to narrowing QTL intervals down to a few candidate genes typically employs the generation of congenic lines, which is time consuming and often not successful. A potential alternative approach is to use a highly genetically informative animal model resource capable of delivering very high resolution gene mapping such as Heterogeneous stock (HS) rat. HS rat was derived from eight inbred progenitors: ACI/N, BN/SsN, BUF/N, F344/N, M520/N, MR/N, WKY/N and WN/N. The genetic recombination pattern generated across 50 generations in these rats has been shown to deliver ultra-high even gene-level resolution for complex genetic studies. The purpose of this study is to investigate the usefulness of the HS rat model for fine mapping and identification of genes underlying bone fragility phenotypes. We compared bone geometry, density and strength phenotypes at multiple skeletal sites in HS rats with those obtained from five of the eight progenitor inbred strains. In addition, we estimated the heritability for different bone phenotypes in these rats and employed principal component analysis to explore relationships among bone phenotypes in the HS rats. Our study demonstrates that significant variability exists for different skeletal phenotypes in HS rats compared with their inbred progenitors. In addition, we estimated high heritability for several bone phenotypes and biologically interpretable factors explaining significant overall variability, suggesting that the HS rat model could be a unique genetic resource for rapid and efficient discovery of the genetic determinants of bone fragility. Copyright

  4. Analysis of cytoplasmic effects and fine-mapping of a genic male sterile line in rice.

    Directory of Open Access Journals (Sweden)

    Peng Qin

    Full Text Available Cytoplasm has substantial genetic effects on progeny and is important for yield improvement in rice breeding. Studies on the cytoplasmic effects of cytoplasmic male sterility (CMS show that most types of CMS have negative effects on yield-related traits and that these negative effects vary among CMS. Some types of genic male sterility (GMS, including photo-thermo sensitive male sterility (PTMS, have been widely used in rice breeding, but the cytoplasmic effects of GMS remain unknown. Here, we identified a GMS mutant line, h2s, which exhibited small, white anthers and failed to produce mature pollen. Unlike CMS, the h2s had significant positive cytoplasmic effects on the seed set rate, weight per panicle, yield, and general combining ability (GCA for plant height, seed set rate, weight per panicle, and yield. These effects indicated that h2s cytoplasm may show promise for the improvement of rice yield. Genetic analysis suggested that the phenotype of h2s was controlled by a single recessive locus. We mapped h2s to a 152 kb region on chromosome 6, where 22 candidate genes were predicted. None of the 22 genes had previously been reported to be responsible for the phenotypes of h2s. Sequencing analysis showed a 12 bp deletion in the sixth exon of Loc_Os06g40550 in h2s in comparison to wild type, suggesting that Loc_Os06g40550 is the best candidate gene. These results lay a strong foundation for cloning of the H2S gene to elucidate the molecular mechanism of male reproduction.

  5. Recurrent selection in inbred popcorn families

    Directory of Open Access Journals (Sweden)

    Daros Máskio

    2004-01-01

    Full Text Available Although much appreciated in Brazil, commercial popcorn is currently cropped on a fairly small scale. A number of problems need to be solved to increase production, notably the obtaintion of seeds with good agronomic traits and good culinary characteristics. With the objective of developing superior genotypes in popcorn, a second cycle of intrapopulation recurrent selection based on inbred S1 families was carried out. From the first cycle of selection over the UNB-2U population, 222 S1 families were obtained, which were then divided into six sets and evaluated in a randomized complete block design with two replications within the sets. Experiments were carried out in two Brazilian localities. The analysis of variance revealed environmental effects for all evaluated traits, except popping and stand, showing that, for most traits, these environments affected genotype behavior in different ways. In addition, the set as source of variation was significant for most of the evaluated traits, indicating that dividing the families into sets was an efficient strategy. Genotype-by-environment interaction was detected for most traits, except popping expansion and stand. Differences among genotypes were also detected (1% F-test, making viable the proposition of using the genetic variability in the popcorn population as a basis for future recurrent selection cycles. Superior families were selected using the Smith and Hazel classic index, with predicted genetic gains of 17.8% for popping expansion and 26.95% for yield.

  6. Internal electric-field-lines distribution in CdZnTe detectors measured using X-ray mapping

    International Nuclear Information System (INIS)

    Bolotnikov, A.E.; Camarda, G.S.; Cui, Y.; Hossain, A.; Yang, G.; Yao, H.W.; James, R.B.

    2009-01-01

    The ideal operation of CdZnTe devices entails having a uniformly distributed internal electric field. Such uniformity especially is critical for thick long-drift-length detectors, such as large-volume CPG and 3-D multi-pixel devices. Using a high-spatial resolution X-ray mapping technique, we investigated the distribution of the electric field in real devices. Our measurements demonstrate that in thin detectors, 1 cm, with a large aspect ratio (thickness-to-width ratio), we observed two effects: the electric field lines bending away from or towards the side surfaces, which we called, respectively, the focusing field-line distribution and the defocusing field-line distribution. In addition to these large-scale variations, the field-line distributions were locally perturbed by the presence of extended defects and residual strains existing inside the crystals. We present our data clearly demonstrating the non-uniformity of the internal electric field

  7. An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

    Science.gov (United States)

    Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W.

    2013-01-01

    We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa. The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. PMID:23550116

  8. An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce.

    Science.gov (United States)

    Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W

    2013-04-09

    We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F 7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. Copyright © 2013 Truco et al.

  9. X-ray and NQR studies of bromoindate(III) complexes. [C2H5NH3]4InBr7, [C(NH2)3]3InBr6, and [H3NCH2C(CH3)2CH2NH3]InBr5

    International Nuclear Information System (INIS)

    Iwakiri, Takeharu; Ishihara, Hideta; Terao, Hiromitsu; Lork, Enno; Gesing, Thorsten M.

    2017-01-01

    The crystal structures of [C 2 H 5 NH 3 ] 4 InBr 7 (1), [C(NH 2 ) 3 ] 3 InBr 6 (2), and [H 3 NCH 2 C(CH 3 ) 2 CH 2 NH 3 ]InBr 5 (3) were determined at 100(2) K: monoclinic, P2 1 /n, a=1061.94(3), b=1186.40(4), c=2007.88(7) pm, β= 104.575(1) , Z=4 for 1; monoclinic, C2/c, a=3128.81(12), b=878.42(3), c=2816.50(10) pm, β=92.1320(10) , Z=16 for 2; orthorhombic, P2 1 2 1 2 1 , a=1250.33(5), b=1391.46(6), c=2503.22(9) pm, Z=4 for 3. The structure of 1 contains an isolated octahedral [InBr 6 ] 3- ion and a Br - ion. The structure of 2 contains three different isolated octahedral [InBr 6 ] 3- ions. The structure of 3 has a corner-shared double-octahedral [In 2 Br 11 ] 5- ion and an isolated tetrahedral [InBr 4 ] - ion. The 81 Br nuclear quadrupole resonance (NQR) lines of the terminal Br atoms of the compounds are widely spread in frequency, and some of them show unusual positive temperature dependence. These observations manifest the N-H..Br-In hydrogen bond networks developed between the cations and anions to stabilize the crystal structures. The 81 Br NQR and differential thermal analysis (DTA) measurements have revealed the occurrence of unique phase transitions in 1 and 3. When the bond angles were estimated from the electric field gradient (EFG) directions calculated by the molecular orbital (MO) methods, accurate values were obtained for [InBr 6 ] 3- of 1 and for [In 2 Br 11 ] 5- and [InBr 4 ] - of 3, except for several exceptions in those for the latter two ions. On the other hand, the calculations of 81 Br NQR frequencies have produced up to 1.4 times higher values than the observed ones.

  10. Model-driven product line engineering for mapping parallel algorithms to parallel computing platforms

    NARCIS (Netherlands)

    Arkin, Ethem; Tekinerdogan, Bedir

    2016-01-01

    Mapping parallel algorithms to parallel computing platforms requires several activities such as the analysis of the parallel algorithm, the definition of the logical configuration of the platform, the mapping of the algorithm to the logical configuration platform and the implementation of the

  11. Map generation in unknown environments by AUKF-SLAM using line segment-type and point-type landmarks

    Science.gov (United States)

    Nishihta, Sho; Maeyama, Shoichi; Watanebe, Keigo

    2018-02-01

    Recently, autonomous mobile robots that collect information at disaster sites are being developed. Since it is difficult to obtain maps in advance in disaster sites, the robots being capable of autonomous movement under unknown environments are required. For this objective, the robots have to build maps, as well as the estimation of self-location. This is called a SLAM problem. In particular, AUKF-SLAM which uses corners in the environment as point-type landmarks has been developed as a solution method so far. However, when the robots move in an environment like a corridor consisting of few point-type features, the accuracy of self-location estimated by the landmark is decreased and it causes some distortions in the map. In this research, we propose AUKF-SLAM which uses walls in the environment as a line segment-type landmark. We demonstrate that the robot can generate maps in unknown environment by AUKF-SLAM, using line segment-type and point-type landmarks.

  12. Confirmation and Fine Mapping of a Major QTL for Aflatoxin Resistance in Maize Using a Combination of Linkage and Association Mapping

    Directory of Open Access Journals (Sweden)

    Yu Zhang

    2016-09-01

    Full Text Available Maize grain contamination with aflatoxin from Aspergillus flavus (A. flavus is a serious health hazard to animals and humans. To map the quantitative trait loci (QTLs associated with resistance to A. flavus, we employed a powerful approach that differs from previous methods in one important way: it combines the advantages of the genome-wide association analysis (GWAS and traditional linkage mapping analysis. Linkage mapping was performed using 228 recombinant inbred lines (RILs, and a highly significant QTL that affected aflatoxin accumulation, qAA8, was mapped. This QTL spanned approximately 7 centi-Morgan (cM on chromosome 8. The confidence interval was too large for positional cloning of the causal gene. To refine this QTL, GWAS was performed with 558,629 single nucleotide polymorphisms (SNPs in an association population comprising 437 maize inbred lines. Twenty-five significantly associated SNPs were identified, most of which co-localised with qAA8 and explained 6.7% to 26.8% of the phenotypic variation observed. Based on the rapid linkage disequilibrium (LD and the high density of SNPs in the association population, qAA8 was further localised to a smaller genomic region of approximately 1500 bp. A high-resolution map of the qAA8 region will be useful towards a marker-assisted selection (MAS of A. flavus resistance and a characterisation of the causal gene.

  13. Biochemical markers of embryogenesis in tissue cultures of the maize inbred B73

    International Nuclear Information System (INIS)

    Everett, N.P.; Wach, M.J.; Ashworth, D.J.

    1985-01-01

    Stable embryogenic, organogenic and undifferentiated cell lines of the maize (Zea mays L.) inbred B73 were used to assess the value of using isozyme analyses and the composition of secreted polysaccharides to identify embryogenic cells. Esterase, glutamate dehydrogenase, alcohol dehydrogenase and β-glucosidase all possessed developmentally regulated isozymes but only esterase and glutamate dehydrogenase could be used to distinguish between embryogenic and shoot-forming cultures. Embryogenic callus and suspension cultures secreted a mucilagenous polysaccharide whose production was stimulated by 2, 4-dichlorophenozyacetic acid (2, 4-D). The polysaccharide was different from root slime and corn hull gum and may be related to the 'cementing layer' in maize kernels (author)

  14. LARGE-AREA [Fe II] LINE MAPPING OF THE SUPERNOVA REMNANT IC 443 WITH THE IRSF/SIRIUS

    Energy Technology Data Exchange (ETDEWEB)

    Kokusho, Takuma; Nagayama, Takahiro; Kaneda, Hidehiro; Ishihara, Daisuke [Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602 (Japan); Lee, Ho-Gyu; Onaka, Takashi, E-mail: kokusho@u.phys.nagoya-u.ac.jp [Department of Astronomy, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033 (Japan)

    2013-05-01

    We present the results of near-infrared (near-IR) [Fe II] line mapping of the supernova remnant IC 443 with IRSF/SIRIUS, using the two narrow-band filters tuned for the [Fe II] 1.257 {mu}m and [Fe II] 1.644 {mu}m lines. Covering a large area of 30' Multiplication-Sign 35', our observations reveal that [Fe II] filamentary structures exist all over the remnant, not only in an ionic shock shell, but also in a molecular shock shell and a central region inside the shells. With the two [Fe II] lines, we performed corrections for dust extinction to derive the intrinsic line intensities. We also obtained the intensities of thermal emission from the warm dust associated with IC 443, using the far- and mid-IR images taken with AKARI and Spitzer, respectively. As a result, we find that the [Fe II] line emission relative to the dust emission notably enhances in the inner central region. We discuss causes of the enhanced [Fe II] line emission, estimating the Fe{sup +} and dust masses.

  15. Experience of MAPS in monitoring of personnel movement with on-line database management system

    International Nuclear Information System (INIS)

    Rajendran, T.S.; Anand, S.D.

    1992-01-01

    As a part of physical protection system, access control system has been installed in Madras Atomic Power Station(MAPS) to monitor and regulate the movement of persons within MAPS. The present system in its original form was meant only for security monitoring. A PC based database management system was added to this to computerize the availability of work force for actual work. (author). 2 annexures

  16. Prospects and pitfalls of occupational hazard mapping: 'between these lines there be dragons'.

    Science.gov (United States)

    Koehler, Kirsten A; Volckens, John

    2011-10-01

    Hazard data mapping is a promising new technique that can enhance the process of occupational exposure assessment and risk communication. Hazard maps have the potential to improve worker health by providing key input for the design of hazard intervention and control strategies. Hazard maps are developed with aid from direct-reading instruments, which can collect highly spatially and temporally resolved data in a relatively short period of time. However, quantifying spatial-temporal variability in the occupational environment is not a straightforward process, and our lack of understanding of how to ascertain and model spatial and temporal variability is a limiting factor in the use and interpretation of workplace hazard maps. We provide an example of how sources of and exposures to workplace hazards may be mischaracterized in a hazard map due to a lack of completeness and representativeness of collected measurement data. Based on this example, we believe that a major priority for research in this emerging area should focus on the development of a statistical framework to quantify uncertainty in spatially and temporally varying data. In conjunction with this need is one for the development of guidelines and procedures for the proper sampling, generation, and evaluation of workplace hazard maps.

  17. Diallel analysis of leaf disease resistance in inbred Brazilian popcorn cultivars.

    Science.gov (United States)

    Vieira, R A; Scapim, C A; Moterle, L M; Tessmann, D J; Conrado, T V; Amaral Júnior, A T

    2009-12-01

    We estimated general and specific combining abilities and examined resistance to northern leaf blight (Exserohilum turcicum) and to gray leaf spot (Cercospora zeae-maydis) in a set of nine inbred popcorn lines. These inbreds were crossed in a complete diallel scheme without reciprocals, which produced 36 F(1) hybrids. Two experiments with a square lattice design and three replications were conducted during the 2008/2009 crop season, in Maringá, PR, Brazil. The severity of northern leaf blight and gray leaf spot was assessed under natural infestation conditions. Data were examined by individual and joint analysis of variance. Individual and joint Griffing's diallel analyses were carried out for adjusted means. General combining ability and specific combining ability were significant (P < 0.10) by the F-test for northern leaf blight and gray leaf spot infestation levels. This denotes that additive and non-additive gene effects both contributed to resistance to these diseases, but that the additive gene effects were more important. Among the inbred lines, P(8) and P(9) gave the highest resistance to northern leaf blight, and P(3) and P(4.3) gave the highest resistance to gray leaf spot. The hybrids P(7.4) x P(8) and P(4.3) x P(9) could be exploited by reciprocal recurrent selection to provide genotypes with both northern leaf blight and gray leaf spot resistance. Significant interaction between general combining ability and crop season (P < 0.10) denotes the importance of environment, even though the disease levels in the hybrids were quite consistent.

  18. Transcriptome Analyses of Mosaic (MSC Mitochondrial Mutants of Cucumber in a Highly Inbred Nuclear Background

    Directory of Open Access Journals (Sweden)

    Tomasz L. Mróz

    2018-03-01

    Full Text Available Cucumber (Cucumis sativus L. has a large, paternally transmitted mitochondrial genome. Cucumber plants regenerated from cell cultures occasionally show paternally transmitted mosaic (MSC phenotypes, characterized by slower growth, chlorotic patterns on the leaves and fruit, lower fertility, and rearrangements in their mitochondrial DNAs (mtDNAs. MSC lines 3, 12, and 16 originated from different cell cultures all established using the highly inbred, wild-type line B. These MSC lines possess different rearrangements and under-represented regions in their mtDNAs. We completed RNA-seq on normalized and non-normalized cDNA libraries from MSC3, MSC12, and MSC16 to study their nuclear gene-expression profiles relative to inbred B. Results from both libraries indicated that gene expression in MSC12 and MSC16 were more similar to each other than MSC3. Forty-one differentially expressed genes (DEGs were upregulated and one downregulated in the MSC lines relative to B. Gene functional classifications revealed that more than half of these DEGs are associated with stress-response pathways. Consistent with this observation, we detected elevated levels of hydrogen peroxide throughout leaf tissue in all MSC lines compared to wild-type line B. These results demonstrate that independently produced MSC lines with different mitochondrial polymorphisms show unique and shared nuclear responses. This study revealed genes associated with stress response that could become selection targets to develop cucumber cultivars with increased stress tolerance, and further support of cucumber as a model plant to study nuclear-mitochondrial interactions.

  19. Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon.

    Directory of Open Access Journals (Sweden)

    Yu Cui

    Full Text Available The ND18 strain of Barley stripe mosaic virus (BSMV infects several lines of Brachypodium distachyon, a recently developed model system for genomics research in cereals. Among the inbred lines tested, Bd3-1 is highly resistant at 20 to 25 °C, whereas Bd21 is susceptible and infection results in an intense mosaic phenotype accompanied by high levels of replicating virus. We generated an F(6:7 recombinant inbred line (RIL population from a cross between Bd3-1 and Bd21 and used the RILs, and an F(2 population of a second Bd21 × Bd3-1 cross to evaluate the inheritance of resistance. The results indicate that resistance segregates as expected for a single dominant gene, which we have designated Barley stripe mosaic virus resistance 1 (Bsr1. We constructed a genetic linkage map of the RIL population using SNP markers to map this gene to within 705 Kb of the distal end of the top of chromosome 3. Additional CAPS and Indel markers were used to fine map Bsr1 to a 23 Kb interval containing five putative genes. Our study demonstrates the power of using RILs to rapidly map the genetic determinants of BSMV resistance in Brachypodium. Moreover, the RILs and their associated genetic map, when combined with the complete genomic sequence of Brachypodium, provide new resources for genetic analyses of many other traits.

  20. Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits.

    Directory of Open Access Journals (Sweden)

    Deepmala Sehgal

    Full Text Available A pearl millet inbred germplasm association panel (PMiGAP comprising 250 inbred lines, representative of cultivated germplasm from Africa and Asia, elite improved open-pollinated cultivars, hybrid parental inbreds and inbred mapping population parents, was recently established. This study presents the first report of genetic diversity in PMiGAP and its exploitation for association mapping of drought tolerance traits. For diversity and genetic structure analysis, PMiGAP was genotyped with 37 SSR and CISP markers representing all seven linkage groups. For association analysis, it was phenotyped for yield and yield components and morpho-physiological traits under both well-watered and drought conditions, and genotyped with SNPs and InDels from seventeen genes underlying a major validated drought tolerance (DT QTL. The average gene diversity in PMiGAP was 0.54. The STRUCTURE analysis revealed six subpopulations within PMiGAP. Significant associations were obtained for 22 SNPs and 3 InDels from 13 genes under different treatments. Seven SNPs associations from 5 genes were common under irrigated and one of the drought stress treatments. Most significantly, an important SNP in putative acetyl CoA carboxylase gene showed constitutive association with grain yield, grain harvest index and panicle yield under all treatments. An InDel in putative chlorophyll a/b binding protein gene was significantly associated with both stay-green and grain yield traits under drought stress. This can be used as a functional marker for selecting high yielding genotypes with 'stay green' phenotype under drought stress. The present study identified useful marker-trait associations of important agronomics traits under irrigated and drought stress conditions with genes underlying a major validated DT-QTL in pearl millet. Results suggest that PMiGAP is a useful panel for association mapping. Expression patterns of genes also shed light on some physiological mechanisms underlying

  1. Comparison between electric-field-navigated and line-navigated TMS for cortical motor mapping in patients with brain tumors.

    Science.gov (United States)

    Sollmann, Nico; Goblirsch-Kolb, Moritz F; Ille, Sebastian; Butenschoen, Vicki M; Boeckh-Behrens, Tobias; Meyer, Bernhard; Ringel, Florian; Krieg, Sandro M

    2016-12-01

    For the navigation of transcranial magnetic stimulation (TMS), various techniques are available. Yet, there are two basic principles underlying them all: electric-field-navigated transcranial magnetic stimulation (En-TMS) and line-navigated transcranial magnetic stimulation (Ln-TMS). The current study was designed to compare both methods. To explore whether there is a difference in clinical applicability, workflow, and mapping results of both techniques, we systematically compared motor mapping via En-TMS and Ln-TMS in 12 patients suffering from brain tumors. The number of motor-positive stimulation spots and the ratio of positive spots per overall stimulation numbers were significantly higher for En-TMS (motor-positive spots: En-TMS vs. Ln-TMS: 128.3 ± 35.0 vs. 41.3 ± 26.8, p mapping in the neurosurgical context for the first time. Although both TMS systems tested in the present study are explicitly designed for application during motor mapping in patients with brain lesions, there are differences in applicability, workflow, and results between En-TMS and Ln-TMS, which should be distinctly considered during clinical use of the technique. However, to draw final conclusions about accuracy, confirmation of motor-positive Ln-TMS spots by intraoperative stimulation is crucial within the scope of upcoming investigations.

  2. Test of the Capability of Laser Line Scan Technology to Support Benthic Habitat Mapping in Coral Reef Ecosystems, Maui Island, November 2006

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The utility of Laser Line Scan (LLS) Technology for optical validation of benthic habitat map data from coral reef ecosystems was tested with a deployment of a...

  3. Power Lines: The Rhetoric of Maps as Social Change in the Post-Cold War Landscape

    Science.gov (United States)

    Barney, Timothy

    2009-01-01

    After the fall of the Berlin Wall and the collapse of state socialism in Eastern and Central Europe, cartographers were faced with choices on how the new post-Cold War political landscape would be mapped. One such group called the Pluto Project had been producing atlases since 1981 with a progressive point of view about the nature of state power…

  4. Information Security Awareness On-Line Materials Design with Knowledge Maps

    Science.gov (United States)

    Shaw, Ruey-Shiang; Keh, Huan-Chao; Huang, Nan-Ching; Huang, Tien-Chuan

    2011-01-01

    Information Security Awareness, though known as a primary and important issue in the domain of Information Security, CSI computer crime and security survey showed poor security awareness training in public and private sectors. In many studies, the authors have found that the usage of knowledge maps helps the process of learning and conception…

  5. THE LICK AGN MONITORING PROJECT: REVERBERATION MAPPING OF OPTICAL HYDROGEN AND HELIUM RECOMBINATION LINES

    International Nuclear Information System (INIS)

    Bentz, Misty C.; Walsh, Jonelle L.; Barth, Aaron J.; Thornton, Carol E.; Yoshii, Yuzuru; Sakata, Yu; Minezaki, Takeo; Woo, Jong-Hak; Malkan, Matthew A.; Wang, Xiaofeng; Steele, Thea N.; Silverman, Jeffrey M.; Serduke, Frank J. D.; Li, Weidong; Lee, Nicholas; Treu, Tommaso; Street, Rachel A.; Hidas, Marton G.; Hiner, Kyle D.; Greene, Jenny E.

    2010-01-01

    We have recently completed a 64-night spectroscopic monitoring campaign at the Lick Observatory 3 m Shane telescope with the aim of measuring the masses of the black holes in 12 nearby (z 6 -10 7 M sun and also the well-studied nearby active galactic nucleus (AGN) NGC 5548. Nine of the objects in the sample (including NGC 5548) showed optical variability of sufficient strength during the monitoring campaign to allow for a time lag to be measured between the continuum fluctuations and the response to these fluctuations in the broad Hβ emission, which we have previously reported. We present here the light curves for the Hα, Hγ, He II λ4686, and He I λ5876 emission lines and the time lags for the emission-line responses relative to changes in the continuum flux. Combining each emission-line time lag with the measured width of the line in the variable part of the spectrum, we determine a virial mass of the central supermassive black hole from several independent emission lines. We find that the masses are generally consistent within the uncertainties. The time-lag response as a function of velocity across the Balmer line profiles is examined for six of the AGNs. We find similar responses across all three Balmer lines for Arp 151, which shows a strongly asymmetric profile, and for SBS 1116+583A and NGC 6814, which show a symmetric response about zero velocity. For the other three AGNs, the data quality is somewhat lower and the velocity-resolved time-lag response is less clear. Finally, we compare several trends seen in the data set against the predictions from photoionization calculations as presented by Korista and Goad. We confirm several of their predictions, including an increase in responsivity and a decrease in the mean time lag as the excitation and ionization level for the species increases. Specifically, we find the time lags of the optical recombination lines to have weighted mean ratios of τ(Hα):τ(Hβ):τ(Hγ):τ(He I):τ(He II) = 1

  6. Intensity Mapping of the [CII] Fine Structure Line during the Epoch of Reionization

    Science.gov (United States)

    Gong, Yan; Cooray, A.; Silva, M.; Santos, M. G.; Bock, J.; Bradford, M.; Zemcov, M.

    2012-01-01

    The atomic CII fine-structure line is one of the brightest lines in a typical star-forming galaxy spectrum with a luminosity 0.1% to 1% of the bolometric luminosity. It is otentially a reliable tracer of the dense gas distribution at high edshifts and could provide an additional probe to the era of reionization. By taking into account of the spontaneous, stimulated and collisional emission of the CII line, we calculate the spin temperature and the mean intensity as a function of the redshift. When averaged over a cosmologically large volume, we find that the CII emission from ionized carbon in individual galaxies is larger than the signal generated by carbon in the intergalactic medium (IGM). Assuming that the CII luminosity is proportional to the carbon mass in dark matter halos, we also compute the power spectrum of the CII line intensity at various redshifts. In order to avoid the contamination from CO rotational lines at low redshift when targeting a CII survey at high redshifts, we propose the cross-correlation of CII and 21-cm line emission from high redshifts. To explore the detectability of the CII signal from reionization, we also evaluate the expected errors on the CII power spectrum and CII-21 cm cross power spectrum based on the design of the future milimeter surveys. We note that the CII-21 cm cross power spectrum contains interesting features that captures physics during reionization, including the ionized bubble sizes and the mean ionization fraction, which are challenging to measure from 21-cm data alone. We propose an instrumental concept for the reionization CII experiment targeting the frequency range of 200 to 300 GHz with 1, 3 and 10 meter apertures and a bolometric spectrometer array with 64 independent spectral pixels with about 20,000 bolometers.

  7. Construction of chromosome segment substitution lines enables QTL mapping for flowering and morphological traits in Brassica rapa

    Directory of Open Access Journals (Sweden)

    Xiaonan eLi

    2015-06-01

    Full Text Available Chromosome segment substitution lines (CSSLs represent a powerful method for precise quantitative trait loci (QTL detection of complex agronomical traits in plants. In this study, we used a marker-assisted backcrossing strategy to develop a population consisting of 63 CSSLs, derived from backcrossing of the F1 generated from a cross between two Brassica rapa subspecies: ‘Chiifu’ (ssp. pekinensis, the Brassica A genome-represented line used as the donor, and ‘49caixin’ (ssp. parachinensis, a non-heading cultivar used as the recipient. The 63 CSSLs covered 87.95% of the B. rapa genome. Among them, 39 lines carried a single segment; 15 lines, two segments; and nine lines, three or more segments of the donor parent chromosomes. To verify the potential advantage of these CSSL lines, we used them to locate QTL for six morphology-related traits. A total of 58 QTL were located on eight chromosomes for all six traits: 17 for flowering time, 14 each for bolting time and plant height, 6 for plant diameter, 2 for leaf width, and 5 for flowering stalk diameter. Co-localized QTL were mainly distributed on eight genomic regions in A01, A02, A05, A06, A08, A09, and A10, present in the corresponding CSSLs. Moreover, new chromosomal fragments that harbored QTL were identified using the findings of previous studies. The CSSL population constructed in our study paves the way for fine mapping and cloning of candidate genes involved in late bolting, flowering, and plant architecture-related traits in B. rapa. Furthermore, it has great potential for future marker-aided gene/QTL pyramiding of other interesting traits in B. rapa breeding.

  8. Body-Map Storytelling as a Health Research Methodology: Blurred Lines Creating Clear Pictures

    Directory of Open Access Journals (Sweden)

    Denise Gastaldo

    2018-03-01

    Full Text Available In this article we review the literature on body-mapping (BM as an approach to health research in order to systematize recent advancements and to contribute to its development. We conducted a critical narrative synthesis of the literature published until September 2016 guided by two questions: 1. How has BM been utilized in health research? 2. How does BM advance a decolonization agenda? Twenty-seven studies in English, Spanish, and Portuguese were analyzed. Most of them were published between 2011 and 2016 and were conducted in South Africa, Canada, Australia, Brazil, Chile, and USA. They narrate stories of marginalized groups and commonly focus on the social determinants of health. Data generation, analysis, and knowledge mobilization strategies differ considerably. Recent developments show that body-mapping is a visual, narrative, and participatory methodology that has several names and is used unevenly by health researchers. Despite its diversity, core methodological elements reveal that participants are considered knowledgeable, reflexive individuals who can better articulate their complex life journeys when painting and drawing their bodies and social circumstances. The decolonization of health research occurs when these unlikely protagonists tell their stories producing counter-hegemonic discourses to exclusionary capitalist, patriarchal and colonialist rationalities. We call this methodology body-map storytelling.

  9. Inheritance and molecular mapping of anthracnose resistance gene present in the differential line PI533918

    Science.gov (United States)

    Anthracnose (Collectrotichum sublineolum) is considered one of the most destructive diseases of sorghum (Sorghum bicolor L. Moench) because it infects all aerial tissues of the plant. The best strategy to control the disease is the incorporation of resistance genes. At present, eighteen sorghum line...

  10. QTL Mapping of Grain Quality Traits Using Introgression Lines Carrying Oryza rufipogon Chromosome Segments in Japonica Rice.

    Science.gov (United States)

    Yun, Yeo-Tae; Chung, Chong-Tae; Lee, Young-Ju; Na, Han-Jung; Lee, Jae-Chul; Lee, Sun-Gye; Lee, Kwang-Won; Yoon, Young-Hwan; Kang, Ju-Won; Lee, Hyun-Sook; Lee, Jong-Yeol; Ahn, Sang-Nag

    2016-12-01

    Improved eating quality is a major breeding target in japonica rice due to market demand. Consequently, quantitative trait loci (QTL) for glossiness of cooked rice and amylose content associated with eating quality have received much research focus because of their importance in rice quality. In this study, QTL associated with 12 grain quality traits were identified using 96 introgression lines (IL) of rice developed from an interspecific cross between the Korean elite O. sativa japonica cultivar 'Hwaseong' and O. rufipogon over 7 years. QTL analyses indicated that QTL qDTH6 for heading date, detected on chromosome 6 is associated with variance in grain traits. Most QTLs detected in this study clustered near the qDTH6 locus on chromosome 6, suggesting the effect of qDTH6. O. rufipogon alleles negatively affected grain quality traits except for a few QTLs, including qGCR9 for glossiness of cooked rice on chromosome 9. To characterize the effect of the O. rufipogon locus harboring qGCR9, four lines with a single but different O. rufipogon segment near qGCR9 were compared to Hwaseong. Three lines (O. rufipopgon ILs) having O. rufipogon segment between RM242 and RM245 in common showed higher glossiness of cooked rice than Hwaseong and the other line (Hwaseong IL), indicating that qGCR9 is located in the 3.4-Mb region between RM242 and RM245. Higher glossiness of cooked rice conferred by the O. rufipogon allele might be associated with protein content considering that three lines had lower protein content than Hwaseong (P < 0.1). These three O. rufipogon ILs showed higher yield than Hwaseong and Hwaseong IL due to increase in spikelets per panicle and grain weight indicating the linkage of qGCR9 and yield component QTLs. The qGCR9 locus is of particular interest because of its independence from other undesirable grain quality traits in O. rufipogon. SSR markers linked to qGCR9 can be used to develop high-quality japonica lines and offer a starting point for map

  11. Central Masses and Broad-Line Region Sizes of Active Galactic Nuclei. II. A Homogeneous Analysis of a Large Reverberation-Mapping Database

    DEFF Research Database (Denmark)

    Peterson, B. M.; Ferrarese, L.; Gilbert, K. M.

    2004-01-01

    We present improved black hole masses for 35 active galactic nuclei (AGNs) based on a complete and consistent reanalysis of broad emission-line reverberation-mapping data. From objects with multiple line measurements, we find that the highest precision measure of the virial product is obtained...

  12. Transient Cnp expression by early progenitors causes Cre-Lox-based reporter lines to map profoundly different fates.

    Science.gov (United States)

    Tognatta, Reshmi; Sun, Wenjing; Goebbels, Sandra; Nave, Klaus-Armin; Nishiyama, Akiko; Schoch, Susanne; Dimou, Leda; Dietrich, Dirk

    2017-02-01

    NG2 expressing oligodendroglial precursor cells are ubiquitous in the central nervous system and the only cell type cycling throughout life. Previous fate mapping studies have remained inconsistent regarding the question whether NG2 cells are capable of generating certain types of neurons. Here, we use CNP-Cre mice to map the fate of a sub-population of NG2 cells assumed to be close to differentiation. When crossing these mice with the ROSA26/YFP Cre-reporter line we discovered large numbers of reporter-expressing pyramidal neurons in the piriform and dorsal cortex. In contrast, when using Z/EG reporter mice to track the fate of Cnp-expressing NG2 cells only oligodendroglial cells were found reporter positive. Using BrdU-based birth dating protocols and inducible NG2CreER:ROSA26/YFP mice we show that YFP positive neurons are generated from radial glial cells and that these radial glial cells display temporary and low level activity of certain oligodendroglial genes sufficient to recombine the Cre-inducible reporter gene in ROSA26/YFP but not in Z/EG mice. Taken together, we did not obtain evidence for generation of neurons from NG2 cells. Our results suggest that with an appropriate reporter system Cnp activity can be used to define a proliferative subpopulation of NG2 cells committed to generate oligodendrocytes. However, the strikingly different results obtained from ROSA26/YFP versus Z/EG mice demonstrate that the choice of Cre-reporter line can be of crucial importance for fate mapping studies and other applications of the Cre-lox technology. GLIA 2017;65:342-359. © 2016 Wiley Periodicals, Inc.

  13. Grain orientation mapping of passivated aluminum interconnect lines with X-ray micro-diffraction

    International Nuclear Information System (INIS)

    Chang, C.H.; Patel, J.R.; MacDowell, A.A.; Padmore, H.A.; Thompson, A.C.

    1998-01-01

    A micro x-ray diffraction facility is under development at the Advanced Light Source. Spot sizes are typically about 1-microm size generated by means of grazing incidence Kirkpatrick-Baez focusing mirrors. Photon energy is either white of energy range 6--14 keV or monochromatic generated from a pair of channel cut crystals. Laue diffraction pattern from a single grain in a passivated 2-microm wide bamboo structured Aluminum interconnect line has been recorded. Acquisition times are of the order of seconds. The Laue pattern has allowed the determination of the crystallographic orientation of individual grains along the line length. The experimental and analysis procedure used is described, as is the latest grain orientation result. The impact of x-ray micro-diffraction and its possible future direction are discussed in the context of other developments in the area of electromigration, and other technological problems

  14. Grain orientation mapping of passivated aluminum interconnect lines by x-ray micro-diffraction

    International Nuclear Information System (INIS)

    Chang, C. H.; Patel, J. R.; MacDowell, A. A.; Padmore, H. A.; Thompson, A. C.

    1998-01-01

    A micro x-ray diffraction facility is under development at the Advanced Light Source. Spot sizes are typically about 1-μm size generated by means of grazing incidence Kirkpatrick-Baez focusing mirrors. Photon energy is either white of energy range 6-14 keV or monochromatic generated from a pair of channel cut crystals. Laue diffraction pattern from a single grain in a passivated 2-μm wide bamboo structured Aluminum interconnect line has been recorded. Acquisition times are of the order of seconds. The Laue pattern has allowed the determination of the crystallographic orientation of individual grains along the line length. The experimental and analysis procedure used is described, as is the latest grain orientation result. The impact of x-ray micro-diffraction and its possible future direction are discussed in the context of other developments in the area of electromigration, and other technological problems

  15. SPITZER MAPPING OF MOLECULAR HYDROGEN PURE ROTATIONAL LINES IN NGC 1333: A DETAILED STUDY OF FEEDBACK IN STAR FORMATION

    International Nuclear Information System (INIS)

    Maret, Sebastien; Bergin, Edwin A.; Neufeld, David A.; Sonnentrucker, Paule; Yuan Yuan; Green, Joel D.; Watson, Dan M.; Harwit, Martin O.; Kristensen, Lars E.; Melnick, Gary J.; Tolls, Volker; Werner, Michael W.; Willacy, Karen

    2009-01-01

    We present mid-infrared spectral maps of the NGC 1333 star-forming region, obtained with the infrared spectrometer on board the Spitzer Space Telescope. Eight pure H 2 rotational lines, from S(0) to S(7), are detected and mapped. The H 2 emission appears to be associated with the warm gas shocked by the multiple outflows present in the region. A comparison between the observed intensities and the predictions of detailed shock models indicates that the emission arises in both slow (12-24 km s -1 ) and fast (36-53 km s -1 ) C-type shocks with an initial ortho-to-para ratio (opr) ∼ 2 opr exhibits a large degree of spatial variations. In the postshocked gas, it is usually about 2, i.e., close to the equilibrium value (∼3). However, around at least two outflows, we observe a region with a much lower (∼0.5) opr. This region probably corresponds to gas which has been heated up recently by the passage of a shock front, but whose ortho-to-para has not reached equilibrium yet. This, together with the low initial opr needed to reproduce the observed emission, provide strong evidence that H 2 is mostly in para form in cold molecular clouds. The H 2 lines are found to contribute to 25%-50% of the total outflow luminosity, and thus can be used to ascertain the importance of star formation feedback on the natal cloud. From these lines, we determine the outflow mass loss rate and, indirectly, the stellar infall rate, the outflow momentum and the kinetic energy injected into the cloud over the embedded phase. The latter is found to exceed the binding energy of individual cores, suggesting that outflows could be the main mechanism for core disruption.

