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Sample records for characterize qtl regions

  1. Using transcriptome profiling to characterize QTL regions on chicken chromosome 5

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    Demeure Olivier

    2009-12-01

    Full Text Available Abstract Background Although many QTL for various traits have been mapped in livestock, location confidence intervals remain wide that makes difficult the identification of causative mutations. The aim of this study was to test the contribution of microarray data to QTL detection in livestock species. Three different but complementary approaches are proposed to improve characterization of a chicken QTL region for abdominal fatness (AF previously detected on chromosome 5 (GGA5. Results Hepatic transcriptome profiles for 45 offspring of a sire known to be heterozygous for the distal GGA5 AF QTL were obtained using a 20 K chicken oligochip. mRNA levels of 660 genes were correlated with the AF trait. The first approach was to dissect the AF phenotype by identifying animal subgroups according to their 660 transcript profiles. Linkage analysis using some of these subgroups revealed another QTL in the middle of GGA5 and increased the significance of the distal GGA5 AF QTL, thereby refining its localization. The second approach targeted the genes correlated with the AF trait and regulated by the GGA5 AF QTL region. Five of the 660 genes were considered as being controlled either by the AF QTL mutation itself or by a mutation close to it; one having a function related to lipid metabolism (HMGCS1. In addition, a QTL analysis with a multiple trait model combining this 5 gene-set and AF allowed us to refine the QTL region. The third approach was to use these 5 transcriptome profiles to predict the paternal Q versus q AF QTL mutation for each recombinant offspring and then refine the localization of the QTL from 31 cM (100 genes at a most probable location confidence interval of 7 cM (12 genes after determining the recombination breakpoints, an interval consistent with the reductions obtained by the two other approaches. Conclusion The results showed the feasibility and efficacy of the three strategies used, the first revealing a QTL undetected using the

  2. Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean

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    Weeks Nathan

    2010-03-01

    Full Text Available Abstract Background The nutritional and economic value of many crops is effectively a function of seed protein and oil content. Insight into the genetic and molecular control mechanisms involved in the deposition of these constituents in the developing seed is needed to guide crop improvement. A quantitative trait locus (QTL on Linkage Group I (LG I of soybean (Glycine max (L. Merrill has a striking effect on seed protein content. Results A soybean near-isogenic line (NIL pair contrasting in seed protein and differing in an introgressed genomic segment containing the LG I protein QTL was used as a resource to demarcate the QTL region and to study variation in transcript abundance in developing seed. The LG I QTL region was delineated to less than 8.4 Mbp of genomic sequence on chromosome 20. Using Affymetrix® Soy GeneChip and high-throughput Illumina® whole transcriptome sequencing platforms, 13 genes displaying significant seed transcript accumulation differences between NILs were identified that mapped to the 8.4 Mbp LG I protein QTL region. Conclusions This study identifies gene candidates at the LG I protein QTL for potential involvement in the regulation of protein content in the soybean seed. The results demonstrate the power of complementary approaches to characterize contrasting NILs and provide genome-wide transcriptome insight towards understanding seed biology and the soybean genome.

  3. GENE LINKAGE MAPPING OF THE PORCINE CHROMOSOME X REGION HARBOURING QTL FOR FAT DEPOSITION

    Science.gov (United States)

    The QTL for backfat thickness and intramuscular fat content on SSCX is well documented in Meishan x Western breed pedigrees. The QTL has been mapped to the chromosome region between microsatellites SW2456 and SW1943. In the French pedigree with more than 1,100 F2 animals the QTL mapped at position 7...

  4. Fine Mapping and Evolution of a QTL Region on Cattle Chromosome 3

    Science.gov (United States)

    Donthu, Ravikiran

    2009-01-01

    The goal of my dissertation was to fine map the milk yield and composition quantitative trait loci (QTL) mapped to cattle chromosome 3 (BTA3) by Heyen et al. (1999) and to identify candidate genes affecting these traits. To accomplish this, the region between "BL41" and "TGLA263" was mapped to the cattle genome sequence assembly Btau 3.1 and a…

  5. Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.)

    Science.gov (United States)

    Kale, Sandip M; Jaganathan, Deepa; Ruperao, Pradeep; Chen, Charles; Punna, Ramu; Kudapa, Himabindu; Thudi, Mahendar; Roorkiwal, Manish; Katta, Mohan AVSK; Doddamani, Dadakhalandar; Garg, Vanika; Kishor, P B Kavi; Gaur, Pooran M; Nguyen, Henry T; Batley, Jacqueline; Edwards, David; Sutton, Tim; Varshney, Rajeev K

    2015-01-01

    A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the “QTL-hotspot” region for drought tolerance present on the Ca4 pseudomolecule in chickpea. In the first approach, a high-density bin map was developed using 53,223 single nucleotide polymorphisms (SNPs) identified in the recombinant inbred line (RIL) population of ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive) cross. QTL analysis using recombination bins as markers along with the phenotyping data for 17 drought tolerance related traits obtained over 1–5 seasons and 1–5 locations split the “QTL-hotspot” region into two subregions namely “QTL-hotspot_a” (15 genes) and “QTL-hotspot_b” (11 genes). In the second approach, gene enrichment analysis using significant marker trait associations based on SNPs from the Ca4 pseudomolecule with the above mentioned phenotyping data, and the candidate genes from the refined “QTL-hotspot” region showed enrichment for 23 genes. Twelve genes were found common in both approaches. Functional validation using quantitative real-time PCR (qRT-PCR) indicated four promising candidate genes having functional implications on the effect of “QTL-hotspot” for drought tolerance in chickpea. PMID:26478518

  6. QTL mapping of genome regions controlling temephos resistance in larvae of the mosquito Aedes aegypti.

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    Guadalupe Del Carmen Reyes-Solis

    2014-10-01

    Full Text Available The mosquito Aedes aegypti is the principal vector of dengue and yellow fever flaviviruses. Temephos is an organophosphate insecticide used globally to suppress Ae. aegypti larval populations but resistance has evolved in many locations.Quantitative Trait Loci (QTL controlling temephos survival in Ae. aegypti larvae were mapped in a pair of F3 advanced intercross lines arising from temephos resistant parents from Solidaridad, México and temephos susceptible parents from Iquitos, Peru. Two sets of 200 F3 larvae were exposed to a discriminating dose of temephos and then dead larvae were collected and preserved for DNA isolation every two hours up to 16 hours. Larvae surviving longer than 16 hours were considered resistant. For QTL mapping, single nucleotide polymorphisms (SNPs were identified at 23 single copy genes and 26 microsatellite loci of known physical positions in the Ae. aegypti genome. In both reciprocal crosses, Multiple Interval Mapping identified eleven QTL associated with time until death. In the Solidaridad×Iquitos (SLD×Iq cross twelve were associated with survival but in the reciprocal IqxSLD cross, only six QTL were survival associated. Polymorphisms at acetylcholine esterase (AchE loci 1 and 2 were not associated with either resistance phenotype suggesting that target site insensitivity is not an organophosphate resistance mechanism in this region of México.Temephos resistance is under the control of many metabolic genes of small effect and dispersed throughout the Ae. aegypti genome.

  7. Phenotypic plasticity, QTL mapping and genomic characterization of bud set in black poplar

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    Fabbrini Francesco

    2012-04-01

    Full Text Available Abstract Background The genetic control of important adaptive traits, such as bud set, is still poorly understood in most forest trees species. Poplar is an ideal model tree to study bud set because of its indeterminate shoot growth. Thus, a full-sib family derived from an intraspecific cross of P. nigra with 162 clonally replicated progeny was used to assess the phenotypic plasticity and genetic variation of bud set in two sites of contrasting environmental conditions. Results Six crucial phenological stages of bud set were scored. Night length appeared to be the most important signal triggering the onset of growth cessation. Nevertheless, the effect of other environmental factors, such as temperature, increased during the process. Moreover, a considerable role of genotype × environment (G × E interaction was found in all phenological stages with the lowest temperature appearing to influence the sensitivity of the most plastic genotypes. Descriptors of growth cessation and bud onset explained the largest part of phenotypic variation of the entire process. Quantitative trait loci (QTL for these traits were detected. For the four selected traits (the onset of growth cessation (date2.5, the transition from shoot to bud (date1.5, the duration of bud formation (subproc1 and bud maturation (subproc2 eight and sixteen QTL were mapped on the maternal and paternal map, respectively. The identified QTL, each one characterized by small or modest effect, highlighted the complex nature of traits involved in bud set process. Comparison between map location of QTL and P. trichocarpa genome sequence allowed the identification of 13 gene models, 67 bud set-related expressional and six functional candidate genes (CGs. These CGs are functionally related to relevant biological processes, environmental sensing, signaling, and cell growth and development. Some strong QTL had no obvious CGs, and hold great promise to identify unknown genes that affect bud set

  8. Association studies in QTL regions linked to bovine trypanotolerance in a West African crossbred population.

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    Dayo, G K; Gautier, M; Berthier, D; Poivey, J P; Sidibe, I; Bengaly, Z; Eggen, A; Boichard, D; Thevenon, S

    2012-04-01

    African animal trypanosomosis is a parasitic blood disease transmitted by tsetse flies and is widespread in sub-Saharan Africa. West African taurine breeds have the ability, known as trypanotolerance, to limit parasitaemia and anaemia and remain productive in enzootic areas. Several quantitative trait loci (QTL) underlying traits related to trypanotolerance have been identified in an experimentally infected F(2) population resulting from a cross between taurine and zebu cattle. Although this information is highly valuable, the QTL remain to be confirmed in populations subjected to natural conditions of infection, and the corresponding regions need to be refined. In our study, 360 West African cattle were phenotyped for the packed cell volume control under natural conditions of infection in south-western Burkina Faso. Phenotypes were assessed by analysing data from previous cattle monitored over 2 years in an area enzootic for trypanosomosis. We further genotyped for 64 microsatellite markers mapping within four previously reported QTL on BTA02, BTA04, BTA07 and BTA13. These data enabled us to estimate the heritability of the phenotype using the kinship matrix between individuals computed from genotyping data. Thus, depending on the estimators considered and the method used, the heritability of anaemia control ranged from 0.09 to 0.22. Finally, an analysis of association identified an allele of the MNB42 marker on BTA04 as being strongly associated with anaemia control, and a candidate gene, INHBA, as being close to that marker. PMID:22404348

  9. Discovering genes underlying QTL

    International Nuclear Information System (INIS)

    A map-based approach has allowed scientists to discover few genes at a time. In addition, the reproductive barrier between cultivated rice and wild relatives has prevented us from utilizing the germ plasm by a map-based approach. Most genetic traits important to agriculture or human diseases are manifested as observable, quantitative phenotypes called Quantitative Trait Loci (QTL). In many instances, the complexity of the phenotype/genotype interaction and the general lack of clearly identifiable gene products render the direct molecular cloning approach ineffective, thus additional strategies like genome mapping are required to identify the QTL in question. Genome mapping requires no prior knowledge of the gene function, but utilizes statistical methods to identify the most likely gene location. To completely characterize genes of interest, the initially mapped region of a gene location will have to be narrowed down to a size that is suitable for cloning and sequencing. Strategies for gene identification within the critical region have to be applied after the sequencing of a potentially large clone or set of clones that contains this gene(s). Tremendous success of positional cloning has been shown for cloning many genes responsible for human diseases, including cystic fibrosis and muscular dystrophy as well as plant disease resistance genes. Genome and QTL mapping, positional cloning: the pre-genomics era, comparative approaches to gene identification, and positional cloning: the genomics era are discussed in the report. (M. Suetake)

  10. Discovering genes underlying QTL

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    Vanavichit, Apichart [Kasetsart University, Kamphaengsaen, Nakorn Pathom (Thailand)

    2002-02-01

    A map-based approach has allowed scientists to discover few genes at a time. In addition, the reproductive barrier between cultivated rice and wild relatives has prevented us from utilizing the germ plasm by a map-based approach. Most genetic traits important to agriculture or human diseases are manifested as observable, quantitative phenotypes called Quantitative Trait Loci (QTL). In many instances, the complexity of the phenotype/genotype interaction and the general lack of clearly identifiable gene products render the direct molecular cloning approach ineffective, thus additional strategies like genome mapping are required to identify the QTL in question. Genome mapping requires no prior knowledge of the gene function, but utilizes statistical methods to identify the most likely gene location. To completely characterize genes of interest, the initially mapped region of a gene location will have to be narrowed down to a size that is suitable for cloning and sequencing. Strategies for gene identification within the critical region have to be applied after the sequencing of a potentially large clone or set of clones that contains this gene(s). Tremendous success of positional cloning has been shown for cloning many genes responsible for human diseases, including cystic fibrosis and muscular dystrophy as well as plant disease resistance genes. Genome and QTL mapping, positional cloning: the pre-genomics era, comparative approaches to gene identification, and positional cloning: the genomics era are discussed in the report. (M. Suetake)

  11. Re-sequencing data for refining candidate genes and polymorphisms in QTL regions affecting adiposity in chicken.

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    Pierre-François Roux

    Full Text Available In this study, we propose an approach aiming at fine-mapping adiposity QTL in chicken, integrating whole genome re-sequencing data. First, two QTL regions for adiposity were identified by performing a classical linkage analysis on 1362 offspring in 11 sire families obtained by crossing two meat-type chicken lines divergently selected for abdominal fat weight. Those regions, located on chromosome 7 and 19, contained a total of 77 and 84 genes, respectively. Then, SNPs and indels in these regions were identified by re-sequencing sires. Considering issues related to polymorphism annotations for regulatory regions, we focused on the 120 and 104 polymorphisms having an impact on protein sequence, and located in coding regions of 35 and 42 genes situated in the two QTL regions. Subsequently, a filter was applied on SNPs considering their potential impact on the protein function based on conservation criteria. For the two regions, we identified 42 and 34 functional polymorphisms carried by 18 and 24 genes, and likely to deeply impact protein, including 3 coding indels and 4 nonsense SNPs. Finally, using gene functional annotation, a short list of 17 and 4 polymorphisms in 6 and 4 functional genes has been defined. Even if we cannot exclude that the causal polymorphisms may be located in regulatory regions, this strategy gives a complete overview of the candidate polymorphisms in coding regions and prioritize them on conservation- and functional-based arguments.

  12. Genetic effects of polymorphisms in candidate genes and the QTL region on chicken age at first egg

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    Zhou Min

    2011-04-01

    Full Text Available Abstract Background The age at first egg (AFE, an important indicator for sexual maturation in female chickens, is controlled by polygenes. Based on our knowledge of reproductive physiology, 6 genes including gonadotrophin releasing hormone-I (GnRH-I, neuropeptide Y (NPY, dopamine D2 receptor (DRD2, vasoactive intestinal polypeptide (VIP, VIP receptor-1 (VIPR-1, and prolactin (PRL, were selected as candidates for influencing AFE. Additionally, the region between ADL0201 and MCW0241 of chromosome Z was chosen as the candidate QTL region according to some QTL databases. The objective of the present study was to investigate the effects of mutations in candidate genes and the QTL region on chicken AFE. Results Marker-trait association analysis of 8 mutations in those 6 genes in a Chinese native population found a highly significant association (P G840327C of the GnRH-I gene with AFE, and it remained significant even with Bonferroni correction. Based on the results of the 2-tailed χ2 test, mutations T32742394C, T32742468C, G32742603A, and C33379782T in the candidate QTL region of chromosome Z were selected for marker-trait association analysis. The haplotypes of T32742394C and T32742468C were significantly associated (P T32742394C and T32742468C were located in the intron region of the SH3-domain GRB2-like 2 (SH3GL2 gene, which appeared to be associated in the endocytosis and development of the oocyte. Conclusion This study found that G840327C of the GnRH-I gene and the haplotypes of T32742394C-T32742468C of the SH3GL2 gene were associated with the chicken AFE.

  13. A maximum likelihood QTL analysis reveals common genome regions controlling resistance to Salmonella colonization and carrier-state

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    Thanh-Son Tran

    2012-05-01

    Full Text Available Abstract Background The serovars Enteritidis and Typhimurium of the Gram-negative bacterium Salmonella enterica are significant causes of human food poisoning. Fowl carrying these bacteria often show no clinical disease, with detection only established post-mortem. Increased resistance to the carrier state in commercial poultry could be a way to improve food safety by reducing the spread of these bacteria in poultry flocks. Previous studies identified QTLs for both resistance to carrier state and resistance to Salmonella colonization in the same White Leghorn inbred lines. Until now, none of the QTLs identified was common to the two types of resistance. All these analyses were performed using the F2 inbred or backcross option of the QTLExpress software based on linear regression. In the present study, QTL analysis was achieved using Maximum Likelihood with QTLMap software, in order to test the effect of the QTL analysis method on QTL detection. We analyzed the same phenotypic and genotypic data as those used in previous studies, which were collected on 378 animals genotyped with 480 genome-wide SNP markers. To enrich these data, we added eleven SNP markers located within QTLs controlling resistance to colonization and we looked for potential candidate genes co-localizing with QTLs. Results In our case the QTL analysis method had an important impact on QTL detection. We were able to identify new genomic regions controlling resistance to carrier-state, in particular by testing the existence of two segregating QTLs. But some of the previously identified QTLs were not confirmed. Interestingly, two QTLs were detected on chromosomes 2 and 3, close to the locations of the major QTLs controlling resistance to colonization and to candidate genes involved in the immune response identified in other, independent studies. Conclusions Due to the lack of stability of the QTLs detected, we suggest that interesting regions for further studies are those that were

  14. QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments

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    Meirmans Patrick G

    2011-03-01

    Full Text Available Abstract Background The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be validated from one experiment to another. The aim of our study was to overcome this limitation by basing QTL detection on the construction of genetic maps highly-enriched in gene markers, and by assessing QTLs across pedigrees, years, and environments. Results Four saturated individual linkage maps representing two unrelated mapping populations of 260 and 500 clonally replicated progeny were assembled from 471 to 570 markers, including from 283 to 451 gene SNPs obtained using a multiplexed genotyping assay. Thence, a composite linkage map was assembled with 836 gene markers. For individual linkage maps, a total of 33 distinct quantitative trait loci (QTLs were observed for bud flush, 52 for bud set, and 52 for height growth. For the composite map, the corresponding numbers of QTL clusters were 11, 13, and 10. About 20% of QTLs were replicated between the two mapping populations and nearly 50% revealed spatial and/or temporal stability. Three to four occurrences of overlapping QTLs between characters were noted, indicating regions with potential pleiotropic effects. Moreover, some of the genes involved in the QTLs were also underlined by recent genome scans or expression profile studies. Overall, the proportion of phenotypic variance explained by each QTL ranged from 3.0 to 16.4% for bud flush, from 2.7 to 22.2% for bud set, and from 2.5 to 10.5% for height growth. Up to 70% of the total character variance could be accounted for by QTLs for bud flush or bud set, and up to 59% for height growth. Conclusions This study provides a basic understanding of the genomic architecture related to bud flush, bud set, and height growth in a conifer species, and a useful indicator to compare with Angiosperms. It will serve as a basic

  15. Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection.

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    Xianfa Xie

    Full Text Available Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativa--indica and tropical japonica--as well as the ancestral wild rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups.

  16. QTL Mapping of Genome Regions Controlling Temephos Resistance in Larvae of the Mosquito Aedes aegypti

    OpenAIRE

    Guadalupe Del Carmen Reyes-Solis; Karla Saavedra-Rodriguez; Adriana Flores Suarez; Black, William C.

    2014-01-01

    Introduction The mosquito Aedes aegypti is the principal vector of dengue and yellow fever flaviviruses. Temephos is an organophosphate insecticide used globally to suppress Ae. aegypti larval populations but resistance has evolved in many locations. Methodology/Principal Findings Quantitative Trait Loci (QTL) controlling temephos survival in Ae. aegypti larvae were mapped in a pair of F3 advanced intercross lines arising from temephos resistant parents from Solidaridad, México and temephos s...

  17. Characterization and mapping of QTL used in breeding of Scots pine (Pinus sylvestris L.)

    OpenAIRE

    Nowicka, Aleksandra; Ukalska, Joanna; Simińska, Joanna; Szyp-Borowska, Iwona

    2013-01-01

    This paper reports the construction a map based on Amplified Fragment Length Polymorphic DNA (AFLP) in Scots pine (Pinus sylvestris L.). The main purpose of map construction was its application to quantitative traits loci (QTL) mapping for breeding traits economically important in Scots pine breeding program such as tree height and diameter at breast height, number of needles and their length, width, and area. Genomic DNA of needles and haploid megagamethophytes from seeds originating from a ...

  18. Pathotype-specific QTL for stem rust resistance in Lolium perenne.

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    Pfender, W F; Slabaugh, M E

    2013-05-01

    A genetic map populated with RAD and SSR markers was created from F1 progeny of a stem rust-susceptible and stem rust-resistant parent of perennial ryegrass (Lolium perenne). The map supplements a previous map of this population by having markers in common with several other Lolium spp. maps including EST-SSR anchor markers from a consensus map published by other researchers. A QTL analysis was conducted with disease severity and infection type data obtained by controlled inoculation of the population with each of two previously characterized pathotypes of Puccinia graminis subsp. graminicola that differ in virulence to different host plant genotypes in the F1 population. Each pathotype activated a specific QTL on one linkage group (LG): qLpPg1 on LG7 for pathotype 101, or qLpPg2 on LG1 for pathotype 106. Both pathotypes also activated a third QTL in common, qLpPg3 on LG6. Anchor markers, present on a consensus map, were located in proximity to each of the three QTL. These QTL had been detected also in previous experiments in which a genetically heterogeneous inoculum of the stem rust pathogen activated all three QTL together. The results of this and a previous study are consistent with the involvement of the pathotype-specific QTL in pathogen recognition and the pathotype-nonspecific QTL in a generalized resistance response. By aligning the markers common to other published reports, it appears that two and possibly all three of the stem rust QTL reported here are in the same general genomic regions containing some of the L. perenne QTL reported to be activated in response to the crown rust pathogen (P. coronata). PMID:23361523

  19. Concordance analysis for QTL detection in dairy cattle: a case study of leg morphology

    DEFF Research Database (Denmark)

    van den Berg, Irene; Rodrigue; Fritz, Sebastien;

    2014-01-01

    conformation trait in dairy cattle. Several QTL were detected for which the QTL status (homozygous or heterozygous for the QTL) was inferred for each individual. Subsequently, the inferred QTL status was used in a concordance analysis to reduce the number of candidate mutations. Methods Twenty QTL for rear leg...... status was concordant with the QTL status were kept as candidate causative mutations. Results QTL status could be inferred for 15 of the 20 QTL. The number of concordant polymorphisms differed between QTL and depended on the number of QTL statuses that could be inferred and the linkage disequilibrium in......The present availability of sequence data gives new opportunities to narrow down from QTL (quantitative trait locus) regions to causative mutations. Our objective was to decrease the number of candidate causative mutations in a QTL region. For this, a concordance analysis was applied for a leg...

  20. QTL for yield and associated traits in the Seri/Babax population grown across several environments in Mexico, in the West Asia, North Africa, and South Asia regions.

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    Lopes, Marta S; Reynolds, Matthew P; McIntyre, C Lynne; Mathews, Ky L; Jalal Kamali, M R; Mossad, Moussa; Feltaous, Yousef; Tahir, Izzat S A; Chatrath, Ravish; Ogbonnaya, Francis; Baum, Michael

    2013-04-01

    Heat and drought adaptive quantitative trait loci (QTL) in a spring bread wheat population resulting from the Seri/Babax cross designed to minimize confounding agronomic traits have been identified previously in trials conducted in Mexico. The same population was grown across a wide range of environments where heat and drought stress are naturally experienced including environments in Mexico, West Asia, North Africa (WANA), and South Asia regions. A molecular genetic linkage map including 475 marker loci associated to 29 linkage groups was used for QTL analysis of yield, days to heading (DH) and to maturity (DM), grain number (GM2), thousand kernel weight (TKW), plant height (PH), canopy temperature at the vegetative and grain filling stages (CTvg and CTgf), and early ground cover. A QTL for yield on chromosome 4A was confirmed across several environments, in subsets of lines with uniform allelic expression of a major phenology QTL, but not independently from PH. With terminal stress, TKW QTL was linked or pleiotropic to DH and DM. The link between phenology and TKW suggested that early maturity would favor the post-anthesis grain growth periods resulting in increased grain size and yields under terminal stress. GM2 and TKW were partially associated with markers at different positions suggesting different genetic regulation and room for improvement of both traits. Prediction accuracy of yield was improved by 5 % when using marker scores of component traits (GM2 and DH) together with yield in multiple regression. This procedure may provide accumulation of more favorable alleles during selection. PMID:23269228

  1. Short-term selective breeding for High and Low prepulse inhibition of the acoustic startle response; pharmacological characterization and QTL mapping in the selected lines

    OpenAIRE

    Hitzemann, Robert; Malmanger, Barry; Belknap, John; Darakjian, Priscila; McWeeney, Shannon

    2008-01-01

    Selective breeding offers several important advantages over using inbred strain panels in detecting genetically correlated traits to the selection phenotype. The purpose of the current study was to selectively breed for prepulse inhibition (PPI) of the acoustic startle response (ASR), to pharmacologically and behaviorally characterize the selected lines and to use the lines for quantitative trait loci (QTL) mapping. Starting with heterogeneous stock mice formed by crossing the C57BL/6J, DBA/2...

  2. Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

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    Blackmon Barbara P

    2011-07-01

    Full Text Available Abstract Background BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. Results This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. Conclusions Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed.

  3. Consistent effects of a major QTL for thermal resistance in field-released Drosophila melanogaster

    DEFF Research Database (Denmark)

    Loeschcke, Volker; Kristensen, Torsten Nygård; Norry, Fabian M

    2011-01-01

    Molecular genetic markers can be used to identify quantitative trait loci (QTL) for thermal resistance and this has allowed characterization of a major QTL for knockdown resistance to high temperature in Drosophila melanogaster. The QTL showed trade-off associations with cold resistance under lab...... field fitness at different environmental temperatures with genotypic variation in a QTL for thermal tolerance. Graphical abstract...

  4. New Breeding Parents Containing Novel QTL for Rice Sheath Blight Resistance Identified by Combining Phenotypic and Molecular Characterizations

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    Rice Sheath Blight (SB) disease, caused by the necrotrophic Rhizoctonia solani Kühn, is a global and annual cause of rice yield losses. Several QTL with small individual impact must be combined to create rice varieties tolerant of SB infection because no single gene confers complete resistance. Mo...

  5. Genetic Dissection of QTL Associated with Grain Yield in Diverse Environments

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    Junli Zhang

    2014-12-01

    Full Text Available Wheat (Triticum aestivum L. breeding programs strive to increase grain yield; however, the progress is hampered due to its quantitative inheritance, low heritability, and confounding environmental effects. In the present study, a winter wheat population of 159 recombinant inbred lines (RILs was evaluated in six trials under rainfed, terminal drought, and fully-irrigated conditions, over four years. Quantitative trait locus/loci (QTL mapping was conducted for grain yield main effect (GY and the genotype × environment interaction (GEI effect. A total of 17 QTL were associated with GY and 13 QTL associated with GEI, and nine QTL were mapped in the flanking chromosomal regions for both GY and GEI. One major QTL Q.Gy.ui-1B.2, explaining up to 22% of grain yield, was identified in all six trials. Besides the additive effect of QTL associated with GY, interactions among QTL (QTL × QTL interaction, QTL × environment, and QTL × QTL × environment were also observed. When combining the interaction effects, QTL Q.Gy.ui-1B.2 along with other QTL explained up to 52% of the variation in grain yield over the six trials. This study suggests that QTL mapping of complex traits such as grain yield should include interaction effects of QTL and environments in marker-assisted selection.

  6. Characterization of QTL for unique agronomic traits of new-plant-type rice varieties using introgression lines of IR64

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    Analiza G. Tagle

    2016-02-01

    Full Text Available To enhance the yield potential of an elite indica rice cultivar, an introgression (BC3-derived line of IR64, YTH288, was developed using a new-plant-type cultivar, IR66215-44-2-3, as a donor parent. YTH288 has agronomically valuable characteristics such as large panicles, few unproductive tillers, and large leaves inherited from NPT. To identify the genetic basis of these traits, we used 167 F2 plants derived from a cross between IR64 and YTH288 to conduct QTL analysis for five agronomic traits: days to heading (DTH, culm length (CL, flag leaf length (FLL, flag leaf width (FLW, and filled spikelet number per panicle (FSN. Six putative QTL were detected: four on chromosome 4 (for CL, FLL, FLW, and FSN and two on chromosome 2 (for DTH and FLL. All QTL with the IR66215-44-2-3 allele, except that for FLL on chromosome 2, had positive effects on each trait. To confirm the effects of these putative QTL, we developed NILs with the IR64 genetic background by marker-assisted selection. We observed significant differences in several agronomic traits between IR64 and NILs that carried these QTL on chromosomes 2 and 4. Additionally, four IR64-NILs carrying chromosomal segments derived from different NPT varieties on the long arm of chromosome 4 exhibited similar pleiotropic effects for unique agronomic traits. These NILs can be used as research materials for studying each trait and as breeding materials for yield improvement of indica rice cultivars. Abbreviations NPT, new plant type; QTL, quantitative trait loci (locus; GF, grain fertility; DTH, days to heading; CL, culm length; PL, panicle length; LL, leaf length; FLL, flag leaf length; LW, leaf width; FLW, flag leaf width; FSN, filled spikelet number per panicle; TSN, total spikelet number per panicle; PN, panicle number per plant; IRRI, International Rice Research Institute; NIL, near-isogenic line; IL, introgression line; SSR, simple sequence repeat; PCR, polymerase chain reaction

  7. QTL Mapping of Sex Determination Loci Supports an Ancient Pathway in Ants and Honey Bees.

    Directory of Open Access Journals (Sweden)

    Misato O Miyakawa

    2015-11-01

    Full Text Available Sex determination mechanisms play a central role in life-history characteristics, affecting mating systems, sex ratios, inbreeding tolerance, etc. Downstream components of sex determination pathways are highly conserved, but upstream components evolve rapidly. Evolutionary dynamics of sex determination remain poorly understood, particularly because mechanisms appear so diverse. Here we investigate the origins and evolution of complementary sex determination (CSD in ants and bees. The honey bee has a well-characterized CSD locus, containing tandemly arranged homologs of the transformer gene [complementary sex determiner (csd and feminizer (fem]. Such tandem paralogs appear frequently in aculeate hymenopteran genomes. However, only comparative genomic, but not functional, data support a broader role for csd/fem in sex determination, and whether species other than the honey bee use this pathway remains controversial. Here we used a backcross to test whether csd/fem acts as a CSD locus in an ant (Vollenhovia emeryi. After sequencing and assembling the genome, we computed a linkage map, and conducted a quantitative trait locus (QTL analysis of diploid male production using 68 diploid males and 171 workers. We found two QTLs on separate linkage groups (CsdQTL1 and CsdQTL2 that jointly explained 98.0% of the phenotypic variance. CsdQTL1 included two tandem transformer homologs. These data support the prediction that the same CSD mechanism has indeed been conserved for over 100 million years. CsdQTL2 had no similarity to CsdQTL1 and included a 236-kb region with no obvious CSD gene candidates, making it impossible to conclusively characterize it using our data. The sequence of this locus was conserved in at least one other ant genome that diverged >75 million years ago. By applying QTL analysis to ants for the first time, we support the hypothesis that elements of hymenopteran CSD are ancient, but also show that more remains to be learned about the

  8. Identification of Polymorphisms Associated with Drought Adaptation QTL in Brassica napus by Resequencing

    Directory of Open Access Journals (Sweden)

    Richard S. Fletcher

    2016-04-01

    Full Text Available Brassica napus is a globally important oilseed for which little is known about the genetics of drought adaptation. We previously mapped twelve quantitative trait loci (QTL underlying drought-related traits in a biparental mapping population created from a cross between winter and spring B. napus cultivars. Here we resequence the genomes of the mapping population parents to identify genetic diversity across the genome and within QTL regions. We sequenced each parental cultivar on the Illumina HiSeq platform to a minimum depth of 23 × and performed a reference based assembly in order to describe the molecular variation differentiating them at the scale of the genome, QTL and gene. Genome-wide patterns of variation were characterized by an overall higher single nucleotide polymorphism (SNP density in the A genome and a higher ratio of nonsynonymous to synonymous substitutions in the C genome. Nonsynonymous substitutions were used to categorize gene ontology terms differentiating the parent genomes along with a list of putative functional variants contained within each QTL. Marker assays were developed for several of the discovered polymorphisms within a pleiotropic QTL on chromosome A10. QTL analysis with the new, denser map showed the most associated marker to be that developed from an insertion/deletion polymorphism located in the candidate gene Bna.FLC.A10, and it was the only candidate within the QTL interval with observed polymorphism. Together, these results provide a glimpse of genome-wide variation differentiating annual and biennial B. napus ecotypes as well as a better understanding of the genetic basis of root and drought phenotypes.

  9. Identification of Polymorphisms Associated with Drought Adaptation QTL in Brassica napus by Resequencing.

    Science.gov (United States)

    Fletcher, Richard S; Herrmann, David; Mullen, Jack L; Li, Qinfei; Schrider, Daniel R; Price, Nicholas; Lin, Junjiang; Grogan, Kelsi; Kern, Andrew; McKay, John K

    2016-01-01

    Brassica napus is a globally important oilseed for which little is known about the genetics of drought adaptation. We previously mapped twelve quantitative trait loci (QTL) underlying drought-related traits in a biparental mapping population created from a cross between winter and spring B. napus cultivars. Here we resequence the genomes of the mapping population parents to identify genetic diversity across the genome and within QTL regions. We sequenced each parental cultivar on the Illumina HiSeq platform to a minimum depth of 23 × and performed a reference based assembly in order to describe the molecular variation differentiating them at the scale of the genome, QTL and gene. Genome-wide patterns of variation were characterized by an overall higher single nucleotide polymorphism (SNP) density in the A genome and a higher ratio of nonsynonymous to synonymous substitutions in the C genome. Nonsynonymous substitutions were used to categorize gene ontology terms differentiating the parent genomes along with a list of putative functional variants contained within each QTL. Marker assays were developed for several of the discovered polymorphisms within a pleiotropic QTL on chromosome A10. QTL analysis with the new, denser map showed the most associated marker to be that developed from an insertion/deletion polymorphism located in the candidate gene Bna.FLC.A10, and it was the only candidate within the QTL interval with observed polymorphism. Together, these results provide a glimpse of genome-wide variation differentiating annual and biennial B. napus ecotypes as well as a better understanding of the genetic basis of root and drought phenotypes. PMID:26801646

  10. QTL analysis of novel genomic regions associated with yield and yield related traits in new plant type based recombinant inbred lines of rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    Marathi Balram

    2012-08-01

    Full Text Available Abstract Background Rice is staple food for more than half of the world’s population including two billion Asians, who obtain 60-70% of their energy intake from rice and its derivatives. To meet the growing demand from human population, rice varieties with higher yield potential and greater yield stability need to be developed. The favourable alleles for yield and yield contributing traits are distributed among two subspecies i.e., indica and japonica of cultivated rice (Oryza sativa L.. Identification of novel favourable alleles in indica/japonica will pave way to marker-assisted mobilization of these alleles in to a genetic background to break genetic barriers to yield. Results A new plant type (NPT based mapping population of 310 recombinant inbred lines (RILs was used to map novel genomic regions and QTL hotspots influencing yield and eleven yield component traits. We identified major quantitative trait loci (QTLs for days to 50% flowering (R2 = 25%, LOD = 14.3, panicles per plant (R2 = 19%, LOD = 9.74, flag leaf length (R2 = 22%, LOD = 3.05, flag leaf width (R2 = 53%, LOD = 46.5, spikelets per panicle (R2 = 16%, LOD = 13.8, filled grains per panicle (R2 = 22%, LOD = 15.3, percent spikelet sterility (R2 = 18%, LOD = 14.24, thousand grain weight (R2 = 25%, LOD = 12.9 and spikelet setting density (R2 = 23%, LOD = 15 expressing over two or more locations by using composite interval mapping. The phenotypic variation (R2 ranged from 8 to 53% for eleven QTLs expressing across all three locations. 19 novel QTLs were contributed by the NPT parent, Pusa1266. 15 QTL hotpots on eight chromosomes were identified for the correlated traits. Six epistatic QTLs effecting five traits at two locations were identified. A marker interval (RM3276-RM5709 on chromosome 4 harboring major QTLs for four traits was identified. Conclusions The present study reveals that favourable alleles for

  11. Identification of CNV and QTL for productive and functional traits in dairy cattle using dense SNP chips

    OpenAIRE

    Bagnato, Alessandro

    2015-01-01

    The thesis identify CNV structural variants as possible markers for genomic selection and identify QTL regions for Fatty Acid Content in the Italian Brown Swiss population. Additionally it maps the QTL for mastitis resistance in the Valdostana Red Pied cattle.

  12. QTL mapping reveals a two-step model for the evolutionary reduction of inner microsporangia within the asteracean genus Microseris.

    Science.gov (United States)

    Gailing, O; Bachmann, K

    2003-09-01

    The reduction of inner (adaxial) pollen sacs (microsporangia, MS) as a diagnostic character for the three asteracean species, Microseris bigelovii, Microseris elegans and Microseris pygmaea, was analysed in an interspecific cross between Microseris douglasii and Microseris bigelovii with 4 MS and 2 MS, respectively, using the average number of MS per plant as a quantitative character. A previous QTL (Quantitative Trait Locus) analysis had revealed one major QTL (3B) and three modifier QTLs (3A, 4A, 7A) with epistatic effects only on the homozygous recessive 2 MS genotype of QTL 3B. Here we performed a bulked segregant analysis on four 2 MS and four 4 MS DNA-bulks with 407 EcoRI/ MseI AFLP-primer combinations each. In this way additional AFLP markers were mapped close to QTL 3B and QTL 3A. Three of them were converted to SCAR (Sequence Characterized Amplified region) markers. All markers were tested in natural populations of the disporangiate (2 MS) species M. bigelovii, M. elegans and M. pygmaea, and in different populations of tetrasporangiate (4 MS) M. douglasii. The marker distribution suggests that locus 3B mutated in a progenitor of the disporangiate species. QTL 3A has evolved in the 2 MS background of the major gene in the disporangiate species. Since M. pygmaea and M. bigelovii are the sister group to M. elegans, the 4 MS genotype for (markers of) QTL 3A in M. pygmaea populations is most likely due to a back mutation to the 4 MS state and could explain the slight instability of the 2 MS phenotype in this species. PMID:12838389

  13. Functional Characterization of Novel Chitinase Genes Present in the Sheath Blight Resistance QTL: qSBR11-1 in Rice Line Tetep.

    Science.gov (United States)

    Richa, Kamboj; Tiwari, Ila M; Kumari, Mandeep; Devanna, B N; Sonah, Humira; Kumari, Archana; Nagar, Ramawatar; Sharma, Vinay; Botella, Jose R; Sharma, Tilak R

    2016-01-01

    Rice sheath blight disease caused by Rhizoctonia solani is one of the most devastating diseases in rice leading to heavy yield losses. Due to the polygenic nature of resistance, no major resistance gene with complete host resistance against R. solani has been reported. In this study, we have performed molecular and functional analysis of the genes associated with the major R. solani-resistance QTL qSBR11-1 in the indica rice line Tetep. Sequence analysis revealed the presence of a set of 11 tandem repeats containing genes with a high degree of homology to class III chitinase defense response genes. Real-time quantitative PCR analysis showed that all the genes are strongly induced 36 h after R. solani infection. Comparison between the resistant Tetep and the susceptible HP2216 lines shows that the induction of the chitinase genes is much higher in the Tetep line. Recombinant protein produced in vitro for six of the eleven genes showed chitinolytic activity in gel assays but we did not detect any xylanase inhibitory activity. All the six in vitro expressed proteins show antifungal activity with a clear inhibitory effect on the growth of the R. solani mycelium. The characterized chitinase genes can provide an important resource for the genetic improvement of R. solani susceptible rice lines for sheath blight resistance breeding. PMID:26973685

  14. An interval of the obesity QTL Nob3.38 within a QTL hotspot on chromosome 1 modulates behavioral phenotypes.

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    Heike Vogel

    Full Text Available A region on mouse distal chromosome 1 (Chr. 1 that is highly enriched in quantitative trait loci (QTLs controlling neural and behavioral phenotypes overlaps with the peak region of a major obesity QTL (Nob3.38, which we identified in an intercross of New Zealand Obese (NZO mice with C57BL/6J (B6. By positional cloning we recently identified a microdeletion within this locus causing the disruption of Ifi202b that protects from adiposity by suppressing expression of 11β-Hsd1. Here we show that the Nob3.38 segment also corresponds with the QTL rich region (Qrr1 on Chr. 1 and associates with increased voluntary running wheel activity, Rota-rod performance, decreased grip strength, and anxiety-related traits. The characterization of a subcongenic line carrying 14.2 Mbp of Nob3.38 with a polymorphic region of 4.4 Mbp indicates that the microdeletion and/or other polymorphisms in its proximity alter body weight, voluntary activity, and exploration. Since 27 out of 32 QTL were identified in crosses with B6, we hypothesized that the microdeletion and or adjacent SNPs are unique for B6 mice and responsible for some of the complex Qrr1-mediated effects. Indeed, a phylogenic study of 28 mouse strains revealed a NZO-like genotype for 22 and a B6-like genotype for NZW/LacJ and 4 other C57BL strains. Thus, we suggest that a Nob3.38 interval (173.0-177.4 Mbp does not only modify adiposity but also neurobehavioral traits by a haplotype segregating with C57BL strains.