  16. Divergence and inheritance of neocortical heterotopia in inbred and genetically-engineered mice.

    Science.gov (United States)

    Toia, Alyssa R; Cuoco, Joshua A; Esposito, Anthony W; Ahsan, Jawad; Joshi, Alok; Herron, Bruce J; Torres, German; Bolivar, Valerie J; Ramos, Raddy L

    2017-01-18

    Cortical function emerges from the intrinsic properties of neocortical neurons and their synaptic connections within and across lamina. Neurodevelopmental disorders affecting migration and lamination of the neocortex result in cognitive delay/disability and epilepsy. Molecular layer heterotopia (MLH), a dysplasia characterized by over-migration of neurons into layer I, are associated with cognitive deficits and neuronal hyperexcitability in humans and mice. The breadth of different inbred mouse strains that exhibit MLH and inheritance patterns of heterotopia remain unknown. A neuroanatomical survey of numerous different inbred mouse strains, 2 first filial generation (F1) hybrids, and one consomic strain (C57BL/6J-Chr 1 A/J /NaJ) revealed MLH only in C57BL/6 mice and the consomic strain. Heterotopia were observed in numerous genetically-engineered mouse lines on a congenic C57BL/6 background. These data indicate that heterotopia formation is a weakly penetrant trait requiring homozygosity of one or more C57BL/6 alleles outside of chromosome 1. These data are relevant toward understanding neocortical development and disorders affecting neocortical lamination. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  17. The mouse as a model for understanding chronic diseases of aging: the histopathologic basis of aging in inbred mice

    Directory of Open Access Journals (Sweden)

    David Harrison

    2011-06-01

    Full Text Available Inbred mice provide a unique tool to study aging populations because of the genetic homogeneity within an inbred strain, their short life span, and the tools for analysis which are available. A large-scale longitudinal and cross-sectional aging study was conducted on 30 inbred strains to determine, using histopathology, the type and diversity of diseases mice develop as they age. These data provide tools that when linked with modern in silico genetic mapping tools, can begin to unravel the complex genetics of many of the common chronic diseases associated with aging in humans and other mammals. In addition, novel disease models were discovered in some strains, such as rhabdomyosarcoma in old A/J mice, to diseases affecting many but not all strains including pseudoxanthoma elasticum, pulmonary adenoma, alopecia areata, and many others. This extensive data set is now available online and provides a useful tool to help better understand strain-specific background diseases that can complicate interpretation of genetically engineered mice and other manipulatable mouse studies that utilize these strains.

  18. THE LICK AGN MONITORING PROJECT: BROAD-LINE REGION RADII AND BLACK HOLE MASSES FROM REVERBERATION MAPPING OF Hβ

    International Nuclear Information System (INIS)

    Bentz, Misty C.; Walsh, Jonelle L.; Barth, Aaron J.; Baliber, Nairn; Bennert, Vardha Nicola; Greene, Jenny E.; Hidas, Marton G.; Canalizo, Gabriela; Hiner, Kyle D.; Filippenko, Alexei V.; Ganeshalingam, Mohan; Lee, Nicholas; Li, Weidong; Serduke, Frank J. D.; Silverman, Jeffrey M.; Steele, Thea N.; Gates, Elinor L.; Malkan, Matthew A.; Minezaki, Takeo; Sakata, Yu

    2009-01-01

    We have recently completed a 64-night spectroscopic monitoring campaign at the Lick Observatory 3-m Shane telescope with the aim of measuring the masses of the black holes in 12 nearby (z 6 -10 7 M sun and also the well-studied nearby active galactic nucleus (AGN) NGC 5548. Nine of the objects in the sample (including NGC 5548) showed optical variability of sufficient strength during the monitoring campaign to allow for a time lag to be measured between the continuum fluctuations and the response to these fluctuations in the broad Hβ emission. We present here the light curves for all the objects in this sample and the subsequent Hβ time lags for the nine objects where these measurements were possible. The Hβ lag time is directly related to the size of the broad-line region (BLR) in AGNs, and by combining the Hβ lag time with the measured width of the Hβ emission line in the variable part of the spectrum, we determine the virial mass of the central supermassive black hole in these nine AGNs. The absolute calibration of the black hole masses is based on the normalization derived by Onken et al., which brings the masses determined by reverberation mapping into agreement with the local M BH -σ * relationship for quiescent galaxies. We also examine the time lag response as a function of velocity across the Hβ line profile for six of the AGNs. The analysis of four leads to rather ambiguous results with relatively flat time lags as a function of velocity. However, SBS 1116+583A exhibits a symmetric time lag response around the line center reminiscent of simple models for circularly orbiting BLR clouds, and Arp 151 shows an asymmetric profile that is most easily explained by a simple gravitational infall model. Further investigation will be necessary to fully understand the constraints placed on the physical models of the BLR by the velocity-resolved response in these objects.

  19. Mapping of imprinted quantitative trait loci using immortalized F2 populations.

    Directory of Open Access Journals (Sweden)

    Yongxian Wen

    Full Text Available Mapping of imprinted quantitative trait loci (iQTLs is helpful for understanding the effects of genomic imprinting on complex traits in animals and plants. At present, the experimental designs and corresponding statistical methods having been proposed for iQTL mapping are all based on temporary populations including F2 and BC1, which can be used only once and suffer some other shortcomings respectively. In this paper, we propose a framework for iQTL mapping, including methods of interval mapping (IM and composite interval mapping (CIM based on conventional low-density genetic maps and point mapping (PM and composite point mapping (CPM based on ultrahigh-density genetic maps, using an immortalized F2 (imF2 population generated by random crosses between recombinant inbred lines or doubled haploid lines. We demonstrate by simulations that imF2 populations are very desirable and the proposed statistical methods (especially CIM and CPM are very powerful for iQTL mapping, with which the imprinting effects as well as the additive and dominance effects of iQTLs can be unbiasedly estimated.

  20. Mapping analysis of scaffold/matrix attachment regions (s/MARs) from two different mammalian cell lines

    Energy Technology Data Exchange (ETDEWEB)

    Pilus, Nur Shazwani Mohd; Ahmad, Azrin; Yusof, Nurul Yuziana Mohd [School of Bioscience and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor (Malaysia); Johari, Norazfa [Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor (Malaysia)

    2014-09-03

    Scaffold/matrix attachment regions (S/MARs) are potential element that can be integrated into expression vector to increase expression of recombinant protein. Many studies on S/MAR have been done but none has revealed the distribution of S/MAR in a genome. In this study, we have isolated S/MAR sequences from HEK293 and Chinese hamster ovary cell lines (CHO DG44) using two different methods utilizing 2 M NaCl and lithium-3,5-diiodosalicylate (LIS). The isolated S/MARs were sequenced using Next Generation Sequencing (NGS) platform. Based on reference mapping analysis against human genome database, a total of 8,994,856 and 8,412,672 contigs of S/MAR sequences were retrieved from 2M NaCl and LIS extraction of HEK293 respectively. On the other hand, reference mapping analysis of S/MAR derived from CHO DG44 against our own CHO DG44 database have generated a total of 7,204,348 and 4,672,913 contigs from 2 M NaCl and LIS extraction method respectively.

  1. Mapping analysis of scaffold/matrix attachment regions (s/MARs) from two different mammalian cell lines

    International Nuclear Information System (INIS)

    Pilus, Nur Shazwani Mohd; Ahmad, Azrin; Yusof, Nurul Yuziana Mohd; Johari, Norazfa

    2014-01-01

    Scaffold/matrix attachment regions (S/MARs) are potential element that can be integrated into expression vector to increase expression of recombinant protein. Many studies on S/MAR have been done but none has revealed the distribution of S/MAR in a genome. In this study, we have isolated S/MAR sequences from HEK293 and Chinese hamster ovary cell lines (CHO DG44) using two different methods utilizing 2 M NaCl and lithium-3,5-diiodosalicylate (LIS). The isolated S/MARs were sequenced using Next Generation Sequencing (NGS) platform. Based on reference mapping analysis against human genome database, a total of 8,994,856 and 8,412,672 contigs of S/MAR sequences were retrieved from 2M NaCl and LIS extraction of HEK293 respectively. On the other hand, reference mapping analysis of S/MAR derived from CHO DG44 against our own CHO DG44 database have generated a total of 7,204,348 and 4,672,913 contigs from 2 M NaCl and LIS extraction method respectively

  2. Hemodynamic Characterization of Recombinant Inbred Strains: Twenty Years Later

    Czech Academy of Sciences Publication Activity Database

    Kuneš, Jaroslav; Dobešová, Zdenka; Musilová, Alena; Zídek, Václav; Vorlíček, Jaroslav; Pravenec, Michal; Křen, Vladimír; Zicha, Josef

    2008-01-01

    Roč. 31, č. 8 (2008), s. 1659-1668 ISSN 0916-9636 R&D Projects: GA MŠk(CZ) 1M0510; GA ČR(CZ) GA305/08/0139; GA AV ČR(CZ) IAA500110604 Institutional research plan: CEZ:AV0Z50110509 Keywords : recombinant inbred strains * blood pressure * telemetry Subject RIV: ED - Physiology Impact factor: 3.146, year: 2008

  3. Molecular-cloud-scale Chemical Composition. II. Mapping Spectral Line Survey toward W3(OH) in the 3 mm Band

    Energy Technology Data Exchange (ETDEWEB)

    Nishimura, Yuri [Institute of Astronomy, The University of Tokyo, 2-21-1, Osawa, Mitaka, Tokyo 181-0015 (Japan); Watanabe, Yoshimasa; Yamamoto, Satoshi [Department of Physics, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Harada, Nanase [Academia Sinica Institute of Astronomy and Astrophysics, No.1, Sec. 4, Roosevelt Road, 10617 Taipei, Taiwan, R.O.C. (China); Shimonishi, Takashi [Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aramakiazaaoba 6-3, Aoba-ku, Sendai, Miyagi 980-8578 (Japan); Sakai, Nami [RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Aikawa, Yuri [Department of Astronomy, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Kawamura, Akiko [Chile Observatory, National Astronomical Observatory of Japan, 2-21-1, Osawa, Mitaka, Tokyo 181-8588 (Japan)

    2017-10-10

    To study a molecular-cloud-scale chemical composition, we conducted a mapping spectral line survey toward the Galactic molecular cloud W3(OH), which is one of the most active star-forming regions in the Perseus arm. We conducted our survey through the use of the Nobeyama Radio Observatory 45 m telescope, and observed the area of 16′ × 16′, which corresponds to 9.0 pc × 9.0 pc. The observed frequency ranges are 87–91, 96–103, and 108–112 GHz. We prepared the spectrum averaged over the observed area, in which eight molecular species (CCH, HCN, HCO{sup +}, HNC, CS, SO, C{sup 18}O, and {sup 13}CO) are identified. On the other hand, the spectrum of the W3(OH) hot core observed at a 0.17 pc resolution shows the lines of various molecules such as OCS, H{sub 2}CS CH{sub 3}CCH, and CH{sub 3}CN in addition to the above species. In the spatially averaged spectrum, emission of the species concentrated just around the star-forming core, such as CH{sub 3}OH and HC{sub 3}N, is fainter than in the hot core spectrum, whereas emission of the species widely extended over the cloud such as CCH is relatively brighter. We classified the observed area into five subregions according to the integrated intensity of {sup 13}CO, and evaluated the contribution to the averaged spectrum from each subregion. The CCH, HCN, HCO{sup +}, and CS lines can be seen even in the spectrum of the subregion with the lowest {sup 13}CO integrated intensity range (<10 K km s{sup −1}). Thus, the contributions of the spatially extended emission is confirmed to be dominant in the spatially averaged spectrum.

  4. Evaluation of the capacity for direct regeneration of maize inbreds of the Lancaster selection group

    Directory of Open Access Journals (Sweden)

    K. V. Derkach

    2013-11-01

    Full Text Available In connection with the necessity of bringing elite maize inbreds of the Lancaster germplasm group, which have potential for cultivation in Ukraine, into the system of genetic tranformation, the aim of this investigation is to identify the ability of maize inbreds of this group to regenerate by direct organogenesis and to determine the optimal mineral basis for their nutritional environment using segments of the node area of shoots. As explantats we used sterile 4-day old seedlings of 4 maize inbreds of Lancaster germplasm and model inbred Chi31 exotic germplasm. The seedlings were obtained by germination of sterile seeds in Petri dishes between two layers of moist sterile filter paper at a temperature of 27 ºC in dark conditions. A single 1 cmlong segment was cut from each from each seedling, running from 0.5 cmbefore the node to 0.5 cmafter the node. A cut was made in each segment of the node in order to create a wounded surface. Explantats were planted in a nutrient environment with mineral bases of MS or N6, modified by the addition of 10 mg/l silver nitrate, 100 mg/l casein hydrolyzate, 690 mg/l L-proline, 30 g/l sucrose, 1.0 mg/l 2,4-dychlorphenoksiacetic acid and 0,1 mg/l abscisic acid. Cultivation was carried out at 25–27 ºC in the light. Direct hemogenesis in this environment on the 14th day of cultivation in vitro reached 100% for each line. This meant that all researched lines of Lancaster germplasm and the model line showed a high capacity for direct regeneration through direct hemogenesis, which does not depend on the composition of the mineral content of their nutritional environment. Callus formation was observed in all genotypes on the 14th day of cultivation in vitro and the extent of its formation increased during the following month of cultivation. The callus formation was observed only at the site of the wounded surface. The calluses were transparent. Although green areas appeared in these calluses, they were

  5. Learning spatial orientation tasks in the radial-maze and structural variation in the hippocampus in inbred mice

    Directory of Open Access Journals (Sweden)

    Schwegler Herbert

    2005-04-01

    Full Text Available Abstract In the present paper we review a series of experiments showing that heritable variations in the size of the hippocampal intra- and infrapyramidal mossy fiber (IIPMF terminal fields correlate with performance in spatial, but not non-spatial radial-maze tasks. Experimental manipulation of the size of this projection by means of early postnatal hyperthyroidism produces the effects predicted from the correlations obtained with inbred mouse strains. Although the physiological mechanisms behind these correlations are unknown as yet, several lines of evidence indicate that these correlations are causal.

  6. Mapping low-frequency carbon radio recombination lines towards Cassiopeia A at 340, 148, 54, and 43 MHz

    Science.gov (United States)

    Salas, P.; Oonk, J. B. R.; van Weeren, R. J.; Wolfire, M. G.; Emig, K. L.; Toribio, M. C.; Röttgering, H. J. A.; Tielens, A. G. G. M.

    2018-04-01

    Quantitative understanding of the interstellar medium requires knowledge of its physical conditions. Low-frequency carbon radio recombination lines (CRRLs) trace cold interstellar gas and can be used to determine its physical conditions (e.g. electron temperature and density). In this work, we present spatially resolved observations of the low-frequency (≤390 MHz) CRRLs centred around C268α, C357α, C494α, and C539α towards Cassiopeia A on scales of ≤1.2 pc. We compare the spatial distribution of CRRLs with other interstellar medium tracers. This comparison reveals a spatial offset between the peak of the CRRLs and other tracers, which is very characteristic for photodissociation regions and that we take as evidence for CRRLs being preferentially detected from the surfaces of molecular clouds. Using the CRRLs, we constrain the gas electron temperature and density. These constraints on the gas conditions suggest variations of less than a factor of 2 in pressure over ˜1 pc scales, and an average hydrogen density of 200-470 cm-3. From the electron temperature and density maps, we also constrain the ionized carbon emission measure, column density, and path length. Based on these, the hydrogen column density is larger than 1022 cm-2, with a peak of ˜4 × 1022 cm-2 towards the south of Cassiopeia A. Towards the southern peak, the line-of-sight length is ˜40 pc over a ˜2 pc wide structure, which implies that the gas is a thin surface layer on a large (molecular) cloud that is only partially intersected by Cassiopeia A. These observations highlight the utility of CRRLs as tracers of low-density extended H I and CO-dark gas halo's around molecular clouds.

  7. Mapping of QTLs for Leaf Malondialdehyde Content Associated with Stress Tolerance in Rice

    Directory of Open Access Journals (Sweden)

    Jing JIANG

    2009-03-01

    Full Text Available Malondialdehyde (MDA is the final product of lipid peroxidation, and MDA content can reflect the stress tolerance of plants. To map QTLs conditioning the MDA content in rice leaves, a recombinant inbred line (RIL population with 247 lines derived from an indica-indica cross Zhenshan 97B×Milyang 46, and a linkage map consisting of 207 DNA markers were used. The RIL population showed a transgressive segregation in the MDA content of rice leaves. Two QTLs for the MDA content in rice leaves were detected in the intervals RG532–RG811 and RG381–RG236 on chromosome 1, with the additive effects from maternal and paternal parents, accounting for 4.33% and 4.62% of phenotype variations, respectively.

  8. Fracture network evaluation program (FraNEP): A software for analyzing 2D fracture trace-line maps

    Science.gov (United States)

    Zeeb, Conny; Gomez-Rivas, Enrique; Bons, Paul D.; Virgo, Simon; Blum, Philipp

    2013-10-01

    Fractures, such as joints, faults and veins, strongly influence the transport of fluids through rocks by either enhancing or inhibiting flow. Techniques used for the automatic detection of lineaments from satellite images and aerial photographs, LIDAR technologies and borehole televiewers significantly enhanced data acquisition. The analysis of such data is often performed manually or with different analysis software. Here we present a novel program for the analysis of 2D fracture networks called FraNEP (Fracture Network Evaluation Program). The program was developed using Visual Basic for Applications in Microsoft Excel™ and combines features from different existing software and characterization techniques. The main novelty of FraNEP is the possibility to analyse trace-line maps of fracture networks applying the (1) scanline sampling, (2) window sampling or (3) circular scanline and window method, without the need of switching programs. Additionally, binning problems are avoided by using cumulative distributions, rather than probability density functions. FraNEP is a time-efficient tool for the characterisation of fracture network parameters, such as density, intensity and mean length. Furthermore, fracture strikes can be visualized using rose diagrams and a fitting routine evaluates the distribution of fracture lengths. As an example of its application, we use FraNEP to analyse a case study of lineament data from a satellite image of the Oman Mountains.

  9. C II forbidden-line 158 micron mapping in Sagittarius A Rotation curve and mass distribution in the galactic center

    Science.gov (United States)

    Lugten, J. B.; Genzel, R.; Crawford, M. K.; Townes, C. H.

    1986-01-01

    Based on data obtained with the NASA Kuiper Airborne Observatory 91.4 cm telescope, the 158-micron fine structure line emission of C(+) is mapped near the galactic center. The strongest emission comes from a 10-pc FWHM diameter disk centered on Sgr A West whose dominant motion is rotation. Extended C(+) emission is also found from the +50 km/s galactic center molecular cloud, and a second cloud at v(LSR) of about -35 km/s. The rotation curve and mass distribution within 10 pc of the galactic center are derived, and the C(+) profiles show a drop-off of rotation velocity between 2 and 10 pc. A mass model is suggested with 2-4 million solar masses in a central point mass, and a M/L ratio of the central stellar cluster of 0.5 solar masses/solar luminosities, suggesting a large abundance of giants and relatively recent star formation in the center.

  10. BXSB/long-lived is a recombinant inbred strain containing powerful disease suppressor loci.

    Science.gov (United States)

    Haywood, Michelle E K; Gabriel, Luisa; Rose, S Jane; Rogers, Nicola J; Izui, Shozo; Morley, Bernard J

    2007-08-15

    The BXSB strain of recombinant inbred mice develops a spontaneous pathology that closely resembles the human disease systemic lupus erythematosus. Six non-MHC loci, Yaa, Bxs1-4, and Bxs6, have been linked to the development of aspects of the disease while a further locus, Bxs5, may be a BXSB-derived disease suppressor. Disease development is delayed in a substrain of BXSB, BXSB/MpJScr-long-lived (BXSB/ll). We compared the genetic derivation of BXSB/ll mice to the original strain, BXSB/MpJ, using microsatellite markers and single nucleotide polymorphisms across the genome. These differences were clustered and included two regions known to be important in the disease-susceptibility of these mice, Bxs5 and 6, as well as regions on chromosomes 5, 6, 9, 11, 12, and 13. We compared BXSB/ll to >20 strains including the BXSB parental SB/Le and C57BL/6 strains. This revealed that BXSB/ll is a separate recombinant inbred line derived from SB/Le and C57BL/6, but distinctly different from BXSB, that most likely arose due to residual heterozygosity in the BXSB stock. Despite the continued presence of the powerful disease-susceptibility locus Bxs3, BXSB/ll mice do not develop disease. We propose that the disappearance of the disease phenotype in the BXSB/ll mice is due to the inheritance of one or more suppressor loci in the differentially inherited intervals between the BXSB/ll and BXSB strains.

  11. A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome

    Science.gov (United States)

    Kou, Qinghe; Jiang, Jiao; Guo, Shaogui; Zhang, Haiying; Hou, Wenju; Zou, Xiaohua; Sun, Honghe; Gong, Guoyi; Levi, Amnon; Xu, Yong

    2012-01-01

    As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of the assembled genomic sequences of the elite Chinese watermelon line 97103 (Citrullus lanatus var. lanatus). The genetic map was constructed using an F8 population of 103 recombinant inbred lines (RILs). The RILs are derived from a cross between the line 97103 and the United States Plant Introduction (PI) 296341-FR (C. lanatus var. citroides) that contains resistance to fusarium wilt (races 0, 1, and 2). The genetic map consists of eleven linkage groups that include 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel) and 36 structure variation (SV) markers and spans ∼800 cM with a mean marker interval of 0.8 cM. Using fluorescent in situ hybridization (FISH) with 11 BACs that produced chromosome-specifc signals, we have depicted watermelon chromosomes that correspond to the eleven linkage groups constructed in this study. The high resolution genetic map developed here should be a useful platform for the assembly of the watermelon genome, for the development of sequence-based markers used in breeding programs, and for the identification of genes associated with important agricultural traits. PMID:22247776

  12. A consensus linkage map of lentil based on DArT markers from three RIL mapping populations.

    Directory of Open Access Journals (Sweden)

    Duygu Ates

    Full Text Available Lentil (Lens culinaris ssp. culinaris Medikus is a diploid (2n = 2x = 14, self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes.A consensus map of lentil (Lens culinaris ssp. culinaris Medikus was constructed using three different lentils recombinant inbred line (RIL populations, including "CDC Redberry" x "ILL7502" (LR8, "ILL8006" x "CDC Milestone" (LR11 and "PI320937" x "Eston" (LR39.The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4. The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps.This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.

  13. A consensus linkage map of lentil based on DArT markers from three RIL mapping populations.

    Science.gov (United States)

    Ates, Duygu; Aldemir, Secil; Alsaleh, Ahmad; Erdogmus, Semih; Nemli, Seda; Kahriman, Abdullah; Ozkan, Hakan; Vandenberg, Albert; Tanyolac, Bahattin

    2018-01-01

    Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including "CDC Redberry" x "ILL7502" (LR8), "ILL8006" x "CDC Milestone" (LR11) and "PI320937" x "Eston" (LR39). The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.

  14. [Visualizing Research Lines in Public Health: An analysis Based on Bibliometric Maps Applied to the Revista Española de Salud Pública (2006-2015)].

    Science.gov (United States)

    Gálvez, Carmen

    2016-12-01

    Identifying research lines is essential to understand the knowledge structure of a scientific domain. The aim of this study was to identify the main research topics of within the domain of public health, in the Revista Española de Saslud Pública during 2006-2015. Original articles included in the Social Sciences Citation Index (SSCI) database, available online through the Web of Science (WoS), were selected. The analysis units used were the keywords, KeyWords Plus (KW+), extracted automatically by SSCI. With KW+ obtained bibliometric, maps were created using a methodology based on the combination of co-word analysis, co-word analysis, clustering techniques and visualization techniques. We analyzed 512 documents, of which 176 KW+ were obtained with a frequency greater than or equal to 3. The results were bidimensional bibliometric maps with thematic groupings of KW+, representing the main research fronts: i) epidemiology, risk control programs disease and, in general, service organization and health policies; ii) infectious diseases, principally HIV; iii) a progressive increase in several lines interrelated with cardiovascular diseases (CVD); iv) a line multidimensional dedicated to different aspects associated to the quality of life related to health (HRQoL); and v) an emerging line linked to binge drinking. For the multidisciplinary and multidimensional nature of public health, the construction of bibliometric maps is an appropriate methodology to understand the knowledge structure of this scientific domain.

  15. LIF-measurements on a low prassure RF-driven InBr lamp

    NARCIS (Netherlands)

    Mulders, H.C.J.; Stoffels, W.W.

    2007-01-01

    A laser induced fluorescence (LIF) experiment has been carried out on a low pressure, capacitively coupled RF driven. Ar discharge with InBr as an additive. The intention is to find the density of the different states of InBr and the metastable states in particular. We measured the density profile

  16. Localisation of genes for resistance against ¤Blumeria graminis¤ f.sp. ¤hordei¤ and ¤Puccinia graminis¤ in a cross between a barley cultivar and a wild barley (¤Hordeum vulgare¤ ssp. ¤spontaneum¤) line

    DEFF Research Database (Denmark)

    Backes, G.; Madsen, L.H.; Jaiser, H.

    2003-01-01

    The aims of this investigation have been to map new (quantitative) resistance genes against powdery mildew, caused by Blumeria graminis f.sp. hordei L., and leaf rust, caused by Puccinia hordei L., in a cross between the barley (Hordeum vulgare ssp. vulgare) cultivar "Vada" and the wild barley...... (Hordeum vulgare ssp. spontaneum) line "1B-87" originating from Israel. The population consisted of 121 recombinant inbred lines. Resistance against leaf rust and powdery mildew was tested on detached leaves. The leaf rust isolate "I-80" and the powdery mildew isolate "Va-4", respectively, were used...

  17. THE ALMA SPECTROSCOPIC SURVEY IN THE HUBBLE ULTRA DEEP FIELD: IMPLICATIONS FOR SPECTRAL LINE INTENSITY MAPPING AT MILLIMETER WAVELENGTHS AND CMB SPECTRAL DISTORTIONS

    Energy Technology Data Exchange (ETDEWEB)

    Carilli, C. L.; Walter, F. [National Radio Astronomy Observatory, P.O. Box 0, Socorro, NM 87801 (United States); Chluba, J. [Jodrell Bank Centre for Astrophysics, University of Manchester, Oxford Road, M13 9PL (United Kingdom); Decarli, R. [Max-Planck Institute for Astronomy, D-69117 Heidelberg (Germany); Aravena, M. [Nucleo de Astronomia, Facultad de Ingenieria, Universidad Diego Portales, Av. Ejercito 441, Santiago (Chile); Wagg, J. [Square Kilometre Array Organisation, Lower Withington, Cheshire (United Kingdom); Popping, G. [European Southern Observatory, Karl-Schwarzschild-Strasse 2, D-85748, Garching (Germany); Cortes, P. [Joint ALMA Observatory—ESO, Av. Alonso de Cordova, 3104, Santiago (Chile); Hodge, J. [Leiden Observatory, Leiden University, Niels Bohrweg 2, NL2333 RA Leiden (Netherlands); Weiss, A. [Max-Planck-Institut für Radioastronomie, Auf dem Hügel 69, D-53121 Bonn (Germany); Bertoldi, F. [Argelander Institute for Astronomy, University of Bonn, Auf dem Hügel 71, D-53121 Bonn (Germany); Riechers, D., E-mail: ccarilli@aoc.nrao.edu [Cornell University, 220 Space Sciences Building, Ithaca, NY 14853 (United States)

    2016-12-10

    We present direct estimates of the mean sky brightness temperature in observing bands around 99 and 242 GHz due to line emission from distant galaxies. These values are calculated from the summed line emission observed in a blind, deep survey for spectral line emission from high redshift galaxies using ALMA (the ALMA spectral deep field observations “ASPECS” survey). In the 99 GHz band, the mean brightness will be dominated by rotational transitions of CO from intermediate and high redshift galaxies. In the 242 GHz band, the emission could be a combination of higher order CO lines, and possibly [C ii] 158 μ m line emission from very high redshift galaxies ( z  ∼ 6–7). The mean line surface brightness is a quantity that is relevant to measurements of spectral distortions of the cosmic microwave background, and as a potential tool for studying large-scale structures in the early universe using intensity mapping. While the cosmic volume and the number of detections are admittedly small, this pilot survey provides a direct measure of the mean line surface brightness, independent of conversion factors, excitation, or other galaxy formation model assumptions. The mean surface brightness in the 99 GHZ band is: T{sub B}  = 0.94 ± 0.09 μ K. In the 242 GHz band, the mean brightness is: T{sub B}  = 0.55 ± 0.033 μ K. These should be interpreted as lower limits on the average sky signal, since we only include lines detected individually in the blind survey, while in a low resolution intensity mapping experiment, there will also be the summed contribution from lower luminosity galaxies that cannot be detected individually in the current blind survey.

  18. Slow inbred lines of Drosophila melanogaster express as much inbreeding depression as fast inbred lines under semi-natural conditions

    DEFF Research Database (Denmark)

    Kristensen, Torsten Nygård; Knudsen, Morten Ravn; Loeschcke, Volker

    2011-01-01

    Selection may reduce the deleterious consequences of inbreeding. This may be due to purging of recessive deleterious alleles or balancing selection favouring heterozygote offspring. Such selection is expected to be more efficient at slower compared to at faster rates of inbreeding. In this study ...

  19. Selection of inbred maize (Zea mays L.) progenies by topcrosses conducted in contrasting environments.

    Science.gov (United States)

    Rodrigues, C S; Pacheco, C A P; Guedes, M L; Pinho, R G V; Castro, C R

    2016-09-23

    The aim of this study was to identify inbred progenies of S 0:1 maize (Zea mays L.) plants that were efficient at a low level of technology and responsive at a high level of technology through the use of topcrosses. Two contrasting environments were created using two levels of base fertilization and topdressing, so that the levels of nitrogen, phosphorus, and potassium were applied four times higher in one environment than in the other. We used S 0:1 progenies derived from commercial hybrids in topcrosses with two testers (an elite line from the flint heterotic group and an elite line from the dent heterotic group). The progenies and three controls were evaluated in an augmented block design in Nossa Senhora das Dores, SE, Brazil in the 2010 crop season. The average grain yield in the high-technological level was 21.44% greater than that in the low-technological level. There were no changes in progeny behavior in the two technological levels for grain yield. The testers did not differ in the average grain yield of the progenies at the two technological levels. Therefore, it is possible to select progenies derived from commercial hybrids that have an efficient response to fertilization.

  20. Mapping QTL for Seed Germinability under Low Temperature Using a New High-Density Genetic Map of Rice

    Directory of Open Access Journals (Sweden)

    Ningfei Jiang

    2017-07-01

    Full Text Available Mapping major quantitative trait loci (QTL responsible for rice seed germinability under low temperature (GULT can provide valuable genetic source for improving cold tolerance in rice breeding. In this study, 124 rice backcross recombinant inbred lines (BRILs derived from a cross indica cv. Changhui 891 and japonica cv. 02428 were genotyped through re-sequencing technology. A bin map was generated which includes 3057 bins covering distance of 1266.5 cM with an average of 0.41 cM between markers. On the basis of newly constructed high-density genetic map, six QTL were detected ranging from 40 to 140 kb on Nipponbare genome. Among these, two QTL qCGR8 and qGRR11 alleles shared by 02428 could increase GULT and seed germination recovery rate after cold stress, respectively. However, qNGR1 and qNGR4 may be two major QTL affecting indica Changhui 891germination under normal condition. QTL qGRR1 and qGRR8 affected the seed germination recovery rate after cold stress and the alleles with increasing effects were shared by the Changhui 891 could improve seed germination rate after cold stress dramatically. These QTL could be a highly valuable genetic factors for cold tolerance improvement in rice lines. Moreover, the BRILs developed in this study will serve as an appropriate choice for mapping and studying genetic basis of rice complex traits.

  1. Causes and consequences of chromatin variation between inbred mice.

    Directory of Open Access Journals (Sweden)

    Mona Hosseini

    2013-06-01

    Full Text Available Variation at regulatory elements, identified through hypersensitivity to digestion by DNase I, is believed to contribute to variation in complex traits, but the extent and consequences of this variation are poorly characterized. Analysis of terminally differentiated erythroblasts in eight inbred strains of mice identified reproducible variation at approximately 6% of DNase I hypersensitive sites (DHS. Only 30% of such variable DHS contain a sequence variant predictive of site variation. Nevertheless, sequence variants within variable DHS are more likely to be associated with complex traits than those in non-variant DHS, and variants associated with complex traits preferentially occur in variable DHS. Changes at a small proportion (less than 10% of variable DHS are associated with changes in nearby transcriptional activity. Our results show that whilst DNA sequence variation is not the major determinant of variation in open chromatin, where such variants exist they are likely to be causal for complex traits.

  2. Heritability and Components of Resistance to Cercospora zeae-maydis Derived from Maize Inbred VO613Y.

    Science.gov (United States)

    Gordon, Stuart G; Lipps, Patrick E; Pratt, Richard C

    2006-06-01

    ABSTRACT Gray leaf spot (GLS), caused by the fungus Cercospora zeae-maydis, is one of the most important foliar diseases of maize. This study was undertaken to estimate heritability of C. zeae-maydis resistance and examine the relationship between previously identified resistance loci and certain components of resistance including incubation period, lesion number, and maximum lesion length. Partially inbred progenies arising from hybridization between maize inbred lines VO613Y (high level of partial resistance) and Pa405 (susceptible) were examined in Ohio and South Africa. Heritability estimates of resistance were calculated based on severity and incubation period values. The range of heritability estimates based on severity was broad, with values ranging from approximately 0.46 to 0.81 (mean = 0.59). Estimates of mean heritability for incubation period were lowest (0.18), indicating that this component would likely be unsuitable for selection of germ plasm intended for deployment in diverse regions. Length of GLS lesions was significantly affected by host genotype, with resistant genotypes having shorter lesions from one site in Ohio during two seasons. Genotype also had a significant effect on incubation period and lesion number; the lower values for these components also were associated with resistant genotypes. The combined action of these resistance components resulted in lower overall disease severity.

  3. The Identification of Two Head Smut Resistance-Related QTL in Maize by the Joint Approach of Linkage Mapping and Association Analysis.

    Directory of Open Access Journals (Sweden)

    Yong-xiang Li

    Full Text Available Head smut, caused by the fungus Sphacelotheca reiliana (Kühn Clint, is a devastating threat to maize production. In this study, QTL mapping of head smut resistance was performed using a recombinant inbred line (RIL population from a cross between a resistant line "QI319" and a susceptible line "Huangzaosi" (HZS with a genetic map constructed from genotyping-by-sequencing (GBS data and composed of 1638 bin markers. Two head smut resistance QTL were identified, located on Chromosome 2 (q2.09HR and Chromosome 5 (q5.03HR, q2.09HR is co-localized with a previously reported QTL for head smut resistance, and the effect of q5.03HR has been validated in backcross populations. It was also observed that pyramiding the resistant alleles of both QTL enhanced the level of resistance to head smut. A genome-wide association study (GWAS using 277 diverse inbred lines was processed to validate the mapped QTL and to identify additional head smut resistance associations. A total of 58 associated SNPs were detected, which were distributed in 31 independent regions. SNPs with significant association to head smut resistance were detected within the q2.09HR and q5.03HR regions, confirming the linkage mapping results. It was also observed that both additive and epistastic effects determine the genetic architecture of head smut resistance in maize. As shown in this study, the combined strategy of linkage mapping and association analysis is a powerful approach in QTL dissection for disease resistance in maize.

  4. Scaling results for the magnetic field line trajectories in the stochastic layer near the separatrix in divertor tokamaks with high magnetic shear using the higher shear map

    International Nuclear Information System (INIS)

    Punjabi, Alkesh; Ali, Halima; Farhat, Hamidullah

    2009-01-01

    Extra terms are added to the generating function of the simple map (Punjabi et al 1992 Phys. Rev. Lett. 69 3322) to adjust shear of magnetic field lines in divertor tokamaks. From this new generating function, a higher shear map is derived from a canonical transformation. A continuous analog of the higher shear map is also derived. The method of maps (Punjabi et al 1994 J. Plasma Phys. 52 91) is used to calculate the average shear, stochastic broadening of the ideal separatrix near the X-point in the principal plane of the tokamak, loss of poloidal magnetic flux from inside the ideal separatrix, magnetic footprint on the collector plate, and its area, and the radial diffusion coefficient of magnetic field lines near the X-point. It is found that the width of the stochastic layer near the X-point and the loss of poloidal flux from inside the ideal separatrix scale linearly with average shear. The area of magnetic footprints scales roughly linearly with average shear. Linear scaling of the area is quite good when the average shear is greater than or equal to 1.25. When the average shear is in the range 1.1-1.25, the area of the footprint fluctuates (as a function of average shear) and scales faster than linear scaling. Radial diffusion of field lines near the X-point increases very rapidly by about four orders of magnitude as average shear increases from about 1.15 to 1.5. For higher values of average shear, diffusion increases linearly, and comparatively very slowly. The very slow scaling of the radial diffusion of the field can flatten the plasma pressure gradient near the separatrix, and lead to the elimination of type-I edge localized modes.

  5. Analysis and Mapping of Flood Line and Flood Zones within the Godavari River in Nasik Municipal Corporation

    Science.gov (United States)

    Thakre, Deepak

    2010-05-01

    Analysis and Mapping of Flood Line within the Godavari River in Nasik(Municipal Corporation Area) Dr.Deepak N.Thakre Lecturer in Geography L.V.H.College, Nasik-3, Maharashtra, India A flood is an overflow or accumulation of an expanse of water that submerges land when the discharge of a river can not be accommodated within the margins of its normal channel so that water spreads over adjoining area and creates havoc. Problem: Since last few years there has been a sudden increase in rainfall,quite intense during a certain period in monsoon,as a result of which the discharge in river Godavari increases and creates problems in low lying areas on the banks of river Godavari like: submergence of houses,major loss of lives,management failure(due to unexpected dimension of floods)and the disruption of normal life. This paper attempts to analyse and draw an averege flood zone and sudden flood zone on the basis of : 1) Actual field work and survey with the help of Dumpy level and GPS 2) Field interviews of affected people 3) Data available from Meteorological and Irrigation department Among several districts that have flourished in the soils of Indian subcontinent the name of Nashik has drawn the attention of people all over the world. Geographical location of Nashik is 20° 01' to 20° 02' North and 73° 30' to 73° 50'East. Nashik city is situated on the banks of river Godavari and tributaries namely Nasardi, Waghadi, Darna and Walvadi.The total area of Nasik is 264.23 Sq.km (102 Sq.mt) and height from M.S.L is 3284 feet (1001 Mt). River Godavari originates in Western mountain range and flows towards East up to Bay of Bengal. On the upstream of Nasik city dams like Gangapur, Darna, Alandi, Kasyapi and Gautami-Godavari are constructed on river Godavari and its tributaries. Gangapur dam is the nearest storage dam constructed 15km away from Nasik city at source area in the year 1965. Due to moderation of floods and construction of dam there is encroachment in low lying areas

  6. Differential screening and mass mapping of proteins from premalignant and cancer cell lines using nonporous reversed-phase HPLC coupled with mass spectrometric analysis.