  15. An Interval of the Obesity QTL Nob3.38 within a QTL Hotspot on Chromosome 1 Modulates Behavioral Phenotypes

    Science.gov (United States)

    Vogel, Heike; Montag, Dirk; Kanzleiter, Timo; Jonas, Wenke; Matzke, Daniela; Scherneck, Stephan; Chadt, Alexandra; Töle, Jonas; Kluge, Reinhart; Joost, Hans-Georg; Schürmann, Annette

    2013-01-01

    A region on mouse distal chromosome 1 (Chr. 1) that is highly enriched in quantitative trait loci (QTLs) controlling neural and behavioral phenotypes overlaps with the peak region of a major obesity QTL (Nob3.38), which we identified in an intercross of New Zealand Obese (NZO) mice with C57BL/6J (B6). By positional cloning we recently identified a microdeletion within this locus causing the disruption of Ifi202b that protects from adiposity by suppressing expression of 11β-Hsd1. Here we show that the Nob3.38 segment also corresponds with the QTL rich region (Qrr1) on Chr. 1 and associates with increased voluntary running wheel activity, Rota-rod performance, decreased grip strength, and anxiety-related traits. The characterization of a subcongenic line carrying 14.2 Mbp of Nob3.38 with a polymorphic region of 4.4 Mbp indicates that the microdeletion and/or other polymorphisms in its proximity alter body weight, voluntary activity, and exploration. Since 27 out of 32 QTL were identified in crosses with B6, we hypothesized that the microdeletion and or adjacent SNPs are unique for B6 mice and responsible for some of the complex Qrr1-mediated effects. Indeed, a phylogenic study of 28 mouse strains revealed a NZO-like genotype for 22 and a B6-like genotype for NZW/LacJ and 4 other C57BL strains. Thus, we suggest that a Nob3.38 interval (173.0–177.4 Mbp) does not only modify adiposity but also neurobehavioral traits by a haplotype segregating with C57BL strains. PMID:23308133

  16. In silico screening of the chicken genome for overlaps between genomic regions: microRNA genes, coding and non-coding transcriptional units, QTL, and genetic variations.

    Science.gov (United States)

    Zorc, Minja; Kunej, Tanja

    2016-05-01

    MicroRNAs (miRNAs) are a class of non-coding RNAs involved in posttranscriptional regulation of target genes. Regulation requires complementarity between target mRNA and the mature miRNA seed region, responsible for their recognition and binding. It has been estimated that each miRNA targets approximately 200 genes, and genetic variability of miRNA genes has been reported to affect phenotypic variability and disease susceptibility in humans, livestock species, and model organisms. Polymorphisms in miRNA genes could therefore represent biomarkers for phenotypic traits in livestock animals. In our previous study, we collected polymorphisms within miRNA genes in chicken. In the present study, we identified miRNA-related genomic overlaps to prioritize genomic regions of interest for further functional studies and biomarker discovery. Overlapping genomic regions in chicken were analyzed using the following bioinformatics tools and databases: miRNA SNiPer, Ensembl, miRBase, NCBI Blast, and QTLdb. Out of 740 known pre-miRNA genes, 263 (35.5 %) contain polymorphisms; among them, 35 contain more than three polymorphisms The most polymorphic miRNA genes in chicken are gga-miR-6662, containing 23 single nucleotide polymorphisms (SNPs) within the pre-miRNA region, including five consecutive SNPs, and gga-miR-6688, containing ten polymorphisms including three consecutive polymorphisms. Several miRNA-related genomic hotspots have been revealed in chicken genome; polymorphic miRNA genes are located within protein-coding and/or non-coding transcription units and quantitative trait loci (QTL) associated with production traits. The present study includes the first description of an exonic miRNA in a chicken genome, an overlap between the miRNA gene and the exon of the protein-coding gene (gga-miR-6578/HADHB), and the first report of a missense polymorphism located within a mature miRNA seed region. Identified miRNA-related genomic hotspots in chicken can serve researchers as a

  17. Discovering Characterizing Regions For Consumer Products

    OpenAIRE

    Mishra, Shashwat; Leroy, Vincent; Amer-Yahia, Sihem

    2015-01-01

    Consumer behaviour holds special importance in the retail industry. Consumer location impacts consumer behaviour by dictating purchase trends. This paper investigates the problem of examining product sales across a chain of stores to extract the geographic regions that characterize a product. Characterizing region for a product is a coherent geographic region where the consumers actively consume the said product. We introduce DICE, a diffusion-based technique to uncover all such regions for a...

  18. Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs

    DEFF Research Database (Denmark)

    Jouffe, Vincent; Rowe, Suzanne; Liaubet, Laurence;

    2009-01-01

    Background: Microarray studies can supplement QTL studies by suggesting potential candidate. Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provi...

  19. Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data

    Directory of Open Access Journals (Sweden)

    Goddard Mike E

    2004-05-01

    Full Text Available Abstract A multi-locus QTL mapping method is presented, which combines linkage and linkage disequilibrium (LD information and uses multitrait data. The method assumed a putative QTL at the midpoint of each marker bracket. Whether the putative QTL had an effect or not was sampled using Markov chain Monte Carlo (MCMC methods. The method was tested in dairy cattle data on chromosome 14 where the DGAT1 gene was known to be segregating. The DGAT1 gene was mapped to a region of 0.04 cM, and the effects of the gene were accurately estimated. The fitting of multiple QTL gave a much sharper indication of the QTL position than a single QTL model using multitrait data, probably because the multi-locus QTL mapping reduced the carry over effect of the large DGAT1 gene to adjacent putative QTL positions. This suggests that the method could detect secondary QTL that would, in single point analyses, remain hidden under the broad peak of the dominant QTL. However, no indications for a second QTL affecting dairy traits were found on chromosome 14.

  20. mQTL-seq delineates functionally relevant candidate gene harbouring a major QTL regulating pod number in chickpea.

    Science.gov (United States)

    Das, Shouvik; Singh, Mohar; Srivastava, Rishi; Bajaj, Deepak; Saxena, Maneesha S; Rana, Jai C; Bansal, Kailash C; Tyagi, Akhilesh K; Parida, Swarup K

    2016-02-01

    The present study used a whole-genome, NGS resequencing-based mQTL-seq (multiple QTL-seq) strategy in two inter-specific mapping populations (Pusa 1103 × ILWC 46 and Pusa 256 × ILWC 46) to scan the major genomic region(s) underlying QTL(s) governing pod number trait in chickpea. Essentially, the whole-genome resequencing of low and high pod number-containing parental accessions and homozygous individuals (constituting bulks) from each of these two mapping populations discovered >8 million high-quality homozygous SNPs with respect to the reference kabuli chickpea. The functional significance of the physically mapped SNPs was apparent from the identified 2,264 non-synonymous and 23,550 regulatory SNPs, with 8-10% of these SNPs-carrying genes corresponding to transcription factors and disease resistance-related proteins. The utilization of these mined SNPs in Δ (SNP index)-led QTL-seq analysis and their correlation between two mapping populations based on mQTL-seq, narrowed down two (Caq(a)PN4.1: 867.8 kb and Caq(a)PN4.2: 1.8 Mb) major genomic regions harbouring robust pod number QTLs into the high-resolution short QTL intervals (Caq(b)PN4.1: 637.5 kb and Caq(b)PN4.2: 1.28 Mb) on chickpea chromosome 4. The integration of mQTL-seq-derived one novel robust QTL with QTL region-specific association analysis delineated the regulatory (C/T) and coding (C/A) SNPs-containing one pentatricopeptide repeat (PPR) gene at a major QTL region regulating pod number in chickpea. This target gene exhibited anther, mature pollen and pod-specific expression, including pronounced higher up-regulated (∼3.5-folds) transcript expression in high pod number-containing parental accessions and homozygous individuals of two mapping populations especially during pollen and pod development. The proposed mQTL-seq-driven combinatorial strategy has profound efficacy in rapid genome-wide scanning of potential candidate gene(s) underlying trait-associated high-resolution robust QTL(s), thereby

  1. Fine Mapping of a Major-Effect QTL Controlling Rhizomatous Growth in Perennial Wildrye Hyrbrids

    OpenAIRE

    Clements, Jenny L.

    2016-01-01

    Quantitative trait loci (QTL) analysis is the science of discovering genes or chromosome regions that influence the expression of quantitative traits. Statistical methods for doing this have evolved from single marker analysis of variance (ANOVA) to more complex approaches such as interval mapping and multiple QTL mapping. The goal of this project was to refine a previously identified QTL chromosome region responsible for rhizome growth in grass hybrids developed from two species of the Triti...

  2. Functional screening of an asthma QTL in YAC transgenic mice

    Energy Technology Data Exchange (ETDEWEB)

    Symula, Derek J.; Frazer, Kelly A.; Ueda, Yukihiko; Denefle, Patrice; Stevens, Mary E.; Wang, Zhi-En; Locksley, Richard; Rubin, Edward M.

    1999-07-02

    While large numbers of quantitative trait loci (QTLs) contributing to genetically complex conditions have been discovered, few causative genes have been identified. This is mainly due to the large size of QTLs and the subtle connection between genotype and quantitative phenotype associated with these conditions. While large numbers of quantitative trait loci (QTLs) contributing to genetically complex conditions have been discovered, few causative genes have been identified. This is mainly due to the large size of QTLs and the subtle connection between genotype and quantitative phenotype associated with these conditions. To screen for genes contributing to an asthma QTL mapped to human chromosome 5q33, the authors characterized a panel of large-insert 5q31 transgenics based on studies demonstrating that altering gene dosage frequently affects quantitative phenotypes normally influenced by that gene. This panel of human YAC transgenics, propagating a one megabase interva2048 chromosome 5q31 containing 23 genes, was screened for quantitative changes in several asthma-associated phenotypes. Multiple independent transgenic lines with altered IgE response to antigen treatment shared a 180 kb region containing 5 genes, including human interleukin 4 (IL4) and interleukin 13 (IL13), which induce IgE class switching in B cells5. Further analysis of these mice and mice transgenic for only murine Il4 and Il13 demonstrated that moderate changes in murine Il4 and Il13 expression affect asthma-associated phenotypes in vivo. This functional screen of large-insert transgenics enabled them to sift through multiple genes in the 5q3 asthma QTL without prior consideration of assumed individual gene function and identify genes that influence the QTL phenotype in vivo.

  3. eQTL Viewer: visualizing how sequence variation affects genome-wide transcription

    OpenAIRE

    Zeng Zhao-Bang; Aylor David L; Zou Wei

    2007-01-01

    Abstract Background Expression Quantitative Trait Locus (eQTL) mapping methods have been used to identify the genetic basis of gene expression variations. To map eQTL, thousands of expression profiles are related with sequence polymorphisms across the genome through their correlated variations. These eQTL distribute in many chromosomal regions, each of which can include many genes. The large number of mapping results produced makes it difficult to consider simultaneously the relationships bet...

  4. Complex trait subtypes identification using transcriptome profiling reveals an interaction between two QTL affecting adiposity in chicken

    Directory of Open Access Journals (Sweden)

    Blum Yuna

    2011-11-01

    Full Text Available Abstract Background Integrative genomics approaches that combine genotyping and transcriptome profiling in segregating populations have been developed to dissect complex traits. The most common approach is to identify genes whose eQTL colocalize with QTL of interest, providing new functional hypothesis about the causative mutation. Another approach includes defining subtypes for a complex trait using transcriptome profiles and then performing QTL mapping using some of these subtypes. This approach can refine some QTL and reveal new ones. In this paper we introduce Factor Analysis for Multiple Testing (FAMT to define subtypes more accurately and reveal interaction between QTL affecting the same trait. The data used concern hepatic transcriptome profiles for 45 half sib male chicken of a sire known to be heterozygous for a QTL affecting abdominal fatness (AF on chromosome 5 distal region around 168 cM. Results Using this methodology which accounts for hidden dependence structure among phenotypes, we identified 688 genes that are significantly correlated to the AF trait and we distinguished 5 subtypes for AF trait, which are not observed with gene lists obtained by classical approaches. After exclusion of one of the two lean bird subtypes, linkage analysis revealed a previously undetected QTL on chromosome 5 around 100 cM. Interestingly, the animals of this subtype presented the same q paternal haplotype at the 168 cM QTL. This result strongly suggests that the two QTL are in interaction. In other words, the "q configuration" at the 168 cM QTL could hide the QTL existence in the proximal region at 100 cM. We further show that the proximal QTL interacts with the previous one detected on the chromosome 5 distal region. Conclusion Our results demonstrate that stratifying genetic population by molecular phenotypes followed by QTL analysis on various subtypes can lead to identification of novel and interacting QTL.

  5. Evaluation and Bulked Segregant Analysis of Major Yield QTL qtl12.1 Introgressed into Indigenous Elite Line for Low Water Availability under Water Stress

    Institute of Scientific and Technical Information of China (English)

    N.Manikanda BOOPATHI; Gat SWAPNASHRI; P.KAVITHA; S.SATHISH; R.NITHYA; Wickneswari RATNAM; Arvind KUMAR

    2013-01-01

    Near isogenic lines carrying large-effect QTL (qtl12.1),which has a consistent influence on grain yield under upland drought stress conditions in a wide range of environments,were evaluated under water stress in the fields.The line which gave higher yield under drought was crossed with a local elite line,PMK3,and forwarded to F2:3 generation.Significant variation was found among the F2:3 lines for agronomic traits under water stress in the fields.Low to high broad sense heritability (H) for investigated traits was also found.Water stress indicators such as leaf rolling and leaf drying were negatively correlated with plant height,biomass and grain yield under stress.Bulked segregant analysis (BSA) was performed with the markers in the vicinity of qtl12.1,and RM27933 was found to be segregated perfectly well in individual components of drought resistant and drought susceptible bulks which were bulked based on yield under water stress among F2:3 lines.Hence,this simple and breeder friendly marker,RM27933,may be useful as a potentially valuable candidate marker for the transfer of the QTL qtl12.1 in the regional breeding program.Bioinformatic analysis of the DNA sequence of the qtl12.1 region was also done to identify and analyze positional candidate genes associated with this QTL and to ascertain the putative molecular basis of qtl12.1.

  6. Mapping QTL influencing gastrointestinal nematode burden in Dutch Holstein-Friesian dairy cattle

    Directory of Open Access Journals (Sweden)

    Georges Michel

    2009-03-01

    Full Text Available Abstract Background Parasitic gastroenteritis caused by nematodes is only second to mastitis in terms of health costs to dairy farmers in developed countries. Sustainable control strategies complementing anthelmintics are desired, including selective breeding for enhanced resistance. Results and Conclusion To quantify and characterize the genetic contribution to variation in resistance to gastro-intestinal parasites, we measured the heritability of faecal egg and larval counts in the Dutch Holstein-Friesian dairy cattle population. The heritability of faecal egg counts ranged from 7 to 21% and was generally higher than for larval counts. We performed a whole genome scan in 12 paternal half-daughter groups for a total of 768 cows, corresponding to the ~10% most and least infected daughters within each family (selective genotyping. Two genome-wide significant QTL were identified in an across-family analysis, respectively on chromosomes 9 and 19, coinciding with previous findings in orthologous chromosomal regions in sheep. We identified six more suggestive QTL by within-family analysis. An additional 73 informative SNPs were genotyped on chromosome 19 and the ensuing high density map used in a variance component approach to simultaneously exploit linkage and linkage disequilibrium in an initial inconclusive attempt to refine the QTL map position.

  7. QTL mapping in new Arabidopsis thaliana advanced intercross-recombinant inbred lines.

    Directory of Open Access Journals (Sweden)

    Sureshkumar Balasubramanian

    Full Text Available BACKGROUND: Even when phenotypic differences are large between natural or domesticated strains, the underlying genetic basis is often complex, and causal genomic regions need to be identified by quantitative trait locus (QTL mapping. Unfortunately, QTL positions typically have large confidence intervals, which can, for example, lead to one QTL being masked by another, when two closely linked loci are detected as a single QTL. One strategy to increase the power of precisely localizing small effect QTL, is the use of an intercross approach before inbreeding to produce Advanced Intercross RILs (AI-RILs. METHODOLOGY/PRINCIPAL FINDINGS: We present two new AI-RIL populations of Arabidopsis thaliana genotyped with an average intermarker distance of 600 kb. The advanced intercrossing design led to expansion of the genetic map in the two populations, which contain recombination events corresponding to 50 kb/cM in an F(2 population. We used the AI-RILs to map QTL for light response and flowering time, and to identify segregation distortion in one of the AI-RIL populations due to a negative epistatic interaction between two genomic regions. CONCLUSIONS/SIGNIFICANCE: The two new AI-RIL populations, EstC and KendC, derived from crosses of Columbia (Col to Estland (Est-1 and Kendallville (Kend-L provide an excellent resource for high precision QTL mapping. Moreover, because they have been genotyped with over 100 common markers, they are also excellent material for comparative QTL mapping.

  8. Combining two Meishan F2 crosses improves the detection of QTL on pig chromosomes 2, 4 and 6

    Directory of Open Access Journals (Sweden)

    Bidanel Jean-Pierre

    2010-11-01

    Full Text Available Abstract Background In pig, a number of experiments have been set up to identify QTL and a multitude of chromosomal regions harbouring genes influencing traits of interest have been identified. However, the mapping resolution remains limited in most cases and the detected QTL are rather inaccurately located. Mapping accuracy can be improved by increasing the number of phenotyped and genotyped individuals and/or the number of informative markers. An alternative approach to overcome the limited power of individual studies is to combine data from two or more independent designs. Methods In the present study we report a combined analysis of two independent design (a French and a Dutch F2 experimental designs, with 2000 F2 individuals. The purpose was to further map QTL for growth and fatness on pig chromosomes 2, 4 and 6. Using QTL-map software, uni- and multiple-QTL detection analyses were applied separately on the two pedigrees and then on the combination of the two pedigrees. Results Joint analyses of the combined pedigree provided (1 greater significance of shared QTL, (2 exclusion of false suggestive QTL and (3 greater mapping precision for shared QTL. Conclusions Combining two Meishan x European breeds F2 pedigrees improved the mapping of QTL compared to analysing pedigrees separately. Our work was facilitated by the access to raw phenotypic data and DNA of animals from both pedigrees and the combination of the two designs with the addition of new markers allowed us to fine map QTL without phenotyping additional animals.

  9. Integrated Metabolo-Transcriptomics Reveals Fusarium Head Blight Candidate Resistance Genes in Wheat QTL-Fhb2

    Science.gov (United States)

    Dhokane, Dhananjay; Karre, Shailesh; Kushalappa, Ajjamada C.; McCartney, Curt

    2016-01-01

    Background Fusarium head blight (FHB) caused by Fusarium graminearum not only causes severe losses in yield, but also reduces quality of wheat grain by accumulating mycotoxins. Breeding for host plant resistance is considered as the best strategy to manage FHB. Resistance in wheat to FHB is quantitative in nature, involving cumulative effects of many genes governing resistance. The poor understanding of genetics and lack of precise phenotyping has hindered the development of FHB resistant cultivars. Though more than 100 QTLs imparting FHB resistance have been reported, none discovered the specific genes localized within the QTL region, nor the underlying mechanisms of resistance. Findings In our study recombinant inbred lines (RILs) carrying resistant (R-RIL) and susceptible (S-RIL) alleles of QTL-Fhb2 were subjected to metabolome and transcriptome profiling to discover the candidate genes. Metabolome profiling detected a higher abundance of metabolites belonging to phenylpropanoid, lignin, glycerophospholipid, flavonoid, fatty acid, and terpenoid biosynthetic pathways in R-RIL than in S-RIL. Transcriptome analysis revealed up-regulation of several receptor kinases, transcription factors, signaling, mycotoxin detoxification and resistance related genes. The dissection of QTL-Fhb2 using flanking marker sequences, integrating metabolomic and transcriptomic datasets, identified 4-Coumarate: CoA ligase (4CL), callose synthase (CS), basic Helix Loop Helix (bHLH041) transcription factor, glutathione S-transferase (GST), ABC transporter-4 (ABC4) and cinnamyl alcohol dehydrogenase (CAD) as putative resistance genes localized within the QTL-Fhb2 region. Conclusion Some of the identified genes within the QTL region are associated with structural resistance through cell wall reinforcement, reducing the spread of pathogen through rachis within a spike and few other genes that detoxify DON, the virulence factor, thus eventually reducing disease severity. In conclusion, we

  10. QTL alleles on chromosome 7 from fatty Meishan pigs reduce fat deposition

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    For detecting QTL in the whole swine genome, 1068 pigs from three F2 populations constructed by crossing European Wild boar and Pietrain (WxP), Meishan and Pietrain (M×P),and Wild Boar and Meishan (W×M) were genotyped for genetic markers evenly spaced at approximately 20 cM intervals. A QTL analysis was performed using a least-squares method. Here the results of the QTL analysis on the porcine chromosome 7 are presented. QTL for carcass composition (e.g. head weight, carcass length, backfat depth, abdominal fat and bacon meat) were mapped in the chromosomal region CYPA/CYPD-TNFB-S0102 in M×P and W×M, but not in W×P.The QTL explained 5.3%-27.2% of the F2 phenotypic variance in the two F2 populations. Most traits affected by the mapped QTL were related to carcass fatness. The mode of gene action of QTL was additive. Surprisingly, in contrast to the parental phenotype, the QTL alleles from fatty Meishan were associated with thinner backfat than Pietrain and Wild Boar alleles, suggesting that the genome of the fatty Meishan pig contains genes which can reduce fat content of carcass substantially.

  11. Sex-specific effects on spatial learning and memory, and sex-independent effects on blood pressure of a <3.3 Mbp rat chromosome 2 QTL region in Dahl salt-sensitive rats.

    Directory of Open Access Journals (Sweden)

    Victoria L Herrera

    Full Text Available Epidemiological studies have consistently found that hypertension is associated with poor cognitive performance. We hypothesize that a putative causal mechanism underlying this association is due to genetic loci affecting both blood pressure and cognition. Consistent with this notion, we reported several blood pressure (BP quantitative trait loci (QTLs that co-localized with navigational performance (Nav-QTLs influencing spatial learning and memory in Dahl rats. The present study investigates a chromosome 2 region harboring BP-f4 and Nav-8 QTLs. We developed two congenic strains, S.R2A and S.R2B introgressing Dahl R-chromosome 2 segments into Dahl S chromosome 2 region spanning BP-f4 and Nav-8 QTLs. Radiotelemetric blood pressure analysis identified only S.R2A congenic rats with lower systolic blood pressure (females: -26.0 mmHg, P = 0.003; males: -30.9 mmHg, P<1×10(-5, diastolic blood pressure (females: -21.2 mmHg, P = 0.01; males: -25.7 mmHg, P<1×10(-5, and mean arterial pressure (females: -23.9 mmHg, P = 0.004; males: -28.0 mmHg, P<1×10(-5 compared with corresponding Dahl S controls, confirming the presence of BP-f4 QTL on rat chromosome 2. The S.R2B congenic segment did not affect blood pressure. Testing of S.R2A, S.R2B, and Dahl S male rats in the Morris water maze (MWM task revealed significantly decreased spatial navigation performance in S.R2A male congenic rats when compared with Dahl S male controls (P<0.05. The S.R2B congenic segment did not affect performance of the MWM task in males. The S.R2A female rats did not differ in spatial navigation when compared with Dahl S female controls, indicating that the Nav-8 effect on spatial navigation is male-specific. Our results suggest the existence of a single QTL on chromosome 2 176.6-179.9 Mbp region which affects blood pressure in both males and females and cognition solely in males.

  12. Statistical Methods for Mapping Multiple QTL

    OpenAIRE

    2008-01-01

    Since Lander and Botstein proposed the interval mapping method for QTL mapping data analysis in 1989, tremendous progress has been made in the last many years to advance new and powerful statistical methods for QTL analysis. Recent research progress has been focused on statistical methods and issues for mapping multiple QTL together. In this article, we review this progress. We focus the discussion on the statistical methods for mapping multiple QTL by maximum likelihood and Bayesian methods ...

  13. Biphasic survival analysis of trypanotolerance QTL in mice

    NARCIS (Netherlands)

    Koudante, O.D.; Thomson, P.C.; Bovenhuis, H.; Iraqi, F.; Gibson, J.P.; Arendonk, van J.A.M.

    2008-01-01

    A marker-assisted introgression (MAI) experiment was conducted to transfer trypanotolerance quantitative trait loci (QTL) from a donor mouse strain, C57BL/6, into a recipient mouse strain, A/J. The objective was to assess the effect of three previously identified chromosomal regions on mouse chromos

  14. Implementation of SNPs in pig genetics: LD and QTL analysis

    NARCIS (Netherlands)

    Jungerius, B.J.

    2004-01-01

    The aim of this thesis was the implementation and application of SNP markers in animal breeding and genetics. The emphasis was on the analysis of fatness traits in pigs, in particular of the imprinted QTL region on SSC2p. Several aspects of the implemetation of SNP markers in genetic analysis of

  15. Differential gene expression in nearly isogenic lines with QTL for partial resistance to Puccinia hordei in barley

    Directory of Open Access Journals (Sweden)

    Marcel Thierry C

    2010-11-01

    Full Text Available Abstract Background The barley-Puccinia hordei (barley leaf rust pathosystem is a model for investigating partial disease resistance in crop plants and genetic mapping of phenotypic resistance has identified several quantitative trait loci (QTL for partial resistance. Reciprocal QTL-specific near-isogenic lines (QTL-NILs have been developed that combine two QTL, Rphq2 and Rphq3, the largest effects detected in a recombinant-inbred-line (RIL population derived from a cross between the super-susceptible line L94 and partially-resistant line Vada. The molecular mechanism underpinning partial resistance in these QTL-NILs is unknown. Results An Agilent custom microarray consisting of 15,000 probes derived from barley consensus EST sequences was used to investigate genome-wide and QTL-specific differential expression of genes 18 hours post-inoculation (hpi with Puccinia hordei. A total of 1,410 genes were identified as being significantly differentially expressed across the genome, of which 55 were accounted for by the genetic differences defined by QTL-NILs at Rphq2 and Rphq3. These genes were predominantly located at the QTL regions and are, therefore, positional candidates. One gene, encoding the transcriptional repressor Ethylene-Responsive Element Binding Factor 4 (HvERF4 was located outside the QTL at 71 cM on chromosome 1H, within a previously detected eQTL hotspot for defence response. The results indicate that Rphq2 or Rphq3 contains a trans-eQTL that modulates expression of HvERF4. We speculate that HvERF4 functions as an intermediate that conveys the response signal from a gene(s contained within Rphq2 or Rphq3 to a host of down-stream defense responsive genes. Our results also reveal that barley lines with extreme or intermediate partial resistance phenotypes exhibit a profound similarity in their spectrum of Ph-responsive genes and that hormone-related signalling pathways are actively involved in response to Puccinia hordei. Conclusions

  16. Identification of Quantitative Trait Loci (QTL) and Candidate Genes for Cadmium Tolerance in Populus

    Energy Technology Data Exchange (ETDEWEB)

    Induri, Brahma R [West Virginia University; Ellis, Danielle R [West Virginia University; Slavov, Gancho [West Virginia University; Yin, Tongming [ORNL; Muchero, Wellington [ORNL; Tuskan, Gerald A [ORNL; DiFazio, Stephen P [West Virginia University

    2012-01-01

    Knowledge of genetic variation in response of Populus to heavy metals like cadmium (Cd) is an important step in understanding the underlying mechanisms of tolerance. In this study, a pseudo-backcross pedigree of Populus trichocarpa and Populus deltoides was characterized for Cd exposure. The pedigree showed significant variation for Cd tolerance thus enabling the identification of relatively tolerant and susceptible genotypes for intensive characterization. A total of 16 QTLs at logarithm of odds (LOD) ratio > 2.5, were found to be associated with total dry weight, its components, and root volume. Four major QTLs for total dry weight were mapped to different linkage groups in control (LG III) and Cd conditions (LG XVI) and had opposite allelic effects on Cd tolerance, suggesting that these genomic regions were differentially controlled. The phenotypic variation explained by Cd QTL for all traits under study varied from 5.9% to 11.6% and averaged 8.2% across all QTL. Leaf Cd contents also showed significant variation suggesting the phytoextraction potential of Populus genotypes, though heritability of this trait was low (0.22). A whole-genome microarray study was conducted by using two genotypes with extreme responses for Cd tolerance in the above study and differentially expressed genes were identified. Candidate genes including CAD2 (CADMIUM SENSITIVE 2), HMA5 (HEAVY METAL ATPase5), ATGTST1 (Arabidopsis thaliana Glutathione S-Transferase1), ATGPX6 (Glutathione peroxidase 6), and ATMRP 14 (Arabidopsis thaliana Multidrug Resistance associated Protein 14) were identified from QTL intervals and microarray study. Functional characterization of these candidate genes could enhance phytoremediation capabilities of Populus.

  17. QTL mapping of powdery mildew resistance in WI 2757 cucumber (Cucumis sativus L.).

    Science.gov (United States)

    He, Xiaoming; Li, Yuhong; Pandey, Sudhakar; Yandell, Brain S; Pathak, Mamta; Weng, Yiqun

    2013-08-01

    Powdery mildew (PM) is a very important disease of cucumber (Cucumis sativus L.). Resistant cultivars have been deployed in production for a long time, but the genetic mechanisms of PM resistance in cucumber are not well understood. A 3-year QTL mapping study of PM resistance was conducted with 132 F2:3 families derived from two cucumber inbred lines WI 2757 (resistant) and True Lemon (susceptible). A genetic map covering 610.4 cM in seven linkage groups was developed with 240 SSR marker loci. Multiple QTL mapping analysis of molecular marker data and disease index of the hypocotyl, cotyledon and true leaf for responses to PM inoculation identified six genomic regions in four chromosomes harboring QTL for PM resistance in WI 2757. Among the six QTL, pm1.1 and pm1.2 in chromosome 1 conferred leaf resistance. Minor QTL pm3.1 (chromosome 3) and pm4.1 (chromosome 4) contributed to disease susceptibility. The two major QTL, pm5.1 and pm5.2 were located in an interval of ~40 cM in chromosome 5 with each explaining 21.0-74.5 % phenotypic variations. Data presented herein support two recessively inherited, linked major QTL in chromosome 5 plus minor QTL in other chromosomes that control the PM resistance in WI 2757. The QTL pm5.2 for hypocotyl resistance plays the most important role in host resistance. Multiple observations in the same year revealed the importance of scoring time in the detection of PM resistance QTL. Results of this study provided new insights into phenotypic and genetic mechanisms of powdery mildew resistance in cucumber. PMID:23689747

  18. Linear models for joint association and linkage QTL mapping

    Directory of Open Access Journals (Sweden)

    Fernando Rohan L

    2009-09-01

    Full Text Available Abstract Background Populational linkage disequilibrium and within-family linkage are commonly used for QTL mapping and marker assisted selection. The combination of both results in more robust and accurate locations of the QTL, but models proposed so far have been either single marker, complex in practice or well fit to a particular family structure. Results We herein present linear model theory to come up with additive effects of the QTL alleles in any member of a general pedigree, conditional to observed markers and pedigree, accounting for possible linkage disequilibrium among QTLs and markers. The model is based on association analysis in the founders; further, the additive effect of the QTLs transmitted to the descendants is a weighted (by the probabilities of transmission average of the substitution effects of founders' haplotypes. The model allows for non-complete linkage disequilibrium QTL-markers in the founders. Two submodels are presented: a simple and easy to implement Haley-Knott type regression for half-sib families, and a general mixed (variance component model for general pedigrees. The model can use information from all markers. The performance of the regression method is compared by simulation with a more complex IBD method by Meuwissen and Goddard. Numerical examples are provided. Conclusion The linear model theory provides a useful framework for QTL mapping with dense marker maps. Results show similar accuracies but a bias of the IBD method towards the center of the region. Computations for the linear regression model are extremely simple, in contrast with IBD methods. Extensions of the model to genomic selection and multi-QTL mapping are straightforward.

  19. Methodologies to characterize uncertainties in regional reanalyses

    Science.gov (United States)

    Borsche, M.; Kaiser-Weiss, A. K.; Undén, P.; Kaspar, F.

    2015-10-01

    When using climate data for various applications, users are confronted with the difficulty to assess the uncertainties of the data. For both in-situ and remote sensing data the issues of representativeness, homogeneity, and coverage have to be considered for the past, and their respective change over time has to be considered for any interpretation of trends. A synthesis of observations can be obtained by employing data assimilation with numerical weather prediction (NWP) models resulting in a meteorological reanalysis. Global reanalyses can be used as boundary conditions for regional reanalyses (RRAs), which run in a limited area (Europe in our case) with higher spatial and temporal resolution, and allow for assimilation of more regionally representative observations. With the spatially highly resolved RRAs, which exhibit smaller scale information, a more realistic representation of extreme events (e.g. of precipitation) compared to global reanalyses is aimed for. In this study, we discuss different methods for quantifying the uncertainty of the RRAs to answer the question to which extent the smaller scale information (or resulting statistics) provided by the RRAs can be relied on. Within the European Union's seventh Framework Programme (EU FP7) project Uncertainties in Ensembles of Regional Re-Analyses (UERRA) ensembles of RRAs (both multi-model and single model ensembles) are produced and their uncertainties are quantified. Here we explore the following methods for characterizing the uncertainties of the RRAs: (A) analyzing the feedback statistics of the assimilation systems, (B) validation against station measurements and (C) grids derived thereof, and (D) against gridded satellite data products. The RRA ensembles (E) provide the opportunity to derive ensemble scores like ensemble spread and other special probabilistic skill scores. Finally, user applications (F) are considered. The various methods are related to user questions they can help to answer.

  20. Mapping quantitative trait loci (QTL in sheep. II. Meta-assembly and identification of novel QTL for milk production traits in sheep

    Directory of Open Access Journals (Sweden)

    Lam Mary K

    2009-10-01

    Full Text Available Abstract An (Awassi × Merino × Merino backcross family of 172 ewes was used to map quantitative trait loci (QTL for different milk production traits on a framework map of 200 loci across all autosomes. From five previously proposed mathematical models describing lactation curves, the Wood model was considered the most appropriate due to its simplicity and its ability to determine ovine lactation curve characteristics. Derived milk traits for milk, fat, protein and lactose yield, as well as percentage composition and somatic cell score were used for single and two-QTL approaches using maximum likelihood estimation and regression analysis. A total of 15 significant (P P http://crcidp.vetsci.usyd.edu.au/cgi-bin/gbrowse/oaries_genome/. Many of the QTL for milk production traits have been reported on chromosomes 1, 3, 6, 16 and 20. Those on chromosomes 3 and 20 are in strong agreement with the results reported here. In addition, novel QTL were found on chromosomes 7, 8, 9, 14, 22 and 24. In a cross-species comparison, we extended the meta-assembly by comparing QTL regions of sheep and cattle, which provided strong evidence for synteny conservation of QTL regions for milk, fat, protein and somatic cell score data between cattle and sheep.

  1. A consensus linkage map of oil palm and a major QTL for stem height.

    Science.gov (United States)

    Lee, May; Xia, Jun Hong; Zou, Zhongwei; Ye, Jian; Rahmadsyah; Alfiko, Yuzer; Jin, Jingjing; Lieando, Jessica Virginia; Purnamasari, Maria Indah; Lim, Chin Huat; Suwanto, Antonius; Wong, Limsoon; Chua, Nam-Hai; Yue, Gen Hua

    2015-01-01

    Oil palm (Elaeis guinensis Jacquin) is the most important source of vegetable oil and fat. Several linkage maps had been constructed using dominant and co-dominant markers to facilitate mapping of QTL. However, dominant markers are not easily transferable among different laboratories. We constructed a consensus linkage map for oil palm using co-dominant markers (i.e. microsatellite and SNPs) and two F1 breeding populations generated by crossing Dura and Pisifera individuals. Four hundreds and forty-four microsatellites and 36 SNPs were mapped onto 16 linkage groups. The map length was 1565.6 cM, with an average marker space of 3.72 cM. A genome-wide scan of QTL identified a major QTL for stem height on the linkage group 5, which explained 51% of the phenotypic variation. Genes in the QTL were predicted using the palm genome sequence and bioinformatic tools. The linkage map supplies a base for mapping QTL for accelerating the genetic improvement, and will be also useful in the improvement of the assembly of the genome sequences. Markers linked to the QTL may be used in selecting dwarf trees. Genes within the QTL will be characterized to understand the mechanisms underlying dwarfing. PMID:25648560

  2. Quantitative trait loci (QTL mapping for growth traits on bovine chromosome 14

    Directory of Open Access Journals (Sweden)

    Marcelo Miyata

    2007-03-01

    Full Text Available Quantitative trait loci (QTL mapping in livestock allows the identification of genes that determine the genetic variation affecting traits of economic interest. We analyzed the birth weight and weight at 60 days QTL segregating on bovine chromosome BTA14 in a F2 resource population using genotypes produced from seven microsatellite markers. Phenotypes were derived from 346 F2 progeny produced from crossing Bos indicus Gyr x Holstein Bos taurus F1 parents. Interval analysis to detect QTL for birth weight revealed the presence of a QTL (p < 0.05 at 1 centimorgan (cM from the centromere with an additive effect of 1.210 ± 0.438 kg. Interval analysis for weight at 60 days revealed the presence of a QTL (p < 0.05 at 0 cM from the centromere with an additive effect of 2.122 ± 0.735 kg. The region to which the QTL were assigned is described in the literature as responsible for some growth traits, milk yield, milk composition, fat deposition and has also been related to reproductive traits such as daughter pregnancy rate and ovulation rate. The effects of the QTL described on other traits were not investigated.

  3. eQTL Viewer: visualizing how sequence variation affects genome-wide transcription

    Directory of Open Access Journals (Sweden)

    Zeng Zhao-Bang

    2007-01-01

    Full Text Available Abstract Background Expression Quantitative Trait Locus (eQTL mapping methods have been used to identify the genetic basis of gene expression variations. To map eQTL, thousands of expression profiles are related with sequence polymorphisms across the genome through their correlated variations. These eQTL distribute in many chromosomal regions, each of which can include many genes. The large number of mapping results produced makes it difficult to consider simultaneously the relationships between multiple genomic regions and multiple expressional profiles. There is a need for informative bioinformatics tools to assist the visualization and interpretation of these mapping results. Results We have developed a web-based tool, called eQTL Viewer, to visualize the relationships between the expression trait genes and the candidate genes in the eQTL regions using Scalable Vector Graphics. The plot generated by eQTL Viewer has the capacity to display mapping results with high resolutions at a variety of scales, and superimpose biological annotations onto the mapping results dynamically. Conclusion Our tool provides an efficient and intuitive way for biologists to explore transcriptional regulation patterns, and to generate hypotheses on the genetic basis of transcriptional regulations.

  4. Characterizing Uncertainty for Regional Climate Change Mitigation and Adaptation Decisions

    Energy Technology Data Exchange (ETDEWEB)

    Unwin, Stephen D.; Moss, Richard H.; Rice, Jennie S.; Scott, Michael J.

    2011-09-30

    This white paper describes the results of new research to develop an uncertainty characterization process to help address the challenges of regional climate change mitigation and adaptation decisions.

  5. Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis.

    Science.gov (United States)

    Wei, Qing-Zhen; Fu, Wen-Yuan; Wang, Yun-Zhu; Qin, Xiao-Dong; Wang, Jing; Li, Ji; Lou, Qun-Feng; Chen, Jin-Feng

    2016-01-01

    The cucumber (Cucumis sativus L.) exhibits extensive variations in fruit size and shape. Fruit length is an important agronomic and domesticated trait controlled by quantitative trait loci (QTLs). Nonetheless, the underlying molecular and genetic mechanisms that determine cucumber fruit length remain unclear. QTL-seq is an efficient strategy for QTL identification that takes advantage of bulked-segregant analysis (BSA) and next-generation sequencing (NGS). In the present study, we conducted QTL mapping and QTL-seq of cucumber fruit length. QTL mapping identified 8 QTLs for immature and mature fruit length. A major-effect QTL fl3.2, which explained a maximum of 38.87% of the phenotypic variation, was detected. A genome-wide comparison of SNP profiles between two DNA bulks identified 6 QTLs for ovary length. QTLs ovl3.1 and ovl3.2 both had major effects on ovary length with a △ (SNP-index) of 0.80 (P < 0.01) and 0.74 (P < 0.01), respectively. Quantitative RT-PCR of fruit size-related homologous genes localized in the consensus QTL FL3.2 was conducted. Four candidate genes exhibited increased expression levels in long fruit genotypes. Our results demonstrated the power of the QTL-seq method in rapid QTL detection and provided reliable QTL regions for fine mapping of fruit length-related loci and for identifying candidate genes. PMID:27271557

  6. Cis-eQTL analysis and functional validation of candidate susceptibility genes for high-grade serous ovarian cancer

    DEFF Research Database (Denmark)

    Lawrenson, Kate; Li, Qiyuan; Kar, Siddhartha;

    2015-01-01

    Genome-wide association studies have reported 11 regions conferring risk of high-grade serous epithelial ovarian cancer (HGSOC). Expression quantitative trait locus (eQTL) analyses can identify candidate susceptibility genes at risk loci. Here we evaluate cis-eQTL associations at 47 regions assoc...

  7. Comparative QTL analysis of maize seed artificial aging between an immortalized F2 population and its corresponding RILs

    Institute of Scientific and Technical Information of China (English)

    Bin Wang; Zhanhui Zhang; Zhiyuan Fu; Zonghua Liu; Yanmin Hu; Jihua Tang

    2016-01-01

    Seed aging decreases the quality and vigor of crop seeds, thereby causing substantial agricultural and economic losses in crops. To identify genetic differences in seed aging between homozygotes and heterozygotes in maize, the seeds of a set of recombinant inbred lines (RILs) and an immortalized F2 (IF2) population were subjected to artificial aging treatments for 0, 2, 3, and 4 days under 45 ºC and 85%relative humidity and seed vigor was then evaluated in a field experiment. Seed vigor of all entries tested decreased sharply with longer aging treatment and seed vigor decreased more slowly in heterozygotes than in homozygotes. Forty-nine QTL were detected for four measured seed vigor traits in the RIL (28 QTL) and IF2 (21 QTL) populations. Only one QTL, qGP5, was detected in both populations, indicating that the genes involved in anti-aging mechanisms differed between inbred lines and hybrids. Several QTL were identified to be responsible for multiple seed vigor traits simultaneously in the RIL and IF2 populations under artificial aging conditions. These QTL may include major genes for seed vigor or seed aging. QTL qVI4b and qGE3a detected in the RIL population coincided with genes ZmLOX1 and ZmPLD1 in the same respective chromosomal regions. These QTL would be useful for screening for anti-aging genes in maize breeding.

  8. QTL and QTL x Environment Effects on Agronomic and Nitrogen Acquisition Traits in Rice

    Institute of Scientific and Technical Information of China (English)

    Senapathy Senthilvel; Kunnummal Kurungara Vinod; Palaniappan Malarvizhi; Marappa Maheswaran

    2008-01-01

    Agricultural environments deteriorate due to excess nitrogen application.Breeding for low nitrogen responsive genotypes can reduce soil nitrogen input.Rice genotypes respond variably to soil available nitrogen.The present study attempted quantification of genotype x nitrogen level interaction and mapping of quantitative trait loci (QTLs) associated with nitrogen use efficiency (NUE) and other associated agronomic traits.Twelve parameters were observed across a set of 82 double haploid (DH) lines derived from IR64/Azucena.Three nitrogen regimes namely,native (0 kg/ha; no nitrogen applied),optimum (100 kg/ha) and high (200 kg/ha) replicated thrice were the environments.The parents and DH lines were significantly varying for all traits under different nitrogen regimes.All traits except plant height recorded significant genotype x environment interaction.Individual plant yield was positively correlated with nitrogen use efficiency and nitrogen uptake.Sixteen QTLs were detected by composite interval mapping.Eleven QTLs showed significant QTL x environment interactions.On chromosome 3,seven QTLs were detected associated with nitrogen use,plant yield and associated traits.A QTL region between markers RZ678,RZ574 and RZ284 was associated with nitrogen use and yield.This chromosomal region was enriched with expressed gene sequences of known key nitrogen assimilation genes.

  9. QTL Information Table: 188 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available 30 RZ801 pha Cao, G.Q., Zhu, J., He, C.X., Gao, Y.M., and Wu, P. (2001). QTL analysis for epistatic effects ...and QTL x environment interaction effects on final height of rice (Oryza sativa L.). Yi Chuan Xue Bao 28, 135-143. ...

  10. QTL Information Table: 732 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qtl12.1 Resistance or Tolerance Drought tolerance Plant heigh at maturity SSR C)Interval F3 Way Rare...m Vandana A RM28048 RM28166 pha Bernier, J., Kumar, A., Ramaiah, V., Spaner, D., and Atlin, G. (2007). A Lar...ge-Effect QTL for Grain Yield under Reproductive-Stage Drought Stress in Upland Rice. Crop

  11. Detection on OAR7 of QTL affecting fat and protein yields in dairy sheep

    Directory of Open Access Journals (Sweden)

    Antonello Carta

    2010-01-01

    Full Text Available The objective of this paper was identifying QTL that affect fat and protein yields in dairy sheep independently of milk yield. Data were collected in an experimental flock of 887 ewes organized in a daughter design. QTL detection focused on OAR7 where 13 microsatellites were available. The genetic abilities to produce fat and protein independently from the ability to produce milk were estimated as the residuals of the regression of EBV for fat and protein yields on EBV for milk yield. One QTL affecting fat yield (CWP=0.00009 and one QTL affecting protein yield (CWP=0.006 were detected. The most probable QTL location was 115.3 cM in the Sheep Best Position Linkage Map Version 4.7 for both traits. No QTL affecting milk yield was detected. The analysis of fat and protein yields independently of milk yield is an effective strategy to identify chromosomal regions affecting milk composition with no detrimental effect on milk yield.

  12. An interaction quantitative trait loci tool implicates epistatic functional variants in an apoptosis pathway in smallpox vaccine eQTL data.

    Science.gov (United States)

    Lareau, C A; White, B C; Oberg, A L; Kennedy, R B; Poland, G A; McKinney, B A

    2016-06-01

    Expression quantitative trait loci (eQTL) studies have functionalized nucleic acid variants through the regulation of gene expression. Although most eQTL studies only examine the effects of single variants on transcription, a more complex process of variant-variant interaction (epistasis) may regulate transcription. Herein, we describe a tool called interaction QTL (iQTL) designed to efficiently detect epistatic interactions that regulate gene expression. To maximize biological relevance and minimize the computational and hypothesis testing burden, iQTL restricts interactions such that one variant is within a user-defined proximity of the transcript (cis-regulatory). We apply iQTL to a data set of 183 smallpox vaccine study participants with genome-wide association study and gene expression data from unstimulated samples and samples stimulated by inactivated vaccinia virus. While computing only 0.15% of possible interactions, we identify 11 probe sets whose expression is regulated through a variant-variant interaction. We highlight the functional epistatic interactions among apoptosis-related genes, DIABLO, TRAPPC4 and FADD, in the context of smallpox vaccination. We also use an integrative network approach to characterize these iQTL interactions in a posterior network of known prior functional interactions. iQTL is an efficient, open-source tool to analyze variant interactions in eQTL studies, providing better understanding of the function of epistasis in immune response and other complex phenotypes. PMID:27052692

  13. qtl.outbred: Interfacing outbred line cross data with the R/qtl mapping software

    Science.gov (United States)

    2011-01-01

    Background qtl.outbred is an extendible interface in the statistical environment, R, for combining quantitative trait loci (QTL) mapping tools. It is built as an umbrella package that enables outbred genotype probabilities to be calculated and/or imported into the software package R/qtl. Findings Using qtl.outbred, the genotype probabilities from outbred line cross data can be calculated by interfacing with a new and efficient algorithm developed for analyzing arbitrarily large datasets (included in the package) or imported from other sources such as the web-based tool, GridQTL. Conclusion qtl.outbred will improve the speed for calculating probabilities and the ability to analyse large future datasets. This package enables the user to analyse outbred line cross data accurately, but with similar effort than inbred line cross data. PMID:21615912

  14. North Central regional environmental characterization report: executive summary - final

    International Nuclear Information System (INIS)

    This Executive Summary of the final North Central Regional Environmental Characterization Report (RECR) is issued primarily for public information purposes and provides a general overview of the report. The complete RECR presents available regional environmental information pertinent to siting a repository for high-level nuclear waste in crystalline rock in Minnesota, Wisconsin, and the Upper Peninsula of Michigan. For each of the States within the North Central Region, information is provided on the environmental disqualifying factors and the environmental regional screening variables to be used in region-to-area screening

  15. Northeastern Regional Environmental Characterization Report. Executive summary. Final report

    International Nuclear Information System (INIS)

    This Executive Summary of the final Northeastern Regional Environmental Characterization Report (RECR) is issued primarily for public information purposes and provides a general overview of the report. The complete RECR presents available regional environmental information pertinent to siting a repository for high-level nuclear waste in crystalline rock in Connecticut, Maine, Massachusetts, New Hampshire, New Jersey, New York, Pennsylvania, Rhode Island, and Vermont. For each of the states within the Northeastern Region, information is provided on the environmental disqualifying factors and the environmental regional screening variables to be used in region-to-area screening

  16. Southeastern Regional Environmental Characterization Report: executive summary. Final report

    International Nuclear Information System (INIS)

    This Executive Summary of the final ''Southeastern Regional Environmental Characterization Report'' (RECR) is issued primarily for public information purposes and provides a general overview of the report. The complete RECR presents available regional environmental information pertinent to siting a repository or high-level nuclear waste in crystalline rock in central Maryland; noncoastal Virginia, North Carolina, and South Carolina; and northern Georgia. For each of the states within the Southeastern Region, information is provided on the environmental disqualifying factors and the environmental regional screening variables to be used in region-to-area screening

  17. Southeastern Regional Geologic Characterization Report. Executive summary. Final report

    International Nuclear Information System (INIS)

    This Executive Summary of the final Southeastern Regional Geologic Characterization Report (RGCR) is issued primarily for public information purposes, and provides a general overview of the report. The complete RGCR presents available regional geologic information pertinent to siting a repository for high-level nuclear waste in crystalline rock in central Maryland; noncoastal Virginia, North Carolina, and South Carolina; and northern Georgia. For each of the states within the Southeastern Region, information is provided on the geologic disqualifying factor and the geologic regional screening variables to be used in region-to-area screening

  18. Identification of QTL controlling meat quality traits in an F2 cross between two chicken lines selected for either low or high growth rate

    Directory of Open Access Journals (Sweden)

    Simon Jean

    2007-06-01

    traits, muscle biochemistry and ultimately meat quality traits. Several QTL regions were identified that are worthy of further characterization. Some QTLs may in fact co-localize, suggesting pleiotropic effects for some chromosomal regions.

  19. QTL analysis for some quantitative traits in bread wheat

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Quantitative trait loci (QTL) analysis was conducted in bread wheat for 14 important traits utilizing data from four different mapping populations involving different approaches of QTL analysis. Analysis for grain protein content (GPC) suggested that the major part of genetic variation for this trait is due to environmental interactions. In contrast, pre-harvest sprouting tolerance (PHST) was controlled mainly by main effect QTL (M-QTL) with very little genetic variation due to environmental interactions; a major QTL for PHST was detected on chromosome arm 3AL. For grain weight, one QTL each was detected on chromosome arms 1AS, 2BS and 7AS. QTL for 4 growth related traits taken together detected by different methods ranged from 37 to 40; nine QTL that were detected by single-locus as well as two-locus analyses were all M-QTL. Similarly, single-locus and two-locus QTL analyses for seven yield and yield contributing traits in two populations respectively allowed detection of 25 and 50 QTL by composite interval mapping (CIM), 16 and 25 QTL by multiple-trait composite interval mapping (MCIM) and 38 and 37 QTL by two-locus analyses. These studies should prove useful in QTL cloning and wheat improvement through marker aided selection.

  20. Co-localization of growth QTL with differentially expressed candidate genes in rainbow trout.

    Science.gov (United States)

    Kocmarek, Andrea L; Ferguson, Moira M; Danzmann, Roy G

    2015-09-01

    We tested whether genes differentially expressed between large and small rainbow trout co-localized with familial QTL regions for body size. Eleven chromosomes, known from previous work to house QTL for weight and length in rainbow trout, were examined for QTL in half-sibling families produced in September (1 XY male and 1 XX neomale) and December (1 XY male). In previous studies, we identified 108 candidate genes for growth expressed in the liver and white muscle in a subset of the fish used in this study. These gene sequences were BLASTN aligned against the rainbow trout and stickleback genomes to determine their location (rainbow trout) and inferred location based on synteny with the stickleback genome. Across the progeny of all three males used in the study, 63.9% of the genes with differential expression appear to co-localize with the QTL regions on 6 of the 11 chromosomes tested in these males. Genes that co-localized with QTL in the mixed-sex offspring of the two XY males primarily showed up-regulation in the muscle of large fish and were related to muscle growth, metabolism, and the stress response. PMID:26360524

  1. QTL Information Table: 119 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Flowering heading date RFLP C)Interval BC1F9 Nipponbare Kasalath A R2171 R21 ... d temperature: a QTL analysis using a phenological model . Theor Appl Genet 110, 778-786. ...

  2. QTL Information Table: 692 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qTRA7 Resistance or Tolerance Other stress resistance tolerance to disturbance trampling toleran ... , M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture ... and Its Ecological Significance in Asian Wild Rice ...

  3. QTL Information Table: 181 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Glu6 Physiological trait Eating quality glutelin subunit polypeptides A)Physical OSJNBa0083F15 p ... . QTL mapping of the root traits in rice seedling. Yi ... Chuan Xue Bao 28, 433-438. ...

  4. QTL Information Table: 468 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Root Root / Shoot Ratio of Dry Weight RFLP C)Interval DHL ZYQ8 Jingxi 17 B R ... . QTL mapping of the root traits in rice seedling. Yi ... Chuan Xue Bao 28, 433-438. ...

  5. QTL Information Table: 843 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available parison between QTLs and expressed sequence tags. TAG Th... T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and com

  6. QTL Information Table: 444 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Resistance or Tolerance Insect resistance Green ... rice hopper RFLP C)Interval RIL Asominori IR24 B ... Yoshimura, A. (1999). QTL mapping of antibiosis to green ... leafhopper, Nephotettix virescens Distant and gree ...

  7. QTL Information Table: 840 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available parison between QTLs and expressed sequence tags. TAG Th... T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and com

  8. QTL Information Table: 837 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available map: QTL analysis and comparison between QTLs and expressed sequence tags. TAG T..., T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function

  9. QTL Information Table: 845 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available map: QTL analysis and comparison between QTLs and expressed sequence tags. TAG T..., T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function

  10. QTL Information Table: 842 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available parison between QTLs and expressed sequence tags. TAG Th... T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and com

  11. QTL Information Table: 735 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available (2007). A Large-Effect QTL for Grain Yield under Reproductive-Stage Drought Stress in Upland Rice. Crop Sci. 47, 507-516. http://crop.scijournals.org/cgi/content/abstract/47/2/507 ...

  12. QTL Information Table: 731 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available 007). A Large-Effect QTL for Grain Yield under Reproductive-Stage Drought Stress in Upland Rice. Crop Sci. 47, 507-516. http://crop.scijournals.org/cgi/content/abstract/47/2/507 ...

  13. QTL Information Table: 733 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available 007). A Large-Effect QTL for Grain Yield under Reproductive-Stage Drought Stress in Upland Rice. Crop Sci. 47, 507-516. http://crop.scijournals.org/cgi/content/abstract/47/2/507 ...

  14. solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database

    Directory of Open Access Journals (Sweden)

    van der Knaap Esther

    2010-10-01

    Full Text Available Abstract Background A common approach to understanding the genetic basis of complex traits is through identification of associated quantitative trait loci (QTL. Fine mapping QTLs requires several generations of backcrosses and analysis of large populations, which is time-consuming and costly effort. Furthermore, as entire genomes are being sequenced and an increasing amount of genetic and expression data are being generated, a challenge remains: linking phenotypic variation to the underlying genomic variation. To identify candidate genes and understand the molecular basis underlying the phenotypic variation of traits, bioinformatic approaches are needed to exploit information such as genetic map, expression and whole genome sequence data of organisms in biological databases. Description The Sol Genomics Network (SGN, http://solgenomics.net is a primary repository for phenotypic, genetic, genomic, expression and metabolic data for the Solanaceae family and other related Asterids species and houses a variety of bioinformatics tools. SGN has implemented a new approach to QTL data organization, storage, analysis, and cross-links with other relevant data in internal and external databases. The new QTL module, solQTL, http://solgenomics.net/qtl/, employs a user-friendly web interface for uploading raw phenotype and genotype data to the database, R/QTL mapping software for on-the-fly QTL analysis and algorithms for online visualization and cross-referencing of QTLs to relevant datasets and tools such as the SGN Comparative Map Viewer and Genome Browser. Here, we describe the development of the solQTL module and demonstrate its application. Conclusions solQTL allows Solanaceae researchers to upload raw genotype and phenotype data to SGN, perform QTL analysis and dynamically cross-link to relevant genetic, expression and genome annotations. Exploration and synthesis of the relevant data is expected to help facilitate identification of candidate genes

  15. QTL Information Table: 730 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qtl12.1 Resistance or Tolerance Drought tolerance Harvest index SSR C)Interval F3 W...ay Rarem Vandana A RM7195 RM28166 pha Bernier, J., Kumar, A., Ramaiah, V., Spaner, D., and Atlin, G. (2007).... A Large-Effect QTL for Grain Yield under Reproductive-Stage Drought Stress in Upland Rice. Crop Sci. 47, 507-516. http://crop.scijournals.org/cgi/content/abstract/47/2/507 ...

  16. QTL Information Table: 729 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qtl12.1 Resistance or Tolerance Drought tolerance Biomass yield SSR C)Interval F3 Way Rare...m Vandana A RM28048 RM28166 pha Bernier, J., Kumar, A., Ramaiah, V., Spaner, D., and Atlin, G. (2007). A Lar...ge-Effect QTL for Grain Yield under Reproductive-Stage Drought Stress in Upland Rice. Crop Sci. 47, 507-516. http://crop.scijournals.org/cgi/content/abstract/47/2/507 ...

  17. QTL Information Table: 728 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qtl12.1 Resistance or Tolerance Drought tolerance Grain yield SSR C)Interval F3 Way Rare...m Vandana A RM28048 RM511 pha Bernier, J., Kumar, A., Ramaiah, V., Spaner, D., and Atlin, G. (2007). A Lar...ge-Effect QTL for Grain Yield under Reproductive-Stage Drought Stress in Upland Rice. Crop Sci. 47, 507-516. http://crop.scijournals.org/cgi/content/abstract/47/2/507 ...

  18. Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits.

    Science.gov (United States)

    Imumorin, Ikhide G; Kim, Eun-Hee; Lee, Yun-Mi; De Koning, Dirk-Jan; van Arendonk, Johan A; De Donato, Marcos; Taylor, Jeremy F; Kim, Jong-Joo

    2011-01-01

    Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We identified 24 POE-QTL on 15 Bos taurus autosomes (BTAs) of which six were significant at 5% genome-wide (GW) level and 18 at the 5% chromosome-wide (CW) significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 (linkage region of 0-9 cM; genomic region of 5.0-10.8 Mb), for which only one imprinted ortholog is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4 ∼ 5.1% of each trait's phenotypic variance. Comparative in silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologs map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only two (GNAS and PEG3) have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologs of imprinted genes so as to investigate their effects on quantitative traits. PMID:22303340

  19. Genome scan for parent-of-origin QTL effects on bovine growth and carcass traits

    Directory of Open Access Journals (Sweden)

    Ikhide G. Imumorin

    2011-07-01

    Full Text Available Parent-of-origin effects (POE such as genomic imprinting influence growth and body composition in livestock, rodents and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL with POE on growth and carcass traits in Angus x Brahman cattle crossbreds. We identified 24 POE-QTL on 15 Bos taurus autosomes (BTAs of which 6 were significant at 5% genome-wide level and 18 at the 5% chromosome-wide significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 [linkage region of 0 – 9 cM; genomic region of 5.0 – 10.8 Mb], for which only one imprinted orthologue is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4% ~ 5.1% of each trait’s phenotypic variance. Comparative in-silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologues map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only 2 (GNAS and PEG3 have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologues of imprinted genes so as to investigate their effects on quantitative traits.

  20. Ancestral QTL alleles from wild emmer wheat improve drought resistance and productivity in modern wheat cultivars

    Directory of Open Access Journals (Sweden)

    Lianne eMerchuk-Ovnat

    2016-04-01

    Full Text Available Wild emmer wheat (Triticum turgidum ssp. dicoccoides is considered a promising source for improving stress resistances in domesticated wheat. Here we explored the potential of selected quantitative trait loci (QTLs from wild emmer wheat, introgressed via marker-assisted selection, to enhance drought resistance in elite durum (T. turgidum ssp. durum and bread (T. aestivum wheat cultivars. The resultant near-isogenic lines (BC3F3 and BC3F4 were genotyped using SNP array to confirm the introgressed genomic regions and evaluated in two consecutive years under well-watered (690–710 mm and water-limited (290–320 mm conditions. Three of the introgressed QTLs were successfully validated, two in the background of durum wheat cv. Uzan (on chromosomes 1BL and 2BS, and one in the background of bread wheat cvs. Bar Nir and Zahir (chromosome 7AS. In most cases, the QTL x environment interaction was validated in terms of improved grain yield and biomass - specifically under drought (7AS QTL in cv. Bar Nir background, under both treatments (2BS QTL, and a greater stability across treatments (1BL QTL. The results provide a first demonstration that introgression of wild emmer QTL alleles can enhance productivity and yield stability across environments in domesticated wheat, thereby enriching the modern gene pool with essential diversity for the improvement of drought resistance.

  1. QTL mapping for two commercial traits in farmed saltwater crocodiles (Crocodylus porosus).

    Science.gov (United States)

    Miles, L G; Isberg, S R; Thomson, P C; Glenn, T C; Lance, S L; Dalzell, P; Moran, C

    2010-04-01

    The recent generation of a genetic linkage map for the saltwater crocodile (Crocodylus porosus) has now made it possible to carry out the systematic searches necessary for the identification of quantitative trait loci (QTL) affecting traits of economic, as well as evolutionary, importance in crocodilians. In this study, we conducted genome-wide scans for two commercially important traits, inventory head length (which is highly correlated with growth rate) and number of scale rows (SR, a skin quality trait), for the existence of QTL in a commercial population of saltwater crocodiles at Darwin Crocodile Farm, Northern Territory, Australia. To account for the uncommonly large difference in sex-specific recombination rates apparent in the saltwater crocodile, a duel mapping strategy was employed. This strategy employed a sib-pair analysis to take advantage of our full-sib pedigree structure, together with a half-sib analysis to account for, and take advantage of, the large difference in sex-specific recombination frequencies. Using these approaches, two putative QTL regions were identified for SR on linkage group 1 (LG1) at 36 cM, and on LG12 at 0 cM. The QTL identified in this investigation represent the first for a crocodilian and indeed for any non-avian member of the Class Reptilia. Mapping of QTL is an important first step towards the identification of genes and causal mutations for commercially important traits and the development of selection tools for implementation in crocodile breeding programmes for the industry. PMID:19917044

  2. Ancestral QTL Alleles from Wild Emmer Wheat Improve Drought Resistance and Productivity in Modern Wheat Cultivars

    Science.gov (United States)

    Merchuk-Ovnat, Lianne; Barak, Vered; Fahima, Tzion; Ordon, Frank; Lidzbarsky, Gabriel A.; Krugman, Tamar; Saranga, Yehoshua

    2016-01-01

    Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is considered a promising source for improving stress resistances in domesticated wheat. Here we explored the potential of selected quantitative trait loci (QTLs) from wild emmer wheat, introgressed via marker-assisted selection, to enhance drought resistance in elite durum (T. turgidum ssp. durum) and bread (T. aestivum) wheat cultivars. The resultant near-isogenic lines (BC3F3 and BC3F4) were genotyped using SNP array to confirm the introgressed genomic regions and evaluated in two consecutive years under well-watered (690–710 mm) and water-limited (290–320 mm) conditions. Three of the introgressed QTLs were successfully validated, two in the background of durum wheat cv. Uzan (on chromosomes 1BL and 2BS), and one in the background of bread wheat cvs. Bar Nir and Zahir (chromosome 7AS). In most cases, the QTL x environment interaction was validated in terms of improved grain yield and biomass—specifically under drought (7AS QTL in cv. Bar Nir background), under both treatments (2BS QTL), and a greater stability across treatments (1BL QTL). The results provide a first demonstration that introgression of wild emmer QTL alleles can enhance productivity and yield stability across environments in domesticated wheat, thereby enriching the modern gene pool with essential diversity for the improvement of drought resistance. PMID:27148287

  3. Microsomal Omega-3 Fatty Acid Desaturase Genes in Low Linolenic Acid Soybean Line RG10 and Validation of Major Linolenic Acid QTL

    Science.gov (United States)

    Reinprecht, Yarmilla; Pauls, K. Peter

    2016-01-01

    High levels of linolenic acid (80 g kg−1) are associated with the development of off-flavors and poor stability in soybean oil. The development of low linolenic acid lines such as RG10 (20 g kg−1 linolenic acid) can reduce these problems. The level of linolenic acid in seed oil is determined by the activities of microsomal omega-3 fatty acid desaturases (FAD3). A major linolenic acid QTL (>70% of variation) on linkage group B2 (chromosome Gm14) was previously detected in a recombinant inbred line population from the RG10 × OX948 cross. The objectives of this study were to validate the major linolenic acid QTL in an independent population and characterize all the soybean FAD3 genes. Four FAD3 genes were sequenced and localized in RG10 and OX948 and compared to the genes in the reference Williams 82 genome. The FAD3A gene sequences mapped to the locus Glyma.14g194300 [on the chromosome Gm14 (B2)], which is syntenic to the FAD3B gene (locus Glyma.02g227200) on the chromosome Gm02 (D1b). The location of the FAD3A gene is the same as was previously determined for the fan allele, that conditions low linolenic acid content and several linolenic acid QTL, including Linolen 3-3, mapped previously with the RG10 × OX948 population and confirmed in the PI 361088B × OX948 population as Linolen-PO (FAD3A). The FAD3B gene-based marker, developed previously, was mapped to the chromosome Gm02 (D1b) in a region containing a newly detected linolenic acid QTL [Linolen-RO(FAD3B)] in the RG10 × OX948 genetic map and corresponds well with the in silico position of the FAD3B gene sequences. FAD3C and FAD3D gene sequences, mapped to syntenic regions on chromosomes Gm18 (locus Glyma.18g062000) and Gm11 (locus Glyma.11g227200), respectively. Association of linolenic acid QTL with the desaturase genes FAD3A and FAD3B, their validation in an independent population, and development of FAD3 gene-specific markers should simplify and accelerate breeding for low linolenic acid soybean

  4. Refining QTL with high-density SNP genotyping and whole genome sequence in three cattle breeds

    DEFF Research Database (Denmark)

    Sahana, Goutam; Guldbrandtsen, Bernt; Lund, Mogens Sandø

    2012-01-01

    Genome-wide association study was carried out in Nordic Holsteins, Nordic Red and Jersey breeds for functional traits using BovineHD Genotyping BreadChip (Illumina, San Diego, CA). The association analyses were carried out using both linear mixed model approach and a Bayesian variable selection...... method. Principal components were used to account for population structure. The QTL segregating in all three breeds were selected and a few of the most significant ones were followed in further analyses. The polymorphisms in the identified QTL regions were imputed using 90 whole genome sequences...

  5. Mapping the quantitative trait loci (QTL) controlling seed morphology in sunflower (Helianthus annuus L.)

    Science.gov (United States)

    This paper reports the results of analyzing the quantitative trait loci (QTL) underlying sunflower seed morphological traits in a segregating population derived from an oilseed by confection cross. A linkage map containing 165 target region amplification polymorphism (TRAP) and 44 simple sequence re...

  6. MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments

    Directory of Open Access Journals (Sweden)

    Charcosset Alain

    2007-02-01

    Full Text Available Abstract Background Integration of multiple results from Quantitative Trait Loci (QTL studies is a key point to understand the genetic determinism of complex traits. Up to now many efforts have been made by public database developers to facilitate the storage, compilation and visualization of multiple QTL mapping experiment results. However, studying the congruency between these results still remains a complex task. Presently, the few computational and statistical frameworks to do so are mainly based on empirical methods (e.g. consensus genetic maps are generally built by iterative projection. Results In this article, we present a new computational and statistical package, called MetaQTL, for carrying out whole-genome meta-analysis of QTL mapping experiments. Contrary to existing methods, MetaQTL offers a complete statistical process to establish a consensus model for both the marker and the QTL positions on the whole genome. First, MetaQTL implements a new statistical approach to merge multiple distinct genetic maps into a single consensus map which is optimal in terms of weighted least squares and can be used to investigate recombination rate heterogeneity between studies. Secondly, assuming that QTL can be projected on the consensus map, MetaQTL offers a new clustering approach based on a Gaussian mixture model to decide how many QTL underly the distribution of the observed QTL. Conclusion We demonstrate using simulations that the usual model choice criteria from mixture model literature perform relatively well in this context. As expected, simulations also show that this new clustering algorithm leads to a reduction in the length of the confidence interval of QTL location provided that across studies there are enough observed QTL for each underlying true QTL location. The usefulness of our approach is illustrated on published QTL detection results of flowering time in maize. Finally, MetaQTL is freely available at http://bioinformatics.org/mqtl.

  7. Identification of carcass and meat quality QTL in an F2 Duroc x Pietrain pig resource population using different least-squares analysis models

    Directory of Open Access Journals (Sweden)

    Igseo eChoi

    2011-05-01

    Full Text Available A three-generation resource population was constructed by crossing pigs from the Duroc and Pietrain breeds. In this study, 954 F2 animals were used to identify quantitative trait loci (QTL affecting carcass and meat quality traits. Based on results of the first scan analyzed with a line-cross model using 124 microsatellite markers and 510 F2 animals, 9 chromosomes were selected for genotyping of additional markers. Twenty additional markers were genotyped for 954 F2 animals and 20 markers used in the first scan were genotyped for 444 additional F2 animals. Three different Mendelian models using least-squares for QTL analysis were applied for the second scan: a line-cross model, a half-sib model, and a combined line-cross and half-sib model. Significance thresholds were determined by false discovery rate (FDR. In total, 50 QTL using the line-cross model, 38 QTL using the half-sib model and 3 additional QTL using the combined line-cross and half-sib model were identified (q < 0.05. The line-cross and half-sib models revealed strong evidence for QTL regions on SSC6 for carcass traits (e.g., 10th-rib backfat; q < 0.0001 and on SSC15 for meat quality traits (e.g., tenderness, color, pH; q < 0.01, respectively. QTL for pH (SSC3, dressing percent (SSC7, marbling score and moisture percent (SSC12, CIE a* (SSC16 and carcass length and spareribs weight (SSC18 were also significant (q < 0.01. Additional marker and animal genotypes increased the statistical power for QTL detection, and applying different analysis models allowed confirmation of QTL and detection of new QTL.

  8. Biphasic survival analysis of trypanotolerance QTL in mice.

    Science.gov (United States)

    Koudandé, O D; Thomson, P C; Bovenhuis, H; Iraqi, F; Gibson, J P; van Arendonk, J A M

    2008-04-01

    A marker-assisted introgression (MAI) experiment was conducted to transfer trypanotolerance quantitative trait loci (QTL) from a donor mouse strain, C57BL/6, into a recipient mouse strain, A/J. The objective was to assess the effect of three previously identified chromosomal regions on mouse chromosomes 1 (MMU1), 5 (MMU5) and 17 (MMU17) in different genetic backgrounds on the survival pattern following infection with Trypanosoma congolense. An exploratory data analysis revealed a biphasic pattern of time to death, with highly distinct early and late mortality phases. In this paper, we present survival analysis methods that account for the biphasic mortality pattern and results of reanalyzing the data from the MAI experiment. The analysis with a Weibull mixture model confirmed the biphasic pattern of time to death. Mortality phase, an unobserved variable, appears to be an important factor influencing survival time and is modeled as a binary outcome variable using logistic regression analysis. Accounting for this biphasic pattern in the analysis reveals that a previously observed sex effect on average survival is rather an effect on proportion of mice in the two mortality phases. The C57BL/6 (donor) QTL alleles on MMU1 and MMU17 act dominantly in the late mortality phase while the A/J (recipient) QTL allele on MMU17 acts dominantly in the early mortality phase. From this study, we found clear evidence for a biphasic survival pattern and provided models for its analysis. These models can also be used when studying defense mechanisms against other pathogens. Finally, these approaches provide further information on the nature of gene actions. PMID:18253157

  9. QTL detection for physicochemical characteristics of cashew apple

    Directory of Open Access Journals (Sweden)

    Francisco Herbeth Costa dos Santos

    2011-08-01

    Full Text Available The identification of quantitative trait loci (QTL and marker-assisted selection have aroused great interest inbreeding programs aiming at fruit quality. The objective of this study was to detect QTL related to the quality of the cashew apple.The physicochemical characteristics oligomeric phenolics, total soluble solids, total titrable acidity and vitamin C contents wereanalyzed in the mapped cashew population. QTL were detected by QTL interval and multiple QTL mapping. The results showedhigh phenotypic variation in the segregating F1 generation for all traits. Eighteen QTL associated with cashew quality wereidentified: three for oligomeric phenolics, five for total soluble solids, six for total acidity and four for vitamin C. QTL are promisingfor marker-assisted selection since they have the greatest phenotypic effects and contribution to phenotypic variation.

  10. Northeastern Regional environmental characterization report. Volume 1. Final report

    International Nuclear Information System (INIS)

    This report presents available environmental information pertinent to siting a repository for high-level nuclear waste in crystalline rock in Maine, New Hampshire, Vermont, northeastern and southeastern New York, Massachusetts, Rhode Island, Connecticut, northern New Jersey, and eastern Pennsylvania. For each of the States within the Northeastern Region, information is provided on those environmental disqualifying factors and regional screening variables to be used in region-to-area screening. These environmental factors and variables include existing and proposed Federal-protected lands, components of National Forest Lands, proximity to Federal-protected lands, existing State-protected lands, proximity to State-protected lands, population density and distribution, proximity to highly populated areas, or to 1-mile-square areas with 1000 or more persons, National and State forest lands, designated critical habitats for threatened and endangered species, surface water bodies, and wetlands. In addition, supplementary descriptive information providing a general characterization of the region is presented, as is information on environmental parameters that will be of use at later phases of screening. Also included is a discussion of the relationship between the US Department of Energy Siting Guidelines (10 CFR 960) and those environmental disqualifying factors and regional screening variables to be used in the region-to-area screening process

  11. Revised draft: North Central Regional environmental characterization report. Volume 1

    International Nuclear Information System (INIS)

    This report presents available environmental information pertinent to siting a repository for high-level nuclear waste in crystalline rock in Minnesota, Wisconsin, and the Upper Peninsula of Michigan. For each of the states within the North Central Region, information is provided on those environmental disqualifying factors and regional screening variables to be used in region-to-area screening. These environmental factors and variables include existing and proposed federal protected lands, proximity to federal protected lands, existing state protected lands, proximity to state protected lands, population density and distribution, proximity to highly populated areas, national and state forest lands, state wildlife lands, designated critical habitats for threatened and endangered species, surface water bodies, and wetlands. In addition, supplementary descriptive information providing a general characterization of the region is presented, as is information on environmental parameters that may be of use at later phases of screening. Also included is a discussion of the relationship between the DOE Siting Guidelines and those environmental disqualifying factors and regional screening variables to be used in the region-to-area screening process

  12. Revised draft: Northeastern Regional environmental characterization report. Volume 1

    International Nuclear Information System (INIS)

    This report presents available environmental information pertinent to siting a repository for high-level nuclear waste in crystalline rock in Maine, New Hampshire, Vermont, northeastern and southeastern New York, Massachusetts, Rhode Island, Connecticut, northern New Jersey, and eastern Pennsylvania. For each of the states within the Northeastern Region, information is provided on those environmental disqualifying factors and regional screening variables to be used in region-to-area screening. These environmental factors and variables include existing and proposed federal protected lands, proximity to federal protected lands, existing state protected lands, proximity to state protected lands, population density and distribution, proximity to highly populated areas, national and state forest lands, state wildlife lands, designated critical habitats for threatened and endangered species, surface water bodies, and wetlands. In addition, supplementary descriptive information providing a general characterization of the region is presented, as is information on environmental parameters that may be of use at later phases of screening. Also included is a discussion of the relationship between the US Department of Energy (DOE) Siting Guidelines and those environmental disqualifying factors and regional screening variables to be used in the region-to-area screening process

  13. Revised draft: Southeastern Regional environmental characterization report. Volume 1

    International Nuclear Information System (INIS)

    This report presents available environmental information pertinent to siting a repository for high-level nuclear waste in crystalline rock in central Maryland; noncoastal Virginia, North Carolina, and South Carolina; and northern Georgia. For each of the states within the Southeastern Region, information is provided on those environmental disqualifying factors and regional screening variables to be used in region-to-area screening. These environmental factors and variables include existing and proposed federal protected lands, proximity to federal protected lands, existing state protected lands, proximity to state protected lands, population density and distribution, proximity to highly populated areas, national and state forest lands, state wild-life lands, designated critical habitats for threatened and endangered species, surface water bodies, and wetlands. In addition, supplementary descriptive information providing a general characterization of the region is presented, as is information on environmental parameters that may be of use at later phases of screening. Also included is a discussion of the relationship between the US Department of Energy (DOE) Siting Guidelines and those environmental disqualifying factors and regional screening variables to be used in the region-to-area screening process

  14. North Central Regional environmental characterization report. Volume 1. Final report

    International Nuclear Information System (INIS)

    This report presents available environmental information pertinent to siting a repository for high-level nuclear waste in crystalline rock in Minnesota, Wisconsin, and the Upper Peninsula of Michigan. For each of the states within the North Central Region, information is provided on those environmental disqualifying factors and regional screening variables to be used in region-to-area screening. These environmental factors and variables include existing and proposed Federal-protected lands, proximity to Federal-protected lands, components of national forest lands, existing state-protected lands, proximity to state-protected lands, population density and distribution, proximity to highly populated areas or to 1-mile square areas with 1000 or more persons, national and state forest lands, designated critical habitats for threatened and endangered spcies, surface water bodies, and wetlands. In addition, supplementary descriptive information providing a general characterization of the region is presented, as is information on environmental parameters that will be of use at later phases of screening. Also included is a discussion of the relationship between the US Department of Energy Siting Guidelines (10CFR 960) and those environmental disqualifying factors and regional screening variables to be used in the region-to-area screening process

  15. Southeastern Regional Environmental Characterization Report. Volume 1. Final report

    International Nuclear Information System (INIS)

    This report presents available environmental information pertinent to siting a repository for high-level nuclear waste in crystalline rock in central Maryland; noncoastal Virginia, North Carolina, and South Carolina; and northern Georgia. For each of the States within the Southeastern Region, information is provided on those environmental disqualifying factors and regional screening variables to be used in region-to-area screening. These environmental factors and variables include existing and proposd Federal-protected lands, components of National Forest Lands, proximity to Federal-protected lands, existing State-protected lands, proximity to State-protected lands, population density and distribution, proximity to highly populated areas, or to 1-mile-square areas with 1000 or more persons, national and State forest lands, designated critical habitats for threatened and endangered species, surface water bodies, and wetlands. In addition, supplementary descriptive information providing a general characterization of the region is presented, as is information on environmental parameters that will be of use at later phases of screening. Also included is a discussion of the relationship between the US Department of Energy Siting Guidelines (10 CFR 960) and those environmental disqualifying factors and regional screening variables to be used in the region-to-area screening process

  16. Mapeamento de QTL para conteúdos de proteína e óleo em soja Mapping QTL for protein and oil content in soybean

    Directory of Open Access Journals (Sweden)

    Josiane Isabela da Silva Rodrigues

    2010-05-01

    explained by QTL ranged from 6.24 to 18.94% and 17.26 to 25.93%, respectively. New QTL associated with protein and oil contents were detected, besides those previously reported in other studies. Other regions may be involved in the genetic control of protein and oil contents in soybean besides those already known.