    Science.gov (United States)

    Chong, B E; Hamler, R L; Lubman, D M; Ethier, S P; Rosenspire, A J; Miller, F R

    2001-03-15

    Nonporous (NPS) RP-HPLC has been used to rapidly separate proteins from whole cell lysates of human breast cell lines. The nonporous separation involves the use of hard-sphere silica beads of 1.5-microm diameter coated with C18, which can be used to separate proteins ranging from 5 to 90 kDa. Using only 30-40 microg of total protein, the protein molecular weights are detectable on-line using an ESI-oaTOF MS. Of hundreds of proteins detected in this mass range, approxinately 75-80 are more highly expressed. The molecular weight profiles can be displayed as a mass map analogous to a virtual "1-D gel" and differentially expressed proteins can be compared by image analysis. The separated proteins can also be detected by UV absorption and differentially expressed proteins quantified. The eluting proteins can be collected in the liquid phase and the molecular weight and peptide maps determined by MALDI-TOF MS for identification. It is demonstrated that the expressed protein profiles change during neoplastic progression and that many oncoproteins are readily detected. It is also shown that the response of premalignant cancer cells to estradiol can be rapidly screened by this method, demonstrating significant changes in response to an external agent. Ultimately, the proteins can be studied by peptide mapping to search for posttranslational modifications of the oncoproteins accompanying progression.

  7. Variation in DNA Methylation Patterns is More Common among Maize Inbreds than among Tissues

    Directory of Open Access Journals (Sweden)

    Steven R. Eichten

    2013-07-01

    Full Text Available Chromatin modifications, such as DNA methylation, can provide heritable, epigenetic regulation of gene expression in the absence of genetic changes. A role for DNA methylation in meiotically stable marking of repetitive elements and other sequences has been demonstrated in plants. Methylation of DNA is also proposed to play a role in development through providing a mitotic memory of gene expression states established during cellular differentiation. We sought to clarify the relative levels of DNA methylation variation among different genotypes and tissues in maize ( L.. We have assessed genomewide DNA methylation patterns in leaf, immature tassel, embryo, and endosperm tissues of two inbred maize lines: B73 and Mo17. There are hundreds of regions of differential methylation present between the two genotypes. In general, the same regions exhibit differential methylation between B73 and Mo17 in each of the tissues that were surveyed. In contrast, there are few examples of tissue-specific DNA methylation variation. Only a subset of regions with tissue-specific variation in DNA methylation show similar patterns in both genotypes of maize and even fewer are associated with altered gene expression levels among the tissues. Our data indicates a limited impact of DNA methylation on developmental gene regulation within maize.

  8. Park Facilities, Boundaries were determined from parcel mapping lines & site specific items, such as shelter locations, were obtained by field GPS observation, Published in 2010, Not Applicable scale, Chippewa County Government.

    Data.gov (United States)

    NSGIC Local Govt | GIS Inventory — Park Facilities dataset current as of 2010. Boundaries were determined from parcel mapping lines & site specific items, such as shelter locations, were obtained...

  9. Delineation of high tide line using DGPS and laser trak instruments: With special reference to mapping techniqus

    Digital Repository Service at National Institute of Oceanography (India)

    Ganesan, P.

    output. A suggestion is being made in this report for an urgent need that CRZ issues should be taken up as a national programme with all mapping agencies using same methodology, same datum, same projection and with similar interpretation, so that, uniform...

  10. The structure of the broad-line region in active galactic nuclei. I. Reconstructed velocity-delay maps

    DEFF Research Database (Denmark)

    Grier, C.J.; Peterson, B.M.; Pogge, R.W.

    2013-01-01

    We present velocity-resolved reverberation results for five active galactic nuclei. We recovered velocity-delay maps using the maximum entropy method for four objects: Mrk 335, Mrk 1501, 3C 120, and PG 2130+099. For the fifth, Mrk 6, we were only able to measure mean time delays in different velo...

  11. GPR applied to mapping utilities along the route of the Line 4 (yellow) subway tunnel construction in São Paulo City, Brazil

    Science.gov (United States)

    Porsani, Jorge Luís; Ruy, Yang Boo; Ramos, Fernanda Pereira; Yamanouth, Gisele R. B.

    2012-05-01

    The rapid industrial development and disorganized population growth in huge cities bring about various urban problems due to intense use of physical space on and below the surface. Subsurface problems in metropolitan areas are caused by subway line construction, which often follows the routes of utility networks, such as electric and telephone cables, water and gas pipes, storm sewers, etc. Usually, the main problems are related to damage or destruction of preexisting utilities, often putting human lives at risk. With the purpose of minimizing risks, GPR-profiling with 200 MHz antennae was done at two sites, both located in downtown São Paulo, Brazil. The objectives of this work were to map utilities or existing infrastructure in the subsurface in order to orient the construction of the Line 4 (yellow) subway tunnel in São Paulo. GPR profiles can detect water pipes, utility networks in the subsurface, and concrete foundation columns or pilings in subsoil up to 2 m depth. In addition, the GPR profiles also provided details of the target shapes in the subsurface. GPR interpretations combined with lithological information from boreholes and trenches opened in the study areas were extremely important in mapping of the correct spatial distribution of buried utilities at these two sites in São Paulo. This information improves and updates maps of utility placement, serves as a basis for planning of the geotechnical excavation of the Line 4 (yellow) subway tunnel in São Paulo, helps minimize problems related to destruction of preexisting utilities in the subsoil, and avoids risk of dangerous accidents.

  12. Inbred or Outbred? Genetic Diversity in Laboratory Rodent Colonies

    Science.gov (United States)

    Brekke, Thomas D.; Steele, Katherine A.; Mulley, John F.

    2017-01-01

    Nonmodel rodents are widely used as subjects for both basic and applied biological research, but the genetic diversity of the study individuals is rarely quantified. University-housed colonies tend to be small and subject to founder effects and genetic drift; so they may be highly inbred or show substantial genetic divergence from other colonies, even those derived from the same source. Disregard for the levels of genetic diversity in an animal colony may result in a failure to replicate results if a different colony is used to repeat an experiment, as different colonies may have fixed alternative variants. Here we use high throughput sequencing to demonstrate genetic divergence in three isolated colonies of Mongolian gerbil (Meriones unguiculatus) even though they were all established recently from the same source. We also show that genetic diversity in allegedly “outbred” colonies of nonmodel rodents (gerbils, hamsters, house mice, deer mice, and rats) varies considerably from nearly no segregating diversity to very high levels of polymorphism. We conclude that genetic divergence in isolated colonies may play an important role in the “replication crisis.” In a more positive light, divergent rodent colonies represent an opportunity to leverage genetically distinct individuals in genetic crossing experiments. In sum, awareness of the genetic diversity of an animal colony is paramount as it allows researchers to properly replicate experiments and also to capitalize on other genetically distinct individuals to explore the genetic basis of a trait. PMID:29242387

  13. Genetic effects in callose content in root apex of inbred resistant and susceptible corn lines to acid soils Efectos genéticos de la formación de calosa en ápices radicales de líneas de maíz resistentes y susceptibles a suelos ácidos

    Directory of Open Access Journals (Sweden)

    Arcos Alba Lucía

    2007-12-01

    Full Text Available

    The main objective of this work was to identify genetic parameters that are related to callose accumulation using tropical inbreeds corn. Fourteen inbreed lines selected for different levels of tolerance to acid soils were chosen and a diallel among them was generated. The seeds were grown under controlled environmental conditions in a growth chamber and transferred to a nutrient solution at pH 4.3. After 12 hours of 25 µM Al (AlCl3 treatment was applied, callose contents of 1 cm root apex were determined with fluorescence spectrophotometer. Significant differences were found for parents, crosses and parents vs crosses. Average callose content varied from 0.746 to 2.035 (µg PE/cm root apex. Heterosis varied from –21.2% to 276.3%. General combining ability (GCA and specific combining ability (SCA were highly significant indicating that both, additive and non–additive gene effects were important for callose inheritance. SCA and GCA sum of squares accounted for 54% and 46%, respectively of crosses of squares sum. Correlation coefficient between callose content and corn grain yield in the field was negative but not significant (r = –0.38.

    Key words: Zea mays; callose; inheritance; diallel; heterosis; acid soils.

    El objetivo de este trabajo fue estudiar la herencia de la producción de calosa utilizando líneas endogámicas de maíz. Seleccionando 14 líneas (7 tolerantes y 7 susceptibles a suelos ácidos se formó un dialelo que fue probado en campo y en invernadero. Se determinó el contenido de calosa en los 91 cruzamientos resultantes y los 14 progenitores. Para ello se colocaron las semillas en cámara de crecimiento en condiciones controladas. Después de 4–5 días las plántulas fueron transferidas a cubetas que contenían solución nutritiva con aireación constante. Luego de 48 horas se adicionaron 25 µM de aluminio (AlCl3 a cada una de las cubetas y se mantuvieron por 12 horas. Se cortaron tres ápices radicales de

  14. High-density Integrated Linkage Map Based on SSR Markers in Soybean

    Science.gov (United States)

    Hwang, Tae-Young; Sayama, Takashi; Takahashi, Masakazu; Takada, Yoshitake; Nakamoto, Yumi; Funatsuki, Hideyuki; Hisano, Hiroshi; Sasamoto, Shigemi; Sato, Shusei; Tabata, Satoshi; Kono, Izumi; Hoshi, Masako; Hanawa, Masayoshi; Yano, Chizuru; Xia, Zhengjun; Harada, Kyuya; Kitamura, Keisuke; Ishimoto, Masao

    2009-01-01

    A well-saturated molecular linkage map is a prerequisite for modern plant breeding. Several genetic maps have been developed for soybean with various types of molecular markers. Simple sequence repeats (SSRs) are single-locus markers with high allelic variation and are widely applicable to different genotypes. We have now mapped 1810 SSR or sequence-tagged site markers in one or more of three recombinant inbred populations of soybean (the US cultivar ‘Jack’ × the Japanese cultivar ‘Fukuyutaka’, the Chinese cultivar ‘Peking’ × the Japanese cultivar ‘Akita’, and the Japanese cultivar ‘Misuzudaizu’ × the Chinese breeding line ‘Moshidou Gong 503’) and have aligned these markers with the 20 consensus linkage groups (LGs). The total length of the integrated linkage map was 2442.9 cM, and the average number of molecular markers was 90.5 (range of 70–114) for the 20 LGs. We examined allelic diversity for 1238 of the SSR markers among 23 soybean cultivars or lines and a wild accession. The number of alleles per locus ranged from 2 to 7, with an average of 2.8. Our high-density linkage map should facilitate ongoing and future genomic research such as analysis of quantitative trait loci and positional cloning in addition to marker-assisted selection in soybean breeding. PMID:19531560

  15. Diagnosing the Kinematics of the Tori in Active Galactic Nuclei with the Velocity-resolved Reverberation Mapping of the Narrow Iron K α Line

    Energy Technology Data Exchange (ETDEWEB)

    Liu Yuan; Li Xiaobo, E-mail: liuyuan@ihep.ac.cn, E-mail: lixb@ihep.ac.cn [Key Laboratory of Particle Astrophysics, Institute of High Energy Physics, Chinese Academy of Sciences, P.O. Box 918-3, Beijing 100049 (China)

    2017-07-20

    The properties of the dusty tori in active galactic nuclei (AGNs) have been investigated in detail, mainly focusing on the geometry and components; however, the kinematics of the torus are still not clear. The narrow iron K α line at 6.4 keV is thought to be produced by the X-ray reflection from the torus. Thus, the velocity-resolved reverberation mapping of it is able to constrain the kinematics of the torus. Such effort is limited by the spectral resolution of current charged coupled device (CCD) detectors and should be possible with the microcalorimeter on the next generation X-ray satellite. In this paper, we first construct the response functions of the torus under a uniform inflow, a Keplerian rotation, and a uniform outflow. Then the energy-dependent light curve of the narrow iron K α line is simulated according to the performance of the X-ray Integral Field Unit in Athena. Finally, the energy-dependent cross-correlation function is calculated to reveal the kinematic signal. According to our results, 100 observations with 5 ks exposure of each are sufficient to distinguish the above three velocity fields. Although the real geometry and velocity field of the torus could be more complex than we assumed, the present result proves the feasibility of the velocity-resolved reverberation mapping of the narrow iron K α line. The combination of the dynamics of the torus with those of the broad-line region and the host galaxy is instructive for the understanding of the feeding and feedback process of AGNs.

  16. Development of genetic and molecular indices for drought tolerance in some inbred and hybrids of maize (Zea mays L.)

    International Nuclear Information System (INIS)

    Saleh, O.M.

    1998-01-01

    From eighteen zea mays inbred lines, two were chosen as drought tolerant and drought sensitive genotypes (G621W and G603W, respectively). They were evaluated along with their F1 and F2 for their relative drought tolerance for some yield traits. The physiological markers cations (Na, K, Ca and Mg) and their ratios (K/Na, Ca/K and Ca/Mg) showed differential association with drought tolerance was observed.SDS-protein profiles indicated the presence of two bands in the tolerant group associated with drought tolerance. Western blotting analysis didn't give polymorphism patterns such as esterase, peroxidase and acid phosphatase showed differential responses with respect to drought tolerance

  17. QTL mapping in multiple populations and development stages reveals dynamic quantitative trait loci for fruit size in cucumbers of different market classes.

    Science.gov (United States)

    Weng, Yiqun; Colle, Marivi; Wang, Yuhui; Yang, Luming; Rubinstein, Mor; Sherman, Amir; Ophir, Ron; Grumet, Rebecca

    2015-09-01

    QTL analysis in multi-development stages with different QTL models identified 12 consensus QTLs underlying fruit elongation and radial growth presenting a dynamic view of genetic control of cucumber fruit development. Fruit size is an important quality trait in cucumber (Cucumis sativus L.) of different market classes. However, the genetic and molecular basis of fruit size variations in cucumber is not well understood. In this study, we conducted QTL mapping of fruit size in cucumber using F2, F2-derived F3 families and recombinant inbred lines (RILs) from a cross between two inbred lines Gy14 (North American picking cucumber) and 9930 (North China fresh market cucumber). Phenotypic data of fruit length and diameter were collected at three development stages (anthesis, immature and mature fruits) in six environments over 4 years. QTL analysis was performed with three QTL models including composite interval mapping (CIM), Bayesian interval mapping (BIM), and multiple QTL mapping (MQM). Twenty-nine consistent and distinct QTLs were detected for nine traits from multiple mapping populations and QTL models. Synthesis of information from available fruit size QTLs allowed establishment of 12 consensus QTLs underlying fruit elongation and radial growth, which presented a dynamic view of genetic control of cucumber fruit development. Results from this study highlighted the benefits of QTL analysis with multiple QTL models and different mapping populations in improving the power of QTL detection. Discussion was presented in the context of domestication and diversifying selection of fruit length and diameter, marker-assisted selection of fruit size, as well as identification of candidate genes for fruit size QTLs in cucumber.

  18. High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth1[OPEN

    Science.gov (United States)

    Huang, Chenglong; Wu, Di; Qiao, Feng; Li, Wenqiang; Duan, Lingfeng; Wang, Ke; Xiao, Yingjie; Chen, Guoxing; Liu, Qian; Yang, Wanneng

    2017-01-01

    With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize (Zea mays) recombinant inbred line population (n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction. PMID:28153923

  19. Prenatal effects of ancestral irradiation in inbred mice

    International Nuclear Information System (INIS)

    Sprackling, L.E.S.

    1975-01-01

    Mice from 13 inbred strains (S, Z, E, Bab, BaB, BrR, C, K, N, Q, G, CFW, CF1) received continuous cobalt 60 irradiation at low dose rates for varying numbers of consecutive generations. Some Bab and BaB mice had received continuous irradiation for from 24 to 31 generations and the other mice had up to six generations of continuous irradiation in their ancestry. At weaning, the mice were removed from the irradiation room and were mated within strains either to sibs or nonsibs. Ancestral and direct irradiation doses were calculated. The ancestral dose was the effective accumulated dose to the progeny of the mated mice. The direct dose was the amount of irradiation received by any mated female from her conception to her weaning. Each irradiated or control female was scored as fertile or sterile and in utero litter counts were made in pregnant females that were dissected past the tenth day of pregnancy; the sum of moles, dead embryos, and live embryos was the total in utero litter size. A ratio of the living embryos to the total number of embryos in utero was determined for each litter. An increase in ancestral or direct irradiation dose significantly decreased fertility in 11 of the 13 strains. The fertility curves for the pooled data were sigmoid in the area of the doses below those that caused complete sterility. Among the controls, there were significant strain differences in total litter size and in the ratio. Strain X--Y plots, with ancestral or direct doses plotted against total litter size or ratio, revealed the tendency for litter size to decrease as dose increased. The only trend shown for ratio was for the litters with ratios of 0.50 or less to appear more frequently among the irradiated mice. The few corpora lutea counts revealed nothing of significance. Generally, there was a definite trend toward fewer mice alive in utero among the irradiated mice

  20. Comparison of global brain gene expression profiles between inbred long-sleep and inbred short-sleep mice by high-density gene array hybridization.

    Science.gov (United States)

    Xu, Y; Ehringer, M; Yang, F; Sikela, J M

    2001-06-01

    Inbred long-sleep (ILS) and short-sleep (ISS) mice show significant central nervous system-mediated differences in sleep time for sedative dose of ethanol and are frequently used as a rodent model for ethanol sensitivity. In this study, we have used complementary DNA (cDNA) array hybridization methodology to identify genes that are differentially expressed between the brains of ILS and ISS mice. To carry out this analysis, we used both the gene discovery array (GDA) and the Mouse GEM 1 Microarray. GDA consists of 18,378 nonredundant mouse cDNA clones on a single nylon filter. Complex probes were prepared from total brain mRNA of ILS or ISS mice by using reverse transcription and 33P labeling. The labeled probes were hybridized in parallel to the gene array filters. Data from GDA experiments were analyzed with SQL-Plus and Oracle 8. The GEM microarray includes 8,730 sequence-verified clones on a glass chip. Two fluorescently labeled probes were used to hybridize a microarray simultaneously. Data from GEM experiments were analyzed by using the GEMTools software package (Incyte). Differentially expressed genes identified from each method were confirmed by relative quantitative reverse transcription-polymerase chain reaction (RT-PCR). A total of 41 genes or expressed sequence tags (ESTs) display significant expression level differences between brains of ILS and ISS mice after GDA, GEM1 hybridization, and quantitative RT-PCR confirmation. Among them, 18 clones were expressed higher in ILS mice, and 23 clones were expressed higher in ISS mice. The individual gene or EST's function and mapping information have been analyzed. This study identified 41 genes that are differentially expressed between brains of ILS and ISS mice. Some of them may have biological relevance in mediation of phenotypic variation between ILS and ISS mice for ethanol sensitivity. This study also demonstrates that parallel gene expression comparison with high-density cDNA arrays is a rapid and

  1. Integrated genetic linkage map of cultivated peanut by three RIL populations

    Institute of Scientific and Technical Information of China (English)

    Yanbin Song; Huifang Jiang; Huaiyong Luo; Li Huang; Yuning Chen; Weigang Chen; Nian Liu; Xiaoping Ren; Bolun Yu; Jianbin Guo

    2017-01-01

    High-density and precise genetic linkage map is fundamental to detect quanti-tative trait locus (QTL) of agronomic and quality related traits in cultivated peanut (Arachis hypogaea L.). In this study, three linkage maps from three RIL (recombinant inbred line) populations were used to construct an integrated map. A total of 2,069 SSR and transposon markers were anchored on the high-density integrated map which covered 2,231.53 cM with 20 linkage groups. Totally, 92 QTLs correlating with pod length (PL), pod width (PW), hun-dred pods weight (HPW) and plant height (PH) from above RIL populations were mapped on it. Seven intervals were found to harbor QTLs controlling the same traits in different pop-ulations, including one for PL, three for PW, two for HPW, and one for PH. Besides, QTLs controlling different traits in different populations were found to be overlapped in four inter-vals. Interval on A05 contains 17 QTLs for different traits from two RIL populations. New markers were added to these intervals to detect QTLs with narrow confidential intervals. Results obtained in this study may facilitate future genomic researches such as QTL study, fine mapping, positional cloning and marker-assisted selection (MAS) in peanut.

  2. Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Thudi, Mahendar; Khan, Aamir W; Kumar, Vinay; Gaur, Pooran M; Katta, Krishnamohan; Garg, Vanika; Roorkiwal, Manish; Samineni, Srinivasan; Varshney, Rajeev K

    2016-01-27

    Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in South Asia and Sub-Saharan Africa. In order to harness the untapped genetic potential available for chickpea improvement, we re-sequenced 35 chickpea genotypes representing parental lines of 16 mapping populations segregating for abiotic (drought, heat, salinity), biotic stresses (Fusarium wilt, Ascochyta blight, Botrytis grey mould, Helicoverpa armigera) and nutritionally important (protein content) traits using whole genome re-sequencing approach. A total of 192.19 Gb data, generated on 35 genotypes of chickpea, comprising 973.13 million reads, with an average sequencing depth of ~10 X for each line. On an average 92.18 % reads from each genotype were aligned to the chickpea reference genome with 82.17 % coverage. A total of 2,058,566 unique single nucleotide polymorphisms (SNPs) and 292,588 Indels were detected while comparing with the reference chickpea genome. Highest number of SNPs were identified on the Ca4 pseudomolecule. In addition, copy number variations (CNVs) such as gene deletions and duplications were identified across the chickpea parental genotypes, which were minimum in PI 489777 (1 gene deletion) and maximum in JG 74 (1,497). A total of 164,856 line specific variations (144,888 SNPs and 19,968 Indels) with the highest percentage were identified in coding regions in ICC 1496 (21 %) followed by ICCV 97105 (12 %). Of 539 miscellaneous variations, 339, 138 and 62 were inter-chromosomal variations (CTX), intra-chromosomal variations (ITX) and inversions (INV) respectively. Genome-wide SNPs, Indels, CNVs, PAVs, and miscellaneous variations identified in different mapping populations are a valuable resource in genetic research and helpful in locating genes/genomic segments responsible for economically important traits. Further, the genome-wide variations identified in the present study can be used for developing high density SNP arrays for

  3. Intergenerational effects of inbreeding in Nicrophorus vespilloides: offspring suffer fitness costs when either they or their parents are inbred.

    Science.gov (United States)

    Mattey, S N; Strutt, L; Smiseth, P T

    2013-04-01

    Inbreeding depression is the reduction in fitness caused by mating between related individuals. Inbreeding is expected to cause a reduction in offspring fitness when the offspring themselves are inbred, but outbred individuals may also suffer a reduction in fitness when they depend on care from inbred parents. At present, little is known about the significance of such intergenerational effects of inbreeding. Here, we report two experiments on the burying beetle Nicrophorus vespilloides, an insect with elaborate parental care, in which we investigated inbreeding depression in offspring when either the offspring themselves or their parents were inbred. We found substantial inbreeding depression when offspring were inbred, including reductions in hatching success of inbred eggs and survival of inbred offspring. We also found substantial inbreeding depression when parents were inbred, including reductions in hatching success of eggs produced by inbred parents and survival of outbred offspring that received care from inbred parents. Our results suggest that intergenerational effects of inbreeding can have substantial fitness costs to offspring, and that future studies need to incorporate such costs to obtain accurate estimates of inbreeding depression. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  4. Multiple disease resistance to fungal and oomycete pathogens using a recombinant inbred line population in pepper

    Science.gov (United States)

    Incorporating disease resistance into cultivars is a primary focus of modern breeding programs. Resistance to pathogens is often introgressed from landrace or wild individuals with poor fruit quality into commercial-quality cultivars. Sites of multiple disease resistance (MDR) are regions or “hotspo...

  5. Combining ability of maize (Zea mays L.) inbred lines resistant to ...

    African Journals Online (AJOL)

    GREGORY

    2011-06-01

    Jun 1, 2011 ... evaluated across four locations in Kenya under artificial and natural infestation in 2009. Genotype (G) ... harvested area of annual food crops and 25% of total ..... to additive rather than non-additive gene effects, and selection ...

  6. Transcriptome analysis of two recombinant inbred lines of common bean contrasting for symbiotic nitrogen fixation

    Science.gov (United States)

    Common bean (Phaseolus vulgaris L.) is able to fix atmospheric nitrogen (N2) through symbiotic nitrogen fixation (SNF). Effective utilization of existing variability for SNF in common bean for genetic improvement requires an understanding of underlying genes and molecular mechanisms. The utility of ...

  7. Molecular characterization of high performance inbred lines of Brazilian common beans.

    Science.gov (United States)

    Cardoso, P C B; Veiga, M M; de Menezes, I P P; Valdisser, P A M R; Borba, T C O; Melo, L C; Del Peloso, M J; Brondani, C; Vianello, R P

    2013-02-06

    The identification of germplasm genetic variability in breeding programs of the common bean (Phaseolus vulgaris) is essential for determining the potential of each combination of parent plants to obtain superior genotypes. The present study aimed to estimated the extent of genetic diversity in 172 lineages and cultivars of the common bean by integrating five tests of value for cultivation and use (VCU) that were conducted over the last eight years by the breeding program of Embrapa Arroz e Feijão in Brazil. Nine multilocus genotyping systems composed of 36 fluorescent microsatellite markers distributed across 11 different chromosomes of the common bean were used, of which 24 were polymorphic in all trials. One hundred and eighty-seven alleles were identified, with an average of 7.79 alleles per locus and an average gene diversity of 0.65. The combined probability of identity for all loci was 1.32 x 10(-16). Lineages that are more genetically divergent between the selection cycles were identified, allowing the breeding program to develop a crossbreed between elite genotypes with a low degree of genetic relatedness. HE values ranged from 0.31 to 0.63, with a large reduction in the genetic base over successive selection cycles. The test showed a significant degree of differentiation (FST = 0.159). Private alleles (26%) were identified and can be directly incorporated into the gene pool of cultivated germplasm, thereby contributing effectively to the expansion of genetic diversity in this bean-breeding program.

  8. Mapping of Powdery Mildew Resistance Gene pmCH89 in a Putative Wheat-Thinopyrum intermedium Introgression Line.

    Science.gov (United States)

    Hou, Liyuan; Zhang, Xiaojun; Li, Xin; Jia, Juqing; Yang, Huizhen; Zhan, Haixian; Qiao, Linyi; Guo, Huijuan; Chang, Zhijian

    2015-07-28

    Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a globally serious disease adversely affecting wheat production. The Bgt-resistant wheat breeding line CH09W89 was derived after backcrossing a Bgt resistant wheat-Thinopyrum intermedium partial amphiploid TAI7045 with susceptible wheat cultivars. At the seedling stage, CH09W89 exhibited immunity or high resistance to Bgt pathotypes E09, E20, E21, E23, E26, Bg1, and Bg2, similar to its donor line TAI7045 and Th. intermedium. No Th. intermedium chromatin was detected based on genomic in situ hybridization of mitotic chromosomes. To determine the mode of inheritance of the Bgt resistance and the chromosomal location of the resistance gene, CH09W89 was crossed with two susceptible wheat cultivars. The results of the genetic analysis showed that the adult resistance to Bgt E09 in CH09W89 was controlled by a single recessive gene, which was tentatively designated as pmCH89. Two polymorphic SSR markers, Xwmc310 and Xwmc125, were linked to the resistance gene with genetic distances 3.1 and 2.7 cM, respectively. Using the Chinese Spring aneuploid and deletion lines, the resistance gene and its linked markers were assigned to chromosome arm 4BL in the bin 0.68-0.78. Due to its unique position on chromosome 4BL, pmCH89 appears to be a new locus for resistance to powdery mildew. These results will be of benefit for improving powdery mildew resistance in wheat breeding programs.

  9. Mapping of Powdery Mildew Resistance Gene pmCH89 in a Putative Wheat-Thinopyrum intermedium Introgression Line

    Directory of Open Access Journals (Sweden)

    Liyuan Hou

    2015-07-01

    Full Text Available Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt, is a globally serious disease adversely affecting wheat production. The Bgt-resistant wheat breeding line CH09W89 was derived after backcrossing a Bgt resistant wheat-Thinopyrum intermedium partial amphiploid TAI7045 with susceptible wheat cultivars. At the seedling stage, CH09W89 exhibited immunity or high resistance to Bgt pathotypes E09, E20, E21, E23, E26, Bg1, and Bg2, similar to its donor line TAI7045 and Th. intermedium. No Th. intermedium chromatin was detected based on genomic in situ hybridization of mitotic chromosomes. To determine the mode of inheritance of the Bgt resistance and the chromosomal location of the resistance gene, CH09W89 was crossed with two susceptible wheat cultivars. The results of the genetic analysis showed that the adult resistance to Bgt E09 in CH09W89 was controlled by a single recessive gene, which was tentatively designated as pmCH89. Two polymorphic SSR markers, Xwmc310 and Xwmc125, were linked to the resistance gene with genetic distances 3.1 and 2.7 cM, respectively. Using the Chinese Spring aneuploid and deletion lines, the resistance gene and its linked markers were assigned to chromosome arm 4BL in the bin 0.68–0.78. Due to its unique position on chromosome 4BL, pmCH89 appears to be a new locus for resistance to powdery mildew. These results will be of benefit for improving powdery mildew resistance in wheat breeding programs.

  10. Joint Analysis of Strain and Parent-of-Origin Effects for Recombinant Inbred Intercrosses Generated from Multiparent Populations with the Collaborative Cross as an Example.

    Science.gov (United States)

    Liu, Yanyan; Xiong, Sican; Sun, Wei; Zou, Fei

    2018-02-02

    Multiparent populations (MPP) have become popular resources for complex trait mapping because of their wider allelic diversity and larger population size compared with traditional two-way recombinant inbred (RI) strains. In mice, the collaborative cross (CC) is one of the most popular MPP and is derived from eight genetically diverse inbred founder strains. The strategy of generating RI intercrosses (RIX) from MPP in general and from the CC in particular can produce a large number of completely reproducible heterozygote genomes that better represent the (outbred) human population. Since both maternal and paternal haplotypes of each RIX are readily available, RIX is a powerful resource for studying both standing genetic and epigenetic variations of complex traits, in particular, the parent-of-origin (PoO) effects, which are important contributors to many complex traits. Furthermore, most complex traits are affected by >1 genes, where multiple quantitative trait locus mapping could be more advantageous. In this paper, for MPP-RIX data but taking CC-RIX as a working example, we propose a general Bayesian variable selection procedure to simultaneously search for multiple genes with founder allelic effects and PoO effects. The proposed model respects the complex relationship among RIX samples, and the performance of the proposed method is examined by extensive simulations. Copyright © 2018 Liu et al.

  11. Microbeam X-ray fluorescence mapping of Cu and Fe in human prostatic carcinoma cell lines using synchrotron radiation

    Energy Technology Data Exchange (ETDEWEB)

    Rocha, K.M.J.; Leitao, R.G.; Oliveira-Barros, E.G.; Oliveira, M.A.; Canellas, C.G.L.; Anjos, M.J.; Nasciutti, L.E.; Lopes, R.T., E-mail: kjose@nuclear.ufrj.br, E-mail: marcelin@lin.ufrj.br, E-mail: ricardo@lin.ufrj.br, E-mail: roberta@lin.ufrj.br, E-mail: eligouveab@gmail.com, E-mail: maria_aparecida_ufrj@yahoo.com.br, E-mail: luiz.nasciutti@histo.ufrj.br, E-mail: roberta.leitao@uerj.br, E-mail: marcelin@uerj.br [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Laboratorio de Instrumentacao Nuclear; Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Instituto de Ciencias Biomedicas; Universidade do Estado do Rio de Janeiro (UERJ), RJ (Brazil). Instituto de Fisica

    2017-11-01

    Cancer is a worldwide public health problem and prostate cancer continues to be one of the most common fatal cancers in men. Copper plays an important role in the aetiology and growth of tumours however, whether intratumoral copper is actually elevated in prostate cancer patients has not been established. Iron, an important trace element, plays a vital function in oxygen metabolism, oxygen uptake, and electron transport in mitochondria, energy metabolism, muscle function, and hematopoiesis. The X-ray microfluorescence technique (μXRF) is a rapid and non-destructive method of elemental analysis that provides useful elemental information about samples without causing damage or requiring extra sample preparations. This study investigated the behavior of cells in spheroids of human prostate cells, tumour cell line (DU145) and normal cell line (RWPE-1), after supplementation with zinc chloride by 24 hours using synchrotron X-ray microfluorescence (μSRXRF). The measurements were performed with a standard geometry of 45 deg of incidence, excited by a white beam using a pixel of 25 μm and a time of 300 ms/pixel at the XRF beamline at the Synchrotron Light National Laboratory (Campinas, Brazil). The results by SRμXRF showed non-uniform Cu and Fe distributions in all the spheroids analyzed. (author)

  12. Microbeam X-ray fluorescence mapping of Cu and Fe in human prostatic carcinoma cell lines using synchrotron radiation

    International Nuclear Information System (INIS)

    Rocha, K.M.J.; Leitao, R.G.; Oliveira-Barros, E.G.; Oliveira, M.A.; Canellas, C.G.L.; Anjos, M.J.; Nasciutti, L.E.; Lopes, R.T.; Universidade Federal do Rio de Janeiro; Universidade do Estado do Rio de Janeiro

    2017-01-01

    Cancer is a worldwide public health problem and prostate cancer continues to be one of the most common fatal cancers in men. Copper plays an important role in the aetiology and growth of tumours however, whether intratumoral copper is actually elevated in prostate cancer patients has not been established. Iron, an important trace element, plays a vital function in oxygen metabolism, oxygen uptake, and electron transport in mitochondria, energy metabolism, muscle function, and hematopoiesis. The X-ray microfluorescence technique (μXRF) is a rapid and non-destructive method of elemental analysis that provides useful elemental information about samples without causing damage or requiring extra sample preparations. This study investigated the behavior of cells in spheroids of human prostate cells, tumour cell line (DU145) and normal cell line (RWPE-1), after supplementation with zinc chloride by 24 hours using synchrotron X-ray microfluorescence (μSRXRF). The measurements were performed with a standard geometry of 45 deg of incidence, excited by a white beam using a pixel of 25 μm and a time of 300 ms/pixel at the XRF beamline at the Synchrotron Light National Laboratory (Campinas, Brazil). The results by SRμXRF showed non-uniform Cu and Fe distributions in all the spheroids analyzed. (author)

  13. Fine-mapping of qGW4.05, a major QTL for kernel weight and size in maize.

    Science.gov (United States)

    Chen, Lin; Li, Yong-xiang; Li, Chunhui; Wu, Xun; Qin, Weiwei; Li, Xin; Jiao, Fuchao; Zhang, Xiaojing; Zhang, Dengfeng; Shi, Yunsu; Song, Yanchun; Li, Yu; Wang, Tianyu

    2016-04-12

    Kernel weight and size are important components of grain yield in cereals. Although some information is available concerning the map positions of quantitative trait loci (QTL) for kernel weight and size in maize, little is known about the molecular mechanisms of these QTLs. qGW4.05 is a major QTL that is associated with kernel weight and size in maize. We combined linkage analysis and association mapping to fine-map and identify candidate gene(s) at qGW4.05. QTL qGW4.05 was fine-mapped to a 279.6-kb interval in a segregating population derived from a cross of Huangzaosi with LV28. By combining the results of regional association mapping and linkage analysis, we identified GRMZM2G039934 as a candidate gene responsible for qGW4.05. Candidate gene-based association mapping was conducted using a panel of 184 inbred lines with variable kernel weights and kernel sizes. Six polymorphic sites in the gene GRMZM2G039934 were significantly associated with kernel weight and kernel size. The results of linkage analysis and association mapping revealed that GRMZM2G039934 is the most likely candidate gene for qGW4.05. These results will improve our understanding of the genetic architecture and molecular mechanisms underlying kernel development in maize.

  14. QTL mapping of resistance to gray leaf spot in maize.

    Science.gov (United States)

    Zhang, Yan; Xu, Ling; Fan, Xingming; Tan, Jing; Chen, Wei; Xu, Mingliang

    2012-12-01

    Gray leaf spot (GLS), caused by the causal fungal pathogen Cercospora zeae-maydis, is one of the most serious foliar diseases of maize worldwide. In the current study, a highly resistant inbred line Y32 and a susceptible line Q11 were used to produce segregating populations for both genetic analysis and QTL mapping. The broad-sense heritability (H (2)) for GLS resistance was estimated to be as high as 0.85, indicating that genetic factors played key roles in phenotypic variation. In initial QTL analysis, four QTL, located on chromosomes 1, 2, 5, and 8, were detected to confer GLS resistance. Each QTL could explain 2.53-23.90 % of the total phenotypic variation, predominantly due to additive genetic effects. Two major QTL, qRgls1 and qRgls2 on chromosomes 8 and 5, were consistently detected across different locations and replicates. Compared to the previous results, qRgls2 is located in a 'hotspot' for GLS resistance; while, qRgls1 does not overlap with any other known resistance QTL. Furthermore, the major QTL-qRgls1 was fine-mapped into an interval of 1.4 Mb, flanked by the markers GZ204 and IDP5. The QTL-qRgls1 could enhance the resistance percentages by 19.70-61.28 %, suggesting its usefulness to improve maize resistance to GLS.