  17. Detecting parent of origin and dominant QTL in a two-generation commercial poultry pedigree using variance component methodology

    Directory of Open Access Journals (Sweden)

    Haley Christopher S

    2009-01-01

    Full Text Available Abstract Introduction Variance component QTL methodology was used to analyse three candidate regions on chicken chromosomes 1, 4 and 5 for dominant and parent-of-origin QTL effects. Data were available for bodyweight and conformation score measured at 40 days from a two-generation commercial broiler dam line. One hundred dams were nested in 46 sires with phenotypes and genotypes on 2708 offspring. Linear models were constructed to simultaneously estimate fixed, polygenic and QTL effects. Different genetic models were compared using likelihood ratio test statistics derived from the comparison of full with reduced or null models. Empirical thresholds were derived by permutation analysis. Results Dominant QTL were found for bodyweight on chicken chromosome 4 and for bodyweight and conformation score on chicken chromosome 5. Suggestive evidence for a maternally expressed QTL for bodyweight and conformation score was found on chromosome 1 in a region corresponding to orthologous imprinted regions in the human and mouse. Conclusion Initial results suggest that variance component analysis can be applied within commercial populations for the direct detection of segregating dominant and parent of origin effects.

  18. QTL Information Table: 324 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSdn-5 Physiological trait Germination/dormancy germination percentage SSR d)Co-seg... J.M. (2004). Comparative mapping of QTL for seed dormancy in cultivated rice: N22 among three populations. Rice Genetics Newsletter 21, 46-49. ...

  19. QTL Information Table: 364 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSD-1-2 Physiological trait Germination/dormancy RFLP d)Co-segregated CSSL Asominor...ion and analysis of QTL for seed dormancy in rice (Oryza sativa L.) using RIL and CSSL population. Yi Chuan Xue Bao 30, 453-458. ...

  20. QTL Information Table: 641 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available ronment interaction for yield components and plant height in rice. Rice Genetics Newsletter 13, 127-129. ... ... RG13 RG573 rgn Zhuang, J.Y., Lin, H.X., Lu, J., Qian, H.R., Hittalman, S., Huang, N., and Zheng, K.L. (1996). Analysis of QTL x envi

  1. QTL Information Table: 131 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available 2-3SY Physiological trait Source activity biomass yield RFLP C)Interval DHL IR64 Az...ucena A RG171 RG157 pha Liu, G.F., Yang, J., and Zhu, J. (2006). Mapping QTL for biomass yield and its components in rice (Oryza sativa L.). Yi Chuan Xue Bao 33, 607-616. ...

  2. QTL Information Table: 687 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSPR4 Morphological trait Panicle/flower spreading of panicle at maturity stage RFLP C)Interval ... , M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture ... and Its Ecological Significance in Asian Wild Rice ...

  3. QTL Information Table: 690 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qAHL6 Morphological trait Panicle/flower apiculus hair length at seed traits SSR C)Interval RIL ... , M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture ... and Its Ecological Significance in Asian Wild Rice ...

  4. QTL Information Table: 689 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSW5 Morphological trait Seed seed width at seed traits RFLP C)Interval RIL A58 W107 (o. rufipog ... , M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture ... and Its Ecological Significance in Asian Wild Rice ...

  5. QTL Information Table: 686 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available q2LSL3 Morphological trait Shoot/Seedling leaf sheath length st seedling stage SSR C)Interval RI ... , M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture ... and Its Ecological Significance in Asian Wild Rice ...

  6. QTL Information Table: 691 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qLT12 Resistance or Tolerance Cold tolerance low-temperature tolerance SSR C)Interval RIL A58 W1 ... , M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture ... and Its Ecological Significance in Asian Wild Rice ...

  7. QTL Information Table: 688 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSH1 Morphological trait Panicle/flower shattring habit at maturity stage SSR C)Interval RIL A58 ... , M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture ... and Its Ecological Significance in Asian Wild Rice ...

  8. QTL Information Table: 467 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Root Maximum Root Length RFLP C)Interval DHL ZYQ8 Jingxi 17 B C711 G103 pha ... . QTL mapping of the root traits in rice seedling. Yi ... Chuan Xue Bao 28, 433-438. ...

  9. QTL Information Table: 210 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Seed Grain yi eld RFLP C)Interval RIL Zhenshan 97B Milyang 46 RG138 RZ398 pha ... .L. (2001). Comparison of the detection of QTL for yi eld traits in different generations of a rice cross ... using two mapping approaches. Yi ... Chuan Xue Bao 28, 458-464. ...

  10. QTL Information Table: 211 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Seed 1000-grain weight RFLP C)Interval RIL Zhenshan 97B Milyang 46 RZ811 RG5 ... .L. (2001). Comparison of the detection of QTL for yi eld traits in different generations of a rice cross ... using two mapping approaches. Yi ... Chuan Xue Bao 28, 458-464. ...

  11. QTL Information Table: 422 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qH2O21 Others Others H2O2 content RFLP C)Interval BIL Nipponbare Kasalath B C86 C813 pha Yang, Q ... , J.M. (2003). QTL and epistatic interaction underlyi ng leaf chlorophyll and H2O2 content variation in r ... ice (Oryza sativa L.). Yi ... Chuan Xue Bao 30, 245-250. ...

  12. QTL Information Table: 209 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Source activity spikelet fertility RFLP C)Interval RIL Zhenshan 97B Milyang ... .L. (2001). Comparison of the detection of QTL for yi eld traits in different generations of a rice cross ... using two mapping approaches. Yi ... Chuan Xue Bao 28, 458-464. ...

  13. QTL Information Table: 207 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Culm/leaf number of panicle RFLP C)Interval RIL Zhenshan 97B Milyang 46 RG65 ... .L. (2001). Comparison of the detection of QTL for yi eld traits in different generations of a rice cross ... using two mapping approaches. Yi ... Chuan Xue Bao 28, 458-464. ...

  14. QTL Information Table: 88 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qGP4 Morphological trait Panicle/flower grain number RFLP d)Co-segregated CSSL Asominori IR24 B ... ng, C.M., Wan, J.M., and Zhu, J.G. (2005). QTL for yi eld and its components responded to elevated CO2 in ... rice (Oryza sativa L.). Yi ... Chuan Xue Bao 32, 1066-1073. ...

  15. QTL Information Table: 206 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Source activity number of filled grains per panicle RFLP C)Interval RIL Zhen ... .L. (2001). Comparison of the detection of QTL for yi eld traits in different generations of a rice cross ... using two mapping approaches. Yi ... Chuan Xue Bao 28, 458-464. ...

  16. QTL Information Table: 421 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qChll1a Morphological trait Culm/leaf Chlorophyll contents RFLP C)Interval BIL Nipponbare Kasala ... , J.M. (2003). QTL and epistatic interaction underlyi ng leaf chlorophyll and H2O2 content variation in r ... ice (Oryza sativa L.). Yi ... Chuan Xue Bao 30, 245-250. ...

  17. QTL Information Table: 208 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Panicle/flower total number of spikelets per panicle RFLP C)Interval RIL Zhe ... .L. (2001). Comparison of the detection of QTL for yi eld traits in different generations of a rice cross ... using two mapping approaches. Yi ... Chuan Xue Bao 28, 458-464. ...

  18. QTL Information Table: 3 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available rb2 Physiological trait Eating quality ... Rice bran SSR C)Interval DH from BC3F1 Caiapo Oryza glabe ... n, C., and Oard, J.H. (2004). QTL mapping of grain quality ... traits from the interspecific cross Oryza sativa x ...

  19. QTL Information Table: 287 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Eating quality ... gel consistency RFLP C)Interval DHL IR64 Azucena A RG331 RG81 ... ui, H.R., and Shu, Q.Y. (2002). QTL for rice grain quality ... based on a DH population derived from parents with ...

  20. QTL Information Table: 2 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available hr6 Physiological trait Eating quality Head rice SSR C)Interval DH from BC3F1 Caiap...C., Bergman, C., and Oard, J.H. (2004). QTL mapping of grain quality traits from the interspecific cross Oryza sativa x O. glaberrima. Theor Appl Genet 109, 630-639. ...

  1. QTL Information Table: 290 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Eating quality breakdown RFLP C)Interval DHL IR64 Azucena A RZ5...90 RG214 pha Bao, J.S., Wu, Y.R., Hu, B., Wu, P., Cui, H.R., and Shu, Q.Y. (2002). QTL for rice grain quality

  2. QTL Information Table: 289 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Eating quality cool paste viscosity RFLP C)Interval DHL IR64 Az...ucena A RZ574 RZ284 pha Bao, J.S., Wu, Y.R., Hu, B., Wu, P., Cui, H.R., and Shu, Q.Y. (2002). QTL for rice grain quality

  3. QTL Information Table: 288 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Eating quality hot paste viscosity RFLP C)Interval DHL IR64 Azu...cena A RG139 RZ58 pha Bao, J.S., Wu, Y.R., Hu, B., Wu, P., Cui, H.R., and Shu, Q.Y. (2002). QTL for rice grain quality

  4. QTL Information Table: 4 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available alk6-1 Physiological trait Eating quality Alkali-spread.score SSR C)Interval DH fro...J., Castano, C., Bergman, C., and Oard, J.H. (2004). QTL mapping of grain quality traits from the interspecific cross Oryza sativa x O. glaberrima. Theor Appl Genet 109, 630-639. ...

  5. QTL Information Table: 454 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available 61 rgn Zhuang, J.Y., Fan, Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Mapping major and minor QTL for rice CMS-WA fertility restoration. Rice Genetics Newsletter 17, 56-59. ...

  6. QTL Information Table: 240 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qGB Physiological trait Eating quality grain breadth Mixture d)Co-segregated F2 Bas...sis to detect main effect QTL associated with grain quality parameters in Basmati 370/ASD 16 cross in rice O

  7. QTL Information Table: 5 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Eating quality Grain l/w ratio SSR C)Interval DH from BC3F1 Cai..., C., Bergman, C., and Oard, J.H. (2004). QTL mapping of grain quality traits from the interspecific cross Oryza sativa x O. glaberrima. Theor Appl Genet 109, 630-639. ...

  8. QTL Information Table: 383 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Pi32(t) Resistance or Tolerance Blast resistance RFLP C)Interval DHL IR64 Azucena A C449 pha Sal ... st-resistant rice variety IR64 using a QTL mapping strategy . Theor Appl Genet 106, 794-803. ...

  9. QTL Information Table: 751 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available ri B RM257 RM242 pha Miyata, M., Yamamoto, T., Komori, T., and Nitta, N. (2007). Marker-assisted selection and evaluation... of the QTL for stigma exsertion under japonica rice genetic background. Theor Appl Genet 114, 539-548. ... ...qGL9 Morphological trait Seed Grain length Mixture C)Interval F2 98SQ1496 Koshihika

  10. QTL Information Table: 749 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Koshihikari B R1943 R2976 pha Miyata, M., Yamamoto, T., Komori, T., and Nitta, N. (2007). Marker-assisted selection and evaluation... of the QTL for stigma exsertion under japonica rice genetic background. Theor Appl Genet 114, 539-548. ... ...qDTH8 Physiological trait Flowering Days-to-heading Mixture C)Interval F2 98SQ1496

  11. QTL Information Table: 752 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available i B C706 C12534S pha Miyata, M., Yamamoto, T., Komori, T., and Nitta, N. (2007). Marker-assisted selection and evaluation... of the QTL for stigma exsertion under japonica rice genetic background. Theor Appl Genet 114, 539-548. ... ...qGW3 Morphological trait Seed Grain width Mixture C)Interval F2 98SQ1496 Koshihikar

  12. QTL Information Table: 673 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available , Xu, X., Mei, H., and Luo, L. (2007). A major QTL associated with cold tolerance at seedling stage in rice ( Oryza sativa L.). Euphytica. http://dx.doi.org/10.1007/s10681-007-9431-5 ...

  13. QTL Information Table: 1041 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qST3-2 Physiological trait Eating quality stickiness SSR B)Fine F3 SL207 Koshihikar...mbe, T. (2007). QTL Detection for Eating Quality Including Glossiness, Stickiness, Taste and Hardness of Cooked Rice. Breeding Science 57, 231-242. ...

  14. QTL Information Table: 1042 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qTA3 Physiological trait Eating quality taste SSR B)Fine F3 SL207 Koshihikari RM133... (2007). QTL Detection for Eating Quality Including Glossiness, Stickiness, Taste and Hardness of Cooked Rice. Breeding Science 57, 231-242. ...

  15. QTL Information Table: 1040 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qOE3-1 Physiological trait Eating quality overall evaluation SSR B)Fine F3 SL207 Ko...., and Imbe, T. (2007). QTL Detection for Eating Quality Including Glossiness, Stickiness, Taste and Hardness of Cooked Rice. Breeding Science 57, 231-242. ...

  16. QTL Information Table: 1039 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qGL3-1 Physiological trait Eating quality glossiness SSR B)Fine F3 SL207 Koshihikar...mbe, T. (2007). QTL Detection for Eating Quality Including Glossiness, Stickiness, Taste and Hardness of Cooked Rice. Breeding Science 57, 231-242. ...

  17. QTL Information Table: 720 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available DHL Yuefu IRAT109 RM253 RM314 pha Guo, Y., Mu, P., Liu, J., Lu, Y., and Li, Z. (2007). QTL mapping and QxE interactions of grain cook...ing and nutrient qualities in rice under upland and lowland environments. J Genet Genomics 34, 420-428. ...

  18. QTL Information Table: 450 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Seed grain yield RFLP C)Interval RIL Zhenshan 97B Milyang 46 RG138 RZ398 rgn ... Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Comparison ... of QTL detection for yield traits using F2 and rec ...

  19. QTL Information Table: 607 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Shoot/Seedling root length SSR C)Interval RIL Lemont Teqing B OSR19 RM225 ph ... .-S., Wan, S., Chen, L.-H., and Zhu, Y.-G. (2005). Comparison ... of QTL Controlling Seedling Vigour under Different ...

  20. QTL Information Table: 605 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSV-3-1 Morphological trait Shoot/Seedling dry weight SSR C)Interval RIL Lemont Teqing A RM156 R ... .-S., Wan, S., Chen, L.-H., and Zhu, Y.-G. (2005). Comparison ... of QTL Controlling Seedling Vigour under Different ...

  1. QTL Information Table: 608 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSV-3-1 Morphological trait Shoot/Seedling shoot length SSR C)Interval RIL Lemont Teqing A RM156 ... .-S., Wan, S., Chen, L.-H., and Zhu, Y.-G. (2005). Comparison ... of QTL Controlling Seedling Vigour under Different ...

  2. QTL Information Table: 453 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Source activity spikelet fertility RFLP C)Interval RIL Zhenshan 97B Milyang ... Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Comparison ... of QTL detection for yield traits using F2 and rec ...

  3. QTL Information Table: 451 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Source activity number of filled grain per paniucle RFLP C)Interval RIL Zhen ... Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Comparison ... of QTL detection for yield traits using F2 and rec ...

  4. QTL Information Table: 606 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSV-3-2 Physiological trait Germination/dormancy germination rate SSR C)Interval RIL Lemont Teqi ... .-S., Wan, S., Chen, L.-H., and Zhu, Y.-G. (2005). Comparison ... of QTL Controlling Seedling Vigour under Different ...

  5. QTL Information Table: 452 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Panicle/flower total number of spikelets per panicle RFLP C)Interval RIL Zhe ... Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Comparison ... of QTL detection for yield traits using F2 and rec ...

  6. QTL Information Table: 449 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Seed 1000 grain weight RFLP C)Interval F2 Zhenshan 97B Milyang 46 RG543 RG81 ... Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Comparison ... of QTL detection for yield traits using F2 and rec ...

  7. QTL Information Table: 821 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Resistance or Tolerance Other soil stress tolerance Plant height (High N level, Soi...l culture , Maturity ) RFLP C)Interval RIL IR64 Azucena B RZ730 RZ801 pha Fang, P., and Wu, P. (2001). QTL × N-level

  8. QTL Information Table: 825 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Resistance or Tolerance Other soil stress tolerance Plant height (Low N level, Soil... culture , Maturity ) RFLP C)Interval RIL IR64 Azucena B RZ730 RZ801 pha Fang, P., and Wu, P. (2001). QTL × N-level

  9. Insight into the genetic components of community genetics: QTL mapping of insect association in a fast-growing forest tree.

    Science.gov (United States)

    DeWoody, Jennifer; Viger, Maud; Lakatos, Ferenc; Tuba, Katalin; Taylor, Gail; Smulders, Marinus J M

    2013-01-01

    Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL) analyses conducted on data from a common garden experiment. The F2 offspring of a hybrid poplar (Populus trichocarpa x P. deltoides) cross were assessed for seven categories of insect leaf damage at two time points, June and August. Positive and negative correlations were detected among damage categories and between sampling times. For example, sap suckers on leaves in June were positively correlated with sap suckers on leaves (P<0.001) but negatively correlated with skeletonizer damage (P<0.01) in August. The seven forms of leaf damage were used as a proxy for seven functional groups of insect species. Significant variation in insect association occurred among the hybrid offspring, including transgressive segregation of susceptibility to damage. NMDS analyses revealed significant variation and modest broad-sense heritability in insect community structure among genets. QTL analyses identified 14 genomic regions across 9 linkage groups that correlated with insect association. We used three genomics tools to test for putative mechanisms underlying the QTL. First, shikimate-phenylpropanoid pathway genes co-located to 9 of the 13 QTL tested, consistent with the role of phenolic glycosides as defensive compounds. Second, two insect association QTL corresponded to genomic hotspots for leaf trait QTL as identified in previous studies, indicating that, in addition to biochemical attributes, leaf morphology may influence insect preference. Third, network analyses identified categories of gene models over-represented in QTL for certain damage types, providing direction for future functional studies. These results provide insight into the genetic components involved in insect community structure in a fast-growing forest tree

  10. Analysis of rice blast resistance genes by QTL mapping

    Institute of Scientific and Technical Information of China (English)

    XU Jichen; WANG Jiulin; LING Zhongzhuan; ZHU Lihuang

    2004-01-01

    Resistance to rice blast pathogen mostly shows a quantitative trait controlled by several minor genes. Its complexity and the mutable characteristic of rice blast isolates both hinder the development of the blast resistance research. The article here tried to explore the resistance gene distribution on rice chromosomes and the way of function. Totally 124 QTLs have been identified against 20 isolates using Cartographer software with a ZYQ8/JX17 DH population, which separately are at 100 loci of 72 marker intervals on 12 rice chromosomes. Of them, 16 QTLs were determined by the isolate HB-97-36-1. 82 QTLs (66.13%) are from the resistant parent alleles, ZYQ8, while 42 QTLs (33.87%) are from the susceptible parent alleles, JX17. In comparison of their positions on chromosome, most QTLs are clustered together and distributed nearby the major genes especially the regions on chromosomes 1, 2, 8, 10 and 12. Each QTL could account for the resistance variation between 3.52%-68.64%. And, a positional QTL might display the resistance to several different isolates with different contributions.

  11. Identification of QTL for maize grain yield and kernel-related traits

    Indian Academy of Sciences (India)

    CONG YANG; LEI ZHANG; AIMIN JIA; TINGZHAO RONG

    2016-06-01

    Grain yield (GY) is one of the most important and complex quantitative traits in maize (Zea maysL.) breeding practice.Quantitative trait loci (QTLs) for GY and three kernel-related traits were detected in a set of recombinant inbred lines (RILs).One hundred and seven simple sequence repeats (SSRs) and 168 insertion/deletion polymorphism markers (Indels) were usedto genotype RILs. Eight QTLs were found to be associated with four yield-related traits: GY, 100-kernel weight (HKW),10-kernel length (KL), and 10-kernel length width (KW). Each QTL explained between 5.96 (qKL2-1) and 13.05 (qKL1-1)per cent of the phenotypic variance. Notably, one common QTL, located at the marker interval betweenbnlg1893andchr2-236477(chromosomal bin 2.09) simultaneously controlled GY and HKW; another common QTL, at bin 2.03 was simulta-neously responsible for HKW and KW. Of the QTLs identified, only one pair of significant epistatic interaction involved inchromosomal region at bin 2.03 was detected for HKW; no significant QTL ×environment interactions were observed. Theseresults provide the common QTLs and for marker-assisted breeding

  12. Multiple QTL Determine Dorsal Abdominal Scale Patterns in the Mosquito Aedes aegypti.

    Science.gov (United States)

    Mori, Akio; Tsuda, Yoshio; Takagi, Masahiro; Higa, Yukiko; Severson, David W

    2016-09-01

    The mosquito, Aedes aegypti (L.) originated in Sub-Saharan Africa as a dark form sylvan species (A. aegypti formosus). Evolution of A. aegypti aegypti type form as a human commensal facilitated its colonization of most semitropical and tropical areas. We investigated the genetic basis for abdominal white scale presence that represents the diagnostic for sylvan A. aegypti formosus (scales absent), from type form (scales present) and A. aegypti queenslandensis form (dense scaling). We performed quantitative trait locus (QTL) mapping using 3 criteria for scale patterns among 192 F1 intercross progeny from matings between a queenslandensis type and an aegypti type form. Results identified 3 QTL determining scale patterns and indicated that classification criteria impact robustness of QTL LOD support. Dark- and light-colored forms exist in sympatry, but vary in multiple phenotypic characteristics, including preferences for vertebrate host, oviposition container, house-entering behavior, and dengue vector competence. Markers associated with 2 QTL regions reflected major reductions in recombination frequencies compared with the standard type form linkage map, suggestive of inversion polymorphisms associated with observed linkage disequilibrium between type-specific characteristics. Understanding the genic basis for differences in A. aegypti forms could inform efforts to develop new mosquito and arboviral disease control strategies. PMID:27130203

  13. Identification of QTL for maize grain yield and kernel-related traits.

    Science.gov (United States)

    Yang, Cong; Zhang, Lei; Jia, Aimin; Rong, Tingzhao

    2016-06-01

    Grain yield (GY) is one of the most important and complex quantitative traits in maize (Zea mays L.) breeding practice. Quantitative trait loci (QTLs) for GY and three kernel-related traits were detected in a set of recombinant inbred lines (RILs). One hundred and seven simple sequence repeats (SSRs) and 168 insertion/deletion polymorphism markers (Indels) were used to genotype RILs. Eight QTLs were found to be associated with four yield-related traits: GY, 100-kernel weight (HKW), 10-kernel length (KL), and 10-kernel length width (KW). Each QTL explained between 5.96 (qKL2-1) and 13.05 (qKL1-1) per cent of the phenotypic variance. Notably, one common QTL, located at the marker interval between bnlg1893 and chr2- 236477 (chromosomal bin 2.09) simultaneously controlled GY and HKW; another common QTL, at bin 2.03 was simultaneously responsible for HKW and KW. Of the QTLs identified, only one pair of significant epistatic interaction involved in chromosomal region at bin 2.03 was detected for HKW; no significant QTL × environment interactions were observed. These results provide the common QTLs and for marker-assisted breeding. PMID:27350665

  14. Cell Wall Composition and Underlying QTL in an F1 Pseudo-Testcross Population of Switchgrass

    Energy Technology Data Exchange (ETDEWEB)

    Serba, Desalegn D.; Sykes, Robert W.; Gjersing, Erica L.; Decker, Stephen R.; Daverdin, Guillaume; Devos, Katrien M.; Brummer, E. Charles; Saha, Malay C.

    2016-09-01

    Natural genetic variation for reduced recalcitrance can be used to improve switchgrass for biofuel production. A full-sib switchgrass mapping population developed by crossing a lowland genotype, AP13, and upland genotype, VS16, was evaluated at three locations (Ardmore and Burneyville, OK and Watkinsville, GA). Biomass harvested after senescence in 2009 and 2010 was evaluated at the National Renewable Energy Laboratory (NREL) for sugar release using enzymatic hydrolysis and for lignin content and syringyl/guaiacyl lignin monomer (S/G) ratio using pyrolysis molecular beam mass spectrometry (py-MBMS). Glucose and xylose release ranged from 120 to 313 and 123 to 263 mg g-1, respectively, while lignin content ranged from 19 to 27% of the dry biomass. Statistically significant differences were observed among the genotypes and the environments for the cell wall composition traits. Regression analysis showed that a unit increase in lignin content reduced total sugar release by an average of 10 mg g-1. Quantitative trait loci (QTL) analysis detected 9 genomic regions underlying sugar release and 14 for lignin content. The phenotypic variation explained by the individual QTL identified for sugar release ranged from 4.5 to 9.4 and for lignin content from 3.8 to 11.1%. Mapping of the QTL regions to the switchgrass genome sequence (v1.1) found that some of the QTL colocalized with genes involved in carbohydrate processing and metabolism, plant development, defense systems, and transcription factors. The markers associated with QTL can be implemented in breeding programs to efficiently develop improved switchgrass cultivars for biofuel production.

  15. Mapping of QTL affecting incidence of blood and meat inclusions in egg layers

    Directory of Open Access Journals (Sweden)

    Vennerström Pia

    2011-06-01

    Full Text Available Abstract Background Occurrence of blood and meat inclusions is an internal egg quality defect. Mass candling reveals most of the spots, but because brown eggshell hampers selection in brown chicken lines it has not been possible to eliminate the defect by selection. Estimated frequency of blood and meat inclusions in brown layers is about 18% whereas it is 0.5% in white egg layers. Several factors are known to increase the incidence of this fault: genetic background, low level of vitamin A and/or D, stress or infections, for instance. To study the genetic background of the defect, a mapping population of 1599 F2 hens from a cross of White Rock and Rhode Island Red lines was set up. Results Our histopathological analyses show that blood spots consist of mainly erythrocytes and that meat spots are accumulations of necrotic material. Linkage analysis of 27 chromosomes with 162 microsatellite markers revealed one significant quantitative trait locus (QTL affecting blood spot and meat spot frequency. We sequenced a fragment of a candidate gene within the region, ZO-2, coding for a tight junction protein. Nine polymorphisms were detected and two of them were included in fine-mapping and association analysis. Fine-mapping defined the QTL result. To further verify the QTL, association analyses were carried out in two independent commercial breeding lines with the marker MCW241 and surrounding SNPs. Association was found mainly in a 0.8 Mb-wide chromosomal area on GGAZ. Conclusions There was good agreement between the location of the QTL region on chromosome Z and the association results in the commercial breeds analyzed. Variations found in tight junction protein ZO-2 and microRNA gga-mir-1556 may predispose egg layers to blood and meat spot defects. This paper describes the first results of detailed QTL analyses of the blood and meat spots trait(s in chickens.

  16. New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL.

    Science.gov (United States)

    Rinaldi, Riccardo; Van Deynze, Allen; Portis, Ezio; Rotino, Giuseppe L; Toppino, Laura; Hill, Theresa; Ashrafi, Hamid; Barchi, Lorenzo; Lanteri, Sergio

    2016-01-01

    Eggplant, pepper, and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage. Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits. The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp. Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation. In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10%) affecting key agronomic traits. Most were confirmed to cluster in orthologous

  17. QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods QTL list Data de...Policy | Contact Us QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  18. Confirmation and fine-mapping of a major QTL for resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar: population-level associations between markers and trait

    Directory of Open Access Journals (Sweden)

    Moen Thomas

    2009-08-01

    Full Text Available Abstract Background Infectious pancreatic necrosis (IPN is one of the most prevalent and economically devastating diseases in Atlantic salmon (Salmo salar farming worldwide. The disease causes large mortalities at both the fry- and post-smolt stages. Family selection for increased IPN resistance is performed through the use of controlled challenge tests, where survival rates of sib-groups are recorded. However, since challenge-tested animals cannot be used as breeding candidates, within-family selection is not performed and only half of the genetic variation for IPN resistance is being exploited. DNA markers linked to quantitative trait loci (QTL affecting IPN resistance would therefore be a powerful selection tool. The aim of this study was to identify and fine-map QTL for IPN-resistance in Atlantic salmon, for use in marker-assisted selection to increase the rate of genetic improvement for this trait. Results A genome scan was carried out using 10 large full-sib families of challenge-tested Atlantic salmon post-smolts and microsatellite markers distributed across the genome. One major QTL for IPN-resistance was detected, explaining 29% and 83% of the phenotypic and genetic variances, respectively. This QTL mapped to the same location as a QTL recently detected in a Scottish Atlantic salmon population. The QTL was found to be segregating in 10 out of 20 mapping parents, and subsequent fine-mapping with additional markers narrowed the QTL peak to a 4 cM region on linkage group 21. Challenge-tested fry were used to show that the QTL had the same effect on fry as on post-smolt, with the confidence interval for QTL position in fry overlapping the confidence interval found in post-smolts. A total of 178 parents were tested for segregation of the QTL, identifying 72 QTL-heterozygous parents. Genotypes at QTL-heterozygous parents were used to determine linkage phases between alleles at the underlying DNA polymorphism and alleles at single markers or

  19. Characterizing regional soil mineral composition using spectroscopyand geostatistics

    Science.gov (United States)

    Mulder, V.L.; de Bruin, S.; Weyermann, J.; Kokaly, Raymond F.; Schaepman, M.E.

    2013-01-01

    This work aims at improving the mapping of major mineral variability at regional scale using scale-dependent spatial variability observed in remote sensing data. Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) data and statistical methods were combined with laboratory-based mineral characterization of field samples to create maps of the distributions of clay, mica and carbonate minerals and their abundances. The Material Identification and Characterization Algorithm (MICA) was used to identify the spectrally-dominant minerals in field samples; these results were combined with ASTER data using multinomial logistic regression to map mineral distributions. X-ray diffraction (XRD)was used to quantify mineral composition in field samples. XRD results were combined with ASTER data using multiple linear regression to map mineral abundances. We testedwhether smoothing of the ASTER data to match the scale of variability of the target sample would improve model correlations. Smoothing was donewith Fixed Rank Kriging (FRK) to represent the mediumand long-range spatial variability in the ASTER data. Stronger correlations resulted using the smoothed data compared to results obtained with the original data. Highest model accuracies came from using both medium and long-range scaled ASTER data as input to the statistical models. High correlation coefficients were obtained for the abundances of calcite and mica (R2 = 0.71 and 0.70, respectively). Moderately-high correlation coefficients were found for smectite and kaolinite (R2 = 0.57 and 0.45, respectively). Maps of mineral distributions, obtained by relating ASTER data to MICA analysis of field samples, were found to characterize major soil mineral variability (overall accuracies for mica, smectite and kaolinite were 76%, 89% and 86% respectively). The results of this study suggest that the distributions of minerals and their abundances derived using FRK-smoothed ASTER data more closely match the spatial

  20. QTL mapping for production traits in Czech Fleckvieh cattle

    DEFF Research Database (Denmark)

    Matejickova, J; Stipkova, M; Sahana, Goutam;

    2013-01-01

    The objective of this study was to find QTL for milk production traits in Czech Fleckvieh cattle on chromosomes 6, 7, 11, 14, and 23 where QTL were previously identified in other dairy cattle populations. Sixteen grandsire families were genotyped for 38 microsatellite markers on the selected...... associated with milk production traits appeared on other studied chromosomes (BTA6, BTA7, BTA11, and BTA23). This first QTL search on five chromosomes in Czech Fleckvieh population showed several suggestive QTL that can be promising for further studies and contribute to better understanding of genetics of...... milk production in the Czech Fleckvieh cattle....

  1. Dynamic analysis of QTL for plant height at different developmental stages in maize (Zea mays L.)

    Institute of Scientific and Technical Information of China (English)

    YAN Jianbing; TANG Hua; HUANG Yiqin; SHI Yonggang; LI Jiansheng; ZHENG Yonglian

    2003-01-01

    Plant height in maize is not only one of important agronomic traits, but also one of model traits suitablefor study of developmental biology. Using data from fieldtests in two locations (Wuhan and Xiangfan) within the sameyear and a molecular linkage map covering all of 10 chro-mosomes, QTLs affecting plant height at five different de-velopmental stages were mapped and analyzed by the com-bination of composite interval mapping and the conditionalanalysis method. Eight QTLs for plant height at differentstages were located at different regions of five chromosomes(LOD≥2.5). The results showed that there were differenteffect values of QTL on plant height at different develop-mental stages. Three QTLs were detected at all of five stages.With different stages, contributory percentage of single QTL to plant height varied between 3.8% and 17.1%. It suggestedthat the expression of each QTL controlling plant height wasdifferent at different stages. With net growth, seven condi-tional QTLs for plant height were detected. Conditional QTLs were nearly detected at each stage, and QTLs of Ph1-1, Ph1-2, Ph3, Ph5-2 and Ph9 were detected at both locations (Wuhan and Xiangfan). The contributory percentage of single conditional QTL to plant height varied between 3.8% and 12.3%, indicating that QTLs for plant height are expressed in different time-space. Therefore, QTL expressed at different stages should be considered when marker assistant selection is conducted for quantitative traits.

  2. QTL Information Table: 750 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available 96 Koshihikari A R1943 R2976 pha Miyata, M., Yamamoto, T., Komori, T., and Nitta, N. (2007). Marker-assisted selection and evaluation... of the QTL for stigma exsertion under japonica rice genetic background. Theor Appl Genet 114, 539-548. ... ...qPL8 Morphological trait Panicle/flower Panicle length Mixture C)Interval F2 98SQ14

  3. QTL Information Table: 848 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Culm/leaf Leaf area RFLP d)Co-segregated BC1F7 Nipponbare Kasalath A R565 pha Ishimar...ison between QTLs and expressed sequence tags. TAG Theoretical...d the mapping of physiological and agronomic characters on a rice function map: QTL analysis and compar...u, K., Yano, M., Aoki, N., Ono, K., Hirose, T., Lin, S.Y., Monna, L., Sasaki, T., and Ohsugi, R. (2001). Towar

  4. QTL Information Table: 576 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available 1.2 Resistance or Tolerance Blast resistance Lesion area RFLP d)Co-segregated RIL B...ala Azucena A C1370 pha Talukder, Z.I., McDonald, A.J., and Price, A.H. (2005). Loci controlling partial res...istance to rice blast do not show marked QTL x environment interaction when plant nitrogen status alters disease severity. New Phytol 168, 455-464. ...

  5. QTL Information Table: 841 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available p: QTL analysis and comparison between QTLs and expressed sequence tags. TAG Theore...Physiological trait Source activity Decreased Chl. content RFLP d)Co-segregated BC1F7 Nipponbare... Kasalath B C607 pha Ishimaru, K., Yano, M., Aoki, N., Ono, K., Hirose, T., Lin, S.Y., Monna, L...., Sasaki, T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function ma

  6. QTL Information Table: 846 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available p: QTL analysis and comparison between QTLs and expressed sequence tags. TAG Theore...Morphological trait Dwarf Elongation of plant height RFLP d)Co-segregated BC1F7 Nipponbare... Kasalath A C506 pha Ishimaru, K., Yano, M., Aoki, N., Ono, K., Hirose, T., Lin, S.Y., Monna, L., Sas...aki, T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function ma

  7. QTL Information Table: 849 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Germination/dormancy Seed dormancy RFLP d)Co-segregated BC1F7 Nipponbare...p: QTL analysis and comparison between QTLs and expressed sequence tags. TAG Theore... Kasalath A C1488 pha Ishimaru, K., Yano, M., Aoki, N., Ono, K., Hirose, T., Lin, S.Y., Monna, L., ...Sasaki, T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function ma

  8. QTL Information Table: 844 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available p: QTL analysis and comparison between QTLs and expressed sequence tags. TAG Theore...Morphological trait Dwarf Plant height (middle stage) RFLP d)Co-segregated BC1F7 Nipponbare... Kasalath B R2414 pha Ishimaru, K., Yano, M., Aoki, N., Ono, K., Hirose, T., Lin, S.Y., Monna, L., S...asaki, T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function ma

  9. Identification of Candidate Genes Associated with Beef Marbling Using QTL and Pathway Analysis in Hanwoo (Korean Cattle)

    OpenAIRE

    Park, Hyesun; Seo, Seongwon; Cho, Yong Min; Oh, Sung Jong; Seong, Hwan-Hoo; Lee, Seung Hwan; Lim, Dajeong

    2012-01-01

    Marbling from intramuscular fat is an important trait of meat quality and has an economic benefit for the beef industry. Quantitative trait loci (QTL) fine mapping was performed to identify the marbling trait in 266 Hanwoo steers using a 10K single nucleotide polymorphism panel with the combined linkage and linkage disequilibrium method. As a result, we found nine putative QTL regions for marbling: three on BTA6, two on BTA17, two on BTA22, and two on BTA29. We detected candidate genes for ma...

  10. Heading Date QTL in Winter Wheat (Triticum aestivum L.) Coincide with Major Developmental Genes VERNALIZATION1 and PHOTOPERIOD1

    Science.gov (United States)

    Hao, Yuan Feng; Johnson, Jerry; Harrison, Steve; Marshall, David

    2016-01-01

    In wheat (Triticum aestivum L.), time from planting to spike emergence is influenced by genes controlling vernalization requirement and photoperiod response. Characterizing the available genetic diversity of known and novel alleles of VERNALIZATION1 (VRN1) and PHOTOPERIOD1 (PPD1) in winter wheat can inform approaches for breeding climate resilient cultivars. This study identified QTL for heading date (HD) associated with multiple VRN1 and PPD1 loci in a population developed from a cross between two early flowering winter wheat cultivars. When the population was grown in the greenhouse after partial vernalization treatment, major heading date QTLs co-located with the VRN-A1 and VRN-B1 loci. Copy number variation at the VRN-A1 locus influenced HD such that RIL having three copies required longer cold exposure to transition to flowering than RIL having two VRN-A1 copies. Sequencing vrn-B1 winter alleles of the parents revealed multiple polymorphisms in the first intron that were the basis of mapping a major HD QTL coinciding with VRN-B1. A 36 bp deletion in the first intron of VRN-B1 was associated with earlier HD after partial vernalization in lines having either two or three haploid copies of VRN-A1. The VRN1 loci interacted significantly and influenced time to heading in field experiments in Louisiana, Georgia and North Carolina. The PPD1 loci were significant determinants of heading date in the fully vernalized treatment in the greenhouse and in all field environments. Heading date QTL were associated with alleles having large deletions in the upstream regions of PPD-A1 and PPD-D1 and with copy number variants at the PPD-B1 locus. The PPD-D1 locus was determined to have the largest genetic effect, followed by PPD-A1 and PPD-B1. Our results demonstrate that VRN1 and PPD1 alleles of varying strength allow fine tuning of flowering time in diverse winter wheat growing environments. PMID:27163605

  11. A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer

    Directory of Open Access Journals (Sweden)

    Feng Felicia

    2011-04-01

    Full Text Available Abstract Background High density linkage maps are essential for comparative analysis of synteny, fine mapping of quantitative trait loci (QTL, searching for candidate genes and facilitating genome sequence assembly. However, in most foodfish species, marker density is still low. We previously reported a first generation linkage map with 240 DNA markers and its application to preliminarily map QTL for growth traits in Asian seabass (Lates calcarifer. Here, we report a high-resolution linkage map with 790 microsatellites and SNPs, comparative analysis of synteny, fine-mapping of QTL and the identification of potential candidate genes for growth traits. Results A second generation linkage map of Asian seabass was developed with 790 microsatellite and SNP markers. The map spanned a genetic length of 2411.5 cM, with an average intermarker distance of 3.4 cM or 1.1 Mb. This high density map allowed for comparison of the map with Tetraodon nigroviridis genome, which revealed 16 synteny regions between the two species. Moreover, by employing this map we refined QTL to regions of 1.4 and 0.2 cM (or 400 and 50 kb in linkage groups 2 and 3 in a population containing 380 progeny; potential candidate genes for growth traits in QTL regions were further identified using comparative genome analysis, whose effects on growth traits were investigated. Interestingly, a QTL cluster at Lca371 underlying growth traits of Asian seabass showed similarity to the cathepsin D gene of human, which is related to cancer and Alzheimer's disease. Conclusions We constructed a high resolution linkage map, carried out comparative mapping, refined the positions of QTL, identified candidate genes for growth traits and analyzed their effects on growth. Our study developed a framework that will be indispensable for further identification of genes and analysis of molecular variation within the refined QTL to enhance understanding of the molecular basis of growth and speed up genetic

  12. Microstructural characterization of second phase regions in cast stainless steels

    International Nuclear Information System (INIS)

    Full text of publication follows: Cast austenitic stainless steels offer the possibility of directly producing large and/or relatively complex structures, such as the first wall shield modules or the divertor cassette for the International Tokamak Experimental Reactor (ITER). Unfortunately, one of the inherent problems associated with casting stainless steel, especially large castings, is the formation of coarse dendrites with possibly inhomogeneously distributed second phases separated by up to several hundred microns in the microstructure. These microstructural features result from temperature and composition gradients that develop during solidification and subsequent cooling. However, detailed characterization of the second phase regions in the cast microstructures can be quite challenging to techniques such as transmission electron microscopy (TEM), which is useful for phase identification. furthermore, the information about the phases that may be present in the cast microstructures, both equilibrium and nonequilibrium, is important as input as well as for confirming predictions made by computational thermodynamics and solidification modeling. In this study, the investigation of second phase regions that formed in a large cast of a 316 stainless steel (equivalent to CF3M) will be presented and compared to simulations of the phases predicted by computational thermodynamic modeling of the solidification process. The preliminary TEM investigation of the cast microstructure was performed with specimens that were prepared by jet-polishing of 3 mm diameter discs. Although this approach allowed for the identification of the sigma and chi phases, which was consistent with the simulations, it was not suitable for detailed analysis of the second phase regions since these specimens often contained only grains of the gamma austenite phase. A better approach for preparing TEM specimens consisted of strategically lifting small sections of material from second phase regions

  13. Subsurface Characterization of Shallow Water Regions using Airborne Bathymetric Lidar

    Science.gov (United States)

    Bradford, B.; Neuenschwander, A. L.; Magruder, L. A.