  15. Incorrect strain information for mouse cell lines: sequential influence of misidentification on sublines.

    Science.gov (United States)

    Uchio-Yamada, Kozue; Kasai, Fumio; Ozawa, Midori; Kohara, Arihiro

    2017-03-01

    Misidentification or cross-contamination of cell lines can cause serious issues. Human cell lines have been authenticated by short tandem repeat profiling; however, mouse cell lines have not been adequately assessed. In this study, mouse cell lines registered with the JCRB cell bank were examined by simple sequence length polymorphism (SSLP) analysis to identify their strains. Based on comparisons with 7 major inbred strains, our results revealed their strains in 80 of 90 cell lines. However, 12 of the 80 cell lines (15%) were found to differ from registered information. Of them, 4 cell lines originated from the same mouse, which had been generated through mating between two different inbred strains. The genotype of the mouse sample had not been examined after the backcross, leading to strain misidentification in those cell lines. Although 8 other cell lines had been established as sublines of a BALB/c cell line, their SSLP profiles are similar to a Swiss cell line. This affects differences in genotypes between inbred and outbred strains. Because the use of inbred samples and interbreeding between strains are not involved in human materials, our results suggest that the cause and influence of misidentification in mouse cell lines are different from those in human.

  16. Characterization of mature maize (Zea mays L.) root system architecture and complexity in a diverse set of Ex-PVP inbreds and hybrids.

    Science.gov (United States)

    Hauck, Andrew L; Novais, Joana; Grift, Tony E; Bohn, Martin O

    2015-01-01

    The mature root system is a vital plant organ, which is critical to plant performance. Commercial maize (Zea mays L.) breeding has resulted in a steady increase in plant performance over time, along with noticeable changes in above ground vegetative traits, but the corresponding changes in the root system are not presently known. In this study, roughly 2500 core root systems from field trials of a set of 10 diverse elite inbreds formerly protected by Plant Variety Protection plus B73 and Mo17 and the 66 diallel intercrosses among them were evaluated for root traits using high throughput image-based phenotyping. Overall root architecture was modeled by root angle (RA) and stem diameter (SD), while root complexity, the amount of root branching, was quantified using fractal analysis to obtain values for fractal dimension (FD) and fractal abundance (FA). For each trait, per se line effects were highly significant and the most important contributor to trait performance. Mid-parent heterosis and specific combining ability was also highly significant for FD, FA, and RA, while none of the traits showed significant general combining ability. The interaction between the environment and the additive line effect was also significant for all traits. Within the inbred and hybrid generations, FD and FA were highly correlated (rp ≥ 0.74), SD was moderately correlated to FD and FA (0.69 ≥ rp ≥ 0.48), while the correlation between RA and other traits was low (0.13 ≥ rp ≥ -0.40). Inbreds with contrasting effects on complexity and architecture traits were observed, suggesting that root complexity and architecture traits are inherited independently. A more comprehensive understanding of the maize root system and the way it interacts with the environment will be useful for defining adaptation to nutrient acquisition and tolerance to stress from drought and high plant densities, critical factors in the yield gains of modern hybrids.

  17. High-throughput behavioral phenotyping of drug and alcohol susceptibility traits in the expanded panel of BXD recombinant inbred strains

    Energy Technology Data Exchange (ETDEWEB)

    Philip, Vivek M [ORNL; Ansah, T [University of Tennessee Health Science Center, Memphis; Blaha, C, [University of Tennessee Health Science Center, Memphis; Cook, Melloni N. [University of Memphis; Hamre, Kristin M. [University of Tennessee Health Science Center, Memphis; Lariviere, William R [University of Pittsburgh; Matthews, Douglas B [Baylor University; Goldowitz, Daniel [University of British Columbia, Vancouver; Chesler, Elissa J [ORNL

    2010-01-01

    Genetic reference populations, particularly the BXD recombinant inbred strains, are a valuable resource for the discovery of the bio-molecular substrates and genetic drivers responsible for trait variation and co- ariation. This approach can be profitably applied in the analysis of susceptibility and mechanisms of drug and alcohol use disorders for which many predisposing behaviors may predict occurrence and manifestation of increased preference for these substances. Many of these traits are modeled by common mouse behavioral assays, facilitating the detection of patterns and sources of genetic co-regulation of predisposing phenotypes and substance consumption. Members of the Tennessee Mouse Genome Consortium have obtained behavioral phenotype data from 260 measures related to multiple behavioral assays across several domains: self-administration, response to, and withdrawal from cocaine, MDMA, morphine and alcohol; novelty seeking; behavioral despair and related neurological phenomena; pain sensitivity; stress sensitivity; anxiety; hyperactivity; and sleep/wake cycles. All traits have been measured in both sexes and the recently expanded panel of 69 additional BXD recombinant inbred strains (N=69). Sex differences and heritability estimates were obtained for each trait, and a comparison of early (N = 32) and recent BXD RI lines was performed. Primary data is publicly available for heritability, sex difference and genetic analyses using www.GeneNetwork.org. These analyses include QTL detection and genetic analysis of gene expression. Stored results from these analyses are available at http://ontologicaldiscovery.org for comparison to other genomic analysis results. Together with the results of related studies, these data form a public resource for integrative systems genetic analysis of neurobehavioral traits.

  18. About Non-Line-Of-Sight Satellite Detection and Exclusion in a 3D Map-Aided Localization Algorithm

    Directory of Open Access Journals (Sweden)

    François Peyret

    2013-01-01

    Full Text Available Reliable GPS positioning in city environment is a key issue: actually, signals are prone to multipath, with poor satellite geometry in many streets. Using a 3D urban model to forecast satellite visibility in urban contexts in order to improve GPS localization is the main topic of the present article. A virtual image processing that detects and eliminates possible faulty measurements is the core of this method. This image is generated using the position estimated a priori by the navigation process itself, under road constraints. This position is then updated by measurements to line-of-sight satellites only. This closed-loop real-time processing has shown very first promising full-scale test results.

  19. About Non-Line-Of-Sight Satellite Detection and Exclusion in a 3D Map-Aided Localization Algorithm

    Science.gov (United States)

    Peyraud, Sébastien; Bétaille, David; Renault, Stéphane; Ortiz, Miguel; Mougel, Florian; Meizel, Dominique; Peyret, François

    2013-01-01

    Reliable GPS positioning in city environment is a key issue actually, signals are prone to multipath, with poor satellite geometry in many streets. Using a 3D urban model to forecast satellite visibility in urban contexts in order to improve GPS localization is the main topic of the present article. A virtual image processing that detects and eliminates possible faulty measurements is the core of this method. This image is generated using the position estimated a priori by the navigation process itself, under road constraints. This position is then updated by measurements to line-of-sight satellites only. This closed-loop real-time processing has shown very first promising full-scale test results. PMID:23344379

  20. Association mapping in sunflower for sclerotinia head rot resistance

    Directory of Open Access Journals (Sweden)

    Fusari Corina M

    2012-06-01

    Full Text Available Abstract Background Sclerotinia Head Rot (SHR is one of the most damaging diseases of sunflower in Europe, Argentina, and USA, causing average yield reductions of 10 to 20 %, but leading to total production loss under favorable environmental conditions for the pathogen. Association Mapping (AM is a promising choice for Quantitative Trait Locus (QTL mapping, as it detects relationships between phenotypic variation and gene polymorphisms in existing germplasm without development of mapping populations. This article reports the identification of QTL for resistance to SHR based on candidate gene AM. Results A collection of 94 sunflower inbred lines were tested for SHR under field conditions using assisted inoculation with the fungal pathogen Sclerotinia sclerotiorum. Given that no biological mechanisms or biochemical pathways have been clearly identified for SHR, 43 candidate genes were selected based on previous transcript profiling studies in sunflower and Brassica napus infected with S. sclerotiorum. Associations among SHR incidence and haplotype polymorphisms in 16 candidate genes were tested using Mixed Linear Models (MLM that account for population structure and kinship relationships. This approach allowed detection of a significant association between the candidate gene HaRIC_B and SHR incidence (P  Conclusions These results suggest that AM will be useful in dissecting other complex traits in sunflower, thus providing a valuable tool to assist in crop breeding.

  1. Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high-density linkage mapping.

    Science.gov (United States)

    Patil, Gunvant; Vuong, Tri D; Kale, Sandip; Valliyodan, Babu; Deshmukh, Rupesh; Zhu, Chengsong; Wu, Xiaolei; Bai, Yonghe; Yungbluth, Dennis; Lu, Fang; Kumpatla, Siva; Grover Shannon, J; Varshney, Rajeev K; Nguyen, Henry T

    2018-04-04

    The cultivated [Glycine max (L) Merr.] and wild [Glycine soja Siebold & Zucc.] soybean species comprise wide variation in seed composition traits. Compared to wild soybean, cultivated soybean contains low protein, high oil and high sucrose. In this study, an inter-specific population was derived from a cross between G. max (Williams 82) and G. soja (PI 483460B). This recombinant inbred line (RIL) population of 188 lines was sequenced at 0.3x depth. Based on 91,342 single nucleotide polymorphisms (SNPs), recombination events in RILs were defined, and a high-resolution bin map was developed (4,070 bins). In addition to bin mapping, QTL analysis for protein, oil and sucrose was performed using 3,343 polymorphic SNPs (3K-SNP), derived from Illumina Infinium BeadChip sequencing platform. The QTL regions from both platforms were compared and a significant concordance was observed between bin and 3K-SNP markers. Importantly, the bin map derived from next generation sequencing technology enhanced mapping resolution (from 1325 Kb to 50 Kb). A total of 5, 9 and 4 QTLs were identified for protein, oil and sucrose content, respectively and some of the QTLs coincided with soybean domestication related genomic loci. The major QTL for protein and oil was mapped on Chr. 20 (qPro_20) and suggested negative correlation between oil and protein. In terms of sucrose content, a novel and major QTL was identified on Chr. 8 (qSuc_08) and harbors putative genes involved in sugar transport. In addition, genome-wide association (GWAS) using 91,342 SNPs confirmed the genomic loci derived from QTL mapping. A QTL based haplotype using whole genome resequencing of 106 diverse soybean lines identified unique allelic variation in wild soybean that could be utilized to widen the genetic base in cultivated soybean. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  2. Quantitative Trait Loci Mapping of Western Corn Rootworm (Coleoptera: Chrysomelidae) Host Plant Resistance in Two Populations of Doubled Haploid Lines in Maize (Zea mays L.).

    Science.gov (United States)

    Bohn, Martin O; Marroquin, Juan J; Flint-Garcia, Sherry; Dashiell, Kenton; Willmot, David B; Hibbard, Bruce E

    2018-02-09

    Over the last 70 yr, more than 12,000 maize accessions have been screened for their level of resistance to western corn rootworm, Diabrotica virgifera virgifera (LeConte; Coleoptera: Chrysomelidae), larval feeding. Less than 1% of this germplasm was selected for initiating recurrent selection or other breeding programs. Selected genotypes were mostly characterized by large root systems and superior root regrowth after root damage caused by western corn rootworm larvae. However, no hybrids claiming native (i.e., host plant) resistance to western corn rootworm larval feeding are currently commercially available. We investigated the genetic basis of western corn rootworm resistance in maize materials with improved levels of resistance using linkage disequilibrium mapping approaches. Two populations of topcrossed doubled haploid maize lines (DHLs) derived from crosses between resistant and susceptible maize lines were evaluated for their level of resistance in three to four different environments. For each DHL topcross an average root damage score was estimated and used for quantitative trait loci (QTL) analysis. We found genomic regions contributing to western corn rootworm resistance on all maize chromosomes, except for chromosome 4. Models fitting all QTL simultaneously explained about 30 to 50% of the genotypic variance for root damage scores in both mapping populations. Our findings confirm the complex genetic structure of host plant resistance against western corn rootworm larval feeding in maize. Interestingly, three of these QTL regions also carry genes involved in ascorbate biosynthesis, a key compound we hypothesize is involved in the expression of western corn rootworm resistance. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. Unconditional and Conditional QTL Mapping for Tiller Numbers at Various Stages with Single Segment Substitution Lines in Rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    ZHAO Fang-ming; LIU Gui-fu; ZHU Hai-tao; DING Xiao-hua; ZENG Rui-zhen; ZHANG Ze-min; LI Wen-tao; ZHANG Gui-quan

    2008-01-01

    Tiller is one of the most important agronomic traits which influences quantity and quality of effective panicles and finally influences yield in rice.It is important to understand "static" and "dynamic" information of the QTLs for tillers in rice.This work was the first time to simultaneously map unconditional and conditional QTLs for tiller numbers at various stages by using single segment substitution lines in rice.Fourteen QTLs for tiller number,distributing on the corresponding substitution segments of chromosomes 1,2,3,4,6,7 and 8 were detected.Both the number and the effect of the QTLs for tiller number were various at different stages,from 6 to 9 in the number and from 1.49 to 3.49 in the effect,respectively. Tiller number QTLs expressed in a time order,mainly detected at three stages of 0-7d,14-21d and 35-42d after transplanting with 6 positive,9 random and 6 negative expressing QTLs,respectively.Each of the QTLs expressed one time at least during the whole duration of rice.The tiller number at a specific stage was determined by sum of QTL effects estimated by the unconditional method,while the increasing or decreasing number in a given time interval was controlled by the total of QTL effects estimated by the conditional method.These results demonstrated that it is highly effective and accurate for mapping of the QTLs by using single segment substitution lines and the conditional analysis methodology.

  4. Heterogeneous Stock Rat: A Unique Animal Model for Mapping Genes Influencing Bone Fragility

    OpenAIRE

    Alam, Imranul; Koller, Daniel L.; Sun, Qiwei; Roeder, Ryan K.; Cañete, Toni; Blázquez, Gloria; López-Aumatell, Regina; Martínez-Membrives, Esther; Vicens-Costa, Elia; Mont, Carme; Díaz, Sira; Tobeña, Adolf; Fernández-Teruel, Alberto; Whitley, Adam; Strid, Pernilla

    2011-01-01

    Previously, we demonstrated that skeletal mass, structure and biomechanical properties vary considerably among 11 different inbred rat strains. Subsequently, we performed quantitative trait loci (QTL) analysis in 4 inbred rat strains (F344, LEW, COP and DA) for different bone phenotypes and identified several candidate genes influencing various bone traits. The standard approach to narrowing QTL intervals down to a few candidate genes typically employs the generation of congenic lines, which ...

  5. Genotyping-by-Sequencing derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat

    Science.gov (United States)

    Hard red winter wheat parents ‘Harry’ (drought tolerant) and ‘Wesley’ (drought susceptible) was used to develop a recombinant inbred population to identify genomic regions associated with drought and adaptation. To precisely map genomic regions high-density linkage maps are a prerequisite. In this s...

  6. Cytogenetic analysis and mapping of leaf rust resistance in Aegilops speltoides Tausch derived bread wheat line Selection2427 carrying putative gametocidal gene(s).

    Science.gov (United States)

    Niranjana, M; Vinod; Sharma, J B; Mallick, Niharika; Tomar, S M S; Jha, S K

    2017-12-01

    Leaf rust (Puccinia triticina) is a major biotic stress affecting wheat yields worldwide. Host-plant resistance is the best method for controlling leaf rust. Aegilops speltoides is a good source of resistance against wheat rusts. To date, five Lr genes, Lr28, Lr35, Lr36, Lr47, and Lr51, have been transferred from Ae. speltoides to bread wheat. In Selection2427, a bread wheat introgresed line with Ae. speltoides as the donor parent, a dominant gene for leaf rust resistance was mapped to the long arm of chromosome 3B (LrS2427). None of the Lr genes introgressed from Ae. speltoides have been mapped to chromosome 3B. Since none of the designated seedling leaf rust resistance genes have been located on chromosome 3B, LrS2427 seems to be a novel gene. Selection2427 showed a unique property typical of gametocidal genes, that when crossed to other bread wheat cultivars, the F 1 showed partial pollen sterility and poor seed setting, whilst Selection2427 showed reasonable male and female fertility. Accidental co-transfer of gametocidal genes with LrS2427 may have occurred in Selection2427. Though LrS2427 did not show any segregation distortion and assorted independently of putative gametocidal gene(s), its utilization will be difficult due to the selfish behavior of gametocidal genes.

  7. Flood-inundation maps for the Hoosic River, North Adams and Williamstown, Massachusetts, from the confluence with the North Branch Hoosic River to the Vermont State line

    Science.gov (United States)

    Lombard, Pamela J.; Bent, Gardner C.

    2015-01-01

    A series of nine digital flood-inundation maps were developed for an 8-mile reach of the Hoosic River in North Adams and Williamstown, Massachusetts, by the U.S. Geological Survey (USGS) in cooperation with the Federal Emergency Management Agency. The coverage of the maps extends from the confluence with the North Branch Hoosic River to the Vermont State line. Peak flows with 20-, 10-, 4-, 2-, 1-, 0.5-, and 0.2-percent annual exceedance probabilities were computed for the reach from updated flood-frequency analyses. These peak flows were routed through a one-dimensional step-backwater hydraulic model to obtain the corresponding peak water-surface elevations, and to place the tropical storm Irene flood of August 28, 2011 into historical context. The hydraulic model was calibrated by using the current (2014) stage-discharge relation at the USGS streamgage Hoosic River near Williamstown, Massachusetts (01332500), and from documented high-water marks from the tropical storm Irene flood, which had approximately a 1-percent annual exceedance probability.

  8. Mapping the end points of large deletions affecting the hprt locus in human peripheral blood cells and cell lines

    International Nuclear Information System (INIS)

    Nelson, S.L.; Grosovsky, A.J.; Jones, I.M.; Burkhart-Schultz, K.; Fuscoe, J.C.

    1995-01-01

    We have examined the extent of of HPRT - total gene deletions in three mutant collections: spontaneous and X-ray-induced deletions in TK6 human B lymphoblasts, and HPRT - deletions arising in vivo in T cells. A set of 13 Xq26 STS markers surrounding hprt and spanning approximately 3.3 Mb was used. Each marker used was observed to be missing in at least one of the hprt deletion mutants analyzed. The largest deletion observed encompassed at least 3 Mb. Nine deletions extended outside of the mapped region in the centromeric direction (>1.7 Mb). In contrast, only two telomeric deletions extended to marker 342R (1.26 Mb), and both exhibited slowed or limited cell growth. These data suggest the existence of a gene, within the vicinity of 342R, which establishes the telomeric limit of recoverable deletions. Most (25/41) X-ray-induced total gene deletion mutants exhibited marker loss, but only 1/8 of the spontaneous deletions encompassed any Xq26 markers (P = 0.0187). Furthermore, nearly half (3/8) of the spontaneous 3' total deletion breakpoints were within 14 kb of the hprt coding sequence. In contrast, 40/41 X-ray-induced HPRT - total deletions extended beyond this point (P = 0.011). Although the overall representation of total gene deletions in the in vivo spectrum is low, 4/5 encompass Xq26 markers flanking hprt. This pattern differs significantly from spontaneous HPRT - large deletions occurring in vitro (P = 0.032) but resembles the spectrum of X-ray-induced deletions. 24 refs., 6 figs., 1 tab

  9. Enzyme markers in inbred rat strains: genetics of new markers and strain profiles.

    Science.gov (United States)

    Adams, M; Baverstock, P R; Watts, C H; Gutman, G A

    1984-08-01

    Twenty-six inbred strains of the laboratory rat (Rattus norvegicus) were examined for electrophoretic variation at an estimated 97 genetic loci. In addition to previously documented markers, variation was observed for the enzymes aconitase, aldehyde dehydrogenase, and alkaline phosphatase. The genetic basis of these markers (Acon-1, Ahd-2, and Akp-1) was confirmed. Linkage analysis between 35 pairwise comparisons revealed that the markers Fh-1 and Pep-3 are linked. The strain profiles of the 25 inbred strains at 11 electrophoretic markers are given.

  10. Pepsin immobilized in dextran-modified fused-silica capillaries for on-line protein digestion and peptide mapping.

    Science.gov (United States)

    Stigter, E C A; de Jong, G J; van Bennekom, W P

    2008-07-07

    On-line digestion of proteins under acidic conditions was studied using micro-reactors consisting of dextran-modified fused-silica capillaries with covalently immobilized pepsin. The proteins used in this study differed in molecular weight, isoelectric point and sample composition. The injected protein samples were completely digested in 3 min and the digest was analyzed with micro-high performance liquid chromatography (HPLC) and tandem mass spectrometry (MS/MS). The different proteins present in the samples could be identified with a Mascot database search on the basis of auto-MS/MS data. It proved also to be possible to digest and analyze protein mixtures with a sequence coverage of 55% and 97% for the haemoglobin beta- and alpha-chain, respectively, and 35-55% for the various casein variants. Protease auto-digestion, sample carry-over and loss of signal due to adsorption of the injected proteins were not observed. The backpressure of the reactor is low which makes coupling to systems such as Surface Plasmon Resonance biosensors, which do not tolerate too high pressure, possible. The reactor was stable for at least 40 days when used continuously.

  11. Pepsin immobilized in dextran-modified fused-silica capillaries for on-line protein digestion and peptide mapping

    Energy Technology Data Exchange (ETDEWEB)

    Stigter, E.C.A. [Division of Biomedical Analysis, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht (Netherlands)], E-mail: e.c.a.stigter@uu.nl; Jong, G.J. de; Bennekom, W.P. van [Division of Biomedical Analysis, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht (Netherlands)

    2008-07-07

    On-line digestion of proteins under acidic conditions was studied using micro-reactors consisting of dextran-modified fused-silica capillaries with covalently immobilized pepsin. The proteins used in this study differed in molecular weight, isoelectric point and sample composition. The injected protein samples were completely digested in 3 min and the digest was analyzed with micro-high performance liquid chromatography (HPLC) and tandem mass spectrometry (MS/MS). The different proteins present in the samples could be identified with a Mascot database search on the basis of auto-MS/MS data. It proved also to be possible to digest and analyze protein mixtures with a sequence coverage of 55% and 97% for the haemoglobin {beta}- and {alpha}-chain, respectively, and 35-55% for the various casein variants. Protease auto-digestion, sample carry-over and loss of signal due to adsorption of the injected proteins were not observed. The backpressure of the reactor is low which makes coupling to systems such as Surface Plasmon Resonance biosensors, which do not tolerate too high pressure, possible. The reactor was stable for at least 40 days when used continuously.

  12. Characterization of early follicular cDNA library suggests evidence for genetic polymorphisms in the inbred strain C108 of Bombyx mori.

    Science.gov (United States)

    Mills, D R; Goldsmith, M R

    2000-04-01

    Recent work towards the completion of a saturated molecular genetic linkage map for the lepidopteran silkworm, Bombyx mori (n = 28), has provided evidence for existing polymorphisms in the inbred strain C108. Two inbred parental strains, p50 and C108, were crossed to produce the F1 (P/C) hybrid offspring. The populations used in this project were comprised of a combination of 29 F2 (F1 x F1) and 31 reciprocal backcross (P/C x C/C, P/C x P/P) progeny. All restriction fragment length polymorphisms (RFLPs) for the initial analysis were hybridized with anonymous probes derived from a random early follicular cDNA (Rcf) library from Bombyx. A total of 19 Rcf probes were selected as showing scorable codominant polymorphic patterns when screened against F2 and backcross DNAs digested with the restriction enzymes EcoRI, HindIII, or PstI, and Southern blotted to nylon membranes for hybridization. Of the newly reported Rcf probes, 7 (37%) were characterized as producing 'simple' polymorphic patterns, while 12 (63%) were characterized as producing 'complex' polymorphic patterns. Further characterization of the complex patterns subdivided this group into two general classes: polymorphisms that contained an additional allele, and multiple bands that contained an easily scored two banded polymorphism. Because the extra allele class was limited to the (P/C x C/C) backcross progeny, it is suggested that the inbred parental strain C108 harbors polymorphic loci that are inherited in a simple Mendelian fashion. A genetic analysis discussing plausible origins and maintenance of these polymorphisms is presented.

  13. Implementation of lean manufacturing to reduce waste in production line with value stream mapping approach and Kaizen in division sanding upright piano, case study in: PT. X

    Directory of Open Access Journals (Sweden)

    Santosa W. A.

    2018-01-01

    Full Text Available PT. XY produces musical instruments such as Upright Pianos and Grand Pianos. Due to a competitive competition, a good quality product is highly required as well as increasing the production scale. To achieve these objectives, company needs to reduce wastes occurred in its production lines, particularly in the division of sanding panel upright piano (UP which produces type of PE B1 pianos. High cycle time and lead-time are caused by wastes in UP panel sanding division. Therefore, it is needed improvements to be applied here so that the production lines will be run more effectively and efficiently. This study aims to identify wastes using Value Stream Mapping (VSM as a tool of lean manufacturing and to implement the improvements using Kaizen. It is found that the wastes are motion and waiting. Furthermore, the improvements (kaizen are focused on reducing motion and waiting wastes. It is shown that cycle time decreased from 51.16 minutes to 41.90 minutes, work in process or inventory can be reduced to 24 pcs over 32 pcs, and the lead-time is 0.167 days of 0.222 days.

  14. Mapping QTLs Controlling Flowering Time and Important Agronomic Traits in Pearl Millet.

    Science.gov (United States)

    Kumar, Sushil; Hash, C Tom; Nepolean, T; Satyavathi, C Tara; Singh, Govind; Mahendrakar, Mahesh D; Yadav, Rattan S; Srivastava, Rakesh K

    2017-01-01

    Pearl millet [ Pennisetum glaucum (L.) R. Br.] is a staple crop for the people of arid and semi-arid regions of the world. It is fast gaining importance as a climate resilient nutricereal. Exploiting the bold seeded, semi-dwarf, and early flowering genotypes in pearl millet is a key breeding strategy to enhance yield, adaptability, and for adequate food in resource-poor zones. Genetic variation for agronomic traits of pearl millet inbreds can be used to dissect complex traits through quantitative trait locus (QTL) mapping. This study was undertaken to map a set of agronomically important traits like flowering time (FT), plant height (PH), panicle length (PL), and grain weight (self and open-pollinated seeds) in the recombinant inbred line (RIL) population of ICMB 841-P3 × 863B-P2 cross. Excluding grain weight (open pollinated), heritabilities for FT, PH, PL, grain weight (selfed) were in high to medium range. A total of six QTLs for FT were detected on five chromosomes, 13 QTLs for PH on six chromosomes, 11 QTLs for PL on five chromosomes, and 14 QTLs for 1,000-grain weight (TGW) spanning five chromosomes. One major QTL on LG3 was common for FT and PH. Three major QTLs for PL, one each on LG1, LG2, and LG6B were detected. The large effect QTL for TGW (self) on LG6B had a phenotypic variance ( R 2 ) of 62.1%. The R 2 for FT, TGW (self), and PL ranged from 22.3 to 59.4%. A total of 21 digenic interactions were discovered for FT ( R 2 = 18-40%) and PL ( R 2 = 13-19%). The epistatic effects did not reveal any significant QTL × QTL × environment (QQE) interactions. The mapped QTLs for flowering time and other agronomic traits in present experiment can be used for marker-assisted selection (MAS) and genomic selection (GS) breeding programs.

  15. Effect of physical and chemical mutagens and male sterile cytoplasm of chaisma frequency in pearl millet inbreds and hybrids

    International Nuclear Information System (INIS)

    Singh, B.D.; Singh, R.B.; Singh, R.M.; Vijay Laxmi

    1977-01-01

    Chiasma frequency was recorded in normal and treated [10, 20, 30 Kr γ-rays, 0.2% ethyl methane-sulphonate (EMS) and 10 Kr γ-rays + 0.2% EMS] populations of 7 inbreds and 3 hybrids of pearl millet. Inbreds in general showed lower chiasma frequency than hybrids. However, inbred Bi13B showed the highest chiasma frequency. The male sterile cytoplasm reduced the chaisma frequency and increased the among-plant-variability in the inbreds and, therefore, possibly in the hybrids which had male sterile cytoplasm. γ-rays were more effective than EMS in reducing chiasma frequency. In most of the genotypes 10Kr γ-rays and 0.2% EMS promoted chiasma frequency. The combination treatments showed greater effect than γ-rays and EMS applied individually. Hybrids as a group, showed lower variation for chiasma number than inbreds in response to the mutagenic treatments. (author)

  16. Resistance to gray leaf spot of maize: genetic architecture and mechanisms elucidated through nested association mapping and near-isogenic line analysis.

    Science.gov (United States)

    Benson, Jacqueline M; Poland, Jesse A; Benson, Brent M; Stromberg, Erik L; Nelson, Rebecca J

    2015-03-01

    Gray leaf spot (GLS), caused by Cercospora zeae-maydis and Cercospora zeina, is one of the most important diseases of maize worldwide. The pathogen has a necrotrophic lifestyle and no major genes are known for GLS. Quantitative resistance, although poorly understood, is important for GLS management. We used genetic mapping to refine understanding of the genetic architecture of GLS resistance and to develop hypotheses regarding the mechanisms underlying quantitative disease resistance (QDR) loci. Nested association mapping (NAM) was used to identify 16 quantitative trait loci (QTL) for QDR to GLS, including seven novel QTL, each of which demonstrated allelic series with significant effects above and below the magnitude of the B73 reference allele. Alleles at three QTL, qGLS1.04, qGLS2.09, and qGLS4.05, conferred disease reductions of greater than 10%. Interactions between loci were detected for three pairs of loci, including an interaction between iqGLS4.05 and qGLS7.03. Near-isogenic lines (NILs) were developed to confirm and fine-map three of the 16 QTL, and to develop hypotheses regarding mechanisms of resistance. qGLS1.04 was fine-mapped from an interval of 27.0 Mb to two intervals of 6.5 Mb and 5.2 Mb, consistent with the hypothesis that multiple genes underlie highly significant QTL identified by NAM. qGLS2.09, which was also associated with maturity (days to anthesis) and with resistance to southern leaf blight, was narrowed to a 4-Mb interval. The distance between major leaf veins was strongly associated with resistance to GLS at qGLS4.05. NILs for qGLS1.04 were treated with the C. zeae-maydis toxin cercosporin to test the role of host-specific toxin in QDR. Cercosporin exposure increased expression of a putative flavin-monooxygenase (FMO) gene, a candidate detoxification-related gene underlying qGLS1.04. This integrated approach to confirming QTL and characterizing the potential underlying mechanisms advances the understanding of QDR and will facilitate the

  17. Resistance to gray leaf spot of maize: genetic architecture and mechanisms elucidated through nested association mapping and near-isogenic line analysis.

    Directory of Open Access Journals (Sweden)

    Jacqueline M Benson

    2015-03-01

    Full Text Available Gray leaf spot (GLS, caused by Cercospora zeae-maydis and Cercospora zeina, is one of the most important diseases of maize worldwide. The pathogen has a necrotrophic lifestyle and no major genes are known for GLS. Quantitative resistance, although poorly understood, is important for GLS management. We used genetic mapping to refine understanding of the genetic architecture of GLS resistance and to develop hypotheses regarding the mechanisms underlying quantitative disease resistance (QDR loci. Nested association mapping (NAM was used to identify 16 quantitative trait loci (QTL for QDR to GLS, including seven novel QTL, each of which demonstrated allelic series with significant effects above and below the magnitude of the B73 reference allele. Alleles at three QTL, qGLS1.04, qGLS2.09, and qGLS4.05, conferred disease reductions of greater than 10%. Interactions between loci were detected for three pairs of loci, including an interaction between iqGLS4.05 and qGLS7.03. Near-isogenic lines (NILs were developed to confirm and fine-map three of the 16 QTL, and to develop hypotheses regarding mechanisms of resistance. qGLS1.04 was fine-mapped from an interval of 27.0 Mb to two intervals of 6.5 Mb and 5.2 Mb, consistent with the hypothesis that multiple genes underlie highly significant QTL identified by NAM. qGLS2.09, which was also associated with maturity (days to anthesis and with resistance to southern leaf blight, was narrowed to a 4-Mb interval. The distance between major leaf veins was strongly associated with resistance to GLS at qGLS4.05. NILs for qGLS1.04 were treated with the C. zeae-maydis toxin cercosporin to test the role of host-specific toxin in QDR. Cercosporin exposure increased expression of a putative flavin-monooxygenase (FMO gene, a candidate detoxification-related gene underlying qGLS1.04. This integrated approach to confirming QTL and characterizing the potential underlying mechanisms advances the understanding of QDR and will

  18. A high-density SNP map for accurate mapping of seed fibre QTL in Brassica napus L.

    Directory of Open Access Journals (Sweden)

    Liezhao Liu

    Full Text Available A high density genetic linkage map for the complex allotetraploid crop species Brassica napus (oilseed rape was constructed in a late-generation recombinant inbred line (RIL population, using genome-wide single nucleotide polymorphism (SNP markers assayed by the Brassica 60 K Infinium BeadChip Array. The linkage map contains 9164 SNP markers covering 1832.9 cM. 1232 bins account for 7648 of the markers. A subset of 2795 SNP markers, with an average distance of 0.66 cM between adjacent markers, was applied for QTL mapping of seed colour and the cell wall fiber components acid detergent lignin (ADL, cellulose and hemicellulose. After phenotypic analyses across four different environments a total of 11 QTL were detected for seed colour and fiber traits. The high-density map considerably improved QTL resolution compared to the previous low-density maps. A previously identified major QTL with very high effects on seed colour and ADL was pinpointed to a narrow genome interval on chromosome A09, while a minor QTL explaining 8.1% to 14.1% of variation for ADL was detected on chromosome C05. Five and three QTL accounting for 4.7% to 21.9% and 7.3% to 16.9% of the phenotypic variation for cellulose and hemicellulose, respectively, were also detected. To our knowledge this is the first description of QTL for seed cellulose and hemicellulose in B. napus, representing interesting new targets for improving oil content. The high density SNP genetic map enables navigation from interesting B. napus QTL to Brassica genome sequences, giving useful new information for understanding the genetics of key seed quality traits in rapeseed.

  19. VERY LARGE ARRAY MAPPING OF THE CO(1-0) LINE IN SMM J14011+0252

    Energy Technology Data Exchange (ETDEWEB)

    Sharon, Chelsea E.; Baker, Andrew J. [Department of Physics and Astronomy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8019 (United States); Harris, Andrew I. [Department of Astronomy, University of Maryland, College Park, MD 20742 (United States); Thomson, Alasdair P., E-mail: csharon@physics.rutgers.edu, E-mail: ajbaker@physics.rutgers.edu, E-mail: harris@astro.umd.edu, E-mail: at@roe.ac.uk [Institute for Astronomy, University of Edinburgh, Blackford Hill, Edinburgh EH9 3HJ (United Kingdom)

    2013-03-01

    We present high-resolution CO(1-0) observations of the lensed submillimeter galaxy (SMG) SMM J14011+0252 at z = 2.6. Comparison to the previously detected CO(3-2) line gives an intensity ratio of r {sub 3,1} = 0.97 {+-} 0.16 in temperature units, larger than is typical for SMGs but within the range seen in the low-z ultraluminous infrared galaxy population. Combining our new data with previous mid-J CO observations, we perform a single-phase large velocity gradient (LVG) analysis to constrain the physical conditions of the molecular gas. Acceptable models have significant degeneracies between parameters, even when we rule out all models that produce optically thin emission, but we find that the bulk of the molecular gas has T {sub kin} = 20-60 K, n{sub H{sub 2}}{approx}10{sup 4}-10{sup 5} cm{sup -3}, and N {sub CO}/{Delta}v = 10{sup 17.00{+-}0.25} cm{sup -2} km{sup -1} s. For our best-fit models to self-consistently recover a typical CO-to-H{sub 2} abundance and a plausible degree of virialization, the local velocity gradient in the molecular gas must be substantially larger than its galaxy-wide average. This conclusion is consistent with a scenario in which SMM J14011+0252 has a fairly face-on orientation and a molecular interstellar medium composed of many unresolved clouds. Using previous H{alpha} observations, we find that SMM J14011+0252 has a spatially resolved star formation rate versus molecular gas surface density relation inconsistent with those of 'normal' local star-forming galaxies, even if we adopt a local 'disk-like' CO-to-H{sub 2} conversion factor as motivated by our LVG analysis. This discrepancy supports the inference of a star formation relation for high-z starbursts distinct from the local relation that is not solely due to differing choices of gas mass conversion factor.

  20. Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

    Science.gov (United States)

    Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R

    2015-02-01

    Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

  1. Genomic selection and association mapping in rice (Oryza sativa: effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

    Directory of Open Access Journals (Sweden)

    Jennifer Spindel

    2015-02-01

    Full Text Available Genomic Selection (GS is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

  2. Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines

    Science.gov (United States)

    Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R.

    2015-01-01

    Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline. PMID:25689273

  3. Identification of X-linked quantitative trait loci affecting cold tolerance in Drosophila melanogaster and fine mapping by selective sweep analysis.

    Science.gov (United States)

    Svetec, Nicolas; Werzner, Annegret; Wilches, Ricardo; Pavlidis, Pavlos; Alvarez-Castro, José M; Broman, Karl W; Metzler, Dirk; Stephan, Wolfgang

    2011-02-01

    Drosophila melanogaster is a cosmopolitan species that colonizes a great variety of environments. One trait that shows abundant evidence for naturally segregating genetic variance in different populations of D. melanogaster is cold tolerance. Previous work has found quantitative trait loci (QTL) exclusively on the second and the third chromosomes. To gain insight into the genetic architecture of cold tolerance on the X chromosome and to compare the results with our analyses of selective sweeps, a mapping population was derived from a cross between substitution lines that solely differed in the origin of their X chromosome: one originates from a European inbred line and the other one from an African inbred line. We found a total of six QTL for cold tolerance factors on the X chromosome of D. melanogaster. Although the composite interval mapping revealed slightly different QTL profiles between sexes, a coherent model suggests that most QTL overlapped between sexes, and each explained around 5-14% of the genetic variance (which may be slightly overestimated). The allelic effects were largely additive, but we also detected two significant interactions. Taken together, this provides evidence for multiple QTL that are spread along the entire X chromosome and whose effects range from low to intermediate. One detected transgressive QTL influences cold tolerance in different ways for the two sexes. While females benefit from the European allele increasing their cold tolerance, males tend to do better with the African allele. Finally, using selective sweep mapping, the candidate gene CG16700 for cold tolerance colocalizing with a QTL was identified. © 2010 Blackwell Publishing Ltd.

  4. Diversity analysis of Ethiopian mustard breeding lines using RAPD ...

    African Journals Online (AJOL)

    Using cluster analysis based on unweighted pair-group method with arithmetic average (UPGMA) and principal coordinate analysis (PCoA), the 21 Ethiopian inbred lines were grouped into three subgroups and the single genotype introduced from Sweden formed a separate group. The clustering pattern failed to show a ...