    2013-12-01

    Understanding the complex interactions between air, land, and water in shallow water regions is becoming increasingly critical in the age of climate change. To effectively monitor and manage these zones, scientific data focused on changing water levels, quality, and subsurface topography are needed. Airborne remote sensing using light detection and ranging (LIDAR) is naturally suited to address this need as it can simultaneously provide detailed three-dimensional spatial data for both topographic and bathymetric applications in an efficient and effective manner. The key to useful data, however, is the correct interpretation of the incoming laser returns to distinguish between land, water, and objects. The full waveform lidar receiver captures the complete returning signal reflected from the Earth, which contains detailed information about the structure of the objects and surfaces illuminated by the beam. This study examines the characterization of this full waveform with respect to water surface depth penetration and subsurface classification, including sand, rock, and vegetation. Three assessments are performed to help characterize the laser interaction within the shallow water zone: evaluation of water surface backscatter as a function of depth and location, effects from water bottom surface roughness and reflectivity, and detection and classification of subsurface structure. Using the Chiroptera dual-laser lidar mapping system from Airborne Hydrography AB (AHAB), both bathymetric and topographic mapping are possible. The Chiroptera system combines a 1064nm near infrared topographic laser with a 515nm green bathymetric laser to seamlessly map the land/water interface in coastal areas. Two survey sites are examined: Lake Travis in Austin, Texas, USA, and Lake Vättern in Jönköping, Sweden. Water quality conditions were found to impact depth penetration of the lidar, as a maximum depth of 5.5m was recorded at Lake Travis and 11m at Lake Vättern.

  14. Fine mapping of a calving QTL on Bos taurus autosome 18 in Holstein cattle.

    Science.gov (United States)

    Mao, X; Kadri, N K; Thomasen, J R; De Koning, D J; Sahana, G; Guldbrandtsen, B

    2016-06-01

    Decreased calving performance not only directly impacts the economic efficiency of dairy cattle farming but also influences public concern for animal welfare. Previous studies have revealed a QTL on Bos taurus autosome (BTA) 18 that has a large effect on calving traits in Holstein cattle. In this study, fine mapping of this QTL was performed using imputed high-density SNP chip (HD) genotypes followed by imputed next-generation sequencing (NGS) variants. BTA18 was scanned for seven direct calving traits in 6113 bulls with imputed HD genotypes. SNP rs136283363 (BTA18: 57 548 213) was consistently the most significantly associated SNP across all seven traits [e.g. p-value = 2.04 × 10(-59) for birth index (BI)]. To finely map the QTL region and to explore pleiotropic effects, we studied NGS variants within the targeted region (BTA18: 57 321 450-57 625 355) for associations with direct calving traits and with three conformation traits. Significant variants were prioritized, and their biological relevance to the traits was interpreted. Considering their functional relationships with direct calving traits, SIGLEC12, CD33 and CEACAM18 were proposed as candidate genes. In addition, pleiotropic effects of this QTL region on direct calving traits and conformation traits were observed. However, the extent of linkage disequilibrium combined with the lack of complete annotation and potential errors in the Bos taurus genome assembly hampered our efforts to pinpoint the causal mutation. PMID:26486911

  15. The Genetic Architecture of Flowering Time and Photoperiod Sensitivity in Maize as Revealed by QTL Review and Meta Analysis

    Institute of Scientific and Technical Information of China (English)

    Jie Xu; Tingzhao Rong; Yaxi Liu; Jian Liu; Moju Cao; Jing Wang; Hai Lan; Yunbi Xu; Yanli Lu; Guangtang Pan

    2012-01-01

    The control of flowering is not only important for reproduction,but also plays a key role in the processes of domestication and adaptation.To reveal the genetic architecture for flowering time and photoperiod sensitivity,a comprehensive evaluation of the relevant literature was performed and followed by meta analysis.A total of 25 synthetic consensus quantitative trait loci (QTL) and four hot-spot genomic regions were identified for photoperiod sensitivity including 11 genes related to photoperiod response or flower morphogenesis and development.Besides,a comparative analysis of the QTL for flowering time and photoperiod sensitivity highlighted the regions containing shared and unique QTL for the two traits.Candidate genes associated with maize flowering were identified through integrated analysis of the homologous genes for flowering time in plants and the consensus QTL regions for photoperiod sensitivity in maize (Zea mays L.).Our results suggest that the combination of literature review,meta-analysis and homologous blast is an efficient approach to identify new candidate genes and create a global view of the genetic architecture for maize photoperiodic flowering.Sequences of candidate genes can be used to develop molecular markers for various models of marker-assisted selection,such as marker-assisted recurrent selection and genomic selection that can contribute significantly to crop environmental adaptation.

  16. 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.

  17. QTL Information Table: 839 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Others Others Ratoon RFLP d)Co-segregated BC1F7 Nipponbare Kasalath A C901 pha Ishimar...ison between QTLs and expressed sequence tags. TAG Theoretical and Applied Genetics 102, 793-800. http://dx.doi.org/10.1007/s001220000467 ... ...u, K., Yano, M., Aoki, N., Ono, K., Hirose, T., Lin, S.Y., Monna, L., Sasaki, T., and Ohsugi, R. (2001). Toward the ma...pping of physiological and agronomic characters on a rice function map: QTL analysis and compar

  18. QTL Information Table: 838 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Seed Yield RFLP d)Co-segregated BC1F7 Nipponbare Kasalath A C136 pha Ishimar...ison between QTLs and expressed sequence tags. TAG Theoretical and Applied Genetics 102, 793-800. http://dx.doi.org/10.1007/s001220000467 ... ...u, K., Yano, M., Aoki, N., Ono, K., Hirose, T., Lin, S.Y., Monna, L., Sasaki, T., and Ohsugi, R. (2001). Toward the ma...pping of physiological and agronomic characters on a rice function map: QTL analysis and compar

  19. Composite interval mapping of QTL for dynamic traits

    Institute of Scientific and Technical Information of China (English)

    GAO Huijiang; YANG Runqing

    2006-01-01

    Many economically important quantitative traits in animals and plants are measured repeatedly over time. These traits are called dynamic traits. Mapping QTL controlling the phenotypic profiles of dynamic traits has become an interesting topic for animal and plant breeders. However, statistical methods of QTL mapping for dynamic traits have not been well developed. We develop a composite interval mapping approach to detecting QTL for dynamic traits. We fit the profile of each QTL effect with Legendre polynomials. Parameter estimation and statistical test are performed on the regression coefficients of the polynomials under the maximum likelihood framework. Maximum likelihood estimates of QTL parameters are obtained via the EM algorithm. Results of simulation study showed that composite interval mapping can improve both the statistcial power of QTL detecting and the accuracy of parameter estimation relative to the simply interval mapping procedure where only one QTL is fit to each model. The method is developed in the context of an F2 mapping population, but extension to other types of mapping populations is straightforward.

  20. QTL Mapping of Chlorophyll Contents in Rice

    Institute of Scientific and Technical Information of China (English)

    SHEN Bo; ZHUANG Jie-yun; ZHANG Ke-qin; DAI Wei-min; LU Ye; FU Li-qing; DING Jia-ming; ZHENG Kang-le

    2007-01-01

    The objectives of this study were to investigate the genetic factors controlling the chlorophyll content of rice leaf using QTL analysis. A linkage map consisting of 207 DNA markers was constructed by using 247 recombinant inbred lines (RILs) derived from an indica-indica rice cross of Zhenshan97B×Milyang 46. In 2002 and 2003, the contents of chlorophyll a and b of the parents and the 247 RILs were measured on the top first leaf, top second leaf, and top third leaf, respectively. The software QTLMapper 1.6 was used to detect quantitative trait loci (QTLs), additive by environment (AE) interactions, and epistatic by environment (AAE) interactions. A total of eight QTLs in four intervals were detected to have significant additive effects on chlorophyll a and b contents at different leaf positions, with 1.96-9.77% of phenotypic variation explained by a single QTL, and two QTLs with significant AE interactions were detected. Epistasis analysis detected nine significant additive-by-additive interactions on chlorophyll a and b contents, and one pair of QTLs with significant AAE interactions was detected. On comparison with QTLs for yield traits detected in the same population, it was found in many cases that the QTLs for chlorophyll a and b contents and those for yield traits were located in the same chromosome intervals.

  1. Characterization of Innovation Situation in a Remote Rural Region

    OpenAIRE

    Minna Sarkkinen; Tuomo Kässi

    2013-01-01

    Innovation debates dealing with regional economic development have generally focused on densely populated, technologically advanced areas and areas around university cities, undervaluing rural regions and their integration in national innovation systems. However, some statistics indicate that remote and rural regions may also have good innovation potential. This study examines more closely the innovation situation of the firms located in a remote rural region in Finland. The...

  2. Dissection of two soybean QTL conferring partial resistance to Phytophthora sojae through sequence and gene expression analysis

    Directory of Open Access Journals (Sweden)

    Wang Hehe

    2012-08-01

    Full Text Available Abstract Background Phytophthora sojae is the primary pathogen of soybeans that are grown on poorly drained soils. Race-specific resistance to P. sojae in soybean is gene-for-gene, although in many areas of the US and worldwide there are populations that have adapted to the most commonly deployed resistance to P. sojae ( Rps genes. Hence, this system has received increased attention towards identifying mechanisms and molecular markers associated with partial resistance to this pathogen. Several quantitative trait loci (QTL have been identified in the soybean cultivar ‘Conrad’ that contributes to the expression of partial resistance to multiple P. sojae isolates. Results In this study, two of the Conrad QTL on chromosome 19 were dissected through sequence and expression analysis of genes in both resistant (Conrad and susceptible (‘Sloan’ genotypes. There were 1025 single nucleotide polymorphisms (SNPs in 87 of 153 genes sequenced from Conrad and Sloan. There were 304 SNPs in 54 genes sequenced from Conrad compared to those from both Sloan and Williams 82, of which 11 genes had SNPs unique to Conrad. Eleven of 19 genes in these regions analyzed with qRT-PCR had significant differences in fold change of transcript abundance in response to infection with P. sojae in lines with QTL haplotype from the resistant parent compared to those with the susceptible parent haplotype. From these, 8 of the 11 genes had SNPs in the upstream, untranslated region, exon, intron, and/or downstream region. These 11 candidate genes encode proteins potentially involved in signal transduction, hormone-mediated pathways, plant cell structural modification, ubiquitination, and basal resistance. Conclusions These findings may indicate a complex defense network with multiple mechanisms underlying these two soybean QTL conferring resistance to P. sojae. SNP markers derived from these candidate genes can contribute to fine mapping of QTL and marker assisted breeding for

  3. solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database

    OpenAIRE

    van der Knaap Esther; Buels Robert M; Menda Naama; Tecle Isaak Y; Mueller Lukas A

    2010-01-01

    Abstract Background A common approach to understanding the genetic basis of complex traits is through identification of associated quantitative trait loci (QTL). Fine mapping QTLs requires several generations of backcrosses and analysis of large populations, which is time-consuming and costly effort. Furthermore, as entire genomes are being sequenced and an increasing amount of genetic and expression data are being generated, a challenge remains: linking phenotypic variation to the underlying...

  4. Mapping quantitative trait loci (QTL in sheep. IV. Analysis of lactation persistency and extended lactation traits in sheep

    Directory of Open Access Journals (Sweden)

    Lam Mary K

    2011-06-01

    Full Text Available Abstract Background In sheep dairy production, total lactation performance, and length of lactation of lactation are of economic significance. A more persistent lactation has been associated with improved udder health. An extended lactation is defined by a longer period of milkability. This study is the first investigation to examine the presence of quantitative trait loci (QTL for extended lactation and lactation persistency in sheep. Methods An (Awassi × Merino × Merino single-sire backcross family with 172 ewes was used to map QTL for lactation persistency and extended lactation traits on a framework map of 189 loci across all autosomes. The Wood model was fitted to data from multiple lactations to estimate parameters of ovine lactation curves, and these estimates were used to derive measures of lactation persistency and extended lactation traits of milk, protein, fat, lactose, useful yield, and somatic cell score. These derived traits were subjected to QTL analyses using maximum likelihood estimation and regression analysis. Results Overall, one highly significant (LOD > 3.0, four significant (2.0 Conclusion This study identified ten novel QTL for lactation persistency and extended lactation in sheep, but results suggest that lactation persistency and extended lactation do not have a major gene in common. These results provide a basis for further validation in extended families and other breeds as well as targeting regions for genome-wide association mapping using high-density SNP arrays.

  5. QTL Mapping of Low Temperature on Germination rate of Rice

    Institute of Scientific and Technical Information of China (English)

    CHEN Liang; LOU Qiao-jun; SUN Zong-xiu; XING Yong-zhong; YU Xin-qiao; LUO Li-jun

    2006-01-01

    To investigate the low temperature on germination capacity (LTG) a double haploid rice (DH) population with 198 lines derived from anther culture of F1 hybrid with indica line Zhenshan 97B and a perennial japonica line AAV002863 was used to construct a linkage map with 140 SSR markers. The germination rate in Zhenshan 97B and AAV002863 was 79.7% and 30.1%, while in DH population it ranged from 0 to 100% at 15℃ after 6 days. Quantitative trait loci (QTLs) controlling low temperature germinability were identified on chromosomes 3 and 10. The percentage of observed phenotypic variance attributed to qLTG-3 and qLTG-10 was 12.6% and 12.9%, respectively. Allele from Zhenshan 97B increased the LTG at qLTG-3 region, while allele from AAV002863 increased the LTG at qLTG-10 region. One pair of epistatic interaction was detected between loci on chromosomes 3 and 10. The main-effect of QTL on chromosome 10 was also involved in epistatic interaction.

  6. North Central Regional geologic characterization report. Volume 1. Final report

    International Nuclear Information System (INIS)

    This report presents available geologic information pertinent to siting a repository for high-level nuclear waste in crystalline rock in Minnesota, Wisconsin, and the Upper Peninsula of Michigan. For each of the states within the North Central Region, information is provided on the geologic disqualifying factor and the geologic regional screening variables to be used in region-to-area screening. The geologic factor and variables include deep mines and quarries, rock mass extent, post-emplacement faulting, suspected Quaternary faulting, seismicity, rock and mineral resources, major groundwater discharge zones, groundwater resources, state of stress, thickness of rock mass, and thickness of overburden. Information is presented on age, areal extent, shape, composition, texture, degree and type of alteration, thickness, and structural features associated with each rock body or complex. Regional seismic and tectonic information is presented, including patterns of earthquake occurrence, earthquake magnitudes, horizontal ground accelerations, and vertical crustal movements. Also included are discussions of the rock and mineral deposits or mines located within or near crystalline rock bodies; groundwater resources and regional hydrology; postulated changes in climate and the associated effects; and landforms, surface processes, and surficial materials on or near the rock bodies. A discussion is also presented of the relationship between the US Department of Energy Siting Guidelines (10 CFR 960) and the geologic disqualifying factor and regional screening variables to be used in the region-to-area screening process. 43 figs., 15 tabs

  7. Northeastern Regional geologic characterization report. Volume 1. Final report

    International Nuclear Information System (INIS)

    This report presents available geologic information pertinent to siting a repository for high-level nuclear waste in crystalline rock in Connecticut, Maine, Massachusetts, New Hampshire, New Jersey, New York, Pennsylvania, Rhode Island, and Vermont. For each of the states within the Northeastern Region, information is provided on the geologic disqualifying factor and the geologic regional screening variables to be used in region-to-area screening. The geologic factor and variables include deep mines and quarries, rock mass extent, postemplacement faulting, suspected Quaternary faulting, seismicity, rock and mineral resources, major ground-water discharge zones, ground-water resources, state of stress, thickness of rock mass, and thickness of overburden. Information is presented on age, areal extent, shape, composition, texture, degree and type of alteration, thickness, and structural features associated with each rock body or complex. Regional seismic and tectonic information is presented, including patterns of earthquake occurrence, earthquake magnitudes, horizontal ground accelerations, and vertical crusal movements. Also included are discussions of the rock and mineral deposits or mines located within or near crystalline bodies; ground-water resources and regional hydrology; postulated changes in climate and the associated effects; and landforms, surface processes, and surficial materials on or near the rock bodies. A discussion is also presented on the relationship between the US Department of Energy (DOE) Siting Guidelines (10 CFR 960) and the geologic disqualifying factor and regional screening variables to be used in the region-to-area screening process

  8. Characterization of Multifloral Honeys of Pervari Region with Different Properties

    OpenAIRE

    EREZ, Mehmet Emre; KARABACAK, Osman; KAYCİ, Lokman; Mehmet FİDAN; KAYA, Yılmaz

    2015-01-01

    The quality of honey from Pervari region was almost known by all over the country in Turkey. This study was undertaken to determine (i) physico-chemical parameters, (ii) antimicrobial analysis and (iii) pollen estimation method with expert computer system obtained from three different sites of Pervari region (Siirt/Turkey). For physico-chemical parameters; moisture, free acidity, diastase activity, hydroxyl methyl furfural (HMF), invert sugar, ash, commercial glucose and proline analysis were...

  9. Logistics characterization for regional spent fuel repositories concept

    International Nuclear Information System (INIS)

    This report summarizes a study of logistics considerations for a four-region repository system for spent fuel disposal. The logistics considerations include: (1) yearly receipt and emplacement; (2) inventory; (3) away-from-reactor (AFR) storage; (4) nuclear capacity growth effects; (5) entire lifetime of reactors served by repository operations; (6) proportions of pressurized-water-reactor (PWR)/boiling-water-reactor (BWR) fuel; (7) proportions of rail and truck shipments; (8) shipping cask fleet requirements; (9) number of annual shipments; (10) mode (rail/truck) and cost of shipment; and (11) initial year for shipment to maintain full core reserve. The nation was divided into Northeast, North Central, Southern, and Western regions for evaluation purposes. Repository logistics were analyzed in each region based on three different capacity projections. For the Southern region, results for seven salt dome sites are presented. The Western region results cover four potential sites. The North Central and Northeastern regions results are not presented on a site specific basis. Conclusions are drawn based on the results. The methodology assumptions and references used in the logistics analysis are described for the convenience of the reader

  10. Revised draft: Southeastern Regional geologic characterization report. Volume 1

    International Nuclear Information System (INIS)

    This report presents available geologic information pertinent to siting a repository for high-level nuclear waste in crystalline rock in Georgia, Maryland, North Carolina, South Carolina, and Virginia. For each of the states within the southeastern region, information is provided on the disqualifying factor and the screening variables to be used in region-to-area screening. These factors and variables include hydrologically significant natural resources, rock mass extent, postemplacement faulting, suspected Quaternary faulting, seismicity, rock and mineral resources, major ground-water discharge zones, water resources, ground-water salinity, and state of stress. Information is presented on the age, areal extent, shape, thickness of overburden, composition, texture, degree and type of alteration, and structural features associated with each rock body or complex. Regional seismic and tectonic information is presented, including patterns of earthquake occurrence, earthquake magnitudes, horizontal ground accelerations, and vertical crustal movements. Also included are discussions of the rock and mineral deposits or mines located within or near crystalline bodies; groundwater resources and regional hydrology; postulated changes in climate and the associated effects; and landforms, surface processes, and surficial materials on or near the subject rock bodies. A discussion of the relationship between the DOE Siting Guidelines and the geologic disqualifying factor and regional screening variables to be used in the region-to-area screening process is also presented

  11. Revised draft: North Central Regional geologic characterization report. Volume 1

    International Nuclear Information System (INIS)

    This report presents available geologic information pertinent to siting a repository for high-level nuclear waste in crystalline rock in Minnesota, Wisconsin, and the Upper Peninsula of Michigan. For each of the states within the North Central Region, information is provided on the disqualifying factor and the screening variables to be used in region-to-area screening. These factors and variables include hydrologically significant natural resources, rock mass extent, post-emplacement faulting, suspected Quaternary faulting, seismicity, rock and mineral resources, major groundwater discharge zones, water resources, groundwater salinity, and state of stress. Information is presented on age, areal extent, shape, thickness of overburden, composition, texture, degree and type of alteration, and structural features associated with each rock body or complex. Regional seismic and tectonic information is presented, including patterns of earthquake occurrence, earthquake magnitudes, horizontal ground accelerations, and vertical crustal movements. Also included are discussions of the rock and mineral deposits or mines located within or near crystalline rock bodies; groundwater resources and regional hydrology; postulated changes in climate and the associated effects; and landforms, surface processes, and surficial materials on or near the subject rock bodies. A discussion of the relationship between the DOE Siting Guidelines and the geologic disqualifying factor and regional screening variables to be used in the region-to-area screening process is also presented

  12. Southeastern Regional geologic characterization report. Volume 1. Final report

    International Nuclear Information System (INIS)

    This report presents available geologic information pertinent to siting a repository for high-level nuclear waste in crystalline rock in central Maryland; noncoastal Virginia, North Carolina, and South Carolina; and northern Georgia. For each of the states within the Southeastern Region, information is provided on the geological disqualifying factor and the geologic regional screening variables to be used in region-to-area screening. The geological factor and variables include deep mines and quarries, rock mass extent, postemplacement faulting, suspected Quaternary faulting, seismicity, rock and mineral resources, major ground-water discharge zones, ground-water resources, state of stress, thickness of rock mass, and thickness of overburden. Information is presented on the age, areal extent, shape, composition, texture, degree and type of alteration, thickness, and structural features associated with each rock body or complex. Regional seismic and tectonic information is presented, including patterns of earthquake occurrence, earthquake magnitudes, horizontal ground accelerations, and vertical crustal movements. Also included are discussions of the rock and mineral deposits or mines located within or near crystalline bodies; ground-water resources and regional hydrology; postulated changes in climate and the associated effects; and landforms, surface processes, and surficial materials on or near the rock bodies

  13. Wheat kernel dimensions: how do they contribute to kernel weight at an individual QTL level?

    Indian Academy of Sciences (India)

    Fa Cui; Anming Ding; Jun Li; Chunhua Zhao; Xingfeng Li; Deshun Feng; Xiuqin Wang; Lin Wang; Jurong Gao; Honggang Wang

    2011-12-01

    Kernel dimensions (KD) contribute greatly to thousand-kernel weight (TKW) in wheat. In the present study, quantitative trait loci (QTL) for TKW, kernel length (KL), kernel width (KW) and kernel diameter ratio (KDR) were detected by both conditional and unconditional QTL mapping methods. Two related F8:9 recombinant inbred line (RIL) populations, comprising 485 and 229 lines, respectively, were used in this study, and the trait phenotypes were evaluated in four environments. Unconditional QTL mapping analysis detected 77 additive QTL for four traits in two populations. Of these, 24 QTL were verified in at least three trials, and five of them were major QTL, thus being of great value for marker assisted selection in breeding programmes. Conditional QTL mapping analysis, compared with unconditional QTL mapping analysis, resulted in reduction in the number of QTL for TKW due to the elimination of TKW variations caused by its conditional traits; based on which we first dissected genetic control system involved in the synthetic process between TKW and KD at an individual QTL level. Results indicated that, at the QTL level, KW had the strongest influence on TKW, followed by KL, and KDR had the lowest level contribution to TKW. In addition, the present study proved that it is not all-inclusive to determine genetic relationships of a pairwise QTL for two related/causal traits based on whether they were co-located. Thus, conditional QTL mapping method should be used to evaluate possible genetic relationships of two related/causal traits.

  14. Analysis and characterization of security regions in power systems

    Energy Technology Data Exchange (ETDEWEB)

    1979-01-01

    Progress is repoted in a study performed to investigate the concept of security regions in the context of power system security analysis. The background and motivation for this research, the results of 2 years of work, and proposed future studies are discussed. (LCL)

  15. Revised draft: Northeastern Regional geologic characterization report. Volume 1

    International Nuclear Information System (INIS)

    This report presents available geologic information pertinent to siting a repository for high-level nuclear waste in crystalline rock in Connecticut, Maine, Massachusetts, New Hampshire, New Jersey, New York, Pennsylvania, Rhode Island, and Vermont. For each of the states within the Northeastern Region, information is provided on the disqualifying factor and the screening variables to be used in region-to-area screening. These factors and variables include: hydrologically significant natural resources, rock mass extent, post-emplacement faulting, suspected Quaternary faulting, seismicity, rock and mineral resources, major ground-water discharge zones, water resources, ground-water salinity, and state of stress. Information is presented on its age, areal extent, shape, thickness of overburden, composition, texture, degree and type of alteration, rock mass thickness, and structural features associated with each rock body or complex. Regional seismic and tectonic information is presented, including patterns of earthquake occurrence, earthquake magnitudes, horizontal ground accelerations, and vertical crustal movements. Also included are discussions of the rock and mineral deposits or mines located within or near crystalline bodies; ground-water resources and regional hydrology; postulated changes in climate and the associated effects; and landforms, surface processes, and surficial materials on or near the subject rock bodies

  16. Physicochemical characterization of natural honeys from different regions in Slovakia

    OpenAIRE

    Sudzina, M.; Melich, Martin; Kňazovická, Vladimíra; Felšöciová, Soňa; Kociubinski, Guillermo; Andreji, Jaroslav; Pavličová, Simona; Kráčmar, Stanislav

    2009-01-01

    This study is intended to determine the physicochemical characteristics of Slovakian honeys, and compare them with specifications described in the Codex Alimentarius Standard, the European Honey directive, the Slovak Codex Alimentarius and Slovak standard No. 1/2006. In addition, we tried to find out correlations between individual constituents of honeys. Physicochemical characterization was carried out following the harmonized methods dictated by the International Honey Commission IHC. Honey...

  17. Heading Date QTL in Winter Wheat (Triticum aestivum L.) Coincide with Major Developmental Genes VERNALIZATION1 and PHOTOPERIOD1

    OpenAIRE

    Guedira, Mohammed; Xiong, Mai; Hao, Yuan Feng; Johnson, Jerry; Harrison, Steve; Marshall, David; Brown-Guedira, Gina

    2016-01-01

    In wheat (Triticum aestivum L.), time from planting to spike emergence is influenced by genes controlling vernalization requirement and photoperiod response. Characterizing the available genetic diversity of known and novel alleles of VERNALIZATION1 (VRN1) and PHOTOPERIOD1 (PPD1) in winter wheat can inform approaches for breeding climate resilient cultivars. This study identified QTL for heading date (HD) associated with multiple VRN1 and PPD1 loci in a population developed from a cross betwe...

  18. AGRONOMIC AND QUALITY QTL MAPPING IN SPRING WHEAT

    Directory of Open Access Journals (Sweden)

    Mohamed Mergoum

    2013-04-01

    Full Text Available Wheat (Triticum aestivum L. flour represents one of the primary sources of calories and proteins for the human diet. The increase in the wheat yield without losing its baking and milling quality is an important breeding objective. The use of QTL analysis is an expedient methodology to help breeders to face this multifaceted challenge. Here, a population of 129 recombinant inbred lines (RILs developed from a cross between ‘Steele-ND’ cultivar and ‘ND 735’ advanced line was used to evaluate several yield and quality traits and map the genomic regions controlling these traits. The phenotypic data were collected from field experiments conducted at four North Dakota (ND, USA environments. Transgressive segregation was observed for all traits, with RILs outperforming the most adapted parent and commercial cultivars. Using a linkage map of 392 markers, composite interval mapping identified a total of 13 environment-specific QTLs, all explaining large phenotypic variations (R2=16-44%. The genotypic values of these “reserve” alleles were directly used as criteria of selection in breeding programs.

  19. Isolation, identification and characterization of regional indigenous Saccharomyces cerevisiae strains

    OpenAIRE

    Hana Šuranská; Dana Vránová; Jiřina Omelková

    2016-01-01

    Abstract In the present work we isolated and identified various indigenous Saccharomyces cerevisiae strains and screened them for the selected oenological properties. These S. cerevisiae strains were isolated from berries and spontaneously fermented musts. The grape berries (Sauvignon blanc and Pinot noir) were grown under the integrated and organic mode of farming in the South Moravia (Czech Republic) wine region. Modern genotyping techniques such as PCR-fingerprinting and interdelta PCR typ...

  20. Isolation, identification and characterization of regional indigenous Saccharomyces cerevisiae strains

    OpenAIRE

    Šuranská, Hana; Vránová, Dana; Omelková, Jiřina

    2016-01-01

    In the present work we isolated and identified various indigenous Saccharomyces cerevisiae strains and screened them for the selected oenological properties. These S. cerevisiae strains were isolated from berries and spontaneously fermented musts. The grape berries (Sauvignon blanc and Pinot noir) were grown under the integrated and organic mode of farming in the South Moravia (Czech Republic) wine region. Modern genotyping techniques such as PCR-fingerprinting and interdelta PCR typing were ...

  1. GENOTIPIC CHARACTERIZATION OF SALMONELLA INFANTIS STRAINS ISOLATED IN MARCHE REGION

    OpenAIRE

    M.B Valli; L. Paoloni; A.M. Dionosi; M. Staffolani; S. Fisichella

    2013-01-01

    In this study thirty-eight strains of Salmonella enterica serovar Infantis isolated in Marche Region from human cases, food, animal and environmental samples were analyzed by Pulsed-Field Gel Electrophoresis (PFGE). All strains were typed by the DNA macro-restriction patterns obtained following PFGE of XbaI digests, while antimicrobial susceptibility testing of isolates was performed by the standardized disk diffusion method. The analysis of PFGE patterns by Bionumerics software demonstrated ...

  2. Hydrochemical characterization of recreational thermal regions in Uruguay

    International Nuclear Information System (INIS)

    The deep drilling in Uruguay yields thermal groundwater aquifer formations contained in Mesozoic and Permo-Carboniferous in the North Basin. This paper characterizes thermal environments from the standpoint of physical-chemical, used primarily recreational, noting also the presence of heavy metals of natural origin. We worked over 62 analytical results from various information sources between 1946 and 2007. Using appropriate software the results were entered selected based on reliability and study area, 11 wells, analyzed different diagrams to characterize the water. Based on the drilling location and classification hydrogeochemistry thermal, thermal environments proposes five sorted from North to South: Arapey, Salto, Guaviyú, Guichon and Paso Ullestie. The proposed thermal environments were differentiated by the constitution hydrochemistry of waters, from north to south evolve bicarbonate calcium bicarbonate to sodium chloride, and increase the presence of sulfates. Groundwater Arapey environments and Salto aquifers are contained in Jurassic-Cretaceous, while for the remaining three environments (Guaviyú, Guichon and Paso Ullestie), aquifers are geological formations Permo - Carboniferous. In the past, it was determined the presence of As, funded by pre-Early Paleozoic formations Guarani Aquifer System: Buena Vista and Yaguarí Resumen ampliado Introducción

  3. Characterization of flow regimes in the post-dryout region

    International Nuclear Information System (INIS)

    A visual study of film boiling using photographic and high speed motion-picture methods was carried out to determine the flow regime transition criteria in the post-CHF region. An idealized inverted annular flow was obtained by introducing a liquid jet of Freon 113 through a nozzle, precisely centered with respect to the internal diameter of the test section, with an annual gas flow. The respective ranges for liquid and gas exit velocities were 0.05-0.5 and 0.03-8.2 m/s. Nitrogen and helium were used in the study

  4. Insight into the Genetic Components of Community Genetics: QTL Mapping of Insect Association in a Fast-Growing Forest Tree

    OpenAIRE

    DeWoody, J.; Viger, M.; Lakatos, F.; Tuba, K.; Taylor, G.; Smulders, M.J.M.

    2013-01-01

    Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL) analyses conducted on data from a common garden experiment. The F2 offspring of a hybrid poplar (Populus trichocarpa x P. deltoides) cross were assessed for seven categories of insect leaf damage at two time points, June and August. Positive ...

  5. Isolation, identification and characterization of regional indigenous Saccharomyces cerevisiae strains

    Science.gov (United States)

    Šuranská, Hana; Vránová, Dana; Omelková, Jiřina

    2016-01-01

    In the present work we isolated and identified various indigenous Saccharomyces cerevisiae strains and screened them for the selected oenological properties. These S. cerevisiae strains were isolated from berries and spontaneously fermented musts. The grape berries (Sauvignon blanc and Pinot noir) were grown under the integrated and organic mode of farming in the South Moravia (Czech Republic) wine region. Modern genotyping techniques such as PCR-fingerprinting and interdelta PCR typing were employed to differentiate among indigenous S. cerevisiae strains. This combination of the methods provides a rapid and relatively simple approach for identification of yeast of S. cerevisiae at strain level. In total, 120 isolates were identified and grouped by molecular approaches and 45 of the representative strains were tested for selected important oenological properties including ethanol, sulfur dioxide and osmotic stress tolerance, intensity of flocculation and desirable enzymatic activities. Their ability to produce and utilize acetic/malic acid was examined as well; in addition, H2S production as an undesirable property was screened. The oenological characteristics of indigenous isolates were compared to a commercially available S. cerevisiae BS6 strain, which is commonly used as the starter culture. Finally, some indigenous strains coming from organically treated grape berries were chosen for their promising oenological properties and these strains will be used as the starter culture, because application of a selected indigenous S. cerevisiae strain can enhance the regional character of the wines. PMID:26887243

  6. Isolation, identification and characterization of regional indigenous Saccharomyces cerevisiae strains.

    Science.gov (United States)

    Šuranská, Hana; Vránová, Dana; Omelková, Jiřina

    2016-01-01

    In the present work we isolated and identified various indigenous Saccharomyces cerevisiae strains and screened them for the selected oenological properties. These S. cerevisiae strains were isolated from berries and spontaneously fermented musts. The grape berries (Sauvignon blanc and Pinot noir) were grown under the integrated and organic mode of farming in the South Moravia (Czech Republic) wine region. Modern genotyping techniques such as PCR-fingerprinting and interdelta PCR typing were employed to differentiate among indigenous S. cerevisiae strains. This combination of the methods provides a rapid and relatively simple approach for identification of yeast of S. cerevisiae at strain level. In total, 120 isolates were identified and grouped by molecular approaches and 45 of the representative strains were tested for selected important oenological properties including ethanol, sulfur dioxide and osmotic stress tolerance, intensity of flocculation and desirable enzymatic activities. Their ability to produce and utilize acetic/malic acid was examined as well; in addition, H2S production as an undesirable property was screened. The oenological characteristics of indigenous isolates were compared to a commercially available S. cerevisiae BS6 strain, which is commonly used as the starter culture. Finally, some indigenous strains coming from organically treated grape berries were chosen for their promising oenological properties and these strains will be used as the starter culture, because application of a selected indigenous S. cerevisiae strain can enhance the regional character of the wines. PMID:26887243

  7. Isolation, identification and characterization of regional indigenous Saccharomyces cerevisiae strains

    Directory of Open Access Journals (Sweden)

    Hana Šuranská

    2016-03-01

    Full Text Available Abstract In the present work we isolated and identified various indigenous Saccharomyces cerevisiae strains and screened them for the selected oenological properties. These S. cerevisiae strains were isolated from berries and spontaneously fermented musts. The grape berries (Sauvignon blanc and Pinot noir were grown under the integrated and organic mode of farming in the South Moravia (Czech Republic wine region. Modern genotyping techniques such as PCR-fingerprinting and interdelta PCR typing were employed to differentiate among indigenous S. cerevisiae strains. This combination of the methods provides a rapid and relatively simple approach for identification of yeast of S. cerevisiae at strain level. In total, 120 isolates were identified and grouped by molecular approaches and 45 of the representative strains were tested for selected important oenological properties including ethanol, sulfur dioxide and osmotic stress tolerance, intensity of flocculation and desirable enzymatic activities. Their ability to produce and utilize acetic/malic acid was examined as well; in addition, H2S production as an undesirable property was screened. The oenological characteristics of indigenous isolates were compared to a commercially available S. cerevisiae BS6 strain, which is commonly used as the starter culture. Finally, some indigenous strains coming from organically treated grape berries were chosen for their promising oenological properties and these strains will be used as the starter culture, because application of a selected indigenous S. cerevisiae strain can enhance the regional character of the wines.

  8. Alternative models for detection of quantitative trait loci (QTL) for growth and carcass traits in pigs chromosomes 4, 5 and 7

    NARCIS (Netherlands)

    Moraes Gonçalves, de T.; Nunes de Oliveira, H.; Bovenhuis, H.; Bink, M.C.A.M.; Arendonk, van J.A.M.

    2005-01-01

    Genome scans can be used to identify chromosomal regions and eventually genes that control quantitative traits (QTL) of economic importance. In an experimental cross between Meishan (male) and Dutch Large White and Landrace lines (female), 298 F1 and 831 F2 animals were evaluated for intramuscular f

  9. QTL consistency for agronomic traits across three generations and potential applications in popcorn

    Institute of Scientific and Technical Information of China (English)

    DONG Yong-bin; ZHANG Zhong-wei; SHI Qing-ling; WANG Qi-lei; ZHOU Qiang; DENG Fei; MA Zhi-yan; QIAO Da-he; LI Yu-ling

    2015-01-01

    Favorable agronomic traits are important to improve productivity of popcorn. In this study, a recombinant inbred line (RIL) population consisting of 258 lines was evaluated to identify quantitative trait loci (QTLs) for nine agronomic traits (plant height, ear height, top height (plant height subtracted ear height), top height/plant height, number of leaves above the top ear, leaf area, stalk diameter, number of tassel branches and the length of tassel) under three environments. Meta-anal-ysis was conducted then to integrate QTLs identiifed across three generations (RIL, F2:3 and BC2F2) developed from the same crosses. In total, 179 QTLs and 36 meta-QTLs (mQTL) were identiifed. The percentage of phenotypic variation (R2) explained by any single QTL varied from 3.86 to 28.4%, and 24 QTLs with contributions over 15%. Nine common QTLs located in the same or similar chromosome regions were detected across three generations. Five meta-QTLs were identiifed including QTLs in three independent studies. Seven important mQTLs were composed of 11–26 QTLs for 4–7 traits, respectively. Only 11 mQTLs were commonly identiifed in the same or similar chromosome regions across agronomic traits, popping characteristics (popping fold, popping volume and popping rate) and grain yield components (ear weight per plant, grain weight per plant, 100-grain weight, ear length, kernel number per row, ear diameter, row number per ear and kernel ratio) by meta-QTL analysis. In conclusion, we identiifed a list of QTLs, some of which with much higher contributions to agronomic traits should be valuable for further study in improving both popping characteristics and grain yield components in popcorn.

  10. Characterization of the flamenco region of the Drosophila melanogaster genome.

    Science.gov (United States)

    Robert, V; Prud'homme, N; Kim, A; Bucheton, A; Pélisson, A

    2001-06-01

    The flamenco gene, located at 20A1-3 in the beta-heterochromatin of the Drosophila X chromosome, is a major regulator of the gypsy/mdg4 endogenous retrovirus. As a first step to characterize this gene, approximately 100 kb of genomic DNA flanking a P-element-induced mutation of flamenco was isolated. This DNA is located in a sequencing gap of the Celera Genomics project, i.e., one of those parts of the genome in which the "shotgun" sequence could not be assembled, probably because it contains long stretches of repetitive DNA, especially on the proximal side of the P insertion point. Deficiency mapping indicated that sequences required for the normal flamenco function are located >130 kb proximal to the insertion site. The distal part of the cloned DNA does, nevertheless, contain several unique sequences, including at least four different transcription units. Dip1, the closest one to the P-element insertion point, might be a good candidate for a gypsy regulator, since it putatively encodes a nuclear protein containing two double-stranded RNA-binding domains. However, transgenes containing dip1 genomic DNA were not able to rescue flamenco mutant flies. The possible nature of the missing flamenco sequences is discussed. PMID:11404334

  11. Revisiting QTL Affecting Clinical Mastitis by High-Density GWAS and Resequencing in the Finnish Ayrshire Dairy Cattle

    DEFF Research Database (Denmark)

    Vilkki, Johanna; Iso-Touru, Terhi; Schulman, Nina F;

    Mastitis is the most common disease of dairy cattle, causing high economic losses each year. Studies to locate QTL affecting clinical mastitis and milk somatic cell counts have been carried out to increase our understanding of the disease. As part of the EU FP7 Quantomics project, we have used most...... recent genomic tools to characterize QTL affecting mastitis incidence in the Finnish Ayrshire cattle. Clinical mastitis diagnoses from -15 to 50 days and 51 to 300 days of first lactation and SCC (geometric mean of SCS observations between 5 to 170 days of first lactation) were included. In total, 1920...... progeny tested bulls were genotyped with the Illumina BovineSNP50 chip. After quality control, 38473 SNPs were analyzed using a mixed linear model (software package DMU). Associations (5% Bonferroni threshold) were detected in 9 peaks on 5 chromosomes. A set of 238 of the bulls were re-genotyped with the...