  5. Comparative Study of Histopathologic Characterization of Azoxymethane-induced Colon Tumors in Three Inbred Rat Strains

    DEFF Research Database (Denmark)

    Kobæk Larsen, Morten; Fenger, Claus; Hansen, Ket

    2002-01-01

    To obtain controlled genetic variation, colon cancer was chemically induced by use of four subcutaneous injections of azoxymethane (15 mg/kg of body weight/wk) to rats of 3 inbred strains (BDIX/OrlIco, F344/NHsd, WAG/Rij). The selection was based on the availability of established colon cancer cell...

  6. Initial locomotor sensitivity to cocaine varies widely among inbred mouse strains.

    Science.gov (United States)

    Wiltshire, T; Ervin, R B; Duan, H; Bogue, M A; Zamboni, W C; Cook, S; Chung, W; Zou, F; Tarantino, L M

    2015-03-01

    Initial sensitivity to psychostimulants can predict subsequent use and abuse in humans. Acute locomotor activation in response to psychostimulants is commonly used as an animal model of initial drug sensitivity and has been shown to have a substantial genetic component. Identifying the specific genetic differences that lead to phenotypic differences in initial drug sensitivity can advance our understanding of the processes that lead to addiction. Phenotyping inbred mouse strain panels are frequently used as a first step for studying the genetic architecture of complex traits. We assessed locomotor activation following a single, acute 20 mg/kg dose of cocaine (COC) in males from 45 inbred mouse strains and observed significant phenotypic variation across strains indicating a substantial genetic component. We also measured levels of COC, the active metabolite, norcocaine and the major inactive metabolite, benzoylecgonine, in plasma and brain in the same set of inbred strains. Pharmacokinetic (PK) and behavioral data were significantly correlated, but at a level that indicates that PK alone does not account for the behavioral differences observed across strains. Phenotypic data from this reference population of inbred strains can be utilized in studies aimed at examining the role of psychostimulant-induced locomotor activation on drug reward and reinforcement and to test theories about addiction processes. Moreover, these data serve as a starting point for identifying genes that alter sensitivity to the locomotor stimulatory effects of COC. © 2015 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

  7. TEMPORAL STRUCTURE OF OPEN-FIELD BEHAVIOR IN INBRED STRAINS OF MICE

    NARCIS (Netherlands)

    MAKINO, J; KATO, K; MAES, FW

    1991-01-01

    Behavior of the inbred mouse strains BALB, C3H, DBA and C57BL in an open field was directly observed for 10 min by a multi-event time sampling method. It was coded into nine behavioral items, the occurrence or absence of which in consecutive 5-s time bins was called a behavioral state. Fourteen

  8. Linkage Map Construction and Quantitative Trait Locus Analysis of Agronomic and Fiber Quality Traits in Cotton

    Directory of Open Access Journals (Sweden)

    Michael A. Gore

    2014-03-01

    Full Text Available The superior fiber properties of L. serve as a source of novel variation for improving fiber quality in Upland cotton ( L., but introgression from has been largely unsuccessful due to hybrid breakdown and a lack of genetic and genomic resources. In an effort to overcome these limitations, we constructed a linkage map and conducted a quantitative trait locus (QTL analysis of 10 agronomic and fiber quality traits in a recombinant inbred mapping population derived from a cross between TM-1, an Upland cotton line, and NM24016, an elite line with stabilized introgression from . The linkage map consisted of 429 simple-sequence repeat (SSR and 412 genotyping-by-sequencing (GBS-based single-nucleotide polymorphism (SNP marker loci that covered half of the tetraploid cotton genome. Notably, the 841 marker loci were unevenly distributed among the 26 chromosomes of tetraploid cotton. The 10 traits evaluated on the TM-1 × NM24016 population in a multienvironment trial were highly heritable, and most of the fiber traits showed considerable transgressive variation. Through the QTL analysis, we identified a total of 28 QTLs associated with the 10 traits. Our study provides a novel resource that can be used by breeders and geneticists for the genetic improvement of agronomic and fiber quality traits in Upland cotton.

  9. Genomic Dissection of Leaf Angle in Maize (Zea mays L. Using a Four-Way Cross Mapping Population.

    Directory of Open Access Journals (Sweden)

    Junqiang Ding

    Full Text Available Increasing grain yield by the selection for optimal plant architecture has been the key focus in modern maize breeding. As a result, leaf angle, an important determinant of plant architecture, has been significantly improved to adapt to the ever-increasing plant density in maize production over the past several decades. To extend our understanding on the genetic mechanisms of leaf angle in maize, we developed the first four-way cross mapping population, consisting of 277 lines derived from four maize inbred lines with varied leaf angles. The four-way cross mapping population together with the four parental lines were evaluated for leaf angle in two environments. In this study, we reported linkage maps built in the population and quantitative trait loci (QTL on leaf angle detected by inclusive composite interval mapping (ICIM. ICIM applies a two-step strategy to effectively separate the cofactor selection from the interval mapping, which controls the background additive and dominant effects at the same time. A total of 14 leaf angle QTL were identified, four of which were further validated in near-isogenic lines (NILs. Seven of the 14 leaf angle QTL were found to overlap with the published leaf angle QTL or genes, and the remaining QTL were unique to the four-way population. This study represents the first example of QTL mapping using a four-way cross population in maize, and demonstrates that the use of specially designed four-way cross is effective in uncovering the basis of complex and polygenetic trait like leaf angle in maize.

  10. Single nucleotide polymorphism of the growth hormone (GH encoding gene in inbred and outbred domestic rabbits

    Directory of Open Access Journals (Sweden)

    Deyana Gencheva Hristova

    2018-03-01

    Full Text Available Taking into consideration that the growth hormone (GH gene in rabbits is a candidate for meat production, understanding the genetic diversity and variation in this locus is of particular relevance. The present study comprised 86 rabbits (Oryctolagus cuniculus divided into 3 groups: New Zealand White (NZW outbred rabbits; first-generation inbred rabbits (F1 and second-generation inbred rabbits (F2. They were analysed by polymerase chain reaction-based restriction fragment length polymorphism method. A 231 bp fragment of the polymorphic site of the GH gene was digested with Bsh1236 restriction enzyme. Single nucleotide polymorphisms for the studied GH locus corresponding to 3 genotypes were detected in the studied rabbit populations: CC, CT and TT. In the synthetic inbred F1 and F2 populations, the frequency of the heterozygous genotype CT was 0.696 and 0.609, respectively, while for the homozygous CC genotype the frequency was lower (0.043 and 0.000, and respective values for the homozygous TT genotype were 0.261 and 0.391. This presumed a preponderance of the T allele (0.609 and 0.696 over the C allele (0.391 and 0.304 in these groups. In outbred rabbits, the allele frequencies were 0.613 (allele C and 0.387 (allele Т; consequently, the frequency of the homozygous CC genotype was higher than that of the homozygous TT genotype (0.300 vs. 0.075. Observed heterozygosity for the GH gene was higher than expected, and the result was therefore a negative inbreeding coefficient (Fis=–0.317 for outbred NZW rabbits; –0.460 for inbred F1 and –0.438 for inbred F2, indicating a sufficient number of heterozygous forms in all studied groups of rabbits. The application of narrow inbreeding by breeding full sibs in the synthetic population did not cause a rapid increase in homozygosity.

  11. Incorrect strain information for mouse cell lines: sequential influence of misidentification on sublines

    OpenAIRE

    Uchio-Yamada, Kozue; Kasai, Fumio; Ozawa, Midori; Kohara, Arihiro

    2016-01-01

    Misidentification or cross-contamination of cell lines can cause serious issues. Human cell lines have been authenticated by short tandem repeat profiling; however, mouse cell lines have not been adequately assessed. In this study, mouse cell lines registered with the JCRB cell bank were examined by simple sequence length polymorphism (SSLP) analysis to identify their strains. Based on comparisons with 7 major inbred strains, our results revealed their strains in 80 of 90 cell lines. However,...

  12. Genomic analysis of CD8+ NK/T cell line, ‘SRIK-NKL’, with array-based CGH (aCGH), SKY/FISH and molecular mapping

    Science.gov (United States)

    Rossi, Michael; LaDuca, Jeff; Cowell, John; Srivastava, Bejai I.S.; Matsui, Sei-ichi

    2010-01-01

    We performed aCGH, SKY /FISH, molecular mapping and expression analyses on a permanent CD8+ NK/T cell line, ‘SRIK-NKL’ established from a lymphoma (ALL) patient, in attempt to define the fundamental genetic profile of its unique NK phenotypes. aCGH revealed hemizygous deletion of 6p containing genes responsible for hematopoietic functions. The SKY demonstrated that a constitutive reciprocal translocation, rcpt(5;14)(p13.2;q11) is a stable marker. Using somatic hybrids containing der(5) derived from SRIK-NKL, we found that the breakpoint in one homologue of no. 5 is located upstream of IL7R and also that the breakpoint in no. 14 is located within TRA@. The FISH analysis using BAC which contains TRA@ and its flanking region further revealed a ~231 kb deletion within 14q11 in the der(5) but not in the normal homologue of no. 14. The RT-PCR analysis detected mRNA for TRA@ transcripts which were extending across, but not including, the deleted region. IL7R was detected at least at mRNA levels. These findings were consistent with the immunological findings that TRA@ and IL7R are both expressed at mRNA levels and TRA@ at cytoplasmic protein levels in SRIK-NKL cells. In addition to rept(5;14), aCGH identified novel copy number abnormalities suggesting that the unique phenotype of the SRIK-NKL cell line is not solely due to the TRA@ rearrangement. These findings provide supportive evidence for the notion that SRIK-NKL cells may be useful for studying not only the function of NK cells but also genetic deregulations associated with leukemiogenesis. PMID:17640729

  13. Properties of Dense Cores Embedded in Musca Derived from Extinction Maps and {sup 13}CO, C{sup 18}O, and NH{sub 3} Emission Lines

    Energy Technology Data Exchange (ETDEWEB)

    Machaieie, Dinelsa A.; Vilas-Boas, José W.; Wuensche, Carlos A. [Instituto Nacional de Pesquisas Espaciais, Av. dos Astronautas 1.758—Jardim da Granja, CEP-12227-010, São José dos Campos, SP (Brazil); Racca, Germán A. [Universidade do Estado do Rio Grande do Norte, Faculdade de Ciências Exatas e Naturais/Depto. de Física, Campus Universitário Central, Setor II BR 110, KM 48, Rua Prof. António Campos, Costa e Silva 59610-090—Mossoró-RN (Brazil); Myers, Philip C. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Hickel, Gabriel R., E-mail: dinelsa.machaieie@inpe.br [Universidade Federal de Itajubá, Departamento de Física, Av. BPS, 1303, Pinheirinho, Itajubá, MG (Brazil)

    2017-02-10

    Using near-infrared data from the Two Micron All Sky Survey catalog and the Near Infrared Color Excess method, we studied the extinction distribution in five dense cores of Musca, which show visual extinction greater than 10 mag and are potential sites of star formation. We analyzed the stability in four of them, fitting their radial extinction profiles with Bonnor–Ebert isothermal spheres, and explored their properties using the J = 1–0 transition of {sup 13}CO and C{sup 18}O and the J = K = 1 transition of NH{sub 3}. One core is not well described by the model. The stability parameter of the fitted cores ranges from 4.5 to 5.7 and suggests that all cores are stable, including Mu13, which harbors one young stellar object (YSO), the IRAS 12322-7023 source. However, the analysis of the physical parameters shows that Mu13 tends to have larger A {sub V}, n {sub c}, and P {sub ext} than the remaining starless cores. The other physical parameters do not show any trend. It is possible that those are the main parameters to explore in active star-forming cores. Mu13 also shows the most intense emission of NH{sub 3}. Its {sup 13}CO and C{sup 18}O lines have double peaks, whose integrated intensity maps suggest that they are due to the superposition of clouds with different radial velocities seen in the line of sight. It is not possible to state whether these clouds are colliding and inducing star formation or are related to a physical process associated with the formation of the YSO.

  14. Single Nucleotide Polymorphism Identification, Characterization, and Linkage Mapping in Quinoa

    Directory of Open Access Journals (Sweden)

    P. J. Maughan

    2012-11-01

    Full Text Available Quinoa ( Willd. is an important seed crop throughout the Andean region of South America. It is important as a regional food security crop for millions of impoverished rural inhabitants of the Andean Altiplano (high plains. Efforts to improve the crop have led to an increased focus on genetic research. We report the identification of 14,178 putative single nucleotide polymorphisms (SNPs using a genomic reduction protocol as well as the development of 511 functional SNP assays. The SNP assays are based on KASPar genotyping chemistry and were detected using the Fluidigm dynamic array platform. A diversity screen of 113 quinoa accessions showed that the minor allele frequency (MAF of the SNPs ranged from 0.02 to 0.50, with an average MAF of 0.28. Structure analysis of the quinoa diversity panel uncovered the two major subgroups corresponding to the Andean and coastal quinoa ecotypes. Linkage mapping of the SNPs in two recombinant inbred line populations produced an integrated linkage map consisting of 29 linkage groups with 20 large linkage groups, spanning 1404 cM with a marker density of 3.1 cM per SNP marker. The SNPs identified here represent important genomic tools needed in emerging plant breeding programs for advanced genetic analysis of agronomic traits in quinoa.

  15. QTL Mapping of Kernel Number-Related Traits and Validation of One Major QTL for Ear Length in Maize.

    Science.gov (United States)

    Huo, Dongao; Ning, Qiang; Shen, Xiaomeng; Liu, Lei; Zhang, Zuxin

    2016-01-01

    The kernel number is a grain yield component and an important maize breeding goal. Ear length, kernel number per row and ear row number are highly correlated with the kernel number per ear, which eventually determines the ear weight and grain yield. In this study, two sets of F2:3 families developed from two bi-parental crosses sharing one inbred line were used to identify quantitative trait loci (QTL) for four kernel number-related traits: ear length, kernel number per row, ear row number and ear weight. A total of 39 QTLs for the four traits were identified in the two populations. The phenotypic variance explained by a single QTL ranged from 0.4% to 29.5%. Additionally, 14 overlapping QTLs formed 5 QTL clusters on chromosomes 1, 4, 5, 7, and 10. Intriguingly, six QTLs for ear length and kernel number per row overlapped in a region on chromosome 1. This region was designated qEL1.10 and was validated as being simultaneously responsible for ear length, kernel number per row and ear weight in a near isogenic line-derived population, suggesting that qEL1.10 was a pleiotropic QTL with large effects. Furthermore, the performance of hybrids generated by crossing 6 elite inbred lines with two near isogenic lines at qEL1.10 showed the breeding value of qEL1.10 for the improvement of the kernel number and grain yield of maize hybrids. This study provides a basis for further fine mapping, molecular marker-aided breeding and functional studies of kernel number-related traits in maize.

  16. Genetic Regulation of Hypothalamic Cocaine and Amphetamine-Regulated Transcript (CART) in BxD Inbred Mice

    Science.gov (United States)

    Hawks, Brian W.; Li, Wei; Garlow, Steven J.

    2009-01-01

    Cocaine-Amphetamine Regulated Transcript (CART) peptides are implicated in a wide range of behaviors including in the reinforcing properties of psychostimulants, feeding and energy balance and stress and anxiety responses. We conducted a complex trait analysis to examine natural variation in the regulation of CART transcript abundance (CARTta) in the hypothalamus. CART transcript abundance was measured in total hypothalamic RNA from 26 BxD recombinant inbred (RI) mouse strains and in the C57BL/6 (B6) and DBA/2J (D2) progenitor strains. The strain distribution pattern for CARTta was continuous across the RI panel, which is consistent with this being a quantitative trait. Marker regression and interval mapping revealed significant quantitative trait loci (QTL) on mouse chromosome 4 (around 58.2cM) and chromosome 11 (between 20–36cM) that influence CARTta and account for 31% of the between strain variance in this phenotype. There are numerous candidate genes and QTL in these chromosomal regions that may indicate shared genetic regulation between CART expression and other neurobiological processes referable to known actions of this neuropeptide. PMID:18199428

  17. Rice genome mapping and its application in rice genetics and breeding

    International Nuclear Information System (INIS)

    Eun, M.Y.; Cho, Y.G.; Hahn, J.H.; Yoon, U.H.; Yi, B.Y.; Chung, T.Y.

    1998-01-01

    An 'MG' recombinant inbred population which consists of 164 F 13 lines has been developed from a cross between a Tongil type variety Milyang 23 and a Japonica type Gihobyeo by single seed descent. A Restriction Fragment Length Polymorphism (RFLP) framework map using this population has been constructed. Morphological markers, isozyme loci, microsatellites, Amplified Fragment Length Polymorphisms (AFLP), and new complementary DNA (cDNA) markers are being integrated in the framework map for a highly saturated comprehensive map. So far, 207 RFLPs, 89 microsatellites, 5 isozymes, 232 AFLPs, and 2 morphological markers have been mapped through international collaboration. The map contains 1,826 cM with an average interval size of 4.5 cM on the framework map and 3.4 cM overall (as of 29 October 1996). The framework map is being used for analyzing, quantitative trait loci (QTL) of agronomic characters and some physico-chemical properties relating to rice quality. The number of significant QTLs affecting each trait ranged from one to five, and 38 QTLs were detected for 17 traits. The percentage of variance explained by each QTL ranged from 5.6 to 66.9%. The isozyme marker, EstI-2, and two RFLP markers, RG109 and RG220, were linked most tightly at a distance less than 1 cM with the semidwarf (sd-1) gene on chromosome 1. These markers could be used for precise in vitro selection of individuals carrying the semidwarf gene using single seeds or very young leaf tissue, before this character is fully expressed. Appropriate application of marker-assisted selection, using EstI-2 and RFLP markers for the semidwarf character, in combination with other markers linked to genes of agronomic importance in rice, holds promise for improving, the efficiency of breeding, and the high-resolution genetic and physical mapping near sd-1, aimed at ultimately cloning this valuable gene

  18. Comparative mapping in watermelon [Citrullus lanatus (Thunb.) Matsum. et Nakai].

    Science.gov (United States)

    Sandlin, Katherine; Prothro, Jason; Heesacker, Adam; Khalilian, Nelly; Okashah, Rebecca; Xiang, Wenwen; Bachlava, Eleni; Caldwell, David G; Taylor, Chris A; Seymour, Danelle K; White, Victoria; Chan, Eva; Tolla, Greg; White, Cathy; Safran, Dolores; Graham, Elaine; Knapp, Steven; McGregor, Cecilia

    2012-12-01

    The first single-nucleotide polymorphism (SNP) maps for watermelon [Citrullus lanatus (Thunb.) Matsum. et Nakai] were constructed and compared. Three populations were developed from crosses between two elite cultivars, Klondike Black Seeded × New Hampshire Midget (KBS × NHM), an elite cultivar and wild egusi accession, Strain II × PI 560023 (SII × Egusi) and an elite cultivar and a wild citron accession, ZWRM50 × PI 244019 (ZWRM × Citroides). The SII × Egusi and ZWRM × Citroides F(2) populations consisted of 187 and 182 individuals respectively while the KBS × NHM recombinant inbred line (RIL) population consisted of 164 lines. The length of the genetic maps were 1,438, 1,514 and 1,144 cM with average marker distances of 3.8, 4.2, and 3.4 cM for the KBS × NHM, SII × Egusi and ZWRM × Citroides populations, respectively. Shared markers were used to align the three maps so that the linkage groups (LGs) represented the 11 chromosomes of the species. Marker segregation distortion were observed in all three populations, but was highest (12.7 %) in the ZWRM × Citroides population, where Citroides alleles were favored. The three maps were used to construct a consensus map containing 378 SNP markers with an average distance of 5.1 cM between markers. Phenotypic data was collected for fruit weight (FWT), fruit length (FL), fruit width (FWD), fruit shape index (FSI), rind thickness (RTH) and Brix (BRX) and analyzed for quantitative trait loci (QTL) associated with these traits. A total of 40 QTL were identified in the three populations, including major QTL for fruit size and shape that were stable across genetic backgrounds and environments. The present study reports the first SNP maps for Citrullus and the first map constructed using two elite parents. We also report the first stable QTL associated with fruit size and shape in Citrullus lanatus. These maps, QTL and SNPs should be useful for the watermelon community and represent a significant step towards the

  19. QTL mapping and transcriptome analysis of cowpea reveals candidate genes for root-knot nematode resistance.

    Science.gov (United States)

    Santos, Jansen Rodrigo Pereira; Ndeve, Arsenio Daniel; Huynh, Bao-Lam; Matthews, William Charles; Roberts, Philip Alan

    2018-01-01

    Cowpea is one of the most important food and forage legumes in drier regions of the tropics and subtropics. However, cowpea yield worldwide is markedly below the known potential due to abiotic and biotic stresses, including parasitism by root-knot nematodes (Meloidogyne spp., RKN). Two resistance genes with dominant effect, Rk and Rk2, have been reported to provide resistance against RKN in cowpea. Despite their description and use in breeding for resistance to RKN and particularly genetic mapping of the Rk locus, the exact genes conferring resistance to RKN remain unknown. In the present work, QTL mapping using recombinant inbred line (RIL) population 524B x IT84S-2049 segregating for a newly mapped locus and analysis of the transcriptome changes in two cowpea near-isogenic lines (NIL) were used to identify candidate genes for Rk and the newly mapped locus. A major QTL, designated QRk-vu9.1, associated with resistance to Meloidogyne javanica reproduction, was detected and mapped on linkage group LG9 at position 13.37 cM using egg production data. Transcriptome analysis on resistant and susceptible NILs 3 and 9 days after inoculation revealed up-regulation of 109 and 98 genes and down-regulation of 110 and 89 genes, respectively, out of 19,922 unique genes mapped to the common bean reference genome. Among the differentially expressed genes, four and nine genes were found within the QRk-vu9.1 and QRk-vu11.1 QTL intervals, respectively. Six of these genes belong to the TIR-NBS-LRR family of resistance genes and three were upregulated at one or more time-points. Quantitative RT-PCR validated gene expression to be positively correlated with RNA-seq expression pattern for eight genes. Future functional analysis of these cowpea genes will enhance our understanding of Rk-mediated resistance and identify the specific gene responsible for the resistance.

  20. QTL mapping and transcriptome analysis of cowpea reveals candidate genes for root-knot nematode resistance.

    Directory of Open Access Journals (Sweden)

    Jansen Rodrigo Pereira Santos

    Full Text Available Cowpea is one of the most important food and forage legumes in drier regions of the tropics and subtropics. However, cowpea yield worldwide is markedly below the known potential due to abiotic and biotic stresses, including parasitism by root-knot nematodes (Meloidogyne spp., RKN. Two resistance genes with dominant effect, Rk and Rk2, have been reported to provide resistance against RKN in cowpea. Despite their description and use in breeding for resistance to RKN and particularly genetic mapping of the Rk locus, the exact genes conferring resistance to RKN remain unknown. In the present work, QTL mapping using recombinant inbred line (RIL population 524B x IT84S-2049 segregating for a newly mapped locus and analysis of the transcriptome changes in two cowpea near-isogenic lines (NIL were used to identify candidate genes for Rk and the newly mapped locus. A major QTL, designated QRk-vu9.1, associated with resistance to Meloidogyne javanica reproduction, was detected and mapped on linkage group LG9 at position 13.37 cM using egg production data. Transcriptome analysis on resistant and susceptible NILs 3 and 9 days after inoculation revealed up-regulation of 109 and 98 genes and down-regulation of 110 and 89 genes, respectively, out of 19,922 unique genes mapped to the common bean reference genome. Among the differentially expressed genes, four and nine genes were found within the QRk-vu9.1 and QRk-vu11.1 QTL intervals, respectively. Six of these genes belong to the TIR-NBS-LRR family of resistance genes and three were upregulated at one or more time-points. Quantitative RT-PCR validated gene expression to be positively correlated with RNA-seq expression pattern for eight genes. Future functional analysis of these cowpea genes will enhance our understanding of Rk-mediated resistance and identify the specific gene responsible for the resistance.

  1. Abiotic stress growth conditions induce different responses in kernel iron concentration across genotypically distinct maize inbred varieties

    Science.gov (United States)

    Kandianis, Catherine B.; Michenfelder, Abigail S.; Simmons, Susan J.; Grusak, Michael A.; Stapleton, Ann E.

    2013-01-01

    The improvement of grain nutrient profiles for essential minerals and vitamins through breeding strategies is a target important for agricultural regions where nutrient poor crops like maize contribute a large proportion of the daily caloric intake. Kernel iron concentration in maize exhibits a broad range. However, the magnitude of genotype by environment (GxE) effects on this trait reduces the efficacy and predictability of selection programs, particularly when challenged with abiotic stress such as water and nitrogen limitations. Selection has also been limited by an inverse correlation between kernel iron concentration and the yield component of kernel size in target environments. Using 25 maize inbred lines for which extensive genome sequence data is publicly available, we evaluated the response of kernel iron density and kernel mass to water and nitrogen limitation in a managed field stress experiment using a factorial design. To further understand GxE interactions we used partition analysis to characterize response of kernel iron and weight to abiotic stressors among all genotypes, and observed two patterns: one characterized by higher kernel iron concentrations in control over stress conditions, and another with higher kernel iron concentration under drought and combined stress conditions. Breeding efforts for this nutritional trait could exploit these complementary responses through combinations of favorable allelic variation from these already well-characterized genetic stocks. PMID:24363659

  2. A RAD-Based Genetic Map for Anchoring Scaffold Sequences and Identifying QTLs in Bitter Gourd (Momordica charantia)

    Science.gov (United States)

    Cui, Junjie; Luo, Shaobo; Niu, Yu; Huang, Rukui; Wen, Qingfang; Su, Jianwen; Miao, Nansheng; He, Weiming; Dong, Zhensheng; Cheng, Jiaowen; Hu, Kailin

    2018-01-01

    Genetic mapping is a basic tool necessary for anchoring assembled scaffold sequences and for identifying QTLs controlling important traits. Though bitter gourd (Momordica charantia) is both consumed and used as a medicinal, research on its genomics and genetic mapping is severely limited. Here, we report the construction of a restriction site associated DNA (RAD)-based genetic map for bitter gourd using an F2 mapping population comprising 423 individuals derived from two cultivated inbred lines, the gynoecious line ‘K44’ and the monoecious line ‘Dali-11.’ This map comprised 1,009 SNP markers and spanned a total genetic distance of 2,203.95 cM across the 11 linkage groups. It anchored a total of 113 assembled scaffolds that covered about 251.32 Mb (85.48%) of the 294.01 Mb assembled genome. In addition, three horticulturally important traits including sex expression, fruit epidermal structure, and immature fruit color were evaluated using a combination of qualitative and quantitative data. As a result, we identified three QTL/gene loci responsible for these traits in three environments. The QTL/gene gy/fffn/ffn, controlling sex expression involved in gynoecy, first female flower node, and female flower number was detected in the reported region. Particularly, two QTLs/genes, Fwa/Wr and w, were found to be responsible for fruit epidermal structure and white immature fruit color, respectively. This RAD-based genetic map promotes the assembly of the bitter gourd genome and the identified genetic loci will accelerate the cloning of relevant genes in the future. PMID:29706980

  3. A RAD-Based Genetic Map for Anchoring Scaffold Sequences and Identifying QTLs in Bitter Gourd (Momordica charantia

    Directory of Open Access Journals (Sweden)

    Junjie Cui

    2018-04-01

    Full Text Available Genetic mapping is a basic tool necessary for anchoring assembled scaffold sequences and for identifying QTLs controlling important traits. Though bitter gourd (Momordica charantia is both consumed and used as a medicinal, research on its genomics and genetic mapping is severely limited. Here, we report the construction of a restriction site associated DNA (RAD-based genetic map for bitter gourd using an F2 mapping population comprising 423 individuals derived from two cultivated inbred lines, the gynoecious line ‘K44’ and the monoecious line ‘Dali-11.’ This map comprised 1,009 SNP markers and spanned a total genetic distance of 2,203.95 cM across the 11 linkage groups. It anchored a total of 113 assembled scaffolds that covered about 251.32 Mb (85.48% of the 294.01 Mb assembled genome. In addition, three horticulturally important traits including sex expression, fruit epidermal structure, and immature fruit color were evaluated using a combination of qualitative and quantitative data. As a result, we identified three QTL/gene loci responsible for these traits in three environments. The QTL/gene gy/fffn/ffn, controlling sex expression involved in gynoecy, first female flower node, and female flower number was detected in the reported region. Particularly, two QTLs/genes, Fwa/Wr and w, were found to be responsible for fruit epidermal structure and white immature fruit color, respectively. This RAD-based genetic map promotes the assembly of the bitter gourd genome and the identified genetic loci will accelerate the cloning of relevant genes in the future.

  4. Digital phenotyping for quantification of genetic diversity in inbred guava (Psidium guajava) families.

    Science.gov (United States)

    Krause, W; Viana, A P; Cavalcante, N R; Ambrósio, M; Santos, E A; Vieira, H D

    2017-03-22

    Digital image analysis of seeds has been used for the identification of cultivars, determination of seed color and mechanical damage, and classification of different seed sizes. The aim of the present study was to evaluate the efficiency of digital image analysis of seeds for the quantification of genetic diversity among genotypes of inbred guava (Psidium guajava L.) families. The SAS Mini equipment, which consists of a capture module and a software program for analysis, was employed for the capture and analysis of the seed images. Different genetic diversity quantification strategies were tested using the Ward-Modified Location Model method. The set of variables related to geometry of the seeds was the largest contributor to divergence among the guava genotypes. The use of seed descriptors obtained by digital image analysis via the SAS system was efficient at quantifying the genetic diversity among genotypes of inbred guava families associated with the use of the Ward-Modified Location Model method.

  5. Novel fluorescent sequence-related amplified polymorphism(FSRAP markers for the construction of a genetic linkage map of wheat(Triticum aestivum L.

    Directory of Open Access Journals (Sweden)

    Zhao Lingbo

    2017-01-01

    Full Text Available Novel fluorescent sequence-related amplified polymorphism (FSRAP markers were developed based on the SRAP molecular marker. Then, the FSRAP markers were used to construct the genetic map of a wheat (Triticum aestivumL. recombinant inbred line population derived from a Chuanmai 42×Chuannong 16 cross. Reproducibility and polymorphism tests indicated that the FSRAP markers have repeatability and better reflect the polymorphism of wheat varieties compared with SRAP markers. A total of 430 polymorphic loci between Chuanmai 42 and Chuannong 16 were detected with 189 FSRAP primer combinations. A total of 281 FSARP markers and 39 SSR markers re classified into 20 linkage groups. The maps spanned a total length of 2499.3cM with an average distance of 7.81cM between markers. A total of 201 markers were mapped on the B genome and covered a distance of 1013cM. On the A genome, 84 markers were mapped and covered a distance of 849.6cM. On the D genome, however, only 35 markers were mapped and covered a distance of 636.7cM. No FSRAP markers were distributed on the 7D chromosome. The results of the present study revealed that the novel FSRAP markers can be used to generate dense, uniform genetic maps of wheat.

  6. Fibre type composition of soleus and extensor digitorum longus muscles in normal female inbred Lewis rats

    Czech Academy of Sciences Publication Activity Database

    Soukup, Tomáš; Zachařová, Gisela; Smerdu, V.

    2002-01-01

    Roč. 104, č. 4 (2002), s. 399-405 ISSN 0065-1281 R&D Projects: GA ČR GA304/00/1653 Grant - others:CZ - SI Czech-Slovenian Intergovernmental S&T Co-operation(XC) - Institutional research plan: CEZ:AV0Z5011922 Keywords : inbred Lewis rats * skeletal muscles * soleus and EDL muscles Subject RIV: FH - Neurology Impact factor: 0.867, year: 2002

  7. A genetic linkage map with 178 SSR and 1 901 SNP markers constructed using a RIL population in wheat (Triticum aestivum L.)

    Institute of Scientific and Technical Information of China (English)

    ZHAI Hui-jie; FENG Zhi-yu; LIU Xin-ye; CHENG Xue-jiao; PENG Hui-ru; YAO Ying-yin; SUN Qi-xin; NI Zhong-fu

    2015-01-01

    The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci (QTLs) controlling agronomically important traits. In this study, simple sequence repeat (SSR) markers and Illumina 9K iSelect single nucleotide polymorphism (SNP) genechip were employed to construct one genetic linkage map of common wheat (Triticum aestivum L.) using 191 recombinant inbred lines (RILs) derived from cross Yu 8679xJing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 cM and 1 000 marker bins, with an average interval distance of 1.66 cM. A, B and D genomes covered 719.1,703.5 and 237.3 cM, with an average interval distance of 1.66, 1.45 and 2.9 cM, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754 (92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184 (97.4%) were located on one single chromosome, and the rest 31 (2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags (ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.

  8. Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers.

    Directory of Open Access Journals (Sweden)

    Huihui Yu

    Full Text Available Huge efforts have been invested in the last two decades to dissect the genetic bases of complex traits including yields of many crop plants, through quantitative trait locus (QTL analyses. However, almost all the studies were based on linkage maps constructed using low-throughput molecular markers, e.g. restriction fragment length polymorphisms (RFLPs and simple sequence repeats (SSRs, thus are mostly of low density and not able to provide precise and complete information about the numbers and locations of the genes or QTLs controlling the traits. In this study, we constructed an ultra-high density genetic map based on high quality single nucleotide polymorphisms (SNPs from low-coverage sequences of a recombinant inbred line (RIL population of rice, generated using new sequencing technology. The quality of the map was assessed by validating the positions of several cloned genes including GS3 and GW5/qSW5, two major QTLs for grain length and grain width respectively, and OsC1, a qualitative trait locus for pigmentation. In all the cases the loci could be precisely resolved to the bins where the genes are located, indicating high quality and accuracy of the map. The SNP map was used to perform QTL analysis for yield and three yield-component traits, number of tillers per plant, number of grains per panicle and grain weight, using data from field trials conducted over years, in comparison to QTL mapping based on RFLPs/SSRs. The SNP map detected more QTLs especially for grain weight, with precise map locations, demonstrating advantages in detecting power and resolution relative to the RFLP/SSR map. Thus this study provided an example for ultra-high density map construction using sequencing technology. Moreover, the results obtained are helpful for understanding the genetic bases of the yield traits and for fine mapping and cloning of QTLs.

  9. Development of Insertion and Deletion Markers based on Biparental Resequencing for Fine Mapping Seed Weight in Soybean

    Directory of Open Access Journals (Sweden)

    Ying-hui Li

    2014-11-01

    Full Text Available As a complement to single nucleotide polymorphisms (SNPs and simple sequence repeats (SSRs, biallelic insertions and deletions (InDels represent powerful molecular markers with desirable features for filling the gap in current genetic linkage maps. In this study, 28,908 small InDel polymorphisms (1–5 base pair, bp distributed genome-wide were identified and annotated by comparison of a whole-genome resequencing data set from two soybean [ (L. Merr.] genotypes, cultivar Zhonghunag13 (ZH and line Zhongpin03-5373 (ZP. The physical distribution of InDel polymorphisms in soybean genome was uneven, and matched closely with the distribution of previously annotated genes. The average density of InDel in the arm region was significantly higher than that in the pericentromeric region. The genomic regions that were fixed between the two elites were elucidated. With this information, five InDel markers within a putative quantitative trait locus (QTL for seed weight (SW, , were developed and used to genotype 254 recombinant inbred lines (RILs derived from the cross of ZP × ZH. Adding these five InDel markers to previously used SNP and SSR markers facilitated the discovery of further recombination events allowing fine-mapping the QTL to a 0.5 Mbp region. Our study clearly underlines the high value of InDel markers for map-based cloning and marker-assisted selection in soybean.

  10. Phenotypic characterization, genetic mapping and candidate gene analysis of a source conferring reduced plant height in sunflower.

    Science.gov (United States)

    Ramos, María Laura; Altieri, Emiliano; Bulos, Mariano; Sala, Carlos A

    2013-01-01

    Reduced height germplasm has the potential to increase stem strength, standability, and also yields potential of the sunflower crop (Helianthus annuus L. var. macrocarpus Ckll.). In this study, we report on the inheritance, mapping, phenotypic and molecular characterization of a reduced plant height trait in inbred lines derived from the source DDR. This trait is controlled by a semidominant allele, Rht1, which maps on linkage group 12 of the sunflower public consensus map. Phenotypic effects of this allele include shorter height and internode length, insensibility to exogenous gibberellin application, normal skotomorphogenetic response, and reduced seed set under self-pollination conditions. This later effect presumably is related to the reduced pollen viability observed in all DDR-derived lines studied. Rht1 completely cosegregated with a haplotype of the HaDella1 gene sequence. This haplotype consists of a point mutation converting a leucine residue in a proline within the conserved DELLA domain. Taken together, the phenotypic, genetic, and molecular results reported here indicate that Rht1 in sunflower likely encodes an altered DELLA protein. If the DELPA motif of the HaDELLA1 sequence in the Rht1-encoded protein determines by itself the observed reduction in height is a matter that remains to be investigated.

  11. Enriching an intraspecific genetic map and identifying QTL for fiber quality and yield component traits across multiple environments in Upland cotton (Gossypium hirsutum L.).

    Science.gov (United States)

    Liu, Xueying; Teng, Zhonghua; Wang, Jinxia; Wu, Tiantian; Zhang, Zhiqin; Deng, Xianping; Fang, Xiaomei; Tan, Zhaoyun; Ali, Iftikhar; Liu, Dexin; Zhang, Jian; Liu, Dajun; Liu, Fang; Zhang, Zhengsheng

    2017-12-01

    Cotton is a significant commercial crop that plays an indispensable role in many domains. Constructing high-density genetic maps and identifying stable quantitative trait locus (QTL) controlling agronomic traits are necessary prerequisites for marker-assisted selection (MAS). A total of 14,899 SSR primer pairs designed from the genome sequence of G. raimondii were screened for polymorphic markers between mapping parents CCRI 35 and Yumian 1, and 712 SSR markers showing polymorphism were used to genotype 180 lines from a (CCRI 35 × Yumian 1) recombinant inbred line (RIL) population. Genetic linkage analysis was conducted on 726 loci obtained from the 712 polymorphic SSR markers, along with 1379 SSR loci obtained in our previous study, and a high-density genetic map with 2051 loci was constructed, which spanned 3508.29 cM with an average distance of 1.71 cM between adjacent markers. Marker orders on the linkage map are highly consistent with the corresponding physical orders on a G. hirsutum genome sequence. Based on fiber quality and yield component trait data collected from six environments, 113 QTLs were identified through two analytical methods. Among these 113 QTLs, 50 were considered stable (detected in multiple environments or for which phenotypic variance explained by additive effect was greater than environment effect), and 18 of these 50 were identified with stability by both methods. These 18 QTLs, including eleven for fiber quality and seven for yield component traits, could be priorities for MAS.

  12. Evidence should trump intuition by preferring inbred strains to outbred stocks in preclinical research.

    Science.gov (United States)

    Festing, Michael F W

    2014-01-01

    Inbred strains of mice such as C57BL and BALB/c are more widely used in published work than outbred stocks of mice such as ICR and CD-1. In contrast, outbred stocks of rats such as Wistar and Sprague-Dawley are more widely used than inbred strains such as F344 and LEW. The properties of inbred and outbred mice and rats are briefly reviewed, and it is concluded that, with some exceptions, there is a strong case for using inbred strains in most controlled experiments. This is because they are usually more uniform, so that fewer animals are usually needed to detect a specified response and they are more repeatable, because they are genetically defined (i.e., the strain can be identified using genetic markers) and less liable to genetic change. Yet many scientists continue to use outbred animals. In Daniel Kahneman's book "Thinking Fast and Slow" he explains that we can answer questions in 2 ways: "fast" by intuition or "slow" by analytical reasoning. The former method is instantaneous, requires no thought but is not evidence based. Analytical reasoning is evidence based but requires hard work, which we all avoid. He has found that "… when faced with a difficult question, we often answer an easier one instead, usually without noticing the substitution." The target question of whether to choose outbred or inbred strains in controlled experiments is a difficult one requiring knowledge of the characteristics of these strains and the principles of experimental design. A substitute question, "are humans and outbred stocks both genetically heterogeneous," is easily answered in the affirmative. It is likely that many scientists are intuitively answering the substitute question and are assuming that they have answered the target question. If so they may be using the wrong animals in their research. Nor is the fact that humans and outbred stocks are alike in being genetically heterogeneous a reason for using them. The whole concept of a "model" is that it is similar to the

  13. Characterization of central and peripheral components of the hypothalamus-pituitary-adrenal axis in the inbred Roman rat strains.

    Science.gov (United States)

    Carrasco, Javier; Márquez, Cristina; Nadal, Roser; Tobeña, Adolfo; Fernández-Teruel, Albert; Armario, Antonio

    2008-05-01

    Several studies performed in outbred Roman high- and low-avoidance lines (RHA and RLA, respectively) have demonstrated that the more anxious line (RLA) is characterized by a higher hypothalamic-pituitary-adrenal (HPA) response to certain stressors than the less anxious one (RHA). However, inconsistent results have also been reported. Taking advantage of the generation of an inbred colony of RLA and RHA rats (RHA-I and RLA-I, respectively), we have characterized in the two strains not only resting and stress levels of peripheral HPA hormones but also central components of the HPA axis, including CRF gene expression in extra-hypothalamic areas. Whereas resting levels of ACTH and corticosterone did not differ between the strains, a greater response to a novel environment was found in RLA-I as compared to RHA-I rats. RLA-I rats showed enhanced CRF gene expression in the paraventricular nucleus (PVN) of the hypothalamus, with normal arginin-vasopressin gene expression in both parvocellular and magnocellular regions of the PVN. This enhanced CRF gene expression is not apparently related to altered negative corticosteroid feedback as similar levels of expression of brain glucorticoid and mineralocorticoid receptors were found in the two rat strains. CRF gene expression tended to be higher in the central amygdala and it was significantly higher in the dorsal region of the bed nucleus of stria terminalis (BNST) of RLA-I rats, while no differences appeared in the ventral region of BNST. Considering the involvement of CRF and the BNST in anxiety and stress-related behavioral alterations, the present data suggest that the CRF system may be a critical neurobiological substrate underlying differences between the two rat strains.

  14. QTL mapping of flag leaf-related traits in wheat (Triticum aestivum L.).

    Science.gov (United States)

    Liu, Kaiye; Xu, Hao; Liu, Gang; Guan, Panfeng; Zhou, Xueyao; Peng, Huiru; Yao, Yingyin; Ni, Zhongfu; Sun, Qixin; Du, Jinkun

    2018-04-01

    QTL controlling flag leaf length, flag leaf width, flag leaf area and flag leaf angle were mapped in wheat. This study aimed to advance our understanding of the genetic mechanisms underlying morphological traits of the flag leaves of wheat (Triticum aestivum L.). A recombinant inbred line (RIL) population derived from ND3331 and the Tibetan semi-wild wheat Zang1817 was used to identify quantitative trait loci (QTLs) controlling flag leaf length (FLL), flag leaf width (FLW), flag leaf area (FLA), and flag leaf angle (FLANG). Using an available simple sequence repeat genetic linkage map, 23 putative QTLs for FLL, FLW, FLA, and FLANG were detected on chromosomes 1B, 2B, 3A, 3D, 4B, 5A, 6B, 7B, and 7D. Individual QTL explained 4.3-68.52% of the phenotypic variance in different environments. Four QTLs for FLL, two for FLW, four for FLA, and five for FLANG were detected in at least two environments. Positive alleles of 17 QTLs for flag leaf-related traits originated from ND3331 and 6 originated from Zang1817. QTLs with pleiotropic effects or multiple linked QTL were also identified on chromosomes 1B, 4B, and 5A; these are potential target regions for fine-mapping and marker-assisted selection in wheat breeding programs.

  15. Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice.

    Science.gov (United States)

    Lou, Qiaojun; Chen, Liang; Mei, Hanwei; Wei, Haibin; Feng, Fangjun; Wang, Pei; Xia, Hui; Li, Tiemei; Luo, Lijun

    2015-08-01

    Deep rooting is a very important trait for plants' drought avoidance, and it is usually represented by the ratio of deep rooting (RDR). Three sets of rice populations were used to determine the genetic base for RDR. A linkage mapping population with 180 recombinant inbred lines and an association mapping population containing 237 rice varieties were used to identify genes linked to RDR. Six quantitative trait loci (QTLs) of RDR were identified as being located on chromosomes 1, 2, 4, 7, and 10. Using 1 019 883 single-nucleotide polymorphisms (SNPs), a genome-wide association study of the RDR was performed. Forty-eight significant SNPs of the RDR were identified and formed a clear peak on the short arm of chromosome 1 in a Manhattan plot. Compared with the shallow-rooting group and the whole collection, the deep-rooting group had selective sweep regions on chromosomes 1 and 2, especially in the major QTL region on chromosome 2. Seven of the nine candidate SNPs identified by association mapping were verified in two RDR extreme groups. The findings from this study will be beneficial to rice drought-resistance research and breeding. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  16. Three millimeter molecular line observations in Sagittarius B2. 1: Full synthesis mapping study of HNO, CCS, and HC(13)CCN

    Science.gov (United States)

    Kuan, Yi-Jehng; Snyder, Lewis E.

    1994-01-01

    We present the first full synthesis maps of the small molecules HNO, CCS, and HC(13)CCN in Sgr B2. We have observed the 3.8 mm continuum, the HNO J(sub K(sub -1)K(sub 1)) = 1(sub O1)-0(sub OO), the CCS J(sub N) = 7(sub 6)-6(sub 5), and the HC(13)CCN J = 9-8 transitions in the core of the Sgr B2 molecular cloud, using the Berkeley Illinois Maryland Association (BIMA) millimeter array and the NRAO 12 m telescope. We have found that HNO exists in five major gas clumps in the Sgr B2 region, which we have labeled HNO(N), HNO(NW), HNO(E), HNO(M), and HNO(S). Of particular interest is HNO(M), a major molecular gas concentration approximately 15 sec west of Sgr B2(M) in a region of young star formation. HNO is found to be closely associated with the ionized gas and might be depleted around bright H II complexes. In general, the peak intensity of the HNO emission is found to be offset from the peak of the continuum emission. We found evidence for some chemical differentiation among the three species, HNO, CCS, and HC(13)CCN, but the abundance ratios are in fair agreement with theoretical models. Two unidentified lines, U81420 and U81518, were observed, and a previously unknown compact dust source was detected. Our HNO data indicate the presence of a rotating approximately (2.2-4.4) x 10(exp 3)solar mass gas envelope surrounding Sgr B2(N), a possible bipolar gas outflow in HNO(M), and possibly a large (approximately 4.2 x 10(exp 4)solar mass) extended rotating disk associated with HNO(S). In addition, the CCS and HC(13)CCN data approximately outline the extended component of Sgr B2 and clearly show that the southern continuum source Sgr B2(S) is actually a major molecular source as well. Consequently, the kinematics of the Sgr B2 molecular cloud is quite complex, but in moving from the northwest to south, the LSR velocity generally changes from 79 to 46 km/s.

  17. Construction of 2 intraspecific linkage maps and identification of resistance QTLs for Phytophthora capsici root-rot and foliar-blight diseases of pepper (Capsicum annuum L.).

    Science.gov (United States)

    Ogundiwin, Ebenezer A; Berke, Terry F; Massoudi, Mark; Black, Lowell L; Huestis, Gordon; Choi, Doil; Lee, Sanghyeob; Prince, James P

    2005-08-01

    Two linkage maps of pepper were constructed and used to identify quantitative trait loci (QTLs) conferring resistance to Phytophthora capsici. Inoculations were done with 7 isolates: 3 from Taiwan, 3 from California, and 1 from New Mexico. The first map was constructed from a set of recombinant inbred lines (RILs) of the PSP-11 (susceptible) x PI201234 (resistant) cross; and the second map was from a set of F(2) lines of the Joe E. Parker' (susceptible) x 'Criollo de Morelos 334' (resistant) cross. The RIL map covered 1466.1 cM of the pepper genome, and it consisted of 144 markers -- 91 amplified fragment length polymorphisms (AFLPs), 34 random amplified polymorphic DNA (RAPDs), 15 simple sequence repeats (SSRs), 1 sequence characterized amplified region (SCAR), and 3 morphological markers -- distributed over 17 linkage groups. The morphological markers mapped on this population were erect fruit habit (up), elongated fruit shape (fs(e)), and fasciculate fruit clusters (fa). The F(2) map consisted of 113 markers (51 AFLPs, 45 RAPDs, 14 SSRs, and 3 SCARs) distributed in 16 linkage groups, covering a total of 1089.2 cM of the pepper genome. Resistance to both root rot and foliar blight were evaluated in the RIL population using the 3 Taiwan isolates; the remaining isolates were used for the root-rot test only. Sixteen chromosomal regions of the RIL map contained single QTLs or clusters of resistance QTLs that had an effect on root rot and (or) foliar blight, revealing a complex set of genetics involved in resistance to P. capsici. Five QTLs were detected in the F(2) map that had an effect on resistance to root rot.

  18. Evaluation of fall armyworm resistance in maize germplasm lines using visual leaf injury rating and predator survey

    Science.gov (United States)

    After examining ear-colonizing pest resistance, 20 maize lines from the USDA-ARS germplasm enhancement of Maize (GEM) Program were evaluated for whorl-feeding fall armyworm (FAW) (Spodoptera frugiperda) resistance using four maize inbred lines as the resistant and susceptible controls. Both FAW inju...

  19. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species.

    Directory of Open Access Journals (Sweden)

    Rebekah E Oliver

    Full Text Available A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42 has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.

  20. Satellite line mapping in Eu3+–Ce3+ and Pr3+–Ce3+ codoped Y2SiO5

    International Nuclear Information System (INIS)

    Serrano, D.; Karlsson, J.; Zheng, L.; Dong, Y.; Ferrier, A.; Goldner, P.; Walther, A.; Rippe, L.; Kröll, S.

    2016-01-01

    In this work we perform a high-resolution spectroscopic investigation of Eu 3+ –Ce 3+ and Pr 3+ –Ce 3+ codoped Y 2 SiO 5 crystals. Satellite line spectra were recorded at low temperatures around the Eu 3+ : 7 F 0 → 5 D 0 and the Pr 3+ : 3 H 4 → 1 D 2 transitions. It is observed that the incorporation of Ce 3+ as a codopant notably changes the Eu 3+ and Pr 3+ satellite line patterns. Satellite lines measured in singly doped Eu 3+ :Y 2 SiO 5 were found at the same spectral positions in Eu 3+ –Ce 3+ codoped crystals. These coincident lines were concluded to be due to pairs of Eu 3+ ions. Extra satellite lines appeared in the codoped crystals, which were assigned to Ce 3+ related structures such as Ce 3+ –Eu 3+ pairs. The analysis of the Pr 3+ satellite line spectra presents further challenges. Satellite lines associated to Pr 3+ pairs show weaker intensity, presumably due to the efficient quenching of the Pr 3+1 D 2 emission through cross-relaxation paths ( 1 D 2 → 1 G 4 ; 3 H 4 → 3 F 4 ). The investigation of the Eu 3+ and Pr 3+ satellite line patterns in Y 2 SiO 5 is particularly interesting for their exploitation in rare-earth based quantum computation schemes. - Highlights: • We recorded Eu and Pr satellite lines in Y 2 SiO 5 with and without Ce as a codopant. • The presence of Ce leads to the appearance of extra satellite lines in the spectra. • The satellite lines are associated to minor crystal sites such as ion pairs. • Less than 100 ion pairs were detected per satellite line. • The exploitation of the satellite line structure is proposed for quantum computing.

  1. A Novel Phytophthora sojae Resistance Rps12 Gene Mapped to a Genomic Region That Contains Several Rps Genes.

    Science.gov (United States)

    Sahoo, Dipak K; Abeysekara, Nilwala S; Cianzio, Silvia R; Robertson, Alison E; Bhattacharyya, Madan K

    2017-01-01

    Phytophthora sojae Kaufmann and Gerdemann, which causes Phytophthora root rot, is a widespread pathogen that limits soybean production worldwide. Development of Phytophthora resistant cultivars carrying Phytophthora resistance Rps genes is a cost-effective approach in controlling this disease. For this mapping study of a novel Rps gene, 290 recombinant inbred lines (RILs) (F7 families) were developed by crossing the P. sojae resistant cultivar PI399036 with the P. sojae susceptible AR2 line, and were phenotyped for responses to a mixture of three P. sojae isolates that overcome most of the known Rps genes. Of these 290 RILs, 130 were homozygous resistant, 12 heterzygous and segregating for Phytophthora resistance, and 148 were recessive homozygous and susceptible. From this population, 59 RILs homozygous for Phytophthora sojae resistance and 61 susceptible to a mixture of P. sojae isolates R17 and Val12-11 or P7074 that overcome resistance encoded by known Rps genes mapped to Chromosome 18 were selected for mapping novel Rps gene. A single gene accounted for the 1:1 segregation of resistance and susceptibility among the RILs. The gene encoding the Phytophthora resistance mapped to a 5.8 cM interval between the SSR markers BARCSOYSSR_18_1840 and Sat_064 located in the lower arm of Chromosome 18. The gene is mapped 2.2 cM proximal to the NBSRps4/6-like sequence that was reported to co-segregate with the Phytophthora resistance genes Rps4 and Rps6. The gene is mapped to a highly recombinogenic, gene-rich genomic region carrying several nucleotide binding site-leucine rich repeat (NBS-LRR)-like genes. We named this novel gene as Rps12, which is expected to be an invaluable resource in breeding soybeans for Phytophthora resistance.

  2. A Novel Phytophthora sojae Resistance Rps12 Gene Mapped to a Genomic Region That Contains Several Rps Genes.

    Directory of Open Access Journals (Sweden)

    Dipak K Sahoo

    Full Text Available Phytophthora sojae Kaufmann and Gerdemann, which causes Phytophthora root rot, is a widespread pathogen that limits soybean production worldwide. Development of Phytophthora resistant cultivars carrying Phytophthora resistance Rps genes is a cost-effective approach in controlling this disease. For this mapping study of a novel Rps gene, 290 recombinant inbred lines (RILs (F7 families were developed by crossing the P. sojae resistant cultivar PI399036 with the P. sojae susceptible AR2 line, and were phenotyped for responses to a mixture of three P. sojae isolates that overcome most of the known Rps genes. Of these 290 RILs, 130 were homozygous resistant, 12 heterzygous and segregating for Phytophthora resistance, and 148 were recessive homozygous and susceptible. From this population, 59 RILs homozygous for Phytophthora sojae resistance and 61 susceptible to a mixture of P. sojae isolates R17 and Val12-11 or P7074 that overcome resistance encoded by known Rps genes mapped to Chromosome 18 were selected for mapping novel Rps gene. A single gene accounted for the 1:1 segregation of resistance and susceptibility among the RILs. The gene encoding the Phytophthora resistance mapped to a 5.8 cM interval between the SSR markers BARCSOYSSR_18_1840 and Sat_064 located in the lower arm of Chromosome 18. The gene is mapped 2.2 cM proximal to the NBSRps4/6-like sequence that was reported to co-segregate with the Phytophthora resistance genes Rps4 and Rps6. The gene is mapped to a highly recombinogenic, gene-rich genomic region carrying several nucleotide binding site-leucine rich repeat (NBS-LRR-like genes. We named this novel gene as Rps12, which is expected to be an invaluable resource in breeding soybeans for Phytophthora resistance.

  3. Mapping QTLs controlling kernel dimensions in a wheat inter-varietal RIL mapping population.

    Science.gov (United States)

    Cheng, Ruiru; Kong, Zhongxin; Zhang, Liwei; Xie, Quan; Jia, Haiyan; Yu, Dong; Huang, Yulong; Ma, Zhengqiang

    2017-07-01

    Seven kernel dimension QTLs were identified in wheat, and kernel thickness was found to be the most important dimension for grain weight improvement. Kernel morphology and weight of wheat (Triticum aestivum L.) affect both yield and quality; however, the genetic basis of these traits and their interactions has not been fully understood. In this study, to investigate the genetic factors affecting kernel morphology and the association of kernel morphology traits with kernel weight, kernel length (KL), width (KW) and thickness (KT) were evaluated, together with hundred-grain weight (HGW), in a recombinant inbred line population derived from Nanda2419 × Wangshuibai, with data from five trials (two different locations over 3 years). The results showed that HGW was more closely correlated with KT and KW than with KL. A whole genome scan revealed four QTLs for KL, one for KW and two for KT, distributed on five different chromosomes. Of them, QKl.nau-2D for KL, and QKt.nau-4B and QKt.nau-5A for KT were newly identified major QTLs for the respective traits, explaining up to 32.6 and 41.5% of the phenotypic variations, respectively. Increase of KW and KT and reduction of KL/KT and KW/KT ratios always resulted in significant higher grain weight. Lines combining the Nanda 2419 alleles of the 4B and 5A intervals had wider, thicker, rounder kernels and a 14% higher grain weight in the genotype-based analysis. A strong, negative linear relationship of the KW/KT ratio with grain weight was observed. It thus appears that kernel thickness is the most important kernel dimension factor in wheat improvement for higher yield. Mapping and marker identification of the kernel dimension-related QTLs definitely help realize the breeding goals.

  4. Detailed mapping of a resistance locus against Fusarium wilt in cultivated eggplant (Solanum melongena).

    Science.gov (United States)

    Miyatake, Koji; Saito, Takeo; Negoro, Satomi; Yamaguchi, Hirotaka; Nunome, Tsukasa; Ohyama, Akio; Fukuoka, Hiroyuki

    2016-02-01

    This is the first report on genetic mapping of a resistance locus against Fusarium wilt caused by the plant pathogen Fusarium oxysporum f. sp. melongenae in cultivated eggplant. Fusarium wilt, caused by the plant pathogen Fusarium oxysporum f. sp. melongenae, is a major soil-borne disease threatening stable production in eggplant (Solanum melongena). Although three eggplant germplasms, LS1934, LS174, and LS2436, are known to be highly resistant to the pathogen, their resistance loci have not been mapped. In this study, we performed quantitative trait locus analyses in F2:3 populations and detected a resistance locus, FM1, at the end of chromosome 2, with two alleles, Fm1(L) and Fm1(E), in the F2 populations LWF2 [LS1934 × WCGR112-8 (susceptible)] and EWF2 [EPL-1 (derived from LS174) × WCGR112-8], respectively. The percentage of phenotypic variance explained by Fm1(L) derived from LS1934 was 75.0% [Logarithm of the odds (LOD) = 29.3], and that explained by Fm1(E) derived from EPL-1 was 92.2% (LOD = 65.8). Using backcrossed inbred lines, we mapped FM1 between two simple sequence repeat markers located ~4.881 cM apart from each other. Comparing the location of the above locus to those of previously reported ones, the resistance locus Rfo-sa1 from an eggplant ally (Solanum aethiopicum gr. Gilo) was mapped very close to FM1, whereas another resistance locus, from LS2436, was mapped to the middle of chromosome 4. This is the first report of mapping of a Fusarium resistance locus in cultivated eggplant. The availability of resistance-linked markers will enable the application of marker-assisted selection to overcome problems posed by self-incompatibility and introduction of negative traits because of linkage drag, and will lead to clear understanding of genetic mechanism of Fusarium resistance.

  5. Hidden Markov model analysis of maternal behavior patterns in inbred and reciprocal hybrid mice.

    Directory of Open Access Journals (Sweden)

    Valeria Carola

    Full Text Available Individual variation in maternal care in mammals shows a significant heritable component, with the maternal behavior of daughters resembling that of their mothers. In laboratory mice, genetically distinct inbred strains show stable differences in maternal care during the first postnatal week. Moreover, cross fostering and reciprocal breeding studies demonstrate that differences in maternal care between inbred strains persist in the absence of genetic differences, demonstrating a non-genetic or epigenetic contribution to maternal behavior. In this study we applied a mathematical tool, called hidden Markov model (HMM, to analyze the behavior of female mice in the presence of their young. The frequency of several maternal behaviors in mice has been previously described, including nursing/grooming pups and tending to the nest. However, the ordering, clustering, and transitions between these behaviors have not been systematically described and thus a global description of maternal behavior is lacking. Here we used HMM to describe maternal behavior patterns in two genetically distinct mouse strains, C57BL/6 and BALB/c, and their genetically identical reciprocal hybrid female offspring. HMM analysis is a powerful tool to identify patterns of events that cluster in time and to determine transitions between these clusters, or hidden states. For the HMM analysis we defined seven states: arched-backed nursing, blanket nursing, licking/grooming pups, grooming, activity, eating, and sleeping. By quantifying the frequency, duration, composition, and transition probabilities of these states we were able to describe the pattern of maternal behavior in mouse and identify aspects of these patterns that are under genetic and nongenetic inheritance. Differences in these patterns observed in the experimental groups (inbred and hybrid females were detected only after the application of HMM analysis whereas classical statistical methods and analyses were not able to

  6. Susceptibility of the wild-derived inbred CAST/Ei mouse to infection by orthopoxviruses analyzed by live bioluminescence imaging

    International Nuclear Information System (INIS)

    Americo, Jeffrey L.; Sood, Cindy L.; Cotter, Catherine A.; Vogel, Jodi L.; Kristie, Thomas M.; Moss, Bernard; Earl, Patricia L.

    2014-01-01

    Classical inbred mice are extensively used for virus research. However, we recently found that some wild-derived inbred mouse strains are more susceptible than classical strains to monkeypox virus. Experiments described here indicated that the 50% lethal dose of vaccinia virus (VACV) and cowpox virus (CPXV) were two logs lower in wild-derived inbred CAST/Ei mice than classical inbred BALB/c mice, whereas there was little difference in the susceptibility of the mouse strains to herpes simplex virus. Live bioluminescence imaging was used to follow spread of pathogenic and attenuated VACV strains and CPXV virus from nasal passages to organs in the chest and abdomen of CAST/Ei mice. Luminescence increased first in the head and then simultaneously in the chest and abdomen in a dose-dependent manner. The spreading kinetics was more rapid with VACV than CPXV although the peak photon flux was similar. These data suggest advantages of CAST/Ei mice for orthopoxvirus studies. - Highlights: • Wild-derived inbred CAST/Ei mice are susceptible to vaccinia virus and cowpox virus. • Morbidity and mortality from orthopoxviruses are greater in CAST/Ei than BALB/c mice. • Morbidity and mortality from herpes simplex virus type 1 are similar in both mice. • Imaging shows virus spread from nose to lungs, abdominal organs and brain. • Vaccinia virus spreads more rapidly than cowpox virus

  7. Susceptibility of the wild-derived inbred CAST/Ei mouse to infection by orthopoxviruses analyzed by live bioluminescence imaging

    Energy Technology Data Exchange (ETDEWEB)

    Americo, Jeffrey L.; Sood, Cindy L.; Cotter, Catherine A.; Vogel, Jodi L.; Kristie, Thomas M.; Moss, Bernard, E-mail: bmoss@nih.gov; Earl, Patricia L., E-mail: pearl@nih.gov

    2014-01-20

    Classical inbred mice are extensively used for virus research. However, we recently found that some wild-derived inbred mouse strains are more susceptible than classical strains to monkeypox virus. Experiments described here indicated that the 50% lethal dose of vaccinia virus (VACV) and cowpox virus (CPXV) were two logs lower in wild-derived inbred CAST/Ei mice than classical inbred BALB/c mice, whereas there was little difference in the susceptibility of the mouse strains to herpes simplex virus. Live bioluminescence imaging was used to follow spread of pathogenic and attenuated VACV strains and CPXV virus from nasal passages to organs in the chest and abdomen of CAST/Ei mice. Luminescence increased first in the head and then simultaneously in the chest and abdomen in a dose-dependent manner. The spreading kinetics was more rapid with VACV than CPXV although the peak photon flux was similar. These data suggest advantages of CAST/Ei mice for orthopoxvirus studies. - Highlights: • Wild-derived inbred CAST/Ei mice are susceptible to vaccinia virus and cowpox virus. • Morbidity and mortality from orthopoxviruses are greater in CAST/Ei than BALB/c mice. • Morbidity and mortality from herpes simplex virus type 1 are similar in both mice. • Imaging shows virus spread from nose to lungs, abdominal organs and brain. • Vaccinia virus spreads more rapidly than cowpox virus.

  8. Effect of. gamma. -radiation on chiasma frequency in four inbred strains of Trigonella L

    Energy Technology Data Exchange (ETDEWEB)

    Venkateswara Rao, T; Lakshmi, N

    1983-12-01

    The effect of ..gamma..-rays on chiasma frequency was studied in M/sub 1/ plants of three inbred strains of T. foenum-graecum and T. corniculata. The response of the varieties to different doses of radiation with respect to chaiasma frequency was found to be different on the basis of students 't' test. In all the treated strains a decrease in chiasma frequency was observed compared to controls and the decrease was found to be inversely proportional to the dose. The possible causes for reduction in chiasma frequency are discussed. 16 refs., 3 tables.

  9. Adult plant leaf rust resistance derived from the soft red winter wheat cultivar Caldwell maps to chromosome 3BS

    Science.gov (United States)

    'Caldwell' is a U.S. soft red winter wheat that has partial, adult plant resistance to the leaf rust pathogen Puccinia triticina. A line of 'Thatcher*2/Caldwell' with adult plant resistance derived from Caldwell was crossed with 'Thatcher' to develop a population of recombinant inbred lines (RILs). ...

  10. Radiation tumorigenesis in inbred laboratory animals and cancer risks in irradiated human populations. Two widely different problems

    International Nuclear Information System (INIS)

    Walinder, G.

    1978-01-01

    The mammal has efficient defence mechanisms against the development of tumours. These mechanisms are successively deteriorated by ionizing radiation when the dose increases beyond certain 'borderline levels'. Consequently, most animal strains demonstrate a bi-phasic dose-tumour relationship with a low-dose limb, the slope of which cannot be distinguished from zero, and a high-dose limb that increases with increasing doses. There are four or five exceptions to this 'rule' but in most of these cases the probable reasons for the deviations are known. Some human tumours as observed in epidemiological investigations do not demonstrate a similar clearly bi-phasic dose response. In all probability, this discrepancy does not reflect a higher susceptibility to radiation-induced tumours in man compared with other mammals. It is rather a consequence of a greater statistical variation in radiosensitivity in heterogeneous human populations than among inbred animals living standardized conditions. Accordingly, when maximum permissible dose levels are to be determined one should extrapolate from epidemiological data. Furthermore, these extrapolations should be linear if the data do not clearly deviate from a straight line, and if there are no scientific reasons to assume that a threshold exists. This formal method would not produce a biological description of what may happen in the low-dose area but rather an upper risk limit for the population studied. The real low-dose risk cannot be known. For the same pragmatic reason other radiological or non-radiological risks should be determined in the same manner, particularly when risks are to be compared. (author)

  11. Labelling subway lines

    NARCIS (Netherlands)

    Garrido, M.A.; Iturriaga, C.; Márquez, A.; Portillo, J.R.; Reyes, P.; Wolff, A.; Eades, P.; Takaoka, T.

    2001-01-01

    Graphical features on map, charts, diagrams and graph drawings usually must be annotated with text labels in order to convey their meaning. In this paper we focus on a problem that arises when labeling schematized maps, e.g. for subway networks. We present algorithms for labeling points on a line

  12. Renal blood flow dynamics in inbred rat strains provides insight into autoregulation.

    Science.gov (United States)

    A Mitrou, Nicholas G; Cupples, William A

    2014-01-01

    Renal autoregulation maintains stable renal blood flow in the face of constantly fluctuating blood pressure. Autoregulation is also the only mechanism that protects the delicate glomerular capillaries when blood pressure increases. In order to understand autoregulation, the renal blood flow response to changing blood pressure is studied. The steadystate response of blood flow is informative, but limits investigation of the individual mechanisms of autoregulation. The dynamics of autoregulation can be probed with transfer function analysis. The frequency-domain analysis of autoregulation allows investigators to probe the relative activity of each mechanism of autoregulation. We discuss the methodology and interpretation of transfer function analysis. Autoregulation is routinely studied in the rat, of which there are many inbred strains. There are multiple strains of rat that are either selected or inbred as models of human pathology. We discuss relevant characteristics of Brown Norway, Spontaneously hypertensive, Dahl, and Fawn-Hooded hypertensive rats and explore differences among these strains in blood pressure, dynamic autoregulation, and susceptibility to hypertensive renal injury. Finally we show that the use of transfer function analysis in these rat strains has contributed to our understanding of the physiology and pathophysiology of autoregulation and hypertensive renal disease.Interestingly all these strains demonstrate effective tubuloglomerular feedback suggesting that this mechanism is not sufficient for effective autoregulation. In contrast, obligatory or conditional failure of the myogenic mechanism suggests that this component is both necessary and sufficient for autoregulation.

  13. Substrains of Inbred Mice Differ in Their Physical Activity as a Behavior

    Directory of Open Access Journals (Sweden)

    Dario Coletti

    2013-01-01

    Full Text Available Recent studies strengthen the belief that physical activity as a behavior has a genetic basis. Screening wheel-running behavior in inbred mouse strains highlighted differences among strains, showing that even very limited genetic differences deeply affect mouse behavior. We extended this observation to substrains of the same inbred mouse strain, that is, BALB/c mice. We found that only a minority of the population of one of these substrains, the BALB/c J, performs spontaneous physical activity. In addition, the runners of this substrain cover a significantly smaller distance than the average runners of two other substrains, namely, the BALB/c ByJ and the BALB/c AnNCrl. The latter shows a striking level of voluntary activity, with the average distance run/day reaching up to about 12 kilometers. These runners are not outstanders, but they represent the majority of the population, with important scientific and economic fallouts to be taken into account during experimental planning. Spontaneous activity persists in pathological conditions, such as cancer-associated cachexia. This important amount of physical activity results in a minor muscle adaptation to endurance exercise over a three-week period; indeed, only a nonsignificant increase in NADH transferase+ fibers occurs in this time frame.

  14. Agrobacterium- and Biolistic-Mediated Transformation of Maize B104 Inbred.

    Science.gov (United States)

    Raji, Jennifer A; Frame, Bronwyn; Little, Daniel; Santoso, Tri Joko; Wang, Kan

    2018-01-01

    Genetic transformation of maize inbred genotypes remains non-routine for many laboratories due to variations in cell competency to induce embryogenic callus, as well as the cell's ability to receive and incorporate transgenes into the genome. This chapter describes two transformation protocols using Agrobacterium- and biolistic-mediated methods for gene delivery. Immature zygotic embryos of maize inbred B104, excised from ears harvested 10-14 days post pollination, are used as starting explant material. Disarmed Agrobacterium strains harboring standard binary vectors and the biolistic gun system Bio-Rad PDS-1000/He are used as gene delivery systems. The herbicide resistant bar gene and selection agent bialaphos are used for identifying putative transgenic type I callus events. Using the step-by-step protocols described here, average transformation frequencies (number of bialaphos resistant T 0 callus events per 100 explants infected or bombarded) of 4% and 8% can be achieved using the Agrobacterium- and biolistic-mediated methods, respectively. An estimated duration of 16-21 weeks is needed using either protocol from the start of transformation experiments to obtaining putative transgenic plantlets with established roots. In addition to laboratory in vitro procedures, detailed greenhouse protocols for producing immature ears as transformation starting material and caring for transgenic plants for seed production are also described.

  15. Unpredictable chronic mild stress differentially impairs social and contextual discrimination learning in two inbred mouse strains.

    Science.gov (United States)

    van Boxelaere, Michiel; Clements, Jason; Callaerts, Patrick; D'Hooge, Rudi; Callaerts-Vegh, Zsuzsanna

    2017-01-01

    Alterations in the social and cognitive domain are considered important indicators for increased disability in many stress-related disorders. Similar impairments have been observed in rodents chronically exposed to stress, mimicking potential endophenotypes of stress-related psychopathologies such as major depression disorder (MDD), anxiety, conduct disorder, and posttraumatic stress disorder (PTSD). Data from numerous studies suggest that deficient plasticity mechanisms in hippocampus (HC) and prefrontal cortex (PFC) might underlie these social and cognitive deficits. Specifically, stress-induced deficiencies in neural plasticity have been associated with a hypodopaminergic state and reduced neural plasticity persistence. Here we assessed the effects of unpredictable chronic mild stress (UCMS) on exploratory, social and cognitive behavior of females of two inbred mouse strains (C57BL/6J and DBA/2J) that differ in their dopaminergic profile. Exposure to chronic stress resulted in impaired circadian rhythmicity, sociability and social cognition in both inbred strains, but differentially affected activity patterns and contextual discrimination performance. These stress-induced behavioral impairments were accompanied by reduced expression levels of brain derived neurotrophic factor (BDNF) in the prefrontal cortex. The strain-specific cognitive impairment was coexistent with enhanced plasma corticosterone levels and reduced expression of genes related to dopamine signaling in hippocampus. These results underline the importance of assessing different strains with multiple test batteries to elucidate the neural and genetic basis of social and cognitive impairments related to chronic stress.

  16. A Maize Inbred Exhibits Resistance Against Western Corn Rootwoorm, Diabrotica virgifera virgifera.

    Science.gov (United States)

    Castano-Duque, Lina; Loades, Kenneth W; Tooker, John F; Brown, Kathleen M; Paul Williams, W; Luthe, Dawn S

    2017-12-01

    Insect resistance against root herbivores like the western corn rootworm (WCR, Diabrotica virgifera virgifera) is not well understood in non-transgenic maize. We studied the responses of two American maize inbreds, Mp708 and Tx601, to WCR infestation using biomechanical, molecular, biochemical analyses, and laser ablation tomography. Previous studies performed on several inbreds indicated that these two maize genotypes differed in resistance to pests including fall armyworm (Spodoptera frugiperda) and WCR. Our data confirmed that Mp708 shows resistance against WCR, and demonstrates that the resistance mechanism is based in a multi-trait phenotype that includes increased resistance to cutting in nodal roots, stable root growth during insect infestation, constitutive and induced expression of known herbivore-defense genes, including ribosomal inhibitor protein 2 (rip2), terpene synthase 23 (tps23) and maize insect resistance cysteine protease-1 (mir1), as well high constitutive levels of jasmonic acid and production of (E)-β-caryophyllene. In contrast, Tx601 is susceptible to WCR. These findings will facilitate the use of Mp708 as a model to explore the wide variety of mechanisms and traits involved in plant defense responses and resistance to herbivory by insects with several different feeding habits.

  17. Cocaine locomotor activation, sensitization and place preference in six inbred strains of mice

    Science.gov (United States)

    2011-01-01

    Background The expanding set of genomics tools available for inbred mouse strains has renewed interest in phenotyping larger sets of strains. The present study aims to explore phenotypic variability among six commonly-used inbred mouse strains to both the rewarding and locomotor stimulating effects of cocaine in a place conditioning task, including several strains or substrains that have not yet been characterized for some or all of these behaviors. Methods C57BL/6J (B6), BALB/cJ (BALB), C3H/HeJ (C3H), DBA/2J (D2), FVB/NJ (FVB) and 129S1/SvImJ (129) mice were tested for conditioned place preference to 20 mg/kg cocaine. Results Place preference was observed in most strains with the exception of D2 and 129. All strains showed a marked increase in locomotor activity in response to cocaine. In BALB mice, however, locomotor activation was context-dependent. Locomotor sensitization to repeated exposure to cocaine was most significant in 129 and D2 mice but was absent in FVB mice. Conclusions Genetic correlations suggest that no significant correlation between conditioned place preference, acute locomotor activation, and locomotor sensitization exists among these strains indicating that separate mechanisms underlie the psychomotor and rewarding effects of cocaine. PMID:21806802

  18. Unpredictable chronic mild stress differentially impairs social and contextual discrimination learning in two inbred mouse strains.

    Directory of Open Access Journals (Sweden)

    Michiel van Boxelaere

    Full Text Available Alterations in the social and cognitive domain are considered important indicators for increased disability in many stress-related disorders. Similar impairments have been observed in rodents chronically exposed to stress, mimicking potential endophenotypes of stress-related psychopathologies such as major depression disorder (MDD, anxiety, conduct disorder, and posttraumatic stress disorder (PTSD. Data from numerous studies suggest that deficient plasticity mechanisms in hippocampus (HC and prefrontal cortex (PFC might underlie these social and cognitive deficits. Specifically, stress-induced deficiencies in neural plasticity have been associated with a hypodopaminergic state and reduced neural plasticity persistence. Here we assessed the effects of unpredictable chronic mild stress (UCMS on exploratory, social and cognitive behavior of females of two inbred mouse strains (C57BL/6J and DBA/2J that differ in their dopaminergic profile. Exposure to chronic stress resulted in impaired circadian rhythmicity, sociability and social cognition in both inbred strains, but differentially affected activity patterns and contextual discrimination performance. These stress-induced behavioral impairments were accompanied by reduced expression levels of brain derived neurotrophic factor (BDNF in the prefrontal cortex. The strain-specific cognitive impairment was coexistent with enhanced plasma corticosterone levels and reduced expression of genes related to dopamine signaling in hippocampus. These results underline the importance of assessing different strains with multiple test batteries to elucidate the neural and genetic basis of social and cognitive impairments related to chronic stress.