  12. A region on chicken chromosome 2 affects both egg white thinning and egg weight

    Directory of Open Access Journals (Sweden)

    Mäki-Tanila Asko

    2005-09-01

    Full Text Available Abstract We describe the results from genetic dissection of a QTL region on chicken chromosome 2, shown to affect egg weight and quality in an earlier genome scan of an F2 intercross between two divergent egg layer lines. As the 90% confidence intervals for the detected QTL covered tens of centiMorgans, new analyses were needed. The datasets were reanalysed with denser marker intervals to characterise the QTL region. Analysis of a candidate gene from the original QTL region, vimentin, did not support its role in controlling egg white thinning. Even after reanalysis with additional seven markers in the QTL area, the 90% confidence intervals remained large or even increased, suggesting the presence of multiple linked QTL for the traits. A grid search fitting two QTL on chromosome 2 for each trait suggested that there are two distinct QTL areas affecting egg white thinning in both production periods and egg weight in the late production period. The results indicate possible pleiotropic effects of some of the QTL on egg quality and egg weight. However, it was not possible to make a distinction between close linkage versus pleiotropic effects.

  13. Identifying QTL for fur quality traits in mink (Neovison vison)

    DEFF Research Database (Denmark)

    Thirstrup, Janne Pia; Anistoroaei, Razvan Marian; Guldbrandtsen, Bernt;

    2012-01-01

    Mapping of quantitative trait loci (QTL) affecting fur quality traits (guard hair length, guard hair thikness, and density of woll) was performed in a 3-generation population (F2-design). In the parental generation, Nordic wild mink were crossed reciprocally with American short nap mink. Twenty one...... wade on all genotyped mink by Kopenhagen Fur. The QTL analyses were performed by least square regression implemented in the software Grid QTL. Evidence was found for QTL for the fur quality on eight autosomal chromosomes (LOD score >3.0). QTL were detected for guard hair thickness on chromosomes 1, 2...

  14. Agronomic characterization variety Quebranta in the Ica region, Peru

    Directory of Open Access Journals (Sweden)

    Cáceres Yparraguirre Hanna

    2015-01-01

    Full Text Available The study was to identify the best strains of the Quebranta variety cultivated in Peruvian region of Ica during campaigns 2011 to 2014. The evaluations were conducted in fourteen vineyards and the criteria to evaluate each one of them was that the same owner vineyard, would identify the best strain Quebranta for their good performance and sanitary quality. Productive parameters as grape weight and number of bunches per vine, average cluster weight, length and width of cluster and Berry weight were evaluated. Within the parameters of vegetative growth was assessed Ravaz index and as parameter for the composition of the grape was evaluated the concentration soluble solids (°Brix, total acidity and pH. Four phenological stages were recorded and defined from observed events in the branch of the year: Phase I comprising bud of winter to sprouting; Phase II of sprouting to full bloom; Phase III of full bloom to veraison and Phase IV of veraison to maturity. At the time of fruit setting were taken leaf samples to assess the State of health of each strain to Grapevine fanleaf virus, Grapevine fleck virus, Grapevine leafroll virus 1, Grapevine leafroll virus 3 and Tomato ringspot virus. The variables average bunch weight (22%, berry weight (20%, bunch length (13% and bunch width (11% presented the lowest values coefficient of variation. The variables of weight of grape per vine (52%, number of bunch (42% and index of Ravaz (60% has the highest values of coefficient of variation. Four variables were used that showed lower values (25% coefficient of variation for the weighted average. The variables that presented perfect correlation were berry weight and width of bunch, berry weight and Ravaz index, length of bunch and Ravaz index. The analysis of conglomerate allowed to group the strains in study in two groups which showed a significant difference between them (p < 0.0001. The principal component analysis identified that the variable of weight per bunch

  15. Cis-eQTL analysis and functional validation of candidate susceptibility genes for high-grade serous ovarian cancer

    Science.gov (United States)

    Lawrenson, Kate; Li, Qiyuan; Kar, Siddhartha; Seo, Ji-Heui; Tyrer, Jonathan; Spindler, Tassja J.; Lee, Janet; Chen, Yibu; Karst, Alison; Drapkin, Ronny; Aben, Katja K. H.; Anton-Culver, Hoda; Antonenkova, Natalia; Bowtell, David; Webb, Penelope M.; deFazio, Anna; Baker, Helen; Bandera, Elisa V.; Bean, Yukie; Beckmann, Matthias W.; Berchuck, Andrew; Bisogna, Maria; Bjorge, Line; Bogdanova, Natalia; Brinton, Louise A.; Brooks-Wilson, Angela; Bruinsma, Fiona; Butzow, Ralf; Campbell, Ian G.; Carty, Karen; Chang-Claude, Jenny; Chenevix-Trench, Georgia; Chen, Anne; Chen, Zhihua; Cook, Linda S.; Cramer, Daniel W.; Cunningham, Julie M.; Cybulski, Cezary; Dansonka-Mieszkowska, Agnieszka; Dennis, Joe; Dicks, Ed; Doherty, Jennifer A.; Dörk, Thilo; du Bois, Andreas; Dürst, Matthias; Eccles, Diana; Easton, Douglas T.; Edwards, Robert P.; Eilber, Ursula; Ekici, Arif B.; Fasching, Peter A.; Fridley, Brooke L.; Gao, Yu-Tang; Gentry-Maharaj, Aleksandra; Giles, Graham G.; Glasspool, Rosalind; Goode, Ellen L.; Goodman, Marc T.; Grownwald, Jacek; Harrington, Patricia; Harter, Philipp; Hasmad, Hanis Nazihah; Hein, Alexander; Heitz, Florian; Hildebrandt, Michelle A. T.; Hillemanns, Peter; Hogdall, Estrid; Hogdall, Claus; Hosono, Satoyo; Iversen, Edwin S.; Jakubowska, Anna; James, Paul; Jensen, Allan; Ji, Bu-Tian; Karlan, Beth Y.; Kruger Kjaer, Susanne; Kelemen, Linda E.; Kellar, Melissa; Kelley, Joseph L.; Kiemeney, Lambertus A.; Krakstad, Camilla; Kupryjanczyk, Jolanta; Lambrechts, Diether; Lambrechts, Sandrina; Le, Nhu D.; Lee, Alice W.; Lele, Shashi; Leminen, Arto; Lester, Jenny; Levine, Douglas A.; Liang, Dong; Lissowska, Jolanta; Lu, Karen; Lubinski, Jan; Lundvall, Lene; Massuger, Leon F. A. G.; Matsuo, Keitaro; McGuire, Valerie; McLaughlin, John R.; Nevanlinna, Heli; McNeish, Ian; Menon, Usha; Modugno, Francesmary; Moysich, Kirsten B.; Narod, Steven A.; Nedergaard, Lotte; Ness, Roberta B.; Azmi, Mat Adenan Noor; Odunsi, Kunle; Olson, Sara H.; Orlow, Irene; Orsulic, Sandra; Weber, Rachel Palmieri; Pearce, Celeste L.; Pejovic, Tanja; Pelttari, Liisa M.; Permuth-Wey, Jennifer; Phelan, Catherine M.; Pike, Malcolm C.; Poole, Elizabeth M.; Ramus, Susan J.; Risch, Harvey A.; Rosen, Barry; Rossing, Mary Anne; Rothstein, Joseph H.; Rudolph, Anja; Runnebaum, Ingo B.; Rzepecka, Iwona K.; Salvesen, Helga B.; Schildkraut, Joellen M.; Schwaab, Ira; Sellers, Thomas A.; Shu, Xiao-Ou; Shvetsov, Yurii B.; Siddiqui, Nadeem; Sieh, Weiva; Song, Honglin; Southey, Melissa C.; Sucheston, Lara; Tangen, Ingvild L.; Teo, Soo-Hwang; Terry, Kathryn L.; Thompson, Pamela J.; Timorek, Agnieszka; Tsai, Ya-Yu; Tworoger, Shelley S.; van Altena, Anne M.; Van Nieuwenhuysen, Els; Vergote, Ignace; Vierkant, Robert A.; Wang-Gohrke, Shan; Walsh, Christine; Wentzensen, Nicolas; Whittemore, Alice S.; Wicklund, Kristine G.; Wilkens, Lynne R.; Woo, Yin-Ling; Wu, Xifeng; Wu, Anna H.; Yang, Hannah; Zheng, Wei; Ziogas, Argyrios; Monteiro, Alvaro; Pharoah, Paul D.; Gayther, Simon A.; Freedman, Matthew L.

    2015-01-01

    Genome-wide association studies have reported 11 regions conferring risk of high-grade serous epithelial ovarian cancer (HGSOC). Expression quantitative trait locus (eQTL) analyses can identify candidate susceptibility genes at risk loci. Here we evaluate cis-eQTL associations at 47 regions associated with HGSOC risk (P≤10−5). For three cis-eQTL associations (P<1.4 × 10−3, FDR<0.05) at 1p36 (CDC42), 1p34 (CDCA8) and 2q31 (HOXD9), we evaluate the functional role of each candidate by perturbing expression of each gene in HGSOC precursor cells. Overexpression of HOXD9 increases anchorage-independent growth, shortens population-doubling time and reduces contact inhibition. Chromosome conformation capture identifies an interaction between rs2857532 and the HOXD9 promoter, suggesting this SNP is a leading causal variant. Transcriptomic profiling after HOXD9 overexpression reveals enrichment of HGSOC risk variants within HOXD9 target genes (P=6 × 10−10 for risk variants (P<10−4) within 10 kb of a HOXD9 target gene in ovarian cells), suggesting a broader role for this network in genetic susceptibility to HGSOC. PMID:26391404

  16. Mapping carcass and meat quality QTL on Sus Scrofa chromosome 2 in commercial finishing pigs

    Directory of Open Access Journals (Sweden)

    van Kampen Tony A

    2009-01-01

    Full Text Available Abstract Quantitative trait loci (QTL affecting carcass and meat quality located on SSC2 were identified using variance component methods. A large number of traits involved in meat and carcass quality was detected in a commercial crossbred population: 1855 pigs sired by 17 boars from a synthetic line, which where homozygous (A/A for IGF2. Using combined linkage and linkage disequilibrium mapping (LDLA, several QTL significantly affecting loin muscle mass, ham weight and ham muscles (outer ham and knuckle ham and meat quality traits, such as Minolta-L* and -b*, ultimate pH and Japanese colour score were detected. These results agreed well with previous QTL-studies involving SSC2. Since our study is carried out on crossbreds, different QTL may be segregating in the parental lines. To address this question, we compared models with a single QTL-variance component with models allowing for separate sire and dam QTL-variance components. The same QTL were identified using a single QTL variance component model compared to a model allowing for separate variances with minor differences with respect to QTL location. However, the variance component method made it possible to detect QTL segregating in the paternal line (e.g. HAMB, the maternal lines (e.g. Ham or in both (e.g. pHu. Combining association and linkage information among haplotypes improved slightly the significance of the QTL compared to an analysis using linkage information only.

  17. Genetic control of rhizomes and genomic localization of a major-effect growth habit QTL in perennial wildrye.

    Science.gov (United States)

    Yun, Lan; Larson, Steve R; Mott, Ivan W; Jensen, Kevin B; Staub, Jack E

    2014-06-01

    Rhizomes are prostrate subterranean stems that provide primitive mechanisms of vegetative dispersal, survival, and regrowth of perennial grasses and other monocots. The extent of rhizome proliferation varies greatly among grasses, being absent in cereals and other annuals, strictly confined in caespitose perennials, or highly invasive in some perennial weeds. However, genetic studies of rhizome proliferation are limited and genes controlling rhizomatous growth habit have not been elucidated. Quantitative trait loci (QTLs) controlling rhizome spreading were compared in reciprocal backcross populations derived from hybrids of rhizomatous creeping wildrye (Leymus triticoides) and caespitose basin wildrye (L. cinereus), which are perennial relatives of wheat. Two recessive QTLs were unique to the creeping wildrye backcross, one dominant QTL was unique to the basin wildrye backcross, and one additive QTL was detectable in reciprocal backcrosses with high log odds (LOD = 31.6) in the basin wildrye background. The dominant QTL located on linkage group (LG)-2a was aligned to a dominant rhizome orthogene (Rhz3) of perennial rice (Oryza longistamina) and perennial sorghum (Sorghum propinquum). Nonparametric 99 % confidence bounds of the 31.6-LOD QTL were localized to a distal 3.8-centiMorgan region of LG-6a, which corresponds to a 0.7-Mb region of Brachypodium Chromosome 3 containing 106 genes. An Aux/IAA auxin signal factor gene was located at the 31.6-LOD peak, which could explain the gravitropic and aphototropic behavior of rhizomes. Findings elucidate genetic mechanisms controlling rhizome development and architectural growth habit differences among plant species. Results have possible applications to improve perennial forage and turf grasses, extend the vegetative life cycle of annual cereals, such as wheat, or control the invasiveness of highly rhizomatous weeds such as quackgrass (Elymus repens). PMID:24509730

  18. Simultaneous QTL detection and genomic breeding value estimation using high density SNP chips

    Directory of Open Access Journals (Sweden)

    Veerkamp Roel F

    2010-03-01

    Full Text Available Abstract Background The simulated dataset of the 13th QTL-MAS workshop was analysed to i detect QTL and ii predict breeding values for animals without phenotypic information. Several parameterisations considering all SNP simultaneously were applied using Gibbs sampling. Results Fourteen QTL were detected at the different time points. Correlations between estimated breeding values were high between models, except when the model was used that assumed that all SNP effects came from one distribution. The model that used the selected 14 SNP found associated with QTL, gave close to unity correlations with the full parameterisations. Conclusions Nine out of 18 QTL were detected, however the six QTL for inflection point were missed. Models for genomic selection were indicated to be fairly robust, e.g. with respect to accuracy of estimated breeding values. Still, it is worthwhile to investigate the number QTL underlying the quantitative traits, before choosing the model used for genomic selection.

  19. Mapping Isoflavone QTL with Main, Epistatic and QTL × Environment Effects in Recombinant Inbred Lines of Soybean

    OpenAIRE

    Yan Wang; Yingpeng Han; Xue Zhao; Yongguang Li; Weili Teng; Dongmei Li; Yong Zhan; Wenbin Li

    2015-01-01

    Soybean (Glycine max (L.) Merr.) isoflavone is important for human health and plant defense system. To identify novel quantitative trait loci (QTL) and epistatic QTL underlying isoflavone content in soybean, F5:6, F5:7 and F5:8 populations of 130 recombinant inbred (RI) lines, derived from the cross of soybean cultivar 'Zhong Dou 27' (high isoflavone) and 'Jiu Nong 20' (low isoflavone), were analyzed with 95 new SSR markers. A new linkage map including 194 SSR markers and covering 2,312 cM wi...

  20. Bayesian multi-QTL mapping for growth curve parameters

    DEFF Research Database (Denmark)

    Heuven, Henri C M; Janss, Luc L G

    2010-01-01

    segregating QTL using a Bayesian algorithm. Results For each individual a logistic growth curve was fitted and three latent variables: asymptote (ASYM), inflection point (XMID) and scaling factor (SCAL) were estimated per individual. Applying an 'animal' model showed heritabilities of approximately 48% for...

  1. Fast and efficient QTL mapper for thousands of molecular phenotypes

    Science.gov (United States)

    Ongen, Halit; Buil, Alfonso; Brown, Andrew Anand; Dermitzakis, Emmanouil T.; Delaneau, Olivier

    2016-01-01

    Motivation: In order to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq require methods that rapidly correlate tens of thousands of molecular phenotypes with millions of genetic variants while appropriately controlling for multiple testing. Results: We have developed FastQTL, a method that implements a popular cis-QTL mapping strategy in a user- and cluster-friendly tool. FastQTL also proposes an efficient permutation procedure to control for multiple testing. The outcome of permutations is modeled using beta distributions trained from a few permutations and from which adjusted P-values can be estimated at any level of significance with little computational cost. The Geuvadis & GTEx pilot datasets can be now easily analyzed an order of magnitude faster than previous approaches. Availability and implementation: Source code, binaries and comprehensive documentation of FastQTL are freely available to download at http://fastqtl.sourceforge.net/ Contact: emmanouil.dermitzakis@unige.ch or olivier.delaneau@unige.ch Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26708335

  2. An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper (Capsicum annuum).

    Science.gov (United States)

    Han, Koeun; Jeong, Hee-Jin; Yang, Hee-Bum; Kang, Sung-Min; Kwon, Jin-Kyung; Kim, Seungill; Choi, Doil; Kang, Byoung-Cheorl

    2016-04-01

    Most agricultural traits are controlled by quantitative trait loci (QTLs); however, there are few studies on QTL mapping of horticultural traits in pepper (Capsicumspp.) due to the lack of high-density molecular maps and the sequence information. In this study, an ultra-high-density map and 120 recombinant inbred lines (RILs) derived from a cross betweenC. annuum'Perennial' andC. annuum'Dempsey' were used for QTL mapping of horticultural traits. Parental lines and RILs were resequenced at 18× and 1× coverage, respectively. Using a sliding window approach, an ultra-high-density bin map containing 2,578 bins was constructed. The total map length of the map was 1,372 cM, and the average interval between bins was 0.53 cM. A total of 86 significant QTLs controlling 17 horticultural traits were detected. Among these, 32 QTLs controlling 13 traits were major QTLs. Our research shows that the construction of bin maps using low-coverage sequence is a powerful method for QTL mapping, and that the short intervals between bins are helpful for fine-mapping of QTLs. Furthermore, bin maps can be used to improve the quality of reference genomes by elucidating the genetic order of unordered regions and anchoring unassigned scaffolds to linkage groups. PMID:26744365

  3. RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome.

    Science.gov (United States)

    Thongjuea, Supat; Ruanjaichon, Vinitchan; Bruskiewich, Richard; Vanavichit, Apichart

    2009-01-01

    RiceGeneThresher is a public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome. It is a compendium of rice genomic resources consisting of genetic markers, genome annotation, expressed sequence tags (ESTs), protein domains, gene ontology, plant stress-responsive genes, metabolic pathways and prediction of protein-protein interactions. RiceGeneThresher system integrates these diverse data sources and provides powerful web-based applications, and flexible tools for delivering customized set of biological data on rice. Its system supports whole-genome gene mining for QTL by querying using DNA marker intervals or genomic loci. RiceGeneThresher provides biologically supported evidences that are essential for targeting groups or networks of genes involved in controlling traits underlying QTL. Users can use it to discover and to assign the most promising candidate genes in preparation for the further gene function validation analysis. The web-based application is freely available at http://rice.kps.ku.ac.th. PMID:18820292

  4. Characterization of the immuno dominant regions within gp41 of env gene of HIV in Pakistan

    International Nuclear Information System (INIS)

    Objective of the present study was to characterize the immuno dominant sequences of gp41 in HIV strain in Pakistani population so that vaccine may be prepared based upon these regions. A total of 25 specimens were collected from HIV patients of different areas of Pakistan. The viral RNA was isolated using QIAamp MinElute Spin Kit manufactured by Quiagen, California, USA. RT-PCR was done for amplification of the required region and confirmed by gel electrophoresis. The nucleotides of the required regions were sequenced using Big Dye terminator. Less than 20% of the specimens had mutations in immuno dominant regions, so it may be concluded that immuno dominant regions of gp41 in HIV strain in Pakistani population are conservatives and vaccine based upon these regions may prove active immunization against the disease. (author)

  5. Analysis of digenic epistatic effects and QE interaction effects QTL controlling grain weight in rice

    Institute of Scientific and Technical Information of China (English)

    高用明; 朱军; 宋佑胜; 何慈信; 石春海; 邢永忠

    2004-01-01

    Immortalized F2 population of rice (Oryza sativa L.) was developed by randomly mating F1 among recombinant inbred (RI) lines derived from (Zhenshan 97B×Minghui 63),which allowed replications within and across environments.QTL (quantitative trait loci) mapping analysis on kilo-grain weight of immortalized F2 population was performed by using newly developed software for QTL mapping,QTL Mapper 2.0. Eleven distinctly digenic epistatic loci included a total of 15 QTL were located on eight chromosomes.QTL main effects of additive,dominance,and additive×additive,additive×dominance,and dominance×dominance interactions were estimated.Interaction effects between QTL main effects and environments (QE) were predicted.Less than 40% of single effects,most of which were additive effects,for identified QTL were significant at 5% level.The directional difference for QTL main effects suggested that these QTL were distributed in parents in the repulsion phase.This should make it feasible to improve kilo-grain weight of both parents by selecting appropriate new recombinants. Only few of the QE interaction effects were significant.Application prospect for QTL mapping achievements in genetic breeding was discussed.

  6. Non-synonymous FGD3 Variant as Positional Candidate for Disproportional Tall Stature Accounting for a Carcass Weight QTL (CW-3 and Skeletal Dysplasia in Japanese Black Cattle.

    Directory of Open Access Journals (Sweden)

    Akiko Takasuga

    2015-08-01

    Full Text Available Recessive skeletal dysplasia, characterized by joint- and/or hip bone-enlargement, was mapped within the critical region for a major quantitative trait locus (QTL influencing carcass weight; previously named CW-3 in Japanese Black cattle. The risk allele was on the same chromosome as the Q allele that increases carcass weight. Phenotypic characterization revealed that the risk allele causes disproportional tall stature and bone size that increases carcass weight in heterozygous individuals but causes disproportionately narrow chest width in homozygotes. A non-synonymous variant of FGD3 was identified as a positional candidate quantitative trait nucleotide (QTN and the corresponding mutant protein showed reduced activity as a guanine nucleotide exchange factor for Cdc42. FGD3 is expressed in the growth plate cartilage of femurs from bovine and mouse. Thus, loss of FDG3 activity may lead to subsequent loss of Cdc42 function. This would be consistent with the columnar disorganization of proliferating chondrocytes in chondrocyte-specific inactivated Cdc42 mutant mice. This is the first report showing association of FGD3 with skeletal dysplasia.

  7. QTL analysis using SNP markers developed by next-generation sequencing for identification of candidate genes controlling 4-methylthio-3-butenyl glucosinolate contents in roots of radish, Raphanus sativus L.

    Directory of Open Access Journals (Sweden)

    Zhongwei Zou

    Full Text Available SNP markers for QTL analysis of 4-MTB-GSL contents in radish roots were developed by determining nucleotide sequences of bulked PCR products using a next-generation sequencer. DNA fragments were amplified from two radish lines by multiplex PCR with six primer pairs, and those amplified by 2,880 primer pairs were mixed and sequenced. By assembling sequence data, 1,953 SNPs in 750 DNA fragments, 437 of which have been previously mapped in a linkage map, were identified. A linkage map of nine linkage groups was constructed with 188 markers, and five QTLs were detected in two F(2 populations, three of them accounting for more than 50% of the total phenotypic variance being repeatedly detected. In the identified QTL regions, nine SNP markers were newly produced. By synteny analysis of the QTLs regions with Arabidopsis thaliana and Brassica rapa genome sequences, three candidate genes were selected, i.e., RsMAM3 for production of aliphatic glucosinolates linked to GSL-QTL-4, RsIPMDH1 for leucine biosynthesis showing strong co-expression with glucosinolate biosynthesis genes linked to GSL-QTL-2, and RsBCAT4 for branched-chain amino acid aminotransferase linked to GSL-QTL-1. Nucleotide sequences and expression of these genes suggested their possible function in 4MTB-GSL biosynthesis in radish roots.

  8. Construction of a BAC library and a physical map of a major QTL for CBB resistance of common bean (Phaseolus vulgaris L.).

    Science.gov (United States)

    Liu, S Y; Yu, K; Huffner, M; Park, S J; Banik, M; Pauls, K P; Crosby, W

    2010-07-01

    A major quantitative trait loci (QTL) conditioning common bacterial blight (CBB) resistance in common bean (Phaseolus vulgaris L.) lines HR45 and HR67 was derived from XAN159, a resistant line obtained from an interspecific cross between common bean lines and the tepary bean (P. acutifolius L.) line PI319443. This source of CBB resistance is widely used in bean breeding. Several other CBB resistance QTL have been identified but none of them have been physically mapped. Four molecular markers tightly linked to this QTL have been identified suitable for marker assisted selection and physical mapping of the resistance gene. A bacterial artificial chromosome (BAC) library was constructed from high molecular weight DNA of HR45 and is composed of 33,024 clones. The size of individual BAC clone inserts ranges from 30 kb to 280 kb with an average size of 107 kb. The library is estimated to represent approximately sixfold genome coverage. The BAC library was screened as BAC pools using four PCR-based molecular markers. Two to seven BAC clones were identified by each marker. Two clones were found to have both markers PV-tttc001 and STS183. One preliminary contig was assembled based on DNA finger printing of those positive BAC clones. The minimum tiling path of the contig contains 6 BAC clones spanning an estimated size of 750 kb covering the QTL region. PMID:20419470

  9. An interspecific backcross of Lycopersicon esculentum x L. hirsutum: linkage analysis and a QTL study of sexual compatibility factors and floral traits.

    Science.gov (United States)

    Bernacchi, D; Tanksley, S D

    1997-10-01

    A BC1 population of the self-compatible tomato Lycopersicon esculentum and its wild self-incompatible relative L. hirsutum f. typicum was used for restriction fragment length polymorphism linkage analysis and quantitative trait loci (QTL) mapping of reproductive behavior and floral traits. The self-incompatibility locus, S, on chromosome 1 harbored the only QTL for self-incompatibility indicating that the transition to self-compatibility in the lineage leading to the cultivated tomato was primarily the result of mutations at the S locus. Moreover, the major QTL controlling unilateral incongruity also mapped to the S locus, supporting the hypothesis that self-incompatibility and unilateral incongruity are not independent mechanisms. The mating behavior of near-isogenic lines carrying the L. hirsutum allele for the S locus on chromosome 1 in an otherwise L. esculentum background support these conclusions. The S locus region of chromosome 1 also harbors most major QTL for several floral traits important to pollination biology (e.g., number and size of flowers), suggesting a gene complex controlling both genetic and morphological mechanisms of reproduction control. Similar associations in other flowering plants suggest that such complex may have been conserved since early periods of plant evolution or else reflect a convergent evolutionary process. PMID:9335620

  10. Identification and mapping QTL for high-temperature adult-plant resistance to stripe rust in winter wheat (Triticum aestivum L.) cultivar 'Stephens'.

    Science.gov (United States)

    Santra, D K; Chen, X M; Santra, M; Campbell, K G; Kidwell, K K

    2008-09-01

    High-temperature adult-plant (HTAP) resistance from the winter wheat (Triticum aestivum) cultivar 'Stephens' has protected wheat crops from stripe rust caused by Puccinia striiformis f. sp. tritici for 30 years. The objectives of this study were to identify quantitative trait loci (QTL) for HTAP resistance in Stephens through genetic linkage analysis and identify DNA markers linked to the QTL for use in marker-assisted breeding. Mapping populations consisted of 101 recombinant inbred lines (RILs) through single-seed descent from 'Stephens' (resistant) x 'Michigan Amber' (susceptible). F(5), F(6) and F(7) RILs were evaluated for stripe rust resistance at Pullman, WA in 1996, 1997 and 1998, respectively, whereas F(8) RILs were evaluated at Mt Vernon, WA, USA in 2005. The 101 F(8) RILs were evaluated with 250 resistance gene analog polymorphism (RGAP), 245 simple sequence repeat (SSR) and 1 sequence tagged site (STS) markers for genetic linkage map construction. Two QTL, which explained 48-61% of the total phenotypic variation of the HTAP resistance in Stephens, were identified. QYrst.wgp-6BS.1 was within a 3.9-cM region flanked by Xbarc101 and Xbarc136. QYrst.wgp-6BS.2 was mapped in a 17.5-cM region flanked by Xgwm132 and Xgdm113. Both two QTL were physically mapped to the short arm of chromosome 6B, but in different bins. Validation and polymorphism tests of the flanking markers in 43 wheat genotypes indicated that the molecular markers associated with these QTL should be useful in marker-assisted breeding programs to efficiently incorporate HTAP resistance into new wheat cultivars. PMID:18584147

  11. Identification of expression QTL (eQTL of genes expressed in porcine M. longissimus dorsi and associated with meat quality traits

    Directory of Open Access Journals (Sweden)

    Schellander Karl

    2010-10-01

    Full Text Available Abstract Background Genetic analysis of transcriptional profiles is a promising approach for identifying and dissecting the genetics of complex traits like meat performance. Accordingly, expression levels obtained by microarray analysis were taken as phenotypes in a linkage analysis to map eQTL. Moreover, expression levels were correlated with traits related to meat quality and principle components with high loadings of these traits. By using an up-to-date annotation and localization of the respective probe-sets, the integration of eQTL mapping data and information of trait correlated expression finally served to point to candidate genes for meat quality traits. Results Genome-wide transcriptional profiles of M. longissimus dorsi RNAs samples of 74 F2 animals of a pig resource population revealed 11,457 probe-sets representing genes expressed in the muscle. Linkage analysis of expression levels of these probe-sets provided 9,180 eQTL at the suggestive significance threshold of LOD > 2. We mapped 653 eQTL on the same chromosome as the corresponding gene and these were designated as 'putative cis-eQTL'. In order to link eQTL to the traits of interest, probe-sets were addressed with relative transcript abundances that showed correlation with meat quality traits at p ≤ 0.05. Out of the 653 'putative cis-eQTL', 262 transcripts were correlated with at least one meat quality trait. Furthermore, association of expression levels with composite traits with high loadings for meat quality traits generated by principle component analysis were taken into account leading to a list of 85 genes exhibiting cis-eQTL and trait dependent expression. Conclusion Holistic expression profiling was integrated with QTL analysis for meat quality traits. Correlations between transcript abundance and meat quality traits, combined with genetic positional information of eQTL allowed us to prioritise candidate genes for further study.

  12. Characterization of seven United States coal regions. The development of optimal terrace pit coal mining systems

    Energy Technology Data Exchange (ETDEWEB)

    Wimer, R.L.; Adams, M.A.; Jurich, D.M.

    1981-02-01

    This report characterizes seven United State coal regions in the Northern Great Plains, Rocky Mountain, Interior, and Gulf Coast coal provinces. Descriptions include those of the Fort Union, Powder River, Green River, Four Corners, Lower Missouri, Illinois Basin, and Texas Gulf coal resource regions. The resource characterizations describe geologic, geographic, hydrologic, environmental and climatological conditions of each region, coal ranks and qualities, extent of reserves, reclamation requirements, and current mining activities. The report was compiled as a basis for the development of hypothetical coal mining situations for comparison of conventional and terrace pit surface mining methods, under contract to the Department of Energy, Contract No. DE-AC01-79ET10023, entitled The Development of Optimal Terrace Pit Coal Mining Systems.

  13. Response to state comments on the draft regional characterization reports for the Crystalline Repository Project

    International Nuclear Information System (INIS)

    In May, 1983, the US Department of Energy (DOE) Crystalline Repository Project Office (CPO) issued six draft Regional Characterization Reports (RCRs) for review and comment to the 17 Crystalline States comprising the Northeastern, Southeastern, and North Central crystalline regions. Comment letters were received from 13 of the 17 states. The more than 2000 comments generally focused on the quality and content of the characterization reports and on their intended use in region-to-area screening. These comments were paraphrased and grouped into 23 subjects within the following four topical areas: (1) General and Programmatic; (2) Geologic; (3) Environmental and Socioeconomic; and (4) Editorial. This document provides responses to the comments submitted by the states

  14. Fine Mapping QTL for mastitis resistance on BTA9 in three Nordic red cattle breeds

    DEFF Research Database (Denmark)

    Sahana, G; Lund, M S; Andersson-Eklund, L;

    2008-01-01

    A QTL affecting clinical mastitis and/or somatic cell score (SCS) has been reported previously on chromosome 9 from studies in 16 families from the Swedish Red and White (SRB), Finnish Ayrshire (FA) and Danish Red (DR) breeds. In order to refine the QTL location, 67 markers were genotyped over the...... mastitis to be mapped to a small interval (BM4208 and INRA084. This QTL showed a pleiotropic effect on SCS in the DR and SRB breeds. Haplotypes associated with variations in mastitis resistance were identified. The haplotypes were predictive in the general population and can be used in marker......-assisted selection. Pleiotropic effects of the mastitis QTL were studied for three milk production traits and eight udder conformation traits. This QTL was also associated with yield traits in DR but not in FA or SRB. No QTL were found for udder conformation traits on chromosome 9...

  15. Identificazione e trasferimento di QTL coinvolti nell’accumulo di antiossidanti nel frutto di pomodoro

    OpenAIRE

    Lombardi, Nadia

    2011-01-01

    L’obiettivo del progetto ha riguardato la combinazione di QTL coinvolti nell’incremento del contenuto in antiossidanti nel frutto di pomodoro. A tale scopo sono state utilizzate le linee di introgressione (IL) di pomodoro. Tali IL sono particolarmente utili per la dissezione di caratteri complessi e consentono l’individuazione ed il mappaggio di QTL di interesse su specifici cromosomi. Il trasferimento dei QTL e la loro combinazione in nuovi genotipi è stato perseguito eseguendo incroci tra l...

  16. Multi-QTL Mapping for Quantitative Traits Using Epistatic Distorted Markers

    OpenAIRE

    Xie, Shang-Qian; Wen, Jia; Zhang, Yuan-Ming

    2013-01-01

    The interaction between segregation distortion loci (SDL) has been often observed in all kinds of mapping populations. However, little has been known about the effect of epistatic SDL on quantitative trait locus (QTL) mapping. Here we proposed a multi-QTL mapping approach using epistatic distorted markers. Using the corrected linkage groups, epistatic SDL was identified. Then, these SDL parameters were used to correct the conditional probabilities of QTL genotypes, and these corrections were ...

  17. An Efficient Hierarchical Generalized Linear Mixed Model for Mapping QTL of Ordinal Traits in Crop Cultivars

    OpenAIRE

    Feng, Jian-Ying; Zhang, Jin; Zhang, Wen-Jie; Wang, Shi-Bo; Han, Shi-Feng; Zhang, Yuan-Ming

    2013-01-01

    Many important phenotypic traits in plants are ordinal. However, relatively little is known about the methodologies for ordinal trait association studies. In this study, we proposed a hierarchical generalized linear mixed model for mapping quantitative trait locus (QTL) of ordinal traits in crop cultivars. In this model, all the main-effect QTL and QTL-by-environment interaction were treated as random, while population mean, environmental effect and population structure were fixed. In the est...

  18. Separation of base allele and sampling term effects gives new insights in variance component QTL analysis

    OpenAIRE

    Carlborg Örjan; Rönnegård Lars

    2007-01-01

    Abstract Background Variance component (VC) models are commonly used for Quantitative Trait Loci (QTL) mapping in outbred populations. Here, the QTL effect is given as a random effect and a critical part of the model is the relationship between the phenotypic values and the random effect. In the traditional VC model, each individual has a unique QTL effect and the relationship between these random effects is given as a covariance structure (known as the identity-by-descent (IBD) matrix). Resu...

  19. Fine mapping of fatness QTL on porcine chromosome X and analyses of three positional candidate genes

    OpenAIRE

    Ma, Junwu; Gilbert, Hélène; Iannuccelli, Nathalie; Duan, Yanyu; Guo, Beili; Huang, Weibing; Ma, Huanban; Riquet, Juliette; Bidanel, Jean Pierre

    2013-01-01

    Background: Porcine chromosome X harbors four QTL strongly affecting backfat thickness (BFT), ham weight (HW), intramuscular fat content (IMF) and loin eye area (LEA). The confidence intervals (CI) of these QTL overlap and span more than 30 cM, or approximately 80 Mb. This study therefore attempts to fine map these QTL by joint analysis of two large-scale F2 populations (Large White × Meishan and White Duroc × Erhualian constructed by INRA and JXAU respectively) and furthermore, to determine ...

  20. Multi-QTL mapping for quantitative traits using epistatic distorted markers.

    Directory of Open Access Journals (Sweden)

    Shang-Qian Xie

    Full Text Available The interaction between segregation distortion loci (SDL has been often observed in all kinds of mapping populations. However, little has been known about the effect of epistatic SDL on quantitative trait locus (QTL mapping. Here we proposed a multi-QTL mapping approach using epistatic distorted markers. Using the corrected linkage groups, epistatic SDL was identified. Then, these SDL parameters were used to correct the conditional probabilities of QTL genotypes, and these corrections were further incorporated into the new QTL mapping approach. Finally, a set of simulated datasets and a real data in 304 mouse F2 individuals were used to validate the new method. As compared with the old method, the new one corrects genetic distance between distorted markers, and considers epistasis between two linked SDL. As a result, the power in the detection of QTL is higher for the new method than for the old one, and significant differences for estimates of QTL parameters between the two methods were observed, except for QTL position. Among two QTL for mouse weight, one significant difference for QTL additive effect between the above two methods was observed, because epistatic SDL between markers C66 and T93 exists (P = 2.94e-4.

  1. A comparison of bivariate and univariate QTL mapping in livestock populations

    Directory of Open Access Journals (Sweden)

    Sorensen Daniel

    2003-11-01

    Full Text Available Abstract This study presents a multivariate, variance component-based QTL mapping model implemented via restricted maximum likelihood (REML. The method was applied to investigate bivariate and univariate QTL mapping analyses, using simulated data. Specifically, we report results on the statistical power to detect a QTL and on the precision of parameter estimates using univariate and bivariate approaches. The model and methodology were also applied to study the effectiveness of partitioning the overall genetic correlation between two traits into a component due to many genes of small effect, and one due to the QTL. It is shown that when the QTL has a pleiotropic effect on two traits, a bivariate analysis leads to a higher statistical power of detecting the QTL and to a more precise estimate of the QTL's map position, in particular in the case when the QTL has a small effect on the trait. The increase in power is most marked in cases where the contributions of the QTL and of the polygenic components to the genetic correlation have opposite signs. The bivariate REML analysis can successfully partition the two components contributing to the genetic correlation between traits.

  2. The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci

    Directory of Open Access Journals (Sweden)

    Xavier Suresh R

    2006-06-01

    Full Text Available Abstract Background Many important agricultural traits such as weight gain, milk fat content and intramuscular fat (marbling in cattle are quantitative traits. Most of the information on these traits has not previously been integrated into a genomic context. Without such integration application of these data to agricultural enterprises will remain slow and inefficient. Our goal was to populate a genomic database with data mined from the bovine quantitative trait literature and to make these data available in a genomic context to researchers via a user friendly query interface. Description The QTL (Quantitative Trait Locus data and related information for bovine QTL are gathered from published work and from existing databases. An integrated database schema was designed and the database (MySQL populated with the gathered data. The bovine QTL Viewer was developed for the integration of QTL data available for cattle. The tool consists of an integrated database of bovine QTL and the QTL viewer to display QTL and their chromosomal position. Conclusion We present a web accessible, integrated database of bovine (dairy and beef cattle QTL for use by animal geneticists. The viewer and database are of general applicability to any livestock species for which there are public QTL data. The viewer can be accessed at http://bovineqtl.tamu.edu.

  3. Major QTL Conferring Resistance to Rice Bacterial Leaf Streak

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Bacterial leaf streak (BLS) is one of the important limiting factors to rice production in southern China and other tropical and sub-tropical areas in Asia. Resistance to BLS was found to be a quantitative trait and no major resistant gene was located in rice until date. In the present study, a new major quantitative trait locus (QTL) conferring resistance to BLS was identified from a highly resistant variety Dular by the employment of Dular/Balilla (DB) and Dular/IR24 (DI) segregation populations and was designated qBLSR-11-1. This QTL was located between the simple sequence repeat (SSR) markers RM120 and RM441 on chromosome 11 and could account for 18.1-21.7% and 36.3% of the variance in DB and DI populations, respectively. The genetic pattern of rice resistance to BLS was discussed.

  4. Sire design power calculation for QTL mapping experiments

    OpenAIRE

    Elsen Jean-Michel; Carta Antonello

    1999-01-01

    Estimates of sire design power for QTL mapping experiments obtained using three different methods of algebraic approximation were analysed by comparing them with the results of data simulations. Even when the binomial probability that any number of sires out of the total number of sires are jointly heterozygous at the marker and the QT loci was taken into consideration, the algebraic approximations overestimated powers. However, they could be used to rank designs differing in the number...

  5. Salt tolerance in Solanum pennellii: antioxidant response and related QTL

    Directory of Open Access Journals (Sweden)

    Şığva Hasan Ö

    2010-04-01

    Full Text Available Abstract Background Excessive soil salinity is an important problem for agriculture, however, salt tolerance is a complex trait that is not easily bred into plants. Exposure of cultivated tomato to salt stress has been reported to result in increased antioxidant content and activity. Salt tolerance of the related wild species, Solanum pennellii, has also been associated with similar changes in antioxidants. In this work, S. lycopersicum M82, S. pennellii LA716 and a S. pennellii introgression line (IL population were evaluated for growth and their levels of antioxidant activity (total water-soluble antioxidant activity, major antioxidant compounds (phenolic and flavonoid contents and antioxidant enzyme activities (superoxide dismutase, catalase, ascorbate peroxidase and peroxidase under both control and salt stress (150 mM NaCl conditions. These data were then used to identify quantitative trait loci (QTL responsible for controlling the antioxidant parameters under both stress and nonstress conditions. Results Under control conditions, cultivated tomato had higher levels of all antioxidants (except superoxide dismutase than S. pennellii. However, under salt stress, the wild species showed greater induction of all antioxidants except peroxidase. The ILs showed diverse responses to salinity and proved very useful for the identification of QTL. Thus, 125 loci for antioxidant content under control and salt conditions were detected. Eleven of the total antioxidant activity and phenolic content QTL matched loci identified in an independent study using the same population, thereby reinforcing the validity of the loci. In addition, the growth responses of the ILs were evaluated to identify lines with favorable growth and antioxidant profiles. Conclusions Plants have a complex antioxidant response when placed under salt stress. Some loci control antioxidant content under all conditions while others are responsible for antioxidant content only under

  6. Identification of seed-related QTL in Brassica rapa

    Directory of Open Access Journals (Sweden)

    H. Bagheri

    2013-10-01

    Full Text Available To reveal the genetic variation, and loci involved, for a range of seed-related traits, a new F2 mapping population was developed by crossing Brassica rapa ssp. parachinensis L58 (CaiXin with B. rapa ssp. trilocularis R-o-18 (spring oil seed, both rapid flowering and self-compatible. A linkage map was constructed using 97 AFLPs and 21 SSRs, covering a map distance of 757 cM with an average resolution of 6.4 cM, and 13 quantitative trait loci (QTL were detected for nine traits. A strong seed colour QTL (LOD 26 co-localized with QTL for seed size (LOD 7, seed weight (LOD 4.6, seed oil content (LOD 6.6, number of siliques (LOD 3 and number of seeds per silique (LOD 3. There was only a significant positive correlation between seed colour and seed oil content in the yellow coloured classes. Seed coat colour and seed size were controlled by the maternal plant genotype. Plants with more siliques tended to have more, but smaller, seeds and higher seed oil content. Seed colour and seed oil content appeared to be controlled by two closely linked loci in repulsion phase. Thus, it may not always be advantageous to select for yellow-seededness when breeding for high seed oil content in Brassicas.

  7. Adaptive linear rank tests for eQTL studies.

    Science.gov (United States)

    Szymczak, Silke; Scheinhardt, Markus O; Zeller, Tanja; Wild, Philipp S; Blankenberg, Stefan; Ziegler, Andreas

    2013-02-10

    Expression quantitative trait loci (eQTL) studies are performed to identify single-nucleotide polymorphisms that modify average expression values of genes, proteins, or metabolites, depending on the genotype. As expression values are often not normally distributed, statistical methods for eQTL studies should be valid and powerful in these situations. Adaptive tests are promising alternatives to standard approaches, such as the analysis of variance or the Kruskal-Wallis test. In a two-stage procedure, skewness and tail length of the distributions are estimated and used to select one of several linear rank tests. In this study, we compare two adaptive tests that were proposed in the literature using extensive Monte Carlo simulations of a wide range of different symmetric and skewed distributions. We derive a new adaptive test that combines the advantages of both literature-based approaches. The new test does not require the user to specify a distribution. It is slightly less powerful than the locally most powerful rank test for the correct distribution and at least as powerful as the maximin efficiency robust rank test. We illustrate the application of all tests using two examples from different eQTL studies. PMID:22933317

  8. QTL Information Table: 229 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available ). Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice. Theor Appl Genet 105, 248-257. ...

  9. QTL Information Table: 753 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Eating ... quality alkali spreading value Mixture C)Interval RIL Zhenshan 97 Del ... traits and viscosity parameters characterizing the eating ... and cooking quality of rice grain. Theor Appl Gene ...

  10. QTL Information Table: 1031 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Resistance or Tolerance Other soil stress tolerance iron ... concentration in shoot tissue Mixture C ... H. (1998). Characterization of tissue tolerance to iron ... by molecular markers in different lines of rice. P ...

  11. Mapping quantitative trait loci (QTL in sheep. I. A new male framework linkage map and QTL for growth rate and body weight

    Directory of Open Access Journals (Sweden)

    Attard Gina

    2009-04-01

    Full Text Available Abstract A male sheep linkage map comprising 191 microsatellites was generated from a single family of 510 Awassi-Merino backcross progeny. Except for ovine chromosomes 1, 2, 10 and 17, all other chromosomes yielded a LOD score difference greater than 3.0 between the best and second-best map order. The map is on average 11% longer than the Sheep Linkage Map v4.7 male-specific map. This map was employed in quantitative trait loci (QTL analyses on body-weight and growth-rate traits between birth and 98 weeks of age. A custom maximum likelihood program was developed to map QTL in half-sib families for non-inbred strains (QTL-MLE and is freely available on request. The new analysis package offers the advantage of enabling QTL × fixed effect interactions to be included in the model. Fifty-four putative QTL were identified on nine chromosomes. Significant QTL with sex-specific effects (i.e. QTL × sex interaction in the range of 0.4 to 0.7 SD were found on ovine chromosomes 1, 3, 6, 11, 21, 23, 24 and 26.

  12. Complete characterization of strictly positive real regions and robust strictly positive real synthesis method

    Institute of Scientific and Technical Information of China (English)

    王龙; 郁文生

    2000-01-01

    The concept of weak strictly positive real regions is introduced, and its properties are discussed . By using the complete discrimination system for polynomials, complete characterization of the (weak) strictly positive real regions for transfer functions in coefficient space is given. A new effective method for robust strictly positive real synthesis is proposed. This method results in necessary and sufficient conditions for low-order stable interval polynomials and segment polynomials, and is also efficient for high-order cases. Numerical examples are provided to illustrate the effectiveness of this method.

  13. Complete characterization of strictly positive real regions and robust strictly positive real synthesis method

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The concept of weak strictly positive real regions is introduced, and its properties are discussed. By using the complete discrimination system for polynomials, complete characterization of the (weak) strictly positive real regions for transfer functions in coefficient space is given. A new effective method for robust strictly positive real synthesis is proposed. This method results in necessary and sufficient conditions for low-order stable interval polynomials and segment polynomials, and is also efficient for high-order cases. Numerical examples are provided to illustrate the effectiveness of this method.

  14. Characterization of the replication and stability regions of Agrobacterium tumefaciens plasmid pTAR.

    OpenAIRE

    Gallie, D R; Zaitlin, D; Perry, K L; Kado, C I

    1984-01-01

    A 5.4-kilobase region containing the origin of replication and stability maintenance of the 44-kilobase Agrobacterium tumefaciens plasmid pTAR has been mapped and characterized. Within this region is a 1.3-kilobase segment that is capable of directing autonomous replication. The remaining segment contains the stability locus for maintenance of pTAR during nonselective growth. Approximately 35% of pTAR shares sequence homology with pAg119, a 44-kilobase cryptic plasmid in grapevine strain 1D11...

  15. Nuclear analytical techniques applied to characterization of atmospheric aerosols in Amazon Region

    International Nuclear Information System (INIS)

    This work presents the atmospheric aerosols characterization that exist in different regions of Amazon basin. The biogenic aerosol emission by forest, as well as the atmospheric emissions of particulate materials due to biomass burning, were analyzed. Samples of aerosol particles were collected during three years in two different locations of Amazon region using Stacked Unit Filters. In order to study these samples some analytical nuclear techniques were used. The high concentrations of aerosols as a result of biomass burning process were observed in the period of june-september

  16. A region growing technique adapted to precise micro calcification characterization in mammography

    International Nuclear Information System (INIS)

    To-day, mammography is the only breast screening technique capable of detecting breast cancer at a very early stage. The presence of a breast tumor is indicated by some features on the mammogram. One sign of malignancy is the presence of clusters of fine, granular micro-calcifications. We present here a new three-step method for detecting and characterizing these micro-calcifications. We design with the detection of potential candidates ('seeds'). The aim of this first step is to detect all the pixels be a micro-calcification. Then we focus on our specific region growing technique which provides an accurate extraction of the shape of the region corresponding to each detected seed. This second step is essential because micro-calcifications shape is a very important feature for the diagnosis. It is then possible to determine precise parameters to characterize these micro-calcifications. (authors)

  17. Detecção de locos de características quantitativas (QTL afetando o crescimento e a carcaça de suínos: um enfoque Bayesiano com o uso de diferentes prioris Detection of quantitative trait loci (QTL affecting growth and carcass traits in swine: a Bayesian approach using differents priors

    Directory of Open Access Journals (Sweden)

    Tarcisio de Moraes Gonçalves

    2008-02-01

    Full Text Available Foram utilizados 1.129 animais, 298 F1 e 831 F2 para gordura intramuscular (GIM, % e ganho de peso (GP, g/dia e 324 F1 e 805 F2 para espessura de toucinho (ET, mm, obtidos por meio do cruzamento de suínos machos da raça Meishan e fêmeas Large White e Landrace. Os animais foram genotipados para marcadores moleculares cobrindo todo o genoma. Foram estudados os cromossomos 1, 2, 4, 5, 6, 7, 13, 14 e19 para ET e GIM e os cromossomos 1, 2, 4, 6, 7, 8, 13, 17 e19 para GP entre 25 e 90 kg de peso vivo (PV. Análises de QTL usando metodologia Bayesiana foram aplicadas mediante o modelo genético estatístico combinando os efeitos Poligênico Infinito (MPI, Poligênico Finito (MPF e de QTL. Os sumários dos parâmetros estimados foram baseados nas distribuições marginais a posteriori obtidas por Cadeia de Markov, algoritmo de Monte Carlo (MCMC. De modo geral, por meio dos resultados, foi possível evidenciar um QTL para ET, independentemente da priori estudada. Não foi possível detectar QTL para as características GIM e GP com a aplicação desta metodologia, o que pode estar relacionado aos marcadores não-informativos ou à ausência de QTL segregando nos cromossomos estudados. Há vantagens em analisar dados experimentais ajustando modelos genéticos combinados e não considerando unicamente o modelo poligênico ou o oligogênico. As análises ilustraram a utilidade e aplicabilidade do método Bayesiano no qual foram utilizados modelos finitos.Genome scan was used to identify chromosomal regions and genes that control quantitative trait loci (QTL of economic importance using 1129 animals from F1 and F2 populations obtained from crosses between Meishan and commercial Dutch breeds (Large White and Landrace. Animals were genotyped for molecular markers covering the entire genome. The chromosomes 1, 2, 4, 5, 6, 7, 13, 14 and 19 were studied for intramuscular fat (IMF, % and backfat thickness (BT, mm and the chromosomes 1, 2, 4, 6, 7, 8, 13, 17 and

  18. Quantitative Trait Locus Analysis of Seed Germination and Seedling Vigor in Brassica rapa Reveals QTL Hotspots and Epistatic Interactions

    OpenAIRE

    Basnet, Ram K.; Duwal, Anita; Tiwari, Dev N.; Xiao, Dong; Monakhos, Sokrat; Bucher, Johan; Visser, Richard G F; Groot, Steven P. C.; Bonnema, Guusje; Maliepaard, Chris

    2015-01-01

    The genetic basis of seed germination and seedling vigor is largely unknown in Brassica species. We performed a study to evaluate the genetic basis of these important traits in a B. rapa doubled haploid population from a cross of a yellow-seeded oil-type yellow sarson and a black-seeded vegetable-type pak choi. We identified 26 QTL regions across all 10 linkage groups for traits related to seed weight, seed germination and seedling vigor under non-stress and salt stress conditions illustratin...

  19. Conditional QTL mapping of protein content in wheat with respect to grain yield and its components

    Indian Academy of Sciences (India)

    Lin Wang; Fa Cui; Jinping Wang; Li Jun; Anming Ding; Chunhua Zhao; Xingfeng Li; Deshun Feng; Jurong Gao; Honggang Wang

    2012-12-01

    Grain protein content in wheat (Triticum aestivum L.) is generally considered a highly heritable character that is negatively correlated with grain yield and yield-related traits. Quantitative trait loci (QTL) for protein content was mapped using data on protein content and protein content conditioned on the putatively interrelated traits to evaluate possible genetic interrelationships between protein content and yield, as well as yield-related traits. Phenotypic data were evaluated in a recombinant inbred line population with 302 lines derived from a cross between the Chinese cultivar Weimai 8 and Luohan 2. Inclusive composite interval mapping using IciMapping 3.0 was employed for mapping unconditional and conditional QTL with additives. A strong genetic relationship was found between protein content and grain yield, and yield-related traits. Unconditional QTL mapping analysis detected seven additive QTL for protein content, with additive effects ranging in absolute size from 0.1898% to 0.3407% protein content, jointly accounting for 43.45% of the trait variance. Conditional QTL mapping analysis indicated two QTL independent from yield, which can be used in marker-assisted selection for increasing yield without affecting grain protein content. Three additional QTL with minor effects were identified in the conditional mapping. Of the three QTLs, two were identified when protein content was conditioned on yield, which had pleiotropic effects on those two traits. Conditional QTL mapping can be used to dissect the genetic interrelationship between two traits at the individual QTL level for closely correlated traits. Further, conditional QTL mapping can reveal additional QTL with minor effects that are undetectable in unconditional mapping.

  20. 基于 SNP 标记的 QTL 组合定位方法%Combined QTL Mapping Method based on SNP Markers

    Institute of Scientific and Technical Information of China (English)

    王倩雯; 郭茂祖; 王春宇; 刘晓燕

    2014-01-01

    QTL 的精确定位对数量性状遗传机制的研究及应用具有重要意义。随着分子生物技术和遗传学的发展,产生了大量可用于 QTL 定位的遗传标记和分析方法。然而,多数方法只能将 QTL 定位到一个区间而非具体位置,且具有较高的假阳性。为此,提出利用全基因组上的 SNP 标记,通过 emBayesB 方法和性状-标记回归区间分析相结合的组合方法进行 QTL 定位研究。组合方法能够筛选出与 QTL 存在较强关联的 SNP 标记,具有较高的计算速度和计算效率;通过性状-标记区间检测,能够较为精确地计算出 QTL 的位置。方法中考虑到染色体上其它标记的背景遗传信息,提高定位成功率和可信度。%Search the precise position of QTL ,is very significant for understanding the genetic mechanisms of quantitative traits and its application.The development of molecular biology and genetics results in a large number of genetic markers and analytical methods can be used for QTL mapping.However,most methods can only map QTL to a interval rather than a specific location with a high false positive.This paper proposes that the use of genome -wide SNP markers and combina-tion strategy which combining emBayesB methods and traits - mark regression interval analysis conducted QTL mapping studies.Combination strategy could screen out SNP markers which associated with QTL in the presence of strong,and hav-ing a high computing speed and efficiency;through trait -mark interval detection,the location of the QTL can be calculat-ed more accurately.The method takes into account the background genetic information of other genetic markers on the chro-mosome,achieves higher position success rate,and improves the positioning reliability.

  1. QTL Information Table: 30 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qUVR-10 Resistance or Tolerance Other stress resistance ultraviolet-B (UVB) resistance Mixture B ... d Yano, M. (2004). Delimitation of the chromosomal region ... for a quantitative trait locus, qUVR- 10, conferri ...

  2. QTL Information Table: 704 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Shoot/Seedling shoot length Mixture C)Interval RIL Lemont Teqing A RM250 RG2 ... me regions associated with seedling vigor in rice. Yi ... Chuan Xue Bao 31, 596-603. ...

  3. QTL Information Table: 91 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Resistance or Tolerance Other soil stress tolerance Cd concentration in brown rice ...somal regions with quantitative trait loci controlling cadmium concentration in brown rice (Oryza sativa). New Phytol 168, 345-350. ...

  4. Validation and Characterization of Ghd7.1, a Major Quantitative Trait Locus with Pleiotropic Effects on Spikelets per Panicle, Plant Height, and Heading Date in Rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    Touming Liu; Haiyang Liu; Huang Zhan; Yongzhong Xing

    2013-01-01

    A quantitative trait locus (QTL) that affects heading date (HD) and the number of spikelets per panicle (SPP) was previously identified in a small region on chromosome 7 in rice (Oryza sativa L.). In order to further characterize the QTL region, near isogenic lines (NILs) were quickly obtained by self-crossing recombinant inbred line 189, which is heterozygous in the vicinity of the target region. The pleiotropic effects of QTL Ghd7.1 on plant height (PH), SPP, and HD, were validated using an NIL-F2 population. Ghd7.1 explained 50.2%, 45.3%, and 76.9%of phenotypic variation in PH, SPP, and HD, respectively. Ghd7.1 was precisely mapped to a 357-kb region on the basis of analysis of the progeny of the NIL-F2 population. Day-length treatment confirmed that Ghd7.1 is sensitive to photoperiod, with long days delaying heading up to 12.5 d. Identification of panicle initiation and development for the pair of NILs showed that Ghd7.1 elongated the photoperiod-sensitive phase more than 10 d, but did not change the basic vegetative phase and the reproductive growth phase. These findings indicated that Ghd7.1 regulates SPP by controlling the rate of panicle differentiation rather than the duration of panicle development.

  5. Response to state comments on the revised draft Southeastern Regional Characterization Reports for the Crystalline Repository Project

    International Nuclear Information System (INIS)

    The purpose of this document is to respond to the comments received from the states of the Southeastern Region on the revised draft Southeastern Regional Characterization Reports (RCRs). The responses in this document indicate the manner in which the suggestions or comments received have been considered in modifying the revised draft Southeastern RCRs. Both general comments related to the overall Crystalline Repository Project (CRP) and comments on specific sections of the RCRs are addressed. This document responds to Southeastern State comments on both the revised draft Southeastern Regional Geologic Characterization Report (RGCR) and the revised draft Southeastern Regional Environmental Characterization Report (RECR)

  6. Response to state comments on the revised draft northeastern regional characterization reports for the Crystalline Repository Project

    International Nuclear Information System (INIS)

    The purpose of this document is to respond to the comments received from the States of the Northeastern Region on the revised draft Northeastern Regional Characterization Reports (RCRs). The responses in this document indicate the manner in which the suggestions or comments received have been considered in modifying the revised draft Northeastern RCRs. Both general comments related to the overall Crystalline Repository Project (CRP) and comments on specific sections of the RCRs are addressed. This document responds to Northeastern State comments on both the revised draft Northeastern Regional Geologic Characterization Report (RGCR) and the revised draft Northeastern Regional Environmental Characterization Report (RECR)

  7. Response to state comments on the revised draft North Central Regional characterization reports for the Crystalline Repository Project

    International Nuclear Information System (INIS)

    The purpose of this document is to respond to the comments received from the states of the North Central Region on the revised draft North Central Regional Characterization Reports (RCRs). The responses in this document indicate the manner in which the suggestions or comments received have been considered in modifying the revised draft North Central RCRs. Both general comments related to the overall Crystalline Repository Project (CRP) and comments on specific sections of the RCRs are addressed. This document responds to North Central State comments on both the revised draft North Central Regional Geologic Characterization Report (RGCR) and the revised draft North Central Regional Environmental Characterization Report (RECR)

  8. Characterization of Partial Coding Region Fibroin Gene on Wild Silkmoth Cricula trifenestrata Helfer (Lepidoptera: Saturniidae

    Directory of Open Access Journals (Sweden)

    Suriana

    2011-04-01

    Full Text Available The study was conducted to characterize coding region of wild silkmoth C. trifenestrata partial fibroin gene, and detect these gene potential as molecular marker. A total of six larvae C. trifenestrata were collected from Bogor, Purwakarta and Bantul Regency. Genomic DNA was extracted from silk gland individual larvae, then amplified by PCR method and sequenced. DNA sequenced result was 986 nucleotide partial fibroin gene of C. trifenestrata, which are comprising complete coding region of first exon (42 nucleotide, an intron (113 nucleotide, and partial of second was exon (831 nucleotide. Only coding region was characterized. Results showed that first exon very conserved in C. trifenestrata. These gene consisted of 31%, thymine, 28% guanine, 21% cytosine, and 19% adenine. Cytosine and thymine (sites of 25th and 35th respectively were marker for C. trifenestrata species. The first exon encoding 14 amino acids. Valine amino acid (12th site was marker to the species C. trifenestrata. The partial second exon consisted of guanine (32.7%, alanine (26.5%, thymine (21% and cytosine (19.7%. These region encoded 277 amino acids, which were dominated by the alanine (27.8% and glycine (21.66%. Alanine formed polyalanine sequence with different motifs namely: AAAAAAASS, AAAAAAAAAAAGSSG, AAAAAAAAAAAAGSGTGFGGYDS, AAAAAAAAAAGSSGRGGYDGVDGGYGSGSS, and AAAAAAAAAAAAGSSGRGLGGYDGWVDDGYGSGSGS.

  9. Characterization of random telegraph noise generated in the space region in NAND flash memory strings

    International Nuclear Information System (INIS)

    We firstly report the observation and characterization of random telegraph noise (RTN) generated in the inter word-line dielectric (IWD) of the region between adjacent word-lines (called the space region) in a cell string of 26 nm NAND flash memory. The RTN is named as space RTN, and its existence is verified by applying our approach. The space RTN is compared with the channel RTN in terms of capture and emission times, depending on a pass bias, and is directly affected by a pass bias of adjacent cells. By considering the simulated electrostatic potential in the space region at various pass biases, we can extract the lateral position of a trap responsible for the space RTN. (paper)

  10. Identification of QTL in soybean underlying resistance to herbivory by Japanese beetles (Popillia japonica, Newman).

    Science.gov (United States)

    Yesudas, C R; Sharma, H; Lightfoot, D A

    2010-07-01

    Soybean [Glycine max (L.) Merr.] was one of the most important legume crops in the world in 2010. Japanese beetles (JB; Popillia japonica, Newman) in the US were an introduced and potentially damaging insect pest for soybean. JBs are likely to spread across the US if global warming occurs. Resistance to JB in soybean was previously reported only in plant introductions. The aims here were to identify loci underlying resistance to JB herbivory in recombinant inbred lines (RILs) derived from the cross of Essex x Forrest cultivars (EF94) and to correlate those with loci with factors that confer insect resistance in soybean cultivars. The RIL population was used to map 413 markers, 238 satellite markers and 177 other DNA markers. Field data were from two environments over 2 years. Pest severity (PS) measured defoliation on a 0-9 scale. Pest incidence (PI) was the percentage of plants within each RIL with beetles on them. Antibiosis and antixenosis data were from feeding assays with detached leaves in petri plates. Five QTL were detected for the mean PS field trait (16% < R (2) < 27%). The loci were within the intervals Satt632-A2D8 on linkage group (LG) A2 (chromosome 8); Satt583-Satt415 on LG B1 (11); Satt009-Satt530 on LG N (3); and close to two markers OB02_140 (LG E; 20 cM from Satt572) and OZ15_150 LG (19 cM from Satt291 C2). Two QTL were detected for the mean PI field trait (16% < R (2) < 18%) close to Satt385 on LG A1 and Satt440 on LG I. The no choice feeding studies detected three QTL that were significant; two for antixenosis (22% < R (2) < 24%) between Satt632-A2D8 on LG A2 (8) and Sat_039-Satt160 on LG F (13); and a major locus effect (R (2) = 54%) for antibiosis on LG D2 (17) between Satt464-Satt488. Therefore, loci underlying resistance to JB herbivory were a mixture of major and minor gene effects. Some loci were within regions underlying resistance to soybean cyst nematode (LGs A2 and I) and root knot nematode (LG F) but not other major loci underlying

  11. QTL Information Table: 228 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available i 63 B C547 C2340 pha Xing, Z., Tan, F., Hua, P., Sun, L., Xu, G., and Zhang, Q. (2002). Characterization of the main effects..., epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice. Theor Appl Genet 105, 248-257. ...

  12. QTL Information Table: 1029 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available ostd(t) Physiological trait Sterility male ... sterility SSR B)Fine F2 ostd(t) Nipponbare RM7434 RM2 ... ng, C.D. (2008). Characterization and mapping of a male -sterility mutant, tapetum desquamation (t), in ric ...

  13. QTL Information Table: 754 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Eating quality Pasting temperature (61-02) Mixture C)Interval R...Xu, C.G., and Zhang, Q. (2007). Genetic basis of 17 traits and viscosity parameters characterizing the eating and cooking quality of rice grain. Theor Appl Genet 115, 463-476. ...

  14. QTL Information Table: 876 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available QSbr3a Resistance or Tolerance Sheath blight resistance sheath blight response ratings (SBRs) RF ... inson, S.R.M., Marchetti, M.A., Stansel, J.W., and Park , W.D. (1995). Characterization of quantitative tra ...

  15. Whole-Genome Mapping Reveals Novel QTL Clusters Associated with Main Agronomic Traits of Cabbage (Brassica oleracea var. capitata L.)

    Science.gov (United States)

    Lv, Honghao; Wang, Qingbiao; Liu, Xing; Han, Fengqing; Fang, Zhiyuan; Yang, Limei; Zhuang, Mu; Liu, Yumei; Li, Zhansheng; Zhang, Yangyong

    2016-01-01

    We describe a comprehensive quantitative trait locus (QTL) analysis for 24 main agronomic traits of cabbage. Field experiments were performed using a 196-line double haploid population in three seasons in 2011 and 2012 to evaluate important agronomic traits related to plant type, leaf, and head traits. In total, 144 QTLs with LOD threshold >3.0 were detected for the 24 agronomic traits: 25 for four plant-type-related traits, 64 for 10 leaf-related traits, and 55 for 10 head-related traits; each QTL explained 6.0–55.7% of phenotype variation. Of the QTLs, 95 had contribution rates higher than 10%, and 51 could be detected in more than one season. Major QTLs included Ph 3.1 (max R2 = 55.7, max LOD = 28.2) for plant height, Ll 3.2 (max R2 = 31.7, max LOD = 13.95) for leaf length, and Htd 3.2 (max R2 = 28.5, max LOD = 9.49) for head transverse diameter; these could all be detected in more than one season. Twelve QTL clusters were detected on eight chromosomes, and the most significant four included Indel481–scaffold18376 (3.20 Mb), with five QTLs for five traits; Indel64–scaffold35418 (2.22 Mb), six QTLs for six traits; scaffold39782–Indel84 (1.78 Mb), 11 QTLs for 11 traits; and Indel353–Indel245 (9.89 Mb), seven QTLs for six traits. Besides, most traits clustered within the same region were significantly correlated with each other. The candidate genes at these regions were also discussed. Robust QTLs and their clusters obtained in this study should prove useful for marker-assisted selection (MAS) in cabbage breeding and in furthering our understanding of the genetic control of these traits.

  16. Whole-Genome Mapping Reveals Novel QTL Clusters Associated with Main Agronomic Traits of Cabbage (Brassica oleracea var. capitata L.).

    Science.gov (United States)

    Lv, Honghao; Wang, Qingbiao; Liu, Xing; Han, Fengqing; Fang, Zhiyuan; Yang, Limei; Zhuang, Mu; Liu, Yumei; Li, Zhansheng; Zhang, Yangyong

    2016-01-01

    We describe a comprehensive quantitative trait locus (QTL) analysis for 24 main agronomic traits of cabbage. Field experiments were performed using a 196-line double haploid population in three seasons in 2011 and 2012 to evaluate important agronomic traits related to plant type, leaf, and head traits. In total, 144 QTLs with LOD threshold >3.0 were detected for the 24 agronomic traits: 25 for four plant-type-related traits, 64 for 10 leaf-related traits, and 55 for 10 head-related traits; each QTL explained 6.0-55.7% of phenotype variation. Of the QTLs, 95 had contribution rates higher than 10%, and 51 could be detected in more than one season. Major QTLs included Ph 3.1 (max R (2) = 55.7, max LOD = 28.2) for plant height, Ll 3.2 (max R (2) = 31.7, max LOD = 13.95) for leaf length, and Htd 3.2 (max R (2) = 28.5, max LOD = 9.49) for head transverse diameter; these could all be detected in more than one season. Twelve QTL clusters were detected on eight chromosomes, and the most significant four included Indel481-scaffold18376 (3.20 Mb), with five QTLs for five traits; Indel64-scaffold35418 (2.22 Mb), six QTLs for six traits; scaffold39782-Indel84 (1.78 Mb), 11 QTLs for 11 traits; and Indel353-Indel245 (9.89 Mb), seven QTLs for six traits. Besides, most traits clustered within the same region were significantly correlated with each other. The candidate genes at these regions were also discussed. Robust QTLs and their clusters obtained in this study should prove useful for marker-assisted selection (MAS) in cabbage breeding and in furthering our understanding of the genetic control of these traits. PMID:27458471

  17. Bayesian Variable Selection to identify QTL affecting a simulated quantitative trait

    NARCIS (Netherlands)

    Schurink, A.; Janss, L.L.G.; Heuven, H.C.M.

    2012-01-01

    Background Recent developments in genetic technology and methodology enable accurate detection of QTL and estimation of breeding values, even in individuals without phenotypes. The QTL-MAS workshop offers the opportunity to test different methods to perform a genome-wide association study on simulat

  18. Bayesian Variable Selection to identify QTL affecting a simulated quantitative trait

    NARCIS (Netherlands)

    Schurink, A.; Janss, L.L.G.; Heuven, H.C.M.

    2012-01-01

    Abstract Background: Recent developments in genetic technology and methodology enable accurate detection of QTL and estimation of breeding values, even in individuals without phenotypes. The QTL-MAS workshop offers the opportunity to test different methods to perform a genome-wide association study

  19. Use of maternal information for QTL detection in a (granddaughter design

    Directory of Open Access Journals (Sweden)

    Boichard Didier

    2002-05-01

    Full Text Available Abstract In a (granddaughter design, maternal information is often neglected because the number of progeny per dam is limited. The number of dams per maternal grandsire (MGS, however, could be large enough to contribute to QTL detection. But dams and MGS usually are not genotyped, there are two recombination opportunities between the MGS and the progeny, and at a given location, only half the progeny receive a MGS chromosomal segment. A 3-step procedure was developed to estimate: (1 the marker phenotypes probabilities of the MGS; (2 the probability of each possible MGS haplotype; (3 the probabilities that the progeny receives either the first, or second MGS segment, or a maternal grandam segment. These probabilities were used for QTL detection in a linear model including the effects of sire, MGS, paternal QTL, MGS QTL and maternal grandam QTL. Including the grandam QTL effect makes it possible to detect QTL in the grandam population, even when MGS are not informative. The detection power, studied by simulation, was rather high, provided that MGS family size was greater than 50. Using maternal information in the French dairy cattle granddaughter design made it possible to detect 23 additional QTL genomewise significant.

  20. Across Breed QTL Detection and Genomic Prediction in French and Danish Dairy Cattle Breeds

    DEFF Research Database (Denmark)

    van den Berg, Irene; Guldbrandtsen, Bernt; Hozé, C;

    Our objective was to investigate the potential benefits of using sequence data to improve across breed genomic prediction, using data from five French and Danish dairy cattle breeds. First, QTL for protein yield were detected using high density genotypes. Part of the QTL detected within breed was...

  1. Detection and modelling of time-dependent QTL in animal populations

    DEFF Research Database (Denmark)

    Lund, Mogens S; Sørensen, Peter; Madsen, Per;

    2008-01-01

    A longitudinal approach is proposed to map QTL affecting function-valued traits and to estimate their effect over time. The method is based on fitting mixed random regression models. The QTL allelic effects are modelled with random coefficient parametric curves and using a gametic relationship ma...

  2. QTL Information Table: 506 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Hd3b Physiological trait Flowering days to heading RFLP B)Fine BC4F2 Nipponbare Kasalath R2291 R ... d Yano, M. (2002). Genetic dissection of a genomic region ... for a quantitative trait locus, Hd3, into two loci ...

  3. Linkage Disequilibrium Mapping of Meat Quality QTL

    Science.gov (United States)

    Previous studies based on linkage analysis have identified broad areas in the bovine genome associated with meat quality. Linkage disequilibrium (LD) analyses have the potential to identify narrower regions and point towards candidate genes. Tenderness and marbling were chosen to be evaluated in a ...

  4. Characterizing moisture delivery mechanisms for extreme precipitation in large geographic regions

    Science.gov (United States)

    Bracken, C.; Rajagopalan, B.; Gangopadhyay, S.

    2014-12-01

    Understanding dominant moisture delivery sources for extreme precipitation events is extremely important for characterizing their statistical behavior and behavior under specific climate regimes. Typically, for a given region, the largest extreme events occur in specific seasons but events occurring in off seasons can be just as socio-economically devastating. A complete picture of how and where events originate in all seasons paves the way for statistical forecasting and simulation of extreme precipitation. We present a data driven methodology applicable to large geographic regions that can partition heterogeneous areas into subregions and then characterize the moisture delivery mechanisms for each subregion under specific climate regimes (e.g., ENSO phases, PDO, etc.) and in each season. Extreme subregions are defined using a new nonparametric extreme value clustering method and moisture delivery characterization is done using the HYSPLIT storm backtracking algorithm. We apply this methodology to the Western United States where the nature of extreme events varies widely due to complex terrain, teleconnections and climate interactions.

  5. QTL analysis of cadmium and zinc accumulation in the heavy metal hyperaccumulator Thlaspi caerulescens.

    Science.gov (United States)

    Deniau, A X; Pieper, B; Ten Bookum, W M; Lindhout, P; Aarts, M G M; Schat, H

    2006-09-01

    Thlaspi caerulescens (Tc; 2n = 14) is a natural Zn, Cd and Ni hyperaccumulator species belonging to the Brassicaceae family. It shares 88% DNA identity in the coding regions with Arabidopsis thaliana (At) (Rigola et al. 2006). Although the physiology of heavy metal (hyper)accumulation has been intensively studied, the molecular genetics are still largely unexplored. We address this topic by constructing a genetic map based on AFLP markers and expressed sequence tags (ESTs). To establish a genetic map, an F(2) population of 129 individuals was generated from a cross between a plant from a Pb/Cd/Zn-contaminated site near La Calamine, Belgium, and a plant from a comparable site near Ganges (GA), France. These two accessions show different degrees of Zn and, particularly, Cd accumulation. We analyzed 181 AFLP markers (of which 4 co-dominant) and 13 co-dominant EST sequences-based markers and mapped them to seven linkage groups (LGs), presumably corresponding to the seven chromosomes of T. caerulescens. The total length of the genetic map is 496 cM with an average density of one marker every 2.5 cM. This map was used for Quantitative Trait Locus (QTL) mapping in the F(2). For Zn as well as Cd concentration in root we mapped two QTLs. Three QTLs and one QTL were mapped for Zn and Cd concentration in shoot, respectively. These QTLs explain 23.8-60.4% of the total variance of the traits measured. We found only one common locus (LG6) for Zn and Cd (concentration in root) and one common locus for shoot and root concentrations of Zn (LG1) and of Cd (LG3). For all QTLs, the GA allele increased the trait value except for two QTLs for Zn accumulation in shoot (LG1 and LG4) and one for Zn concentration in root (LG1). PMID:16850314

  6. Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex

    Directory of Open Access Journals (Sweden)

    Portis Ezio

    2012-05-01

    Full Text Available Abstract Background The Asteraceae species Cynara cardunculus (2n = 2x = 34 includes the two fully cross-compatible domesticated taxa globe artichoke (var. scolymus L. and cultivated cardoon (var. altilis DC. As both are out-pollinators and suffer from marked inbreeding depression, linkage analysis has focussed on the use of a two way pseudo-test cross approach. Results A set of 172 microsatellite (SSR loci derived from expressed sequence tag DNA sequence were integrated into the reference C. cardunculus genetic maps, based on segregation among the F1 progeny of a cross between a globe artichoke and a cultivated cardoon. The resulting maps each detected 17 major linkage groups, corresponding to the species’ haploid chromosome number. A consensus map based on 66 co-dominant shared loci (64 SSRs and two SNPs assembled 694 loci, with a mean inter-marker spacing of 2.5 cM. When the maps were used to elucidate the pattern of inheritance of head production earliness, a key commercial trait, seven regions were shown to harbour relevant quantitative trait loci (QTL. Together, these QTL accounted for up to 74% of the overall phenotypic variance. Conclusion The newly developed consensus as well as the parental genetic maps can accelerate the process of tagging and eventually isolating the genes underlying earliness in both the domesticated C. cardunculus forms. The largest single effect mapped to the same linkage group in each parental maps, and explained about one half of the phenotypic variance, thus representing a good candidate for marker assisted selection.

  7. Characterization of difference of Gaussian filters in the detection of mammographic regions

    International Nuclear Information System (INIS)

    In this article, we present a characterization of the effect of difference of Gaussians (DoG) filters in the detection of mammographic regions. DoG filters have been used previously in mammographic mass computer-aided detection (CAD) systems. As DoG filters are constructed from the subtraction of two bivariate Gaussian distributions, they require the specification of three parameters: the size of the filter template and the standard deviations of the constituent Gaussians. The influence of these three parameters in the detection of mammographic masses has not been characterized. In this work, we aim to determine how the parameters affect (1) the physical descriptors of the detected regions (2) the true and false positive rates, and (3) the classification performance of the individual descriptors. To this end, 30 DoG filters are created from the combination of three template sizes and four values for each of the Gaussians' standard deviations. The filters are used to detect regions in a study database of 181 craniocaudal-view mammograms extracted from the Digital Database for Screening Mammography. To describe the physical characteristics of the identified regions, morphological and textural features are extracted from each of the detected regions. Differences in the mean values of the features caused by altering the DoG parameters are examined through statistical and empirical comparisons. The parameters' effects on the true and false positive rate are determined by examining the mean malignant sensitivities and false positives per image (FPpI). Finally, the effect on the classification performance is described by examining the variation in FPpI at the point where 81% of the malignant masses in the study database are detected. Overall, the findings of the study indicate that increasing the standard deviations of the Gaussians used to construct a DoG filter results in a dramatic decrease in the number of regions identified at the expense of missing a small number of

  8. Sequence Ready Characterization of the Pericentromeric Region of 19p12

    Energy Technology Data Exchange (ETDEWEB)

    Evan E. Eichler

    2006-08-31

    Current mapping and sequencing strategies have been inadequate within the proximal portion of 19p12 due, in part, to the presence of a recently expanded ZNF (zinc-finger) gene family and the presence of large (25-50 kb) inverted beta-satellite repeat structures which bracket this tandemly duplicated gene family. The virtual of absence of classically defined “unique” sequence within the region has hampered efforts to identify and characterize a suitable minimal tiling path of clones which can be used as templates required for finished sequencing of the region. The goal of this proposal is to develop and implement a novel sequence-anchor strategy to generate a contiguous BAC map of the most proximal portion of chromosome 19p12 for the purpose of complete sequence characterization. The target region will be an estimated 4.5 Mb of DNA extending from STS marker D19S450 (the beginning of the ZNF gene cluster) to the centromeric (alpha-satellite) junction of 19p11. The approach will entail 1) pre-selection of 19p12 BAC and cosmid clones (NIH approved library) utilizing both 19p12 -unique and 19p12-SPECIFIC repeat probes (Eichler et al., 1998); 2) the generation of a BAC/cosmid end-sequence map across the region with a density of one marker every 8kb; 3) the development of a second-generation of STS (sequence tagged sites) which will be used to identify and verify clonal overlap at the level of the sequence; 4) incorporation of these sequence-anchored overlapping clones into existing cosmid/BAC restriction maps developed at Livermore National Laboratory; and 5) validation of the organization of this region utilizing high-resolution FISH techniques (extended chromatin analysis) on monochromosomal 19 somatic cell hybrids and parental cell lines of source material. The data generated will be used in the selection of the most parsimonious tiling path of BAC clones to be sequenced as part of the JGI effort on chromosome 19 and should serve as a model for the sequence

  9. QTL-mapping in mink (Neovison vison) shows evidence for QTL for guard hair thickness, guard hair length and skin length

    DEFF Research Database (Denmark)

    Thirstrup, Janne Pia; Labouriau, Rodrigo; Guldbrandtsen, Bernt; Anistoroaei, Razvan Marian; Christensen, Knud; Fredholm, Merete; Nielsen, Vivi Hunnicke

    2011-01-01

    short nap, 103 F1 and 934 F2) were marker typed and recorded for the three presented fur quality traits. For the QTL-analyses a regression analysis implemented in QTL Express software was used. Evidence was found for the existence of QTL for guard hair length, guard hair thickness and density of wool on......Fur quality in mink (Neovison vison) is a composite trait, consisting of e.g. guard hair length, guard hair thickness and density of wool. A genome wide QTL search was performed to detect QTL for fur quality traits in mink. Here we present the results of QTL analyses for guard hair length, guard...... hair thickness and density of wool. Data from an F2-cross was analysed across fourteen chromosomes using 100 microsatellites as markers with a spacing of approximately 20 cM. The two lines used for the F2-cross were Nordic wild mink and American short nap mink. In total 1,083 animals (21 wild type, 25...