  19. Abundance and distribution of transposable elements in two Drosophila QTL mapping resources.

    Science.gov (United States)

    Cridland, Julie M; Macdonald, Stuart J; Long, Anthony D; Thornton, Kevin R

    2013-10-01

    Here we present computational machinery to efficiently and accurately identify transposable element (TE) insertions in 146 next-generation sequenced inbred strains of Drosophila melanogaster. The panel of lines we use in our study is composed of strains from a pair of genetic mapping resources: the Drosophila Genetic Reference Panel (DGRP) and the Drosophila Synthetic Population Resource (DSPR). We identified 23,087 TE insertions in these lines, of which 83.3% are found in only one line. There are marked differences in the distribution of elements over the genome, with TEs found at higher densities on the X chromosome, and in regions of low recombination. We also identified many more TEs per base pair of intronic sequence and fewer TEs per base pair of exonic sequence than expected if TEs are located at random locations in the euchromatic genome. There was substantial variation in TE load across genes. For example, the paralogs derailed and derailed-2 show a significant difference in the number of TE insertions, potentially reflecting differences in the selection acting on these loci. When considering TE families, we find a very weak effect of gene family size on TE insertions per gene, indicating that as gene family size increases the number of TE insertions in a given gene within that family also increases. TEs are known to be associated with certain phenotypes, and our data will allow investigators using the DGRP and DSPR to assess the functional role of TE insertions in complex trait variation more generally. Notably, because most TEs are very rare and often private to a single line, causative TEs resulting in phenotypic differences among individuals may typically fail to replicate across mapping panels since individual elements are unlikely to segregate in both panels. Our data suggest that "burden tests" that test for the effect of TEs as a class may be more fruitful.

  20. A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

    Directory of Open Access Journals (Sweden)

    Ashley S. Chaffin

    2016-07-01

    Full Text Available Hexaploid oat ( L., 2 = 6 = 42 is a member of the Poaceae family and has a large genome (∼12.5 Gb containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP array and genotyping-by-sequencing (GBS were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice ( L. reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.

  1. Allelism analysis of BrRfp locus in different restorer lines and map-based cloning of a fertility restorer gene, BrRfp1, for pol CMS in Chinese cabbage (Brassica rapa L.).

    Science.gov (United States)

    Zhang, Huamin; Wu, Junqing; Dai, Zihui; Qin, Meiling; Hao, Lingyu; Ren, Yanjing; Li, Qingfei; Zhang, Lugang

    2017-03-01

    In Chinese cabbage, there are two Rf loci for pol CMS and one of them was mapped to a 12.6-kb region containing a potential candidate gene encoding PPR protein. In Chinese cabbage (Brassica rapa), polima cytoplasmic male sterility (pol CMS) is an important CMS type and is widely used for hybrid breeding. By extensive test crossing in Chinese cabbage, four restorer lines (92s105, 01s325, 00s109, and 88s148) for pol CMS were screened. By analyzing the allelism of the four restorer lines, it was found that 92s105, 01s325, and 00s109 had the same "restorers of fertility" (Rf) locus (designated as BrRfp1), but 88s148 had a different Rf locus (designated as BrRfp2). For fine mapping the BrRfp1 locus of 92s105, a BC 1 F 1 population with 487 individuals and a BC 1 F 2 population with 2485 individuals were successively constructed. Using simple sequence repeat (SSR) markers developed from Brassica rapa reference genome and InDel markers derived from whole-genome resequencing data of 94c9 and 92s105, BrRfp1 was mapped to a 12.6-kb region containing a potential candidate gene encoding pentatricopeptide repeat-containing protein. Based on the nucleotide polymorphisms of the candidate gene sequence between the restoring and nonrestoring alleles, a co-segregating marker SC718 was developed, which would be helpful for hybrid breeding by marker-assisted screening and for detecting new restorer lines.

  2. The First Genetic and Comparative Map of White Lupin (Lupinus albus L.): Identification of QTLs for Anthracnose Resistance and Flowering Time, and a Locus for Alkaloid Content

    Science.gov (United States)

    Phan, Huyen T. T.; Ellwood, Simon R.; Adhikari, Kedar; Nelson, Matthew N.; Oliver, Richard P.

    2007-01-01

    Abstract We report the first genetic linkage map of white lupin (Lupinus albus L.). An F8 recombinant inbred line population developed from Kiev mutant × P27174 was mapped with 220 amplified fragment length polymorphism and 105 gene-based markers. The genetic map consists of 28 main linkage groups (LGs) that varied in length from 22.7 cM to 246.5 cM and spanned a total length of 2951 cM. There were seven additional pairs and 15 unlinked markers, and 12.8% of markers showed segregation distortion at P anthracnose resistance, flowering time, and alkaloid content allowed loci governing these traits to be defined. Two quantitative trait loci (QTLs) with significant effects were identified for anthracnose resistance on LG4 and LG17, and two QTLs were detected for flowering time on the top of LG1 and LG3. Alkaloid content was mapped as a Mendelian trait to LG11. PMID:17526914

  3. High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth.

    Science.gov (United States)

    Zhang, Xuehai; Huang, Chenglong; Wu, Di; Qiao, Feng; Li, Wenqiang; Duan, Lingfeng; Wang, Ke; Xiao, Yingjie; Chen, Guoxing; Liu, Qian; Xiong, Lizhong; Yang, Wanneng; Yan, Jianbing

    2017-03-01

    With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize ( Zea mays ) recombinant inbred line population ( n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction. © 2017 American Society of Plant Biologists. All Rights Reserved.

  4. QTL mapping for controlling anthesis-silking interval based on RIL ...

    African Journals Online (AJOL)

    To realize the genetic basis of ASI, a recombinant inbred line (RIL) population consisting of 239 RILs, derived from the cross between Mo17 and Huangzao4, was used to identify the quantitative trait loci (QTLs) controlling ASI under different N environments. As a result, 6 QTLs were detected under high N environment on ...

  5. Mapping out Map Libraries

    Directory of Open Access Journals (Sweden)

    Ferjan Ormeling

    2008-09-01

    Full Text Available Discussing the requirements for map data quality, map users and their library/archives environment, the paper focuses on the metadata the user would need for a correct and efficient interpretation of the map data. For such a correct interpretation, knowledge of the rules and guidelines according to which the topographers/cartographers work (such as the kind of data categories to be collected, and the degree to which these rules and guidelines were indeed followed are essential. This is not only valid for the old maps stored in our libraries and archives, but perhaps even more so for the new digital files as the format in which we now have to access our geospatial data. As this would be too much to ask from map librarians/curators, some sort of web 2.0 environment is sought where comments about data quality, completeness and up-to-dateness from knowledgeable map users regarding the specific maps or map series studied can be collected and tagged to scanned versions of these maps on the web. In order not to be subject to the same disadvantages as Wikipedia, where the ‘communis opinio’ rather than scholarship, seems to be decisive, some checking by map curators of this tagged map use information would still be needed. Cooperation between map curators and the International Cartographic Association ( ICA map and spatial data use commission to this end is suggested.

  6. SNP-based linkage mapping for validation of QTLs for resistance to ascochyta blight in lentil

    Directory of Open Access Journals (Sweden)

    Shimna Sudheesh

    2016-11-01

    Full Text Available Lentil (Lens culinaris Medik. is a self-pollinating, diploid, annual, cool-season, food legume crop that is cultivated throughout the world. Ascochyta blight (AB, caused by Ascochyta lentis Vassilievsky, is an economically important and widespread disease of lentil. Development of cultivars with high levels of durable resistance provides an environmentally acceptable and economically feasible method for AB control. A detailed understanding of the genetic basis of AB resistance is hence highly desirable, in order to obtain insight into the number and influence of resistance genes. Genetic linkage maps based on single nucleotide polymorphisms (SNP and simple sequence repeat (SSR markers have been developed from three recombinant inbred line (RIL populations. The IH x NF map contained 460 loci across 1461.6 cM, while the IH x DIG map contained 329 loci across 1302.5 cM and the third map, NF x DIG contained 330 loci across 1914.1 cM. Data from these maps were combined with a map from a previously published study through use of bridging markers to generate a consensus linkage map containing 689 loci distributed across 7 linkage groups (LGs, with a cumulative length of 2429.61 cM at an average density of one marker per 3.5 cM. Trait dissection of AB resistance was performed for the RIL populations, identifying totals of two and three quantitative trait loci (QTLs explaining 52% and 69% of phenotypic variation for resistance to infection in the IH x DIG and IH x NF populations, respectively. Presence of common markers in the vicinity of the AB_IH1- and AB_IH2.1/AB_IH2.2-containing regions on both maps supports the inference that a common genomic region is responsible for conferring resistance and is associated with the resistant parent, Indianhead. The third QTL was derived from Northfield. Evaluation of markers associated with AB resistance across a diverse lentil germplasm panel revealed that the identity of alleles associated with AB_IH1 predicted

  7. Immunohistochemical characterisation of the local immune response in azoxymethane-induced colon tumours in the BDIX inbred rat strain

    DEFF Research Database (Denmark)

    Kobæk Larsen, Morten; Diederichsen, Axel Cosmus Pyndt; Agger, Ralf

    2004-01-01

    by four weekly subcutaneous azoxymethane injections in inbred rats of the BDIX/OrlIco strain in two separate studies. Azoxymethane-induced tumours show many similarities to spontaneously occurring human colon carcinomas with respect to histopathological appearance. In our studies, the overall inflammatory...

  8. A Dynamic Model of Heavy Ion 7Li Irradiation Mutagenesis Based on Maize Inbred Line Nutrition Difference

    Science.gov (United States)

    Hu, Jin-Shan; Geng, Jin-Peng; Li, Duo-Fang; Sui, Li; Zhan, Yong

    2018-04-01

    Not Available Supported by the National Natural Science Foundation of China under Grant No 11735006, the Hebei Natural Science Foundation of China under Grant No B2014209314, and the Hebei Science and Technology Research Project of Higher Education under Grant No ZD2017023.

  9. Evaluation of maize inbred lines for resistance to pre-harvest aflatoxin and fumonisin contamination in the field

    Science.gov (United States)

    Two important mycotoxins, aflatoxin and fumonisin, are among the most potent naturally occurring carcinogens, contaminating maize (Zea mays L.) and affecting the crop yield and quality. Resistance of maize to pre-harvest mycotoxin contamination, specifically aflatoxin produced by Aspergillus flavus ...

  10. Selection of common bean lines with high grain yield and high grain calcium and iron concentrations

    Directory of Open Access Journals (Sweden)

    Nerinéia Dalfollo Ribeiro

    2014-02-01

    Full Text Available Genetic improvement of common bean nutritional quality has advantages in marketing and can contribute to society as a food source. The objective of this study was to evaluate the genetic variability for grain yield, calcium and iron concentrations in grains of inbred common bean lines obtained by different breeding methods. For this, 136 F7 inbred lines were obtained using the Pedigree method and 136 F7 inbred lines were obtained using the Single-Seed Descent (SSD method. The lines showed genetic variability for grain yield, and concentrations of calcium and iron independently of the method of advancing segregating populations. The Pedigree method allows obtaining a greater number of lines with high grain yield. Selection using the SSD method allows the identification of a larger number of lines with high concentrations of calcium and iron in grains. Weak negative correlations were found between grain yield and calcium concentration (r = -0.0994 and grain yield and iron concentration (r = -0.3926. Several lines show genetic superiority for grain yield and concentrations of calcium and iron in grains and their selection can result in new common bean cultivars with high nutritional quality.

  11. Correlation between DNA repair of embryonic fibroblasts and different life span of 3 inbred mouse strains

    Energy Technology Data Exchange (ETDEWEB)

    Paffenholz, V.

    1978-02-01

    Primary mouse fibroblast cultures were established from 10 day old embryos of 3 inbred strains with a genetically determined different life expectancy. The capacity for unscheduled DNA synthesis following uv irradiation was studied in these cells at various passage levels of the in vitro ageing process. The mouse fibroblasts show considerable repair synthesis corresponding to the duration of exposure time. The capacity for induction of unscheduled DNA synthesis was different in the cells of each strain and correlated to the natural life span of the animal. In each case, however, the ability to perform repair synthesis was subjected to an age-associated decline, although semiconservative DNA synthesis and proliferative potential of the cell was not changed until the cultures entered phase III passages.

  12. Genetic basis of resistance to trauma in inbred strains of mice

    International Nuclear Information System (INIS)

    Radojicic, C.; Andric, B.; Simovic, M.; Dujic, A.; Marinkovic, D.

    1990-01-01

    In this study the resistance to mechanical, thermal, and radiation trauma in four inbred strains of mice (AKR, BALB/c, CBA, and C57Bl/6) was compared with the degree of genetic resemblance, by analyzing the allozyme variabilities of these strains. It was shown that the highest degree of genetic resemblance was among CBA and AKR strains, which correlated with a similar degree of resistance to trauma. On the other hand, BALB/c and C57Bl/6 strains expressed significant differences, both genetically and with respect to the responses to trauma. The hypothesis is introduced that the genetic determination of the resistance to trauma is based on: (a) a polygenic control of general physiological homeostasis, with the possibility that (b) some specific genes or single loci may contribute more than others to such adaptations of the strains tested

  13. Electrophoretic variation in low molecular weight lens crystallins from inbred strains of rats.

    Science.gov (United States)

    Donner, M E; Skow, L C; Kunz, H W; Gill, T J

    1985-10-01

    Analysis of rat lens soluble proteins by analytical isoelectric focusing detected two inherited electrophoretic differences in low molecular weight (LM) crystallins from inbred strains of rats (Rattus norvegicus). The polymorphic lens crystallins were shown to be similar to a genetically variant LM crystallin, LEN-1, previously described in mice (Mus musculus) and encoded on chromosome 1, at a locus linked to Pep-3 (dipeptidase). Linkage analysis demonstrated that the rat crystallin locus was loosely linked to Pep-3 at a recombination distance of 38 +/- 4.5 U. These data suggest the conservation of a large chromosomal region during the evolution of Rodentia and support the hypothesis that the gamma-crystallins are evolving more rapidly than alpha- or beta-crystallins.

  14. In-silico QTL mapping of postpubertal mammary ductal development in the mouse uncovers potential human breast cancer risk loci

    Science.gov (United States)

    Genetic background plays a dominant role in mammary gland development and breast cancer (BrCa). Despite this, the role of genetics is only partially understood. This study used strain-dependent variation in an inbred mouse mapping panel, to identify quantitative trait loci (QTL) underlying structura...

  15. Comparison of inbred mouse substrains reveals segregation of maladaptive fear phenotypes

    Directory of Open Access Journals (Sweden)

    Stephanie J Temme

    2014-08-01

    Full Text Available Maladaptive fear, such as fear that is persistent or easily generalized to a nonthreatening stimuli, is associated with anxiety-related disorders in humans. In the laboratory, maladaptive fear can be modeled in rodents using Pavlovian fear conditioning. Recently, an inbred mouse strain known as 129S1/SvImJ, or 129S1 have been reported as exhibiting impairments in fear extinction and enhanced fear generalization. With a long-term goal of identifying segregating genetic markers of maladaptive fear, we used Pavlovian fear conditioning to characterize a closely related substrain designated as 129S6/SvEvTac, or 129S6. Here we report that, like 129S1 animals, 129S6 mice exhibit appropriate levels of fear upon conditioning, but are unable to extinguish fear memories once they are consolidated. Importantly, the maladaptive fear phenotype in this inbred stain can be segregated by sub-strain when probed using conditioning protocols designed to assess generalized fear. We find that unlike the 129S1 substrain, mice from the 129S6 sub-strain do not generalize conditioned fear to previously novel contexts and can learn to discriminate between two similar contexts when trained using a discrimination protocol. These results suggest that at least two forms of maladaptive fear (deficits in fear extinction and fear generalization can be can be functionally segregated, further suggesting that the underlying neurobiology is heritable. Given the observation that two closely related sub-strains can exhibit different constellations of maladaptive fear suggests that these findings could be exploited to facilitate the identification of candidate genes for anxiety-related disorders.

  16. The CNS in inbred transgenic models of 4-repeat Tauopathy develops consistent tau seeding capacity yet focal and diverse patterns of protein deposition.

    Science.gov (United States)

    Eskandari-Sedighi, Ghazaleh; Daude, Nathalie; Gapeshina, Hristina; Sanders, David W; Kamali-Jamil, Razieh; Yang, Jing; Shi, Beipei; Wille, Holger; Ghetti, Bernardino; Diamond, Marc I; Janus, Christopher; Westaway, David

    2017-10-04

    MAPT mutations cause neurodegenerative diseases such as frontotemporal dementia but, strikingly, patients with the same mutation may have different clinical phenotypes. Given heterogeneities observed in a transgenic (Tg) mouse line expressing low levels of human (2 N, 4R) P301L Tau, we backcrossed founder stocks of mice to C57BL/6Tac, 129/SvEvTac and FVB/NJ inbred backgrounds to discern the role of genetic versus environmental effects on disease-related phenotypes. Three inbred derivatives of a TgTau P301L founder line had similar quality and steady-state quantity of Tau production, accumulation of abnormally phosphorylated 64-68 kDa Tau species from 90 days of age onwards and neuronal loss in aged Tg mice. Variegation was not seen in the pattern of transgene expression and seeding properties in a fluorescence-based cellular assay indicated a single "strain" of misfolded Tau. However, in other regards, the aged Tg mice were heterogeneous; there was incomplete penetrance for Tau deposition despite maintained transgene expression in aged animals and, for animals with Tau deposits, distinctions were noted even within each subline. Three classes of rostral deposition in the cortex, hippocampus and striatum accounted for 75% of pathology-positive mice yet the mean ages of mice scored as class I, II or III were not significantly different and, hence, did not fit with a predictable progression from one class to another defined by chronological age. Two other patterns of Tau deposition designated as classes IV and V, occurred in caudal structures. Other pathology-positive Tg mice of similar age not falling within classes I-V presented with focal accumulations in additional caudal neuroanatomical areas including the locus coeruleus. Electron microscopy revealed that brains of Classes I, II and IV animals all exhibit straight filaments, but with coiled filaments and occasional twisted filaments apparent in Class I. Most strikingly, Class I, II and IV animals presented

  17. Fine mapping TaFLW1, a major QTL controlling flag leaf width in bread wheat (Triticum aestivum L.).

    Science.gov (United States)

    Xue, Shulin; Xu, Feng; Li, Guoqiang; Zhou, Yan; Lin, Musen; Gao, Zhongxia; Su, Xiuhong; Xu, Xiaowu; Jiang, Ge; Zhang, Shuang; Jia, Haiyan; Kong, Zhongxin; Zhang, Lixia; Ma, Zhengqiang

    2013-08-01

    Flag leaf width (FLW) is directly related to photosynthetic capacity and yield potential in wheat. In a previous study, Qflw.nau-5A controlling FLW was detected on chromosome 5A in the interval possessing Fhb5 for type I Fusarium head blight (FHB) resistance using a recombinant inbred line population derived from Nanda2419 × Wangshuibai. Qflw.nau-5A near-isogenic line (NIL) with the background of Mianyang 99-323 and PH691 was developed and evaluated. FLW inheritance was investigated using two F2 populations developed from crossing the Qflw.nau-5A NILs with their recurrent parents. One hundred ten and 28 recombinants, which included 10 and 5 types of recombinants, were identified from 2816 F2 plants with Mianyang 99-323 background and 1277 F2 plants with PH691 background, respectively, and phenotyped in field trials for FLW and type I FHB resistance. Deletion bin mapping was applied to physically map Qflw.nau-5A. The introduction of Wangshuibai Qflw.nau-5A allele reduced the FLW up to 3 mm. In the F2 populations, Qflw.nau-5A was inherited like a semi-dominant gene, and was therefore designated as TaFLW1. The FLW of the recombinant lines displayed a distinct two-peak distribution. Recombinants with wider leaves commonly have Mianyang 99-323 or PH691 chromatin in the 0.2 cM Xwmc492-Xwmc752 interval that resided in the 5AL12-0.35-0.57 deletion bin, and recombinants with narrow leaves were Wangshuibai genotype in this interval. Phenotypic recombination between FLW and type I FHB resistance was identified, implying TaFLW1 was in close linkage with Fhb5. These results should aid wheat breeders to break the linkage drag through marker-assisted selection and assist in the map-based cloning of TaFLW1.

  18. Virus-induced gene silencing in diverse maize lines using the Brome Mosaic virus-based silencing vector

    Science.gov (United States)

    Virus-induced gene silencing (VIGS) is a widely used tool for gene function studies in many plant species, though its use in monocots has been limited. Using a Brome mosaic virus (BMV) vector designed to silence the maize phytoene desaturase gene, a genetically diverse set of maize inbred lines was ...

  19. Grain Yield and Fusarium Ear Rot of Maize Hybrids Developed From Lines With Varying Levels of Resistance

    Science.gov (United States)

    Fusarium ear rot, caused by Fusarium verticillioides and other Fusarium spp. is found in all U.S. maize growing regions. Affected grain often contains carcinogenic mycotoxins called fumonisins. We tested the hypothesis that inbred lines with greater resistance to fumonisin contamination would pro...

  20. A missense mutation in ALDH1A3 causes isolated microphthalmia/anophthalmia in nine individuals from an inbred Muslim kindred.

    Science.gov (United States)

    Mory, Adi; Ruiz, Francesc X; Dagan, Efrat; Yakovtseva, Evgenia A; Kurolap, Alina; Parés, Xavier; Farrés, Jaume; Gershoni-Baruch, Ruth

    2014-03-01

    Nine affected individuals with isolated anophthalmia/microphthalmia from a large Muslim-inbred kindred were investigated. Assuming autosomal-recessive mode of inheritance, whole-genome linkage analysis, on DNA samples from four affected individuals, was undertaken. Homozygosity mapping techniques were employed and a 1.5-Mbp region, homozygous in all affected individuals, was delineated. The region contained nine genes, one of which, aldehyde dehydrogenase 1 (ALDH1A3), was a clear candidate. This gene seems to encode a key enzyme in the formation of a retinoic-acid gradient along the dorsoventral axis during an early eye development and the development of the olfactory system. Sanger sequence analysis revealed a missense mutation, causing a substitution of valine (Val) to methionine (Met) at position 71. Analyzing the p.Val71Met missense mutation using standard open access software (MutationTaster online, PolyPhen, SIFT/PROVEAN) predicts this variant to be damaging. Enzymatic activity, studied in vitro, showed no changes between the mutated and the wild-type ALDH1A3 protein.

  1. Fine mapping of a Phytophthora-resistance gene RpsWY in soybean (Glycine max L.) by high-throughput genome-wide sequencing.

    Science.gov (United States)

    Cheng, Yanbo; Ma, Qibin; Ren, Hailong; Xia, Qiuju; Song, Enliang; Tan, Zhiyuan; Li, Shuxian; Zhang, Gengyun; Nian, Hai

    2017-05-01

    Using a combination of phenotypic screening, genetic and statistical analyses, and high-throughput genome-wide sequencing, we have finely mapped a dominant Phytophthora resistance gene in soybean cultivar Wayao. Phytophthora root rot (PRR) caused by Phytophthora sojae is one of the most important soil-borne diseases in many soybean-production regions in the world. Identification of resistant gene(s) and incorporating them into elite varieties are an effective way for breeding to prevent soybean from being harmed by this disease. Two soybean populations of 191 F 2 individuals and 196 F 7:8 recombinant inbred lines (RILs) were developed to map Rps gene by crossing a susceptible cultivar Huachun 2 with the resistant cultivar Wayao. Genetic analysis of the F 2 population indicated that PRR resistance in Wayao was controlled by a single dominant gene, temporarily named RpsWY, which was mapped on chromosome 3. A high-density genetic linkage bin map was constructed using 3469 recombination bins of the RILs to explore the candidate genes by the high-throughput genome-wide sequencing. The results of genotypic analysis showed that the RpsWY gene was located in bin 401 between 4466230 and 4502773 bp on chromosome 3 through line 71 and 100 of the RILs. Four predicted genes (Glyma03g04350, Glyma03g04360, Glyma03g04370, and Glyma03g04380) were found at the narrowed region of 36.5 kb in bin 401. These results suggest that the high-throughput genome-wide resequencing is an effective method to fine map PRR candidate genes.

  2. High Resolution Consensus Mapping of Quantitative Trait Loci for Fiber Strength, Length and Micronaire on Chromosome 25 of the Upland Cotton (Gossypium hirsutum L..

    Directory of Open Access Journals (Sweden)

    Zhen Zhang

    Full Text Available Cotton (Gossypium hirsutum L. is an important agricultural crop that provides renewable natural fiber resources for the global textile industry. Technological developments in the textile industry and improvements in human living standards have increased the requirement for supplies and better quality cotton. Upland cotton 0-153 is an elite cultivar harboring strong fiber strength genes. To conduct quantitative trait locus (QTL mapping for fiber quality in 0-153, we developed a population of 196 recombinant inbred lines (RILs from a cross between 0-153 and sGK9708. The fiber quality traits in 11 environments were measured and a genetic linkage map of chromosome 25 comprising 210 loci was constructed using this RIL population, mainly using simple sequence repeat markers and single nucleotide polymorphism markers. QTLs were identified across diverse environments using the composite interval mapping method. A total of 37 QTLs for fiber quality traits were identified on chromosome 25, of which 17 were stably expressed in at least in two environments. A stable fiber strength QTL, qFS-chr25-4, which was detected in seven environments and was located in the marker interval between CRI-SNP120491 and BNL2572, could explain 6.53%-11.83% of the observed phenotypic variations. Meta-analysis also confirmed the above QTLs with previous reports. Application of these QTLs could contribute to improving fiber quality and provide information for marker-assisted selection.

  3. High Resolution Consensus Mapping of Quantitative Trait Loci for Fiber Strength, Length and Micronaire on Chromosome 25 of the Upland Cotton (Gossypium hirsutum L.).

    Science.gov (United States)

    Zhang, Zhen; Li, Junwen; Muhammad, Jamshed; Cai, Juan; Jia, Fei; Shi, Yuzhen; Gong, Juwu; Shang, Haihong; Liu, Aiying; Chen, Tingting; Ge, Qun; Palanga, Koffi Kibalou; Lu, Quanwei; Deng, Xiaoying; Tan, Yunna; Li, Wei; Sun, Linyang; Gong, Wankui; Yuan, Youlu

    2015-01-01

    Cotton (Gossypium hirsutum L.) is an important agricultural crop that provides renewable natural fiber resources for the global textile industry. Technological developments in the textile industry and improvements in human living standards have increased the requirement for supplies and better quality cotton. Upland cotton 0-153 is an elite cultivar harboring strong fiber strength genes. To conduct quantitative trait locus (QTL) mapping for fiber quality in 0-153, we developed a population of 196 recombinant inbred lines (RILs) from a cross between 0-153 and sGK9708. The fiber quality traits in 11 environments were measured and a genetic linkage map of chromosome 25 comprising 210 loci was constructed using this RIL population, mainly using simple sequence repeat markers and single nucleotide polymorphism markers. QTLs were identified across diverse environments using the composite interval mapping method. A total of 37 QTLs for fiber quality traits were identified on chromosome 25, of which 17 were stably expressed in at least in two environments. A stable fiber strength QTL, qFS-chr25-4, which was detected in seven environments and was located in the marker interval between CRI-SNP120491 and BNL2572, could explain 6.53%-11.83% of the observed phenotypic variations. Meta-analysis also confirmed the above QTLs with previous reports. Application of these QTLs could contribute to improving fiber quality and provide information for marker-assisted selection.

  4. Mapping of Leaf Rust Resistance Genes and Molecular Characterization of the 2NS/2AS Translocation in the Wheat Cultivar Jagger.

    Science.gov (United States)

    Xue, Shulin; Kolmer, James A; Wang, Shuwen; Yan, Liuling

    2018-04-19

    Winter wheat cultivar 'Jagger' was recently found to have an alien chromosomal segment 2NS that has Lr37 , a gene conferring resistance against leaf rust caused by Puccinia triticina The objective of this study was to map and characterize the gene(s) for seedling leaf rust resistance in Jagger. The recombinant inbred line (RIL) population of Jagger × '2174' was inoculated with leaf rust pathogen THBJG and BBBDB, and evaluated for infection type (IT) response. A major quantitative trait locus (QTL) for THBJG and BBBDB was coincidently mapped to chromosome arm 2AS, and the QTL accounted for 56.6% - 66.2% of total phenotypic variation in infection type (IT) response to THBJG, and 72.1% - 86.9% to BBBDB. The causal gene for resistance to these rust races was mapped to the 2NS segment in Jagger. The 2NS segment was located in a region of approximately 27.8 Mb starting from the telomere of chromosome arm 2AS, based on the sequences of the A genome in tetraploid wheat. The Lr17a gene on chromosome arm 2AS was delimited to 3.1 Mb in the genomic region, which was orthologous to the 2NS segment. Therefore, the Lr37 gene in the 2NS segment can be pyramided with other effective resistance genes, rather than Lr17a in wheat, to improve resistance to rust diseases. Copyright © 2018, G3: Genes, Genomes, Genetics.

  5. A high-density genetic map for anchoring genome sequences and identifying QTLs associated with dwarf vine in pumpkin (Cucurbita maxima Duch.).

    Science.gov (United States)

    Zhang, Guoyu; Ren, Yi; Sun, Honghe; Guo, Shaogui; Zhang, Fan; Zhang, Jie; Zhang, Haiying; Jia, Zhangcai; Fei, Zhangjun; Xu, Yong; Li, Haizhen

    2015-12-24

    Pumpkin (Cucurbita maxima Duch.) is an economically important crop belonging to the Cucurbitaceae family. However, very few genomic and genetic resources are available for this species. As part of our ongoing efforts to sequence the pumpkin genome, high-density genetic map is essential for anchoring and orienting the assembled scaffolds. In addition, a saturated genetic map can facilitate quantitative trait locus (QTL) mapping. A set of 186 F2 plants derived from the cross of pumpkin inbred lines Rimu and SQ026 were genotyped using the genotyping-by-sequencing approach. Using the SNPs we identified, a high-density genetic map containing 458 bin-markers was constructed, spanning a total genetic distance of 2,566.8 cM across the 20 linkage groups of C. maxima with a mean marker density of 5.60 cM. Using this map we were able to anchor 58 assembled scaffolds that covered about 194.5 Mb (71.7%) of the 271.4 Mb assembled pumpkin genome, of which 44 (183.0 Mb; 67.4%) were oriented. Furthermore, the high-density genetic map was used to identify genomic regions highly associated with an important agronomic trait, dwarf vine. Three QTLs on linkage groups (LGs) 1, 3 and 4, respectively, were recovered. One QTL, qCmB2, which was located in an interval of 0.42 Mb on LG 3, explained 21.4% phenotypic variations. Within qCmB2, one gene, Cma_004516, encoding the gibberellin (GA) 20-oxidase in the GA biosynthesis pathway, had a 1249-bp deletion in its promoter in bush type lines, and its expression level was significantly increased during the vine growth and higher in vine type lines than bush type lines, supporting Cma_004516 as a possible candidate gene controlling vine growth in pumpkin. A high-density pumpkin genetic map was constructed, which was used to successfully anchor and orient the assembled genome scaffolds, and to identify QTLs highly associated with pumpkin vine length. The map provided a valuable resource for gene cloning and marker assisted breeding in pumpkin and

  6. Multi-environment analysis and improved mapping of a yield-related QTL on chromosome 3B of wheat.

    Science.gov (United States)

    Bonneau, Julien; Taylor, Julian; Parent, Boris; Bennett, Dion; Reynolds, Matthew; Feuillet, Catherine; Langridge, Peter; Mather, Diane

    2013-03-01

    Improved mapping, multi-environment quantitative trait loci (QTL) analysis and dissection of allelic effects were used to define a QTL associated with grain yield, thousand grain weight and early vigour on chromosome 3BL of bread wheat (Triticum aestivum L.) under abiotic stresses. The QTL had pleiotropic effects and showed QTL x environment interactions across 21 diverse environments in Australia and Mexico. The occurrence and the severity of water deficit combined with high temperatures during the growing season affected the responsiveness of this QTL, resulting in a reversal in the direction of allelic effects. The influence of this QTL can be substantial, with the allele from one parent (RAC875) increasing grain yield by up to 12.5 % (particularly in environments where both heat and drought stress occurred) and the allele from the other parent (Kukri) increasing grain yield by up to 9 % in favourable environments. With the application of additional markers and the genotyping of additional recombinant inbred lines, the genetic map in the QTL region was refined to provide a basis for future positional cloning.

  7. Study of improvement of indices maize line to establish their position in hybrids

    Directory of Open Access Journals (Sweden)

    Oxana DIRZU-COCOS

    2015-12-01

    Full Text Available Corn (Zea mays L. crop that is grown on large areas - over 140 million hectares worldwide, and 400-500 thousand ha in Moldova due to production potential broad diversity of use as food for humans, animals, birds raw material for industrial processing. The upward trend in average yields achieved is largely attributed to the improvement of scientific programs. Select the line with the characters and traits that are transmitted hereditary hybrids and contribute to their performance, ensure progress in improvement. Therefore, the process of creating inbred lines associated with combining ability testing as a measure of productivity conferred hybrids, is significant research programs. Orientation purpose of improved maize hybrids to formulas and simple change to a superior capitalization heterosis effect and perfect uniformity of plant requires changes in methodology for the creation, evaluation and classification of inbred lines.

  8. Reward-related behavioral paradigms for addiction research in the mouse: performance of common inbred strains.

    Directory of Open Access Journals (Sweden)

    Lauren Lederle

    2011-01-01

    Full Text Available The mouse has emerged as a uniquely valuable species for studying the molecular and genetic basis of complex behaviors and modeling neuropsychiatric disease states. While valid and reliable preclinical assays for reward-related behaviors are critical to understanding addiction-related processes, and various behavioral procedures have been developed and characterized in rats and primates, there have been relatively few studies using operant-based addiction-relevant behavioral paradigms in the mouse. Here we describe the performance of the C57BL/6J inbred mouse strain on three major reward-related paradigms, and replicate the same procedures in two other commonly used inbred strains (DBA/2J, BALB/cJ. We examined Pavlovian-instrumental transfer (PIT by measuring the ability of an auditory cue associated with food reward to promote an instrumental (lever press response. In a separate experiment, we assessed the acquisition and extinction of a simple stimulus-reward instrumental behavior on a touch screen based task. Reinstatement of this behavior was then examined following either continuous exposure to cues (conditioned reinforcers, CRs associated with reward, brief reward and CR exposure, or brief reward exposure followed by continuous CR exposure. The third paradigm examined sensitivity of an instrumental (lever press response to devaluation of food reward (a probe for outcome insensitive, habitual behavior by repeated pairing with malaise. Results showed that C57BL/6J mice displayed robust PIT, as well as clear extinction and reinstatement, but were insensitive to reinforcer devaluation. DBA/2J mice showed good PIT and (rewarded reinstatement, but were slow to extinguish and did not show reinforcer devaluation or significant CR-reinstatement. BALB/cJ mice also displayed good PIT, extinction and reinstatement, and retained instrumental responding following devaluation, but, unlike the other strains, demonstrated reduced Pavlovian approach

  9. Temporal factors in the extinction of fear in inbred mouse strains differing in extinction efficacy.

    Science.gov (United States)

    MacPherson, Kathryn; Whittle, Nigel; Camp, Marguerite; Gunduz-Cinar, Ozge; Singewald, Nicolas; Holmes, Andrew

    2013-07-05

    Various neuropsychiatric conditions, including posttraumatic stress disorder (PTSD), are characterized by deficient fear extinction, but individuals differ greatly in risk for these. While there is growing evidence that fear extinction is influenced by certain procedural variables, it is unclear how these influences might vary across individuals and subpopulations. To model individual differences in fear extinction, prior studies identified a strain of inbred mouse, 129S1/SvImJ (S1), which exhibits a profound deficit in fear extinction, as compared to other inbred strains, such as C57BL/6J (B6). Here, we assessed the effects of procedural variables on the impaired extinction phenotype of the S1 strain and, by comparison, the extinction-intact B6 strain. The variables studied were 1) the interval between conditioning and extinction, 2) the interval between cues during extinction training, 3) single-cue exposure before extinction training, and 4) extinction of a second-order conditioned cue. Conducting extinction training soon after ('immediately') conditioning attenuated fear retrieval in S1 mice and impaired extinction in B6 mice. Spacing cue presentations with long inter-trial intervals during extinction training augmented fear in S1 and B6 mice. The effect of spacing was lost with one-trial fear conditioning in B6, but not S1 mice. A single exposure to a conditioned cue before extinction training did not alter extinction retrieval, either in B6 or S1 mice. Both the S1 and B6 strains exhibited robust second-order fear conditioning, in which a cue associated with footshock was sufficient to serve as a conditioned exciter to condition a fear association to a second cue. B6 mice extinguished the fear response to the second-order conditioned cue, but S1 mice failed to do so. These data provide further evidence that fear extinction is strongly influenced by multiple procedural variables and is so in a highly strain-dependent manner. This suggests that the efficacy of

  10. Inbred Rats as a Model to Study Persistent Renal Leptospirosis and Associated Cellular Immune Responsiveness

    Directory of Open Access Journals (Sweden)

    Jarlath E. Nally

    2018-03-01

    Full Text Available Pathogenic species of Leptospira cause leptospirosis, a bacterial zoonotic disease with a global distribution affecting over one million people annually. Rats are regarded as one of the most significant reservoir hosts of infection for human disease, and in the absence of clinical signs of infection, excrete large numbers of organisms in their urine. A unique biological equilibrium exists between pathogenic leptospires and reservoir hosts of infection, but surprisingly, little is known concerning the host's cellular immune response that facilitates persistent renal colonization. To address this deficiency, we established and applied an immunocompetent inbred rat model of persistent renal colonization; leptospires were detected in urine of experimentally infected rats by 3 weeks post-infection and remained positive until 8 weeks post-infection. However, there was little, if any, evidence of inflammation in colonized renal tubules. At 8 weeks post-infection, a robust antibody response was detected against lipopolysaccharide and protein outer membrane (OM components. Purified B and T cells derived from the spleen of infected and non-infected rats proliferated in response to stimulation with 0.5 μg of OM fractions of Leptospira, including CD4+ T cells, which comprised 40% of proliferating cells, compared to 25% in non-infected controls. However, analysis of gene expression did not determine which immunoregulatory pathways were activated. Lymphocytes purified from the lymph node draining the site of colonization, the renal lymph node, also showed an increase in percentage of proliferating B and T cells. However, in contrast to a phenotype of 40% CD4+ T cells in the spleen, the phenotype of proliferating T cells in the renal lymph node comprised 65% CD4+ T cells. These results confirm that the renal lymph node, the local lymphoid organ, is a dominant site containing Leptospira reactive CD4+ T cells and highlight the need to consider the local, vs

  11. Reward-related behavioral paradigms for addiction research in the mouse: performance of common inbred strains.

    Science.gov (United States)

    Lederle, Lauren; Weber, Susanna; Wright, Tara; Feyder, Michael; Brigman, Jonathan L; Crombag, Hans S; Saksida, Lisa M; Bussey, Timothy J; Holmes, Andrew

    2011-01-10

    The mouse has emerged as a uniquely valuable species for studying the molecular and genetic basis of complex behaviors and modeling neuropsychiatric disease states. While valid and reliable preclinical assays for reward-related behaviors are critical to understanding addiction-related processes, and various behavioral procedures have been developed and characterized in rats and primates, there have been relatively few studies using operant-based addiction-relevant behavioral paradigms in the mouse. Here we describe the performance of the C57BL/6J inbred mouse strain on three major reward-related paradigms, and replicate the same procedures in two other commonly used inbred strains (DBA/2J, BALB/cJ). We examined Pavlovian-instrumental transfer (PIT) by measuring the ability of an auditory cue associated with food reward to promote an instrumental (lever press) response. In a separate experiment, we assessed the acquisition and extinction of a simple stimulus-reward instrumental behavior on a touch screen based task. Reinstatement of this behavior was then examined following either continuous exposure to cues (conditioned reinforcers, CRs) associated with reward, brief reward and CR exposure, or brief reward exposure followed by continuous CR exposure. The third paradigm examined sensitivity of an instrumental (lever press) response to devaluation of food reward (a probe for outcome insensitive, habitual behavior) by repeated pairing with malaise. Results showed that C57BL/6J mice displayed robust PIT, as well as clear extinction and reinstatement, but were insensitive to reinforcer devaluation. DBA/2J mice showed good PIT and (rewarded) reinstatement, but were slow to extinguish and did not show reinforcer devaluation or significant CR-reinstatement. BALB/cJ mice also displayed good PIT, extinction and reinstatement, and retained instrumental responding following devaluation, but, unlike the other strains, demonstrated reduced Pavlovian approach behavior (food

  12. Gene-based single nucleotide polymorphism markers for genetic and association mapping in common bean.

    Science.gov (United States)

    Galeano, Carlos H; Cortés, Andrés J; Fernández, Andrea C; Soler, Álvaro; Franco-Herrera, Natalia; Makunde, Godwill; Vanderleyden, Jos; Blair, Matthew W

    2012-06-26

    In common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies. In this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364 × G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93 × JALO EEP558 and DOR364 × BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041 cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings. In short, this study illustrates the power of intron-based markers for linkage and association mapping in

  13. Analysis of some coplanar transmission lines: coplanar coupled lines, coplanar coupled striplines, and coplanar coupled lines with rectangular microshield

    Science.gov (United States)

    Yuan, Naichang; He, Jianguo; Yao, Demiao; Dai, Qin; Lin, Weigan

    1995-06-01

    Two types of coplanar transmission lines, rectangular microshield coplanar coupled lines (RMCCL) and coplanar coupled rectangular microshield lines (CCRML), are proposed for MMIC applications. These are developed from coplanar coupled lines (CCL) and coplanar coupled strip lines (CCS). Analytic formulas are presented for calculating the quasistatic TEM parameters of these coupled lines by means of exact conformal mapping techniques. Numerical results are also presented to illustrate the properties of these coplanar transmission lines.