  10. Molecular characterization of tea mosquito bug from tea growing regions of India.

    Science.gov (United States)

    Suganthi, M; Chandrashekara, K N; Arvinth, S; Raj Kumar, R

    2016-09-01

    The tea mosquito bug, Helopeltis (Hemiptera: Miridae), is an insidious pest that poses a significant economical threat to tea plantations. As a basic first step to control this pest is authentic identification, but the inability to determine morphological characters of Helopeltis species makes this process very difficult. DNA barcoding is a reliable alternative to traditional morphological identification of this pest. Since tea is cultivated in different parts of the country, an attempt was made to molecular characterization of Helopeltis. This is the first report on molecular identification and diversity characterization of Helopeltis collected from tea growing regions of southern and north India, using cytochrome c oxidase subunit I (COI) gene of mitochondrial (mt) DNA. Beginning with the molecular identification of this pest is essential to start an effective pest management strategy, and will provide basic information for diffusion pattern, population dynamics and chemical application. PMID:26186305

  11. Isotope characterization of shallow aquifers in the Horombe region, South of Madagascar

    CERN Document Server

    Fareze, L P; Ramaroson, V; Andriambololona, Raoelina; Andriamiarintsoa, G; Razafitsalama, P R; Rahobisoa, J J; Randrianarison, H; Ranaivoarisoa, A; Marah, H

    2012-01-01

    The present study deals with the problem of evaluation of the recharge mechanism and the characterization of the groundwater flow system in the basement shallow aquifer, which is one of the groundwater resource in the semi-arid South region of Madagascar. Stable isotopes (deuterium and oxygen-18) and tritium are used to achieve with accuracy the hydrogeological and geochemical dynamics study. Chemical analysis is used to provide complementary information to the investigation. A space distribution of tritium concentration and isotopic composition in groundwater shows evidence of two opposite categories of aquifers, which is confirmed by the chemical analysis results and by the geological features of the study site. Some groundwater flow path directions have been identified in the study area thanks to the tritium concentration space distribution and the geological formation. Besides, the groundwater recharge of the shallow aquifers in the South of Madagascar has been characterized by the exponential mixing mode...

  12. Genomic dissection and prioritizing of candidate genes of QTL for regulating spontaneous arthritis on chromosome 1 in mice deficient for interleukin-1 receptor antagonist

    Indian Academy of Sciences (India)

    Yanhong Cao; Jifei Zhang; Yan Jiao; Jian Yan; Feng Jiao; Xiaoyun Liu; Robert W. Williams; Karen A. Hasty; John M. Stuart; Weikuan Gu

    2012-08-01

    Rheumatoid arthritis is a heterogeneous disease with clinical and biological polymorphisms. IL-1RN is a protein that binds to interleukin-1 (IL-1) receptors and inhibits the binding of IL-1-alpha and IL-1-beta. IL-1RN levels are elevated in the blood of patients with a variety of infectious, immune, and traumatic conditions. Balb/c mice deficient in IL-1ra (mouse gene of IL-1RN) develop spontaneous autoimmune arthritis while DBA/1 mice deficient in IL-1ra do not. Previously, we identified a major QTL that regulates the susceptibility to arthritis in Balb/c mice with IL-1ra deficiency. In this study, we found that the QTL may contain two peaks that are regulated by two sets of candidate genes. By haplotype analysis, the total genomic regions of candidate genes were reduced from about 19 Mbp to approximately 9 Mbp. The total number of candidate genes was reduced from 208 to 21.

  13. Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. I. Growth and average daily gain

    Science.gov (United States)

    A genome scan was used to detect chromosomal regions and QTL that control quantitative traits of economic importance in chickens. Two unique F2 crosses generated from a commercial broiler male line and 2 genetically distinct inbred lines (Leghorn and Fayoumi) were used to identify QTL affecting BW a...

  14. Hydrogeochemical characterization of groundwater in the Outaouais Region (Québec, Canada) - A regional scale study

    Science.gov (United States)

    Montcoudiol, N.; Molson, J. W.; Lemieux, J.

    2013-12-01

    As part of the Québec regional groundwater characterization program (PACES), a detailed groundwater quality survey was undertaken in the Outaouais Region (Québec, Canada). During the summers of 2011 and 2012, 139 samples were taken from municipal and private wells which were analysed for major ions, nutrients, metals and sulphides. About 70% of the samples were obtained from bedrock wells, mainly in the Canadian Shield and the remainder from wells screened in Quaternary deposit aquifers. Hydrogeochemical facies were determined for 127 samples which had anion-cation charge balance errors within ×10 %. Ca-HCO3 is the dominant water type (65%) which was mainly found in unconfined aquifers, especially Quaternary deposits, and is typical of recently infiltrated rainwater. Other relevant water types are Na-HCO3 and Na-Cl (17 and 6% respectively), characteristic of confined aquifers. This classification by water type is supported by multivariate statistical analysis, namely Principal Component Analysis (PCA) and Hierarchical Clustering Analysis (HCA). PCA allows the identification of three factors controlling groundwater chemistry: salinity, silicate dissolution and F-bearing mineral dissolution. HCA results show that the samples can be grouped into seven clusters. Clusters 1 to 4 are mostly Ca-HCO3 water type and are representative of the enrichment in major ions due to carbonate and silicate dissolution, cluster 1 being closer to rainwater and cluster 4 the most evolved. Cluster 5, made of one sample with a particular chemistry, is not yet fully understood. Samples from cluster 6 present various degrees of Na-Ca exchange, a consequence of remnant Champlain Sea water (some samples from cluster 7 in confined zones) being replaced by infiltrating recharge water. Samples from cluster 7 are evolved waters with high Total Dissolved Solid (TDS) concentrations: they are remnants of the Champlain Sea in confined aquifers (bromide detected) or diluted/mixed by infiltrating

  15. 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.

  16. Linkage of an ABCC transporter to a single QTL that controls Ostrinia nubilalis larval resistance to the Bacillus thuringiensis Cry1Fa toxin.

    Science.gov (United States)

    Coates, Brad S; Siegfried, Blair D

    2015-08-01

    Field evolved resistance of insect populations to Bacillus thuringiensis (Bt) crystalline (Cry) toxins expressed by crop plants has resulted in reduced control of insect feeding damage to field crops, and threatens the sustainability of Bt transgenic technologies. A single quantitative trait locus (QTL) that determines resistance in Ostrinia nubilalis larvae capable of surviving on reproductive stage transgenic corn that express the Bt Cry1Fa toxin was previously mapped to linkage group 12 (LG12) in a backcross pedigree. Fine mapping with high-throughput single nucleotide polymorphism (SNP) anchor markers, a candidate ABC transporter (abcc2) marker, and de novo mutations predicted from a genotyping-by-sequencing (GBS) data redefined a 268.8 cM LG12. The single QTL on LG12 spanned an approximate 46.1 cM region, in which marker 02302.286 and abcc2 were ≤ 2.81 cM, and the GBS marker 697 was an estimated 1.89 cM distant from the causal genetic factor. This positional mapping data showed that an O. nubilalis genome region encoding an abcc2 transporter is in proximity to a single QTL involved in the inheritance of Cry1F resistance, and will assist in the future identification the mutation(s) involved with this phenotype. PMID:26093031

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

    Science.gov (United States)

    Zhang, Yu; Cui, Min; Zhang, Jimin; Zhang, Lei; Li, Chenliu; Kan, Xin; Sun, Qian; Deng, Dexiang; Yin, Zhitong

    2016-01-01

    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. PMID:27598199

  18. Characterization of biomasses from the north and northeast regions of Brazil for processes in biorefineries

    Directory of Open Access Journals (Sweden)

    Magale Karine Diel RAMBO

    2015-01-01

    Full Text Available AbstractIn search for renewable energy sources, the Brazilian residual biomasses stand out due to their favorable physical and chemical properties, low cost, and their being less pollutant. Therefore, they are likely to be used in biorefineries in the production of chemical inputs to substitute fossil fuels. This substitution is possible due to the high contents of carbohydrates (>40%, low contents of extractives (<20%, ashes (<8% and moisture (<8% found in these residual biomasses. High calorific values of all residues also offer them the chance to be used in combustion. A principal components analysis (PCA was performed for better understanding of the samples and their hysic-chemical properties. Thus, this study aimed to characterize biomasses from the north (babassu residues, such as mesocarp and endocarp; pequi and Brazil nut and northeast (agave and coconut regions of Brazil, in order to contribute to the preservation of the environment and strengthen the economy of the region.

  19. A Kelch Motif-Containing Serine/Threonine Protein Phosphatase Determines the Large Grain QTL Trait in Rice

    Institute of Scientific and Technical Information of China (English)

    Zejun Hu; Haohua He; Shiyong Zhang; Fan Sun; Xiaoyun Xin; Wenxiang Wang; Xi Qian; Jingshui Yang; Xiaojin Luo

    2012-01-01

    A thorough understanding of the genetic basis of rice grain traits is critical for the improvement of rice (Oryza sativa L.) varieties.In this study,we generated an F2 population by crossing the large-grain japonica cultivar CW23 with Peiai 64 (PA64),an elite indica small-grain cultivar.Using QTL analysis,17 QTLs for five grain traits were detected on four different chromosomes.Eight of the QTLs were newly-identified in this study.In particular,qGL3-1,a newly-identified grain length QTL with the highest LOD value and largest phenotypic variation,was fine-mapped to the 17 kb region of chromosome 3.A serine/threonine protein phosphatase gene encoding a repeat domain containing two Kelch motifs was identified as the unique candidate gene corresponding to this QTL.A comparison of PA64 and CW23 sequences revealed a single nucleotide substitution (C→A) at position 1092 in exon 10,resulting in replacement of Asp (D) in PA64 with Glu (E) in CW23 for the 364th amino acid.This variation is located at the D position of the conserved sequence motif AVLDT of the Kelch repeat.Genetic analysis of a near-isogenic line (NIL) for qGL3-1 revealed that the allele qGL3-1 from CW23 has an additive or partly dominant effect,and is suitable for use in molecular marker-assisted selection.

  20. QTL Information Table: 139 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available af 1. Aberrant katanin-mediated microtubule organization causes up-regulation of ...dgl1 Morphological trait Dwarf dwarf phenotype and leaves with abnormally rounded tip regions A)Physica...l P0445E10,P0019E03 pha Komorisono, M., Ueguchi-Tanaka, M., Aichi, I., Hasegawa, Y., Ash...ikari, M., Kitano, H., Matsuoka, M., and Sazuka, T. (2005). Analysis of the rice mutant dwarf and gladius le...gibberellin biosynthetic genes independently of gibberellin signaling. Plant Physiol 138, 1982-1993. ...

  1. High-resolution physical mapping and construction of a porcine contig spanning the intramuscular fat content QTL.

    Science.gov (United States)

    Sato, S; Hasebe, H; Sato, S; Asahi, Y; Hayashi, T; Kobayashi, E; Sugimoto, Y

    2006-04-01

    We previously mapped a locus for porcine intramuscular fat content (IMF) by linkage analysis to a 17.1-cM chromosome interval on Sus scrofa chromosome 7 (SSC7) flanked by microsatellite markers SW1083 and SW581. In this study, we identified 34 microsatellite markers and 14 STSs from the 17.1-cM IMF quantitative trait loci (QTL) region corresponding to HSA14q and aligned those loci using the INRA-University of Minnesota porcine radiation hybrid (IMpRH) panel. We then constructed a 5.2-Mb porcine bacterial artificial chromosome (BAC) contig of this region that was aligned using the RH panel. Finally, the IMF QTL was fine-mapped to 12.6 cM between SJ169 and MM70 at the 0.1% chromosome-wise significance level by genotyping the previously studied F2 resource family with 17 additional microsatellites. We also demonstrated that the SJ169-MM70 interval spans approximately 3.0 Mb and contains at least 12 genes: GALC, GPR65, KCNK10, SPATA7, PTPN21, FLJ11806, EML5, TTC8, CHES1, CAP2P1, CHORDC2P and C14orf143. PMID:16573525

  2. Identification and Characterization of Performance Limiting Regions in Poly-Si Wafers for PV Cells

    International Nuclear Information System (INIS)

    As demand for silicon photovoltaic (PV) material increases, so does the need for cost-effective feedstock and production methods that will allow enhanced penetration of silicon PV into the total energy market. The focus on cost minimization for production of polycrystalline silicon (poly-Si) PV has led to relaxed feedstock purity requirements, which has also introduced undesirable characteristics into cast poly-Si PV wafers. To produce cells with the highest possible conversion efficiencies, it is crucial to understand how reduced purity requirements and defects that are introduced through the casting process can impair minority carrier properties in poly-Si PV cells. This is only possible by using multiple characterization techniques that give macro-scale information (such as the spatial distribution of performance-limiting regions), as well as micro and nano-scale information about the structural and chemical nature of such performance-limiting regions. This study demonstrates the usefulness of combining multiple techniques to analyze performance-limiting regions in the poly-Si wafers that are used for PV cells. This is done by first identifying performance-limiting regions using macro-scale techniques including photoluminescence (PL) imaging, microwave photoconductive decay (μPCD), and reflectometry), then using smaller-scale techniques such as scanning electron microscopy (SEM), electron backscattered diffraction (EBSD), laser ablation inductively coupled mass spectrometry (LA-ICP-MS), cathodoluminescence (CL), and transmission electron microscopy (TEM) to understand the nature of such regions. This analysis shows that structural defects as well as metallic impurities are present in performance-limiting regions, which together act to decrease conversion efficiencies in poly-Si PV cells.

  3. Regional Characterization of Soil Properties via a Combination of Methods from Remote Sensing, Geophysics and Geopedology

    Science.gov (United States)

    Meyer, Uwe; Fries, Elke; Frei, Michaela

    2016-04-01

    Soil is one of the most precious resources on Earth. Preserving, using and enriching soils are most complex processes that fundamentally need a sound regional data base. Many countries lack this sort of extensive data or the existing data must be urgently updated when land use recently changed in major patterns. The project "RECHARBO" (Regional Characterization of Soil Properties) aims at the combination of methods from remote sensing, geophysics and geopedology in order to develop a new system to map soils on a regional scale in a quick and efficient manner. First tests will be performed on existing soil monitoring districts, using newly available sensing systems as well as established techniques. Especially hyperspectral and infrared data measured from satellites or airborne platforms shall be combined. Moreover, a systematic correlation between hyperspectral imagery and gamma-ray spectroscopy shall be established. These recordings will be compared and correlated to measurements upon ground and on soil samples to get hold of properties such as soil moisture, soil density, specific resistance plus analytic properties like clay content, anorganic background, organic matter etc. The goal is to generate a system that enables users to map soil patterns on a regional scale using airborne or satellite data and to fix their characteristics with only a limited number of soil samples.

  4. Karst characterization in a semi-arid region using gravity, seismic, and resistivity geophysical techniques.

    Energy Technology Data Exchange (ETDEWEB)

    Barnhart, Kevin Scott

    2013-10-01

    We proposed to customize emerging in situ geophysical monitoring technology to generate time-series data during sporadic rain events in a semi-arid region. Electrodes were to be connected to wireless %5Cnodes%22 which can be left in the eld for many months. Embedded software would then increase sampling frequency during periods of rainfall. We hypothesized that this contrast between no-volume ow in karst passageways dur- ing dry periods and partial- or saturated-volume ow during a rain event is detectable by these Wireless Sensor Network (WSN) geophysical nodes, we call this a Wireless Resistivity Network (WRN). The development of new methodologies to characterize semi-arid karst hydrology is intended to augment Sandia National Laboratorys mission to lead e orts in energy technologies, waste disposal and climate security by helping to identify safe and secure regions and those that are at risk. Development and initial eld testing identi ed technological barriers to using WRNs for identifying semi-arid karst, exposing R&D which can be targeted in the future. Gravity, seismic, and resis- tivity surveys elucidated how each technique might e ectively be used to characterize semi-arid karst. This research brings to light the importance and challenges with char- acterizing semi-arid karst through a multi-method geophysical study. As there have been very few studies with this emphasis, this study has expanded the body of practical experience needed to protect the nations water and energy security interests.

  5. Optimizing purebred selection for crossbred performance using QTL with different degrees of dominance

    Directory of Open Access Journals (Sweden)

    Chakraborty Reena

    2004-05-01

    Full Text Available Abstract A method was developed to optimize simultaneous selection for a quantitative trait with a known QTL within a male and a female line to maximize crossbred performance from a two-way cross. Strategies to maximize cumulative discounted response in crossbred performance over ten generations were derived by optimizing weights in an index of a QTL and phenotype. Strategies were compared to selection on purebred phenotype. Extra responses were limited for QTL with additive and partial dominance effects, but substantial for QTL with over-dominance, for which optimal QTL selection resulted in differential selection in male and female lines to increase the frequency of heterozygotes and polygenic responses. For over-dominant QTL, maximization of crossbred performance one generation at a time resulted in similar responses as optimization across all generations and simultaneous optimal selection in a male and female line resulted in greater response than optimal selection within a single line without crossbreeding. Results show that strategic use of information on over-dominant QTL can enhance crossbred performance without crossbred testing.

  6. A somatic cell hybrid panel for pig regional gene mapping characterized by molecular cytogenetics.

    Science.gov (United States)

    Yerle, M; Echard, G; Robic, A; Mairal, A; Dubut-Fontana, C; Riquet, J; Pinton, P; Milan, D; Lahbib-Mansais, Y; Gellin, J

    1996-01-01

    A panel of 27 pig x rodent somatic cell hybrids was produced and characterized cytogenetically. The first step of this study consisted of hybridizing a SINE probe to GTG-banded metaphases of each hybrid clone in order to count and identify the normal pig chromosomes and to detect rearranged ones. The second step consisted of using the DNA of each clone as a probe after pIRS-PCR (porcine interspersed repetitive sequence-polymerase chain reaction) amplification to highly enrich it in pig sequences. These probes, hybridized to normal pig metaphase chromosomes, enabled the identification of the complete porcine complement in the hybrid lines. Whole chromosomes and fragments were characterized quickly and precisely, and results were compared. In addition to this cytogenetic characterization, molecular verification was also carried out by using primers specific to six microsatellites and to one gene previously mapped to pig chromosomes. The results obtained allow us to conclude that we have produced a panel that is informative for all porcine chromosomes. This panel constitutes a highly efficient tool to establish not only assignments of genes and markers but also regional localizations on pig chromosomes. PMID:8697807

  7. Characterization of municipal solid waste in high-altitude sub-tropical regions.

    Science.gov (United States)

    Kumar, Sunil; Dhar, Hiya; Nair, Vijay V; Bhattacharyya, J K; Vaidya, A N; Akolkar, A B

    2016-10-01

    Solid waste management (SWM) is one of the most challenging issues owing to lack of authentic data on different elements of SWM, namely, storage, collection, transportation, separation, processing and disposal. This study presents an assessment of existing status of SWM in conjunction with municipal solid waste (MSW) generation rates, physical and chemical characterization of MSW in high-altitude sub-tropical regions. Weighing of empty and fully loaded trucks per trip revealed total quantity of MSW collected. The average efficiency of MSW collection was 70%. From the baseline data, it is inferred that the population and MSW generation rates are not co-related. The collected MSW included biodegradables (organic wastes), paper, plastic, glass, ceramics, metals, inert materials, ash and debris. The data analysis indicated that the biodegradable components dominate the characterization at 54.83% followed by inert, ash and debris at 21.06%, paper at 8.77%, plastic at 8.18%, glass and ceramics at 4.45% and metals at 2.71%. Statistical measures were also applied and 90% confidence interval (CI) was generated for the characterization data measuring its statistical significance. PMID:26915419

  8. Two Examples of Integrated Aquifer Characterization at Local and Regional Scales

    Science.gov (United States)

    Lefebvre, R.; Gloaguen, E.; Rivard, C.; Parent, M.; Morin, R. H.; Pugin, A.; Pullan, S.; Crow, H.; Paradis, D.; Tremblay, L.; Blouin, M.; Laurencelle, M.

    2012-12-01

    approach is currently being used for regional groundwater resources assessment of a 9 000 km2 fractured sedimentary rock aquifer system for which the quaternary sediment cover controls in large part recharge, confinement and discharge conditions. Results of this study will be applied to regional resource management, the numerical modeling of the effects of historical geological events on aquifer conditions and hydrogeochemistry. Field methods adapted to the scales and conditions of these study areas were used. The detailed understanding of aquifer systems gained from integrated characterization is also needed for the development of scientifically sound and representative conceptual and numerical models of aquifer systems. The characterization approach is general in nature and could be applied at different scales.

  9. The evolution of gene expression QTL in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    James Ronald

    Full Text Available Understanding the evolutionary forces that influence patterns of gene expression variation will provide insights into the mechanisms of evolutionary change and the molecular basis of phenotypic diversity. To date, studies of gene expression evolution have primarily been made by analyzing how gene expression levels vary within and between species. However, the fundamental unit of heritable variation in transcript abundance is the underlying regulatory allele, and as a result it is necessary to understand gene expression evolution at the level of DNA sequence variation. Here we describe the evolutionary forces shaping patterns of genetic variation for 1206 cis-regulatory QTL identified in a cross between two divergent strains of Saccharomyces cerevisiae. We demonstrate that purifying selection against mildly deleterious alleles is the dominant force governing cis-regulatory evolution in S. cerevisiae and estimate the strength of selection. We also find that essential genes and genes with larger codon bias are subject to slightly stronger cis-regulatory constraint and that positive selection has played a role in the evolution of major trans-acting QTL.

  10. Novel Methodology for Characterizing Regional Variations in the Material Properties of Murine Aortas.

    Science.gov (United States)

    Bersi, Matthew R; Bellini, Chiara; Di Achille, Paolo; Humphrey, Jay D; Genovese, Katia; Avril, Stéphane

    2016-07-01

    Many vascular disorders, including aortic aneurysms and dissections, are characterized by localized changes in wall composition and structure. Notwithstanding the importance of histopathologic changes that occur at the microstructural level, macroscopic manifestations ultimately dictate the mechanical functionality and structural integrity of the aortic wall. Understanding structure-function relationships locally is thus critical for gaining increased insight into conditions that render a vessel susceptible to disease or failure. Given the scarcity of human data, mouse models are increasingly useful in this regard. In this paper, we present a novel inverse characterization of regional, nonlinear, anisotropic properties of the murine aorta. Full-field biaxial data are collected using a panoramic-digital image correlation (p-DIC) system. An inverse method, based on the principle of virtual power (PVP), is used to estimate values of material parameters regionally for a microstructurally motivated constitutive relation. We validate our experimental-computational approach by comparing results to those from standard biaxial testing. The results for the nondiseased suprarenal abdominal aorta from apolipoprotein-E null mice reveal material heterogeneities, with significant differences between dorsal and ventral as well as between proximal and distal locations, which may arise in part due to differential perivascular support and localized branches. Overall results were validated for both a membrane and a thick-wall model that delineated medial and adventitial properties. Whereas full-field characterization can be useful in the study of normal arteries, we submit that it will be particularly useful for studying complex lesions such as aneurysms, which can now be pursued with confidence given the present validation. PMID:27210500

  11. Regional Characterization of the Crust in Metropolitan Areas for Prediction of Strong Ground Motion

    Science.gov (United States)

    Hirata, N.; Sato, H.; Koketsu, K.; Umeda, Y.; Iwata, T.; Kasahara, K.

    2003-12-01

    Introduction: After the 1995 Kobe earthquake, the Japanese government increased its focus and funding of earthquake hazards evaluation, studies of man-made structures integrity, and emergency response planning in the major urban centers. A new agency, the Ministry of Education, Science, Sports and Culture (MEXT) has started a five-year program titled as Special Project for Earthquake Disaster Mitigation in Urban Areas (abbreviated to Dai-dai-toku in Japanese) since 2002. The project includes four programs: I. Regional characterization of the crust in metropolitan areas for prediction of strong ground motion. II. Significant improvement of seismic performance of structure. III. Advanced disaster management system. IV. Investigation of earthquake disaster mitigation research results. We will present the results from the first program conducted in 2002 and 2003. Regional Characterization of the Crust in Metropolitan Areas for Prediction of Strong Ground Motion: A long-term goal is to produce map of reliable estimations of strong ground motion. This requires accurate determination of ground motion response, which includes a source process, an effect of propagation path, and near surface response. The new five-year project was aimed to characterize the "source" and "propagation path" in the Kanto (Tokyo) region and Kinki (Osaka) region. The 1923 Kanto Earthquake is one of the important targets to be addressed in the project. The proximity of the Pacific and Philippine Sea subducting plates requires study of the relationship between earthquakes and regional tectonics. This project focuses on identification and geometry of: 1) Source faults, 2) Subducting plates and mega-thrust faults, 3) Crustal structure, 4) Seismogenic zone, 5) Sedimentary basins, 6) 3D velocity properties We have conducted a series of seismic reflection and refraction experiment in the Kanto region. In 2002 we have completed to deploy seismic profiling lines in the Boso peninsula (112 km) and the

  12. Long-range regulatory polymorphisms affecting a GABA receptor constitute a quantitative trait locus (QTL for social behavior in Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Andres Bendesky

    Full Text Available Aggregation is a social behavior that varies between and within species, providing a model to study the genetic basis of behavioral diversity. In the nematode Caenorhabditis elegans, aggregation is regulated by environmental context and by two neuromodulatory pathways, one dependent on the neuropeptide receptor NPR-1 and one dependent on the TGF-β family protein DAF-7. To gain further insight into the genetic regulation of aggregation, we characterize natural variation underlying behavioral differences between two wild-type C. elegans strains, N2 and CB4856. Using quantitative genetic techniques, including a survey of chromosome substitution strains and QTL analysis of recombinant inbred lines, we identify three new QTLs affecting aggregation in addition to the two known N2 mutations in npr-1 and glb-5. Fine-mapping with near-isogenic lines localized one QTL, accounting for 5%-8% of the behavioral variance between N2 and CB4856, 3' to the transcript of the GABA neurotransmitter receptor gene exp-1. Quantitative complementation tests demonstrated that this QTL affects exp-1, identifying exp-1 and GABA signaling as new regulators of aggregation. exp-1 interacts genetically with the daf-7 TGF-β pathway, which integrates food availability and population density, and exp-1 mutations affect the level of daf-7 expression. Our results add to growing evidence that genetic variation affecting neurotransmitter receptor genes is a source of natural behavioral variation.

  13. Dynamic QTL analysis and candidate gene mapping for waterlogging tolerance at maize seedling stage.

    Directory of Open Access Journals (Sweden)

    Khalid A Osman

    Full Text Available Soil waterlogging is one of the major abiotic stresses adversely affecting maize growth and yield. To identify dynamic expression of genes or quantitative trait loci (QTL, QTL associated with plant height, root length, root dry weight, shoot dry weight and total dry weight were identified via conditional analysis in a mixed linear model and inclusive composite interval mapping method at three respective periods under waterlogging and control conditions. A total of 13, 19 and 23 QTL were detected at stages 3D|0D (the period during 0-3 d of waterlogging, 6D|3D and 9D|6D, respectively. The effects of each QTL were moderate and distributed over nine chromosomes, singly explaining 4.14-18.88% of the phenotypic variation. Six QTL (ph6-1, rl1-2, sdw4-1, sdw7-1, tdw4-1 and tdw7-1 were identified at two consistent stages of seedling development, which could reflect a continuous expression of genes; the remaining QTL were detected at only one stage. Thus, expression of most QTL was influenced by the developmental status. In order to provide additional evidence regarding the role of corresponding genes in waterlogging tolerance, mapping of Expressed Sequence Tags markers and microRNAs were conducted. Seven candidate genes were observed to co-localize with the identified QTL on chromosomes 1, 4, 6, 7 and 9, and may be important candidate genes for waterlogging tolerance. These results are a good starting point for understanding the genetic basis for selectively expressing of QTL in different stress periods and the common genetic control mechanism of the co-localized traits.

  14. Detection of nitrogen deficiency QTL in juvenile wild barley introgression lines growing in a hydroponic system

    Directory of Open Access Journals (Sweden)

    Hoffmann Astrid

    2012-10-01

    Full Text Available Abstract Background In this report we studied the genetic regulation of juvenile development of wild barley introgression lines (S42ILs under two contrasting hydroponic nitrogen (N supplies. Ten shoot and root related traits were examined among 42 S42ILs and the recurrent parent ‘Scarlett’. The traits included tiller number, leaf number, plant height, leaf and root length, leaf to root length ratio, shoots and root dry weight, shoot to root weight ratio, and chlorophyll content. Our aims were (1 to test the suitability of a hydroponic system for early detection of favourable S42ILs, (2 to locate quantitative trait loci (QTL that control the examined traits, (3 to identify favourable wild barley alleles that improve trait performances in regard to N treatment and, finally, (4 to validate the identified QTL through comparison with previously reported QTL originating from the same parental cross. Results The phenotypic data were analysed in a mixed model association study to detect QTL. The post-hoc Dunnett test identified 28 S42ILs that revealed significant (P Hsp effects for tiller number, leaf number, leaf length, plant height and leaf to root ratio on the long arm of chromosome 7H. These QTL correspond to QTL for ears per plant and plant height that were previously detected in field trials conducted with the same S42ILs or with the S42 population. Conclusion Our results suggest that the QTL we identified under hydroponic N cultivation partly correspond to QTL detected in field experiments. Due to this finding, screening of plants in early developmental stages grown in a hydroponic system may be a fast and cost effective method for early QTL detection and marker-assisted allelic selection, potentially speeding up elite barley breeding programs.

  15. Characterizing soil preferential flow using iodine--starch staining experiments and the active region model

    Energy Technology Data Exchange (ETDEWEB)

    Sheng, Feng; Wang, Kang; Zhang, Renduo; Liu, Hui-Hai

    2009-03-01

    Thirteen iodine-starch staining experiments with different boundary conditions and measurement scales were conducted at two sites to study preferential flow processes in natural unsaturated soils. Digital imaging analyses were implemented to obtain the corresponding preferential flow patterns. The test results are used to evaluate a recently proposed active region model in terms of its usefulness and robustness for characterizing unsaturated flow processes at field scale. Test results provide useful insights into flow patterns in unsaturated soils. They show that flow pattern depends on the top boundary condition. As the total infiltrating-water depth increased form 20 mm to 80 mm for the 100 x 100 cm{sup 2} plots, the corresponding flow pattern changed from few preferential flow paths associated with a relatively small degree of stained coverage and a small infiltration depth, to a pattern characterized by a higher stained coverage and a larger infiltration depth, and to (finally) a relatively homogeneous flow pattern with few unstained area and a much larger infiltration depth. Test results also show that the preferential flow pattern became generally more heterogeneous and complex for a larger measurement scale (or size of infiltration plot). These observations support the general idea behind the active region model that preferential flow pattern in unsaturated soils are dynamic and depend on water flow conditions. Further analyses of the test results indicate that the active-region model is able to capture the major features of the observed flow pattern at the scale of interest, and the determined parameter values do not significantly depend on the test conditions (initial water content and total amount of infiltrating water) for a given test site. This supports the validity of the active region model that considers that parameter to be a property of the corresponding unsaturated soil. Results also show that some intrinsic relation seems to exist between active

  16. Characterization of CagA variable region of Helicobacter pylori isolates from Chinese patients

    Institute of Scientific and Technical Information of China (English)

    Yong-Liang Zhu; Shu Zheng; Qin Du; Ke-Da Qian; Ping-Chu Fang

    2005-01-01

    AIM: To characterize the CagA variable region of Helicobacter pylori isolates from Chinese patients.METHODS: DNA fragments in CagA variable region were amplified and sequenced respectively from genomic DNA of 19 isolates from patients with gastric cancer and 20isolates from patients with chronic gastritis. The tendency of phosphorylation in tyrosine(s) of CagA proteins was evaluated subsequently by phosphorylation assay in vivo and in vitro respectively.RESULTS: About 97.44% (38/39) H pylori isolates possessed CagA gene. CagA+ strains contained 2-4tandem five-amino-acid motifs EPIYA but only one EPIYA had repeated sequence in CagA variable region in different isolates. There was no significant difference between the number of EPIYA motifs in H pylori from patients with different diseases. However, only tyrosine site in EPIYA within repeated sequence could be phosphorylated by AGS cells in vivo although all tyrosine sites in EPIYA could be phosphorylated in vitro.CONCLUSION: CagA in Chinese has no functional difference in perturbing cellular signal pathway among different H pylori isolates.

  17. Rapid detection of self-biting disease of mink by specific sequence-characterized amplified regions

    Institute of Scientific and Technical Information of China (English)

    LIU Zong-yue; NING Fang-yong; YANG Hong-yan; WEI Lai; BAI Xiu-juan

    2011-01-01

    Self-biting disease occurred in most farmed fur animals in the world. The mechanism and rapid detection method of this disease has not been reported. We applied bulked sergeant analysis (BSA) in combination with RAPD method to analyze a molecular genetic marker linked with self-biting trait in mink group. The molecular marker was converted into sequence-characterized amplified regions (SCAR) marker for rapid detection of this disease. A single RAPD marker A8 amplified a specific band of 263bp in self-biting minks, which was designated as SRA8-250,and non-specific band of 315bp in both self-biting and healthy minks.The sequences of the bands exhibited 75% and 88% similarity to Canis familiarizes major histocompatibility complex (MHC) class Ⅱ region and Macaca mulatta MHC class Ⅰ region, respectively. A SCAR marker SCAR-A8 was designed for the specific fragment SRA8-250 and validated in 30 self-biting minks and 30 healthy minks. Positive amplification of SCAR-A8 was detected in 24 self-biting minks and 12 healthy minks. x2 test showed significant difference (p<0.01) in the detection rate between the two groups. This indicated that SRA8-250 can be used as a positive marker to detect self-biting disease in minks. Furthermore, the finding that self-biting disease links with MHC genes has significant implications for the mechanism of the disease.

  18. Cloning and characterizing of the murine IRF-3 gene promoter region.

    Science.gov (United States)

    Xu, Hua-Guo; Liu, Lifei; Gao, Shan; Jin, Rui; Ren, Wei; Zhou, Guo-Ping

    2016-08-01

    The interferon regulatory factor 3 (IRF-3) plays essential roles in inflammation and immune response. Here, we cloned the nucleotide sequence of the 5'-flanking region of the murine IRF-3 gene (mIRF-3) and characterized the molecular mechanisms controlling the mIRF-3 transcriptional activity in NIH3T3 cells. Analyses of a series of 5' deletion constructs demonstrated that a 301 bp region (-255/+46) of the mIRF-3 gene is sufficient for full promoter activity. This region contains IK1, Egr2, Cmyb, E2F1 and YY1 putative transcription factor binding sites. Mutation of Egr2 or YY1 site led to 52-68 % decrease of the mIRF-3 promoter activity, and double Egr2 and YY1 mutation reduced the promoter activity to 20 % of the wild-type promoter activity. Furthermore, knockingdown of endogenous Egr2 or YY1 by a siRNA strategy markedly inhibited the mIRF-3 promoter activity. Chromatin immunoprecipitation assays showed that Egr2 and YY1 interact with the mIRF-3 promoter in vivo. These results suggested that the basal promoter activity of the mIRF-3 gene is regulated by transcription factors Egr2 and YY1 in NIH3T3 cells. PMID:26740329

  19. Molecular cloning and characterization of the promoter region of the porcine apolipoprotein E gene.

    Science.gov (United States)

    Xia, Jihan; Hu, Bingjun; Mu, Yulian; Xin, Leilei; Yang, Shulin; Li, Kui

    2014-05-01

    Apolipoprotein E (APOE), a component of lipoproteins plays an important role in the transport and metabolism of cholesterol, and is associated with hyperlipoproteinemia and Alzheimer's disease. In order to further understand the characterization of APOE gene, the promoter of APOE gene of Landrace pigs was analyzed in the present study. The genomic structure and amino acid sequence in pigs were analyzed and found to share high similarity in those of human but low similarity in promoter region. Real-time PCR revealed the APOE gene expression pattern of pigs in diverse tissues. The highest expression level was observed in liver, relatively low expression in other tissues, especially in stomach and muscle. Furthermore, the promoter expressing in Hepa 1-6 was significantly better at driving luciferase expression compared with C2C12 cell. After analysis of porcine APOE gene promoter regions, potential transcription factor binding sites were predicted and two GC signals, a TATA box were indicated. Results of promoter activity analysis indicated that one of potential regulatory elements was located in the region -669 to -259, which was essential for a high expression of the APOE gene. Promoter mutation and deletion analysis further suggested that the C/EBPA binding site within the APOE promoter was responsible for the regulation of APOE transcription. Electrophoretic mobility shift assays also showed the binding site of the transcription factor C/EBPA. This study advances our knowledge of the promoter of the porcine APOE gene. PMID:24464129

  20. Pathology of camel tuberculosis and molecular characterization of its causative agents in pastoral regions of Ethiopia.

    Directory of Open Access Journals (Sweden)

    Gezahegne Mamo

    Full Text Available A cross sectional study was conducted on 906 apparently healthy camels slaughtered at Akaki and Metehara abattoirs to investigate the pathology of camel tuberculosis (TB and characterize its causative agents using postmortem examination, mycobacteriological culturing, and multiplex polymerase chain reaction (PCR, region of difference-4 (RD4-based PCR and spoligotyping. The prevalence of camel TB was 10.04% (91/906 on the basis of pathology and it was significantly higher in females (χ(2 = 4.789; P = 0.029. The tropism of TB lesions was significantly different among the lymph nodes (χ(2 = 22.697; P = 0.002 and lung lobes (χ(2 = 17.901; P = 0.006. Mycobacterial growth was observed in 34% (31/91 of camels with grossly suspicious TB lesions. Upon further molecular characterization using multiplex PCR, 68% (21/31 of the colonies showed a positive signal for the genus Mycobacterium, of which two were confirmed Mycobacterium bovis (M. bovis by RD4 deletion typing. Further characterization of the two M. bovis at strains level revealed that one of the strains was SB0133 while the other strain was new and had not been reported to the M. bovis database prior to this study. Hence, it has now been reported to the database, and designated as SB1953. In conclusion, the results of the present study have shown that the majority of camel TB lesions are caused by mycobacteria other than Mycobacterium tuberculosis complex. And hence further identification and characterization of these species would be useful towards the efforts made to control TB in camels.

  1. Genome scan for parent-of-origin QTL effects on bovine growth and carcass traits

    OpenAIRE

    Ikhide G. Imumorin; Eun-Hee eKim; Yun-Mi eLee; Dirk-Jan eDe Koning; Johan eVan Arendonk; Marcos eDe Donato; Jeremy Francis Taylor; Jong-Joo eKim

    2011-01-01

    Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus x Brahman cattle crossbreds. We identified 24 POE-QTL on 15 Bos taurus autosomes (BTAs) of which 6 were significant at 5% genome-wide level and 18 at the 5% chromosome-wide significance level. Six QTL were paternally expressed while 15...

  2. Self-Confirmation and Ascertainment of the Candidate Genomic Regions of Complex Trait Loci - A None-Experimental Solution.

    Directory of Open Access Journals (Sweden)

    Lishi Wang

    Full Text Available Over the past half century, thousands of quantitative trait loci (QTL have been identified by using animal models and plant populations. However, the none-reliability and imprecision of the genomic regions of these loci have remained the major hurdle for the identification of the causal genes for the correspondent traits. We used a none-experimental strategy of strain number reduction for testing accuracy and ascertainment of the candidate region for QTL. We tested the strategy in over 400 analyses with data from 47 studies. These studies include: 1 studies with recombinant inbred (RI strains of mice. We first tested two previously mapped QTL with well-defined genomic regions; We then tested additional four studies with known QTL regions; and finally we examined the reliability of QTL in 38 sets of data which are produced from relatively large numbers of RI strains, derived from C57BL/6J (B6 X DBA/2J (D2, known as BXD RI mouse strains; 2 studies with RI strains of rats and plants; and 3 studies using F2 populations in mice, rats and plants. In these cases, our method identified the reliability of mapped QTL and localized the candidate genes into the defined genomic regions. Our data also suggests that LRS score produced by permutation tests does not necessarily confirm the reliability of the QTL. Number of strains are not the reliable indicators for the accuracy of QTL either. Our strategy determines the reliability and accuracy of the genomic region of a QTL without any additional experimental study such as congenic breeding.

  3. Self-Confirmation and Ascertainment of the Candidate Genomic Regions of Complex Trait Loci - A None-Experimental Solution.

    Science.gov (United States)

    Wang, Lishi; Jiao, Yan; Wang, Yongjun; Zhang, Mengchen; Gu, Weikuan

    2016-01-01

    Over the past half century, thousands of quantitative trait loci (QTL) have been identified by using animal models and plant populations. However, the none-reliability and imprecision of the genomic regions of these loci have remained the major hurdle for the identification of the causal genes for the correspondent traits. We used a none-experimental strategy of strain number reduction for testing accuracy and ascertainment of the candidate region for QTL. We tested the strategy in over 400 analyses with data from 47 studies. These studies include: 1) studies with recombinant inbred