  14. Map of Nasca Geoglyphs

    Science.gov (United States)

    Hanzalová, K.; Pavelka, K.

    2013-07-01

    The Czech Technical University in Prague in the cooperation with the University of Applied Sciences in Dresden (Germany) work on the Nasca Project. The cooperation started in 2004 and much work has been done since then. All work is connected with Nasca lines in southern Peru. The Nasca project started in 1995 and its main target is documentation and conservation of the Nasca lines. Most of the project results are presented as WebGIS application via Internet. In the face of the impending destruction of the soil drawings, it is possible to preserve this world cultural heritage for the posterity at least in a digital form. Creating of Nasca lines map is very useful. The map is in a digital form and it is also available as a paper map. The map contains planimetric component of the map, map lettering and altimetry. Thematic folder in this map is a vector layer of the geoglyphs in Nasca/Peru. Basis for planimetry are georeferenced satellite images, altimetry is created from digital elevation model. This map was created in ArcGis software.

  15. MAP OF NASCA GEOGLYPHS

    Directory of Open Access Journals (Sweden)

    K. Hanzalová

    2013-07-01

    Full Text Available The Czech Technical University in Prague in the cooperation with the University of Applied Sciences in Dresden (Germany work on the Nasca Project. The cooperation started in 2004 and much work has been done since then. All work is connected with Nasca lines in southern Peru. The Nasca project started in 1995 and its main target is documentation and conservation of the Nasca lines. Most of the project results are presented as WebGIS application via Internet. In the face of the impending destruction of the soil drawings, it is possible to preserve this world cultural heritage for the posterity at least in a digital form. Creating of Nasca lines map is very useful. The map is in a digital form and it is also available as a paper map. The map contains planimetric component of the map, map lettering and altimetry. Thematic folder in this map is a vector layer of the geoglyphs in Nasca/Peru. Basis for planimetry are georeferenced satellite images, altimetry is created from digital elevation model. This map was created in ArcGis software.

  16. Drawing subway maps : a survey

    NARCIS (Netherlands)

    Wolff, A.

    2007-01-01

    This paper deals with automating the drawing of subway maps. There are two features of schematic subway maps that make them different from drawings of other networks such as flow charts or organigrams. First, most schematic subway maps use not only horizontal and vertical lines, but also diagonals.

  17. Genetic mapping and legume synteny of aphid resistance in African cowpea (Vigna unguiculata L. Walp.) grown in California.

    Science.gov (United States)

    Huynh, Bao-Lam; Ehlers, Jeffrey D; Ndeve, Arsenio; Wanamaker, Steve; Lucas, Mitchell R; Close, Timothy J; Roberts, Philip A

    The cowpea aphid Aphis craccivora Koch (CPA) is a destructive insect pest of cowpea, a staple legume crop in Sub-Saharan Africa and other semiarid warm tropics and subtropics. In California, CPA causes damage on all local cultivars from early vegetative to pod development growth stages. Sources of CPA resistance are available in African cowpea germplasm. However, their utilization in breeding is limited by the lack of information on inheritance, genomic location and marker linkage associations of the resistance determinants. In the research reported here, a recombinant inbred line (RIL) population derived from a cross between a susceptible California blackeye cultivar (CB27) and a resistant African breeding line (IT97K-556-6) was genotyped with 1,536 SNP markers. The RILs and parents were phenotyped for CPA resistance using field-based screenings during two main crop seasons in a 'hotspot' location for this pest within the primary growing region of the Central Valley of California. One minor and one major quantitative trait locus (QTL) were consistently mapped on linkage groups 1 and 7, respectively, both with favorable alleles contributed from IT97K-556-6. The major QTL appeared dominant based on a validation test in a related F2 population. SNP markers flanking each QTL were positioned in physical contigs carrying genes involved in plant defense based on synteny with related legumes. These markers could be used to introgress resistance alleles from IT97K-556-6 into susceptible local blackeye varieties by backcrossing.

  18. Molecular mapping and genetic analysis of a rice brown planthopper (Nilaparvata lugens Stål) resistance gene.

    Science.gov (United States)

    Yang, Haiyuan; Ren, Xiang; Weng, Qingmei; Zhu, Lili; He, Guangcun

    2002-01-01

    The brown planthopper (BPH), Nilaparvata lugens Stål, is a serious insect pest of rice (Oryza saliva L.). We have determined the chromosomal location of a BPH resistance gene in rice using SSR and RFLP techniques. A rice line 'B14', derived from the wild rice Oryza latifolia, showed high resistance to BPH. For tagging the resistance gene in 'B14X', an F2 population and a recombinant inbred (RI) population from a cross between Taichung Native 1 and 'B14' were developed and evaluated for BPH resistance. The results showed that a single dominant gene controlled the resistance of 'B14' to BPH. Bulked segregant SSR analysis was employed for identification of DNA markers linked to the resistance gene. From the survey of 302 SSR primer pairs, three SSR (RM335, RM261, RM185) markers linked to the resistance gene were identified. The closest SSR marker RM261 was linked to the resistance gene at a distance of 1.8 cM. Regions surrounding the resistance gene and the SSR markers were examined with additional RFLP markers on chromosome 4 to define the location of the resistance gene. Linkage of RFLP markers C820, R288, C946 with the resistance gene further confirmed its location on the short arm of chromosome 4. Closely linked DNA markers will facilitate selection for resistant lines in breeding programs and provide the basis for map-based cloning of this resistance gene.

  19. A spatially encoded dose difference maximal intensity projection map for patient dose evaluation: A new first line patient quality assurance tool

    Energy Technology Data Exchange (ETDEWEB)

    Hu Weigang; Graff, Pierre; Boettger, Thomas; Pouliot, Jean [Department of Radiation Oncology, University of California, San Francisco, San Francisco, California 94143 (United States); and others

    2011-04-15

    Purpose: To develop a spatially encoded dose difference maximal intensity projection (DD-MIP) as an online patient dose evaluation tool for visualizing the dose differences between the planning dose and dose on the treatment day. Methods: Megavoltage cone-beam CT (MVCBCT) images acquired on the treatment day are used for generating the dose difference index. Each index is represented by different colors for underdose, acceptable, and overdose regions. A maximal intensity projection (MIP) algorithm is developed to compress all the information of an arbitrary 3D dose difference index into a 2D DD-MIP image. In such an algorithm, a distance transformation is generated based on the planning CT. Then, two new volumes representing the overdose and underdose regions of the dose difference index are encoded with the distance transformation map. The distance-encoded indices of each volume are normalized using the skin distance obtained on the planning CT. After that, two MIPs are generated based on the underdose and overdose volumes with green-to-blue and green-to-red lookup tables, respectively. Finally, the two MIPs are merged with an appropriate transparency level and rendered in planning CT images. Results: The spatially encoded DD-MIP was implemented in a dose-guided radiotherapy prototype and tested on 33 MVCBCT images from six patients. The user can easily establish the threshold for the overdose and underdose. A 3% difference between the treatment and planning dose was used as the threshold in the study; hence, the DD-MIP shows red or blue color for the dose difference >3% or {<=}3%, respectively. With such a method, the overdose and underdose regions can be visualized and distinguished without being overshadowed by superficial dose differences. Conclusions: A DD-MIP algorithm was developed that compresses information from 3D into a single or two orthogonal projections while hinting the user whether the dose difference is on the skin surface or deeper.

  20. A spatially encoded dose difference maximal intensity projection map for patient dose evaluation: a new first line patient quality assurance tool.

    Science.gov (United States)

    Hu, Weigang; Graff, Pierre; Boettger, Thomas; Pouliot, Jean

    2011-04-01

    To develop a spatially encoded dose difference maximal intensity projection (DD-MIP) as an online patient dose evaluation tool for visualizing the dose differences between the planning dose and dose on the treatment day. Megavoltage cone-beam CT (MVCBCT) images acquired on the treatment day are used for generating the dose difference index. Each index is represented by different colors for underdose, acceptable, and overdose regions. A maximal intensity projection (MIP) algorithm is developed to compress all the information of an arbitrary 3D dose difference index into a 2D DD-MIP image. In such an algorithm, a distance transformation is generated based on the planning CT. Then, two new volumes representing the overdose and underdose regions of the dose difference index are encoded with the distance transformation map. The distance-encoded indices of each volume are normalized using the skin distance obtained on the planning CT. After that, two MIPs are generated based on the underdose and overdose volumes with green-to-blue and green-to-red lookup tables, respectively. Finally, the two MIPs are merged with an appropriate transparency level and rendered in planning CT images. The spatially encoded DD-MIP was implemented in a dose-guided radiotherapy prototype and tested on 33 MVCBCT images from six patients. The user can easily establish the threshold for the overdose and underdose. A 3% difference between the treatment and planning dose was used as the threshold in the study; hence, the DD-MIP shows red or blue color for the dose difference > 3% or < or = 3%, respectively. With such a method, the overdose and underdose regions can be visualized and distinguished without being overshadowed by superficial dose differences. A DD-MIP algorithm was developed that compresses information from 3D into a single or two orthogonal projections while hinting the user whether the dose difference is on the skin surface or deeper.

  1. Genetic mapping of QTLs controlling fatty acids provided insights into the genetic control of fatty acid synthesis pathway in peanut (Arachis hypogaea L..

    Directory of Open Access Journals (Sweden)

    Ming Li Wang

    Full Text Available Peanut, a high-oil crop with about 50% oil content, is either crushed for oil or used as edible products. Fatty acid composition determines the oil quality which has high relevance to consumer health, flavor, and shelf life of commercial products. In addition to the major fatty acids, oleic acid (C18:1 and linoleic acid (C18:2 accounting for about 80% of peanut oil, the six other fatty acids namely palmitic acid (C16:0, stearic acid (C18:0, arachidic acid (C20:0, gadoleic acid (C20:1, behenic acid (C22:0, and lignoceric acid (C24:0 are accounted for the rest 20%. To determine the genetic basis and to improve further understanding on effect of FAD2 genes on these fatty acids, two recombinant inbred line (RIL populations namely S-population (high oleic line 'SunOleic 97R' × low oleic line 'NC94022' and T-population (normal oleic line 'Tifrunner' × low oleic line 'GT-C20' were developed. Genetic maps with 206 and 378 marker loci for the S- and the T-population, respectively were used for quantitative trait locus (QTL analysis. As a result, a total of 164 main-effect (M-QTLs and 27 epistatic (E-QTLs QTLs associated with the minor fatty acids were identified with 0.16% to 40.56% phenotypic variation explained (PVE. Thirty four major QTLs (>10% of PVE mapped on five linkage groups and 28 clusters containing more than three QTLs were also identified. These results suggest that the major QTLs with large additive effects would play an important role in controlling composition of these minor fatty acids in addition to the oleic and linoleic acids in peanut oil. The interrelationship among these fatty acids should be considered while breeding for improved peanut genotypes with good oil quality and desired fatty acid composition.

  2. Mapping quantitative trait loci affecting fatness and breast muscle weight in meat-type chicken lines divergently selected on abdominal fatness

    Directory of Open Access Journals (Sweden)

    Neau André

    2006-01-01

    Full Text Available Abstract Quantitative trait loci (QTL for abdominal fatness and breast muscle weight were investigated in a three-generation design performed by inter-crossing two experimental meat-type chicken lines that were divergently selected on abdominal fatness. A total of 585 F2 male offspring from 5 F1 sires and 38 F1 dams were recorded at 8 weeks of age for live body, abdominal fat and breast muscle weights. One hundred-twenty nine microsatellite markers, evenly located throughout the genome and heterozygous for most of the F1 sires, were used for genotyping the F2 birds. In each sire family, those offspring exhibiting the most extreme values for each trait were genotyped. Multipoint QTL analyses using maximum likelihood methods were performed for abdominal fat and breast muscle weights, which were corrected for the effects of 8-week body weight, dam and hatching group. Isolated markers were assessed by analyses of variance. Two significant QTL were identified on chromosomes 1 and 5 with effects of about one within-family residual standard deviation. One breast muscle QTL was identified on GGA1 with an effect of 2.0 within-family residual standard deviation.

  3. Hypervitaminosis D and Metastatic Calcification in a Colony of Inbred Strain 13 Guinea Pigs, Cavia porcellus.

    Science.gov (United States)

    Holcombe, H; Parry, N M; Rick, M; Brown, D E; Albers, T M; Refsal, K R; Morris, J; Kelly, R; Marko, S T

    2015-07-01

    A commercial diet fed to a colony of inbred strain 13 guinea pigs for approximately 6 weeks was subsequently recalled for excessive levels of vitamin D. Twenty-one of 62 animals exhibited clinical signs, including anorexia, lethargy, and poor body condition. Nine affected and 4 clinically normal animals were euthanized for further evaluation, including serum chemistry, urinalysis, and gross and/or histopathology. Macroscopic findings included white discoloration in multiple organs in 8 animals, and microscopic evaluation confirmed multiorgan mineralization in tissues from 7 animals. Serum 25-hydroxyvitamin D levels were elevated in 10 animals. Serum inorganic phosphorus and alkaline phosphatase levels were increased in all exposed animals; however, total calcium and ionized calcium levels were not significantly higher in exposed animals than in control strain 13 guinea pigs from a different institution. The data support a diagnosis of hypervitaminosis D with metastatic calcification. Following the diet recall, the remaining guinea pigs increased their food intake and regained body condition. Diagnostic testing of 8 animals euthanized approximately 3 months after returning to a normal diet demonstrated that serum parathyroid hormone remained significantly lower, and ionized calcium and ionized magnesium were significantly higher, in recovered animals compared to controls and exposed animals. These results indicate that diagnostic tests other than serum calcium are necessary for a diagnosis of hypervitaminosis D in guinea pigs. © The Author(s) 2014.

  4. Bone Morphology in 46 BXD Recombinant Inbred Strains and Femur-Tibia Correlation

    Directory of Open Access Journals (Sweden)

    Yueying Zhang

    2015-01-01

    Full Text Available We examined the bone properties of BXD recombinant inbred (RI mice by analyzing femur and tibia and compared their phenotypes of different compartments. 46 BXD RI mouse strains were analyzed including progenitor C57BL/6J (n=16 and DBA/2J (n=15 and two first filial generations (D2B6F1 and B6D2F1. Strain differences were observed in bone quality and structural properties (P<0.05 in each bone profile (whole bone, cortical bone, or trabecular bone. It is well known that skeletal phenotypes are largely affected by genetic determinants and genders, such as bone mineral density (BMD. While genetics and gender appear expectedly as the major determinants of bone mass and structure, significant correlations were also observed between femur and tibia. More importantly, positive and negative femur-tibia associations indicated that genetic makeup had an influence on skeletal integrity. We conclude that (a femur-tibia association in bone morphological properties significantly varies from strain to strain, which may be caused by genetic differences among strains, and (b strainwise variations were seen in bone mass, bone morphology, and bone microarchitecture along with bone structural property.

  5. Genetic analysis of resistance to radiation lymphomagenesis with recombinant inbred strains of mice

    International Nuclear Information System (INIS)

    Okumoto, M.; Nishikawa, R.; Imai, S.; Hilgers, J.

    1990-01-01

    Induction of lymphomas by radiation in mice is controlled by genetic factors. We analyzed the genetic control of radiation lymphomagenesis using the CXS series of recombinant inbred strains derived from two progenitor strains: one highly susceptible to radiation induction of lymphoma [BALB/cHeA (C)] and one extremely resistant [STS/A (S)]. The best concordances between strain distribution patterns of genetic markers and resistance (or susceptibility) to radiation lymphomagenesis were observed in a region with the b and Ifa genes on chromosome 4. This indicates that one major locus controls the incidence of radiogenic lymphomas in mice. We designated this locus as the Lyr (lymphoma resistance) locus. Backcrosses of (CXS)F1 to the two progenitor strains showed an intermediate incidence of lymphomas between their parental mice and did not significantly differ from (CXS)F1 mice. This and previous observations that (CXS)F1 mice also showed an intermediate incidence, differing from both progenitor strains, indicate that more genes are involved in the resistance (or susceptibility) to lymphoma induced by irradiation

  6. Novel approach to the behavioural characterization of inbred mice: automated home cage observations.

    Science.gov (United States)

    de Visser, L; van den Bos, R; Kuurman, W W; Kas, M J H; Spruijt, B M

    2006-08-01

    Here we present a newly developed tool for continuous recordings and analysis of novelty-induced and baseline behaviour of mice in a home cage-like environment. Aim of this study was to demonstrate the strength of this method by characterizing four inbred strains of mice, C57BL/6, DBA/2, C3H and 129S2/Sv, on locomotor activity. Strains differed in circadian rhythmicity, novelty-induced activity and the time-course of specific behavioural elements. For instance, C57BL/6 and DBA/2 mice showed a much faster decrease in activity over time than C3H and 129S2/Sv mice. Principal component analysis revealed two major factors within locomotor activity, which were defined as 'level of activity' and 'velocity/stops'. These factors were able to distinguish strains. Interestingly, mice that displayed high levels of activity in the initial phase of the home cage test were also highly active during an open-field test. Velocity and the number of stops during movement correlated positively with anxiety-related behaviour in the elevated plus maze. The use of an automated home cage observation system yields temporal changes in elements of locomotor activity with an advanced level of spatial resolution. Moreover, it avoids the confounding influence of human intervention and saves time-consuming human observations.

  7. Digital Line Graphs (DLG) 24K

    Data.gov (United States)

    Kansas Data Access and Support Center — Digital line graph (DLG) data are digital representations of cartographic information. DLG's of map features are converted to digital form from maps and related...

  8. Digital Line Graphs (DLG) 100K

    Data.gov (United States)

    Kansas Data Access and Support Center — Digital line graph (DLG) data are digital representations of cartographic information. DLG's of map features are converted to digital form from maps and related...

  9. High-resolution genetic mapping at the Bph15 locus for brown planthopper resistance in rice (Oryza sativa L.).

    Science.gov (United States)

    Yang, Haiyuan; You, Aiqing; Yang, Zhifan; Zhang, Futie; He, Ruifeng; Zhu, Lili; He, Guangcun

    2004-12-01

    Resistance to the brown planthopper (BPH), Nilaparvata lugens Stal, a devastating sucking insect pest of rice, is an important breeding objective in rice improvement programs. Bph15, one of the 17 major BPH resistance genes so far identified in both cultivated and wild rice, has been identified in an introgression line, B5, and mapped on chromosome 4 flanked by restriction fragment length polymorphism markers C820 and S11182. In order to pave the way for positional cloning of this gene, we have developed a high-resolution genetic map of Bph15 by positioning 21 DNA markers in the target chromosomal region. Mapping was based on a PCR-based screening of 9,472 F(2) individuals derived from a cross between RI93, a selected recombinant inbred line of B5 bearing the resistance gene Bph15, and a susceptible variety, Taichung Native 1, in order to identify recombinant plants within the Bph15 region. Recombinant F(2) individuals with the Bph15 genotype were determined by phenotype evaluation. Analysis of recombination events in the Bph15 region delimited the gene locus to an interval between markers RG1 and RG2 that co-segregated with the M1 marker. A genomic library of B5 was screened using these markers, and bacterial artificial chromosome clones spanning the Bph15 chromosome region were obtained. An assay of the recombinants using the sub-clones of these clones in combination with sequence analysis delimited the Bph15 gene to a genomic segment of approximately 47 kb. This result should serve as the basis for eventual isolation of the Bph15 resistance gene.

  10. QTL Analysis and Nested Association Mapping for Adult Plant Resistance to Powdery Mildew in Two Bread Wheat Populations

    Directory of Open Access Journals (Sweden)

    Yan Ren

    2017-07-01

    Full Text Available CIMMYT wheat (Triticum aestivum L. lines Francolin#1 and Quaiu#3 displayed effective and stable adult plant resistance (APR to Chinese Blumeria graminis f. sp. tritici isolates in the field. To elucidate their genetic basis of resistance, two recombinant inbred line (RIL populations of their crosses with Avocet, the susceptible parent, were phenotyped in Zhengzhou and Shangqiu in the 2014–2015 and 2015–2016 cropping seasons. These populations were also genotyped with SSR (simple sequence repeat markers and DArT (diversity arrays technology markers. Two common significant quantitative trait loci (QTL on wheat chromosomes 1BL and 4BL were detected in both populations by joint and individual inclusive composite interval mapping, explaining 20.3–28.7% and 9.6–15.9% of the phenotypic variance in Avocet × Francolin#1 and 4.8–11.5% and 10.8–18.9% in Avocet × Quaiu#3, respectively. Additional QTL were mapped on chromosomes 1DL and 5BL in Avocet × Francolin#1 and on 2DL and 6BS in Avocet × Quaiu#3. Among these, QPm.heau-1DL is probably a novel APR gene contributing 6.1–8.5% of total phenotypic variance. The QTL on 1BL corresponds to the pleiotropic multi-pathogen resistance gene Yr29/Lr46/Pm39, whereas the QTL on 2DL maps to a similar region where stripe rust resistance gene Yr54 is located. The QTL identified can potentially be used for the improvement of powdery mildew and rust resistance in wheat breeding.

  11. Genome-Wide Association Mapping of Seed Coat Color in Brassica napus.

    Science.gov (United States)

    Wang, Jia; Xian, Xiaohua; Xu, Xinfu; Qu, Cunmin; Lu, Kun; Li, Jiana; Liu, Liezhao

    2017-07-05

    Seed coat color is an extremely important breeding characteristic of Brassica napus. To elucidate the factors affecting the genetic architecture of seed coat color, a genome-wide association study (GWAS) of seed coat color was conducted with a diversity panel comprising 520 B. napus cultivars and inbred lines. In total, 22 single-nucleotide polymorphisms (SNPs) distributed on 7 chromosomes were found to be associated with seed coat color. The most significant SNPs were found in 2014 near Bn-scaff_15763_1-p233999, only 43.42 kb away from BnaC06g17050D, which is orthologous to Arabidopsis thaliana TRANSPARENT TESTA 12 (TT12), an important gene involved in the transportation of proanthocyanidin precursors into the vacuole. Two of eight repeatedly detected SNPs can be identified and digested by restriction enzymes. Candidate gene mining revealed that the relevant regions of significant SNP loci on the A09 and C08 chromosomes are highly homologous. Moreover, a comparison of the GWAS results to those of previous quantitative trait locus (QTL) studies showed that 11 SNPs were located in the confidence intervals of the QTLs identified in previous studies based on linkage analyses or association mapping. Our results provide insights into the genetic basis of seed coat color in B. napus, and the beneficial allele, SNP information, and candidate genes should be useful for selecting yellow seeds in B. napus breeding.

  12. Genetic mapping of a major dominant gene for resistance to Ralstonia solanacearum in eggplant.

    Science.gov (United States)

    Lebeau, A; Gouy, M; Daunay, M C; Wicker, E; Chiroleu, F; Prior, P; Frary, A; Dintinger, J

    2013-01-01

    Resistance of eggplant against Ralstonia solanacearum phylotype I strains was assessed in a F(6) population of recombinant inbred lines (RILs) derived from a intra-specific cross between S. melongena MM738 (susceptible) and AG91-25 (resistant). Resistance traits were determined as disease score, percentage of wilted plants, and stem-based bacterial colonization index, as assessed in greenhouse experiments conducted in Réunion Island, France. The AG91-25 resistance was highly efficient toward strains CMR134, PSS366 and GMI1000, but only partial toward the highly virulent strain PSS4. The partial resistance found against PSS4 was overcome under high inoculation pressure, with heritability estimates from 0.28 to 0.53, depending on the traits and season. A genetic map was built with 119 AFLP, SSR and SRAP markers positioned on 18 linkage groups (LG), for a total length of 884 cM, and used for quantitative trait loci (QTL) analysis. A major dominant gene, named ERs1, controlled the resistance to strains CMR134, PSS366, and GMI1000. Against strain PSS4, this gene was not detected, but a significant QTL involved in delay of disease progress was detected on another LG. The possible use of the major resistance gene ERs1 in marker-assisted selection and the prospects offered for academic studies of a possible gene for gene system controlling resistance to bacterial wilt in solanaceous plants are discussed.

  13. Identification and mapping of two powdery mildew resistance genes in Triticum boeoticum L.

    Science.gov (United States)

    Chhuneja, Parveen; Kumar, Krishan; Stirnweis, Daniel; Hurni, Severine; Keller, Beat; Dhaliwal, Harcharan S; Singh, Kuldeep

    2012-04-01

    Powdery mildew (PM) caused by Blumeria graminis f. sp. tritici (Bgt), is one of the important foliar diseases of wheat that can cause serious yield losses. Breeding for cultivars with diverse resources of resistance is the most promising approach for combating this disease. The diploid A genome progenitor species of wheat are an important resource for new variability for disease resistance genes. An accession of Triticum boeoticum (A(b)A(b)) showed resistance against a number of Bgt isolates, when tested using detached leaf segments. Inheritance studies in a recombinant inbred line population (RIL), developed from crosses of PM resistant T. boeoticum acc. pau5088 with a PM susceptible T. monococcum acc. pau14087, indicated the presence of two powdery mildew resistance genes in T. boeoticum acc. pau5088. Analysis of powdery mildew infection and molecular marker data of the RIL population revealed that both powdery mildew resistance genes are located on the long arm of chromosome 7A. Mapping was conducted using an integrated linkage map of 7A consisting of SSR, RFLP, STS, and DArT markers. These powdery mildew resistance genes are tentatively designated as PmTb7A.1 and PmTb7A.2. The PmTb7A.2 is closely linked to STS markers MAG2185 and MAG1759 derived from RFLP probes which are linked to powdery mildew resistance gene Pm1. This indicated that PmTb7A.2 might be allelic to Pm1. The PmTb7A.1, flanked by a DArT marker wPt4553 and an SSR marker Xcfa2019 in a 4.3 cM interval, maps proximal to PmT7A.2. PmTb7A.1 is putatively a new powdery mildew resistance gene. The powdery mildew resistance genes from T. boeoticum are currently being transferred to cultivated wheat background through marker-assisted backcrossing, using T. durum as bridging species.

  14. Mapping resistance to the Ug99 race group of the stem rust pathogen in a spring wheat landrace.

    Science.gov (United States)

    Babiker, E M; Gordon, T C; Chao, S; Newcomb, M; Rouse, M N; Jin, Y; Wanyera, R; Acevedo, M; Brown-Guedira, G; Williamson, S; Bonman, J M

    2015-04-01

    A new gene for Ug99 resistance from wheat landrace PI 374670 was detected on the long arm of chromosome 7A. Wheat landrace PI 374670 has seedling and field resistance to stem rust caused by Puccinia graminis f. sp tritici Eriks. & E. Henn (Pgt) race TTKSK. To elucidate the inheritance of resistance, 216 BC1F2 families, 192 double haploid (DH) lines, and 185 recombinant inbred lines (RILs) were developed by crossing PI 374670 and the susceptible line LMPG-6. The parents and progeny were evaluated for seedling resistance to Pgt races TTKSK, MCCFC, and TPMKC. The DH lines were tested in field stem rust nurseries in Kenya and Ethiopia. The DH lines were genotyped with the 90K wheat iSelect SNP genotyping platform. Goodness-of-fit tests indicated that a single dominant gene in PI 374670 conditioned seedling resistance to the three Pgt races. The seedling resistance locus mapped to the long arm of chromosome 7A and this result was verified in the RIL population screened with the flanking SNP markers using KASP assays. In the same region, a major QTL for field resistance was detected in a 7.7 cM interval and explained 34-54 and 29-36% of the variation in Kenya and Ethiopia, respectively. Results from tests with specific Pgt races and the csIH81 marker showed that the resistance was not due to Sr22. Thus, a new stem rust resistance gene or allele, either closely linked or allelic to Sr15, is responsible for the seedling and field resistance of PI 374670 to Ug99.

  15. Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line

    Science.gov (United States)

    Lizio, Marina; Ishizu, Yuri; Itoh, Masayoshi; Lassmann, Timo; Hasegawa, Akira; Kubosaki, Atsutaka; Severin, Jessica; Kawaji, Hideya; Nakamura, Yukio; Suzuki, Harukazu; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R. R.

    2015-01-01

    Mammals are composed of hundreds of different cell types with specialized functions. Each of these cellular phenotypes are controlled by different combinations of transcription factors. Using a human non islet cell insulinoma cell line (TC-YIK) which expresses insulin and the majority of known pancreatic beta cell specific genes as an example, we describe a general approach to identify key cell-type-specific transcription factors (TFs) and their direct and indirect targets. By ranking all human TFs by their level of enriched expression in TC-YIK relative to a broad collection of samples (FANTOM5), we confirmed known key regulators of pancreatic function and development. Systematic siRNA mediated perturbation of these TFs followed by qRT-PCR revealed their interconnections with NEUROD1 at the top of the regulation hierarchy and its depletion drastically reducing insulin levels. For 15 of the TF knock-downs (KD), we then used Cap Analysis of Gene Expression (CAGE) to identify thousands of their targets genome-wide (KD-CAGE). The data confirm NEUROD1 as a key positive regulator in the transcriptional regulatory network (TRN), and ISL1, and PROX1 as antagonists. As a complimentary approach we used ChIP-seq on four of these factors to identify NEUROD1, LMX1A, PAX6, and RFX6 binding sites in the human genome. Examining the overlap between genes perturbed in the KD-CAGE experiments and genes with a ChIP-seq peak within 50 kb of their promoter, we identified direct transcriptional targets of these TFs. Integration of KD-CAGE and ChIP-seq data shows that both NEUROD1 and LMX1A work as the main transcriptional activators. In the core TRN (i.e., TF-TF only), NEUROD1 directly transcriptionally activates the pancreatic TFs HSF4, INSM1, MLXIPL, MYT1, NKX6-3, ONECUT2, PAX4, PROX1, RFX6, ST18, DACH1, and SHOX2, while LMX1A directly transcriptionally activates DACH1, SHOX2, PAX6, and PDX1. Analysis of these complementary datasets suggests the need for caution in interpreting Ch

  16. Mapping and characterization of the new adult plant leaf rust resistance gene Lr77 derived from Santa Fe winter wheat.

    Science.gov (United States)

    Kolmer, James A; Su, Zhenqi; Bernardo, Amy; Bai, Guihua; Chao, Shiaoman

    2018-04-25

    A new gene for adult plant leaf rust resistance in wheat was mapped to chromosome 3BL. This gene was designated as Lr77. 'Santa Fe' is a hard red winter cultivar that has had long-lasting resistance to the leaf rust fungus, Puccinia triticina. The objective of this study was to determine the chromosome location of the adult plant leaf rust resistance in Santa Fe wheat. A partial backcross line of 'Thatcher' (Tc) wheat with adult plant leaf rust resistance derived from Santa Fe was crossed with Thatcher to develop a Thatcher//Tc*2/Santa Fe F 6 recombinant inbred line (RIL) population. The RIL population and parental lines were evaluated for segregation of leaf rust resistance in three field plot tests and in an adult plant greenhouse test. A genetic map of the RIL population was constructed using 90,000 single-nucleotide polymorphism (SNP) markers with the Illumina Infinium iSelect 90K wheat bead array. A significant quantitative trait locus for reduction of leaf rust severity in all four tests was found on chromosome 3BL that segregated as a single adult plant resistance gene. The RILs with the allele from the resistant parent for SNP marker IWB10344 had lower leaf rust severity and a moderately resistant to moderately susceptible response compared to the susceptible RILs and Thatcher. The gene derived from Santa Fe on chromosome 3BL was designated as Lr77. Kompetitive allele-specific polymerase chain reaction assay markers linked to Lr77 on 3BL should be useful for selection of wheat germplasm with this gene.

  17. Base Flood Elevation (BFE) Lines

    Data.gov (United States)

    Department of Homeland Security — The Base Flood Elevation (BFE) table is required for any digital data where BFE lines will be shown on the corresponding Flood Insurance Rate Map (FIRM). Normally if...

  18. Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.).

    Science.gov (United States)

    Ma, Yu; Coyne, Clarice J; Grusak, Michael A; Mazourek, Michael; Cheng, Peng; Main, Dorrie; McGee, Rebecca J

    2017-02-13

    Marker-assisted breeding is now routinely used in major crops to facilitate more efficient cultivar improvement. This has been significantly enabled by the use of next-generation sequencing technology to identify loci and markers associated with traits of interest. While rich in a range of nutritional components, such as protein, mineral nutrients, carbohydrates and several vitamins, pea (Pisum sativum L.), one of the oldest domesticated crops in the world, remains behind many other crops in the availability of genomic and genetic resources. To further improve mineral nutrient levels in pea seeds requires the development of genome-wide tools. The objectives of this research were to develop these tools by: identifying genome-wide single nucleotide polymorphisms (SNPs) using genotyping by sequencing (GBS); constructing a high-density linkage map and comparative maps with other legumes, and identifying quantitative trait loci (QTL) for levels of boron, calcium, iron, potassium, magnesium, manganese, molybdenum, phosphorous, sulfur, and zinc in the seed, as well as for seed weight. In this study, 1609 high quality SNPs were found to be polymorphic between 'Kiflica' and 'Aragorn', two parents of an F 6 -derived recombinant inbred line (RIL) population. Mapping 1683 markers including 75 previously published markers and 1608 SNPs developed from the present study generated a linkage map of size 1310.1 cM. Comparative mapping with other legumes demonstrated that the highest level of synteny was observed between pea and the genome of Medicago truncatula. QTL analysis of the RIL population across two locations revealed at least one QTL for each of the mineral nutrient traits. In total, 46 seed mineral concentration QTLs, 37 seed mineral content QTLs, and 6 seed weight QTLs were discovered. The QTLs explained from 2.4% to 43.3% of the phenotypic variance. The genome-wide SNPs and the genetic linkage map developed in this study permitted QTL identification for pea seed mineral

  19. Shortest-paths preserving metro maps

    NARCIS (Netherlands)

    Milea, T.Y.; Schrijvers, O.J.; Buchin, K.; Haverkort, H.J.; Kreveld, van M.J.; Speckmann, B.

    2012-01-01

    A metro map, or subway map, is a schematic representation of a metro system of a city. The main goal of a metro map is to provide a traveler with information on which lines to take to get from station A to station B, and at which stations he needs to switch lines. It is often not beneficial to use

  20. System of automated map design

    International Nuclear Information System (INIS)

    Ponomarjov, S.Yu.; Rybalko, S.I.; Proskura, N.I.

    1992-01-01

    Preprint 'System of automated map design' contains information about the program shell for construction of territory map, performing level line drawing of arbitrary two-dimension field (in particular, the radionuclide concentration field). The work schedule and data structures are supplied, as well as data on system performance. The preprint can become useful for experts in radioecology and for all persons involved in territory pollution mapping or multi-purpose geochemical mapping. (author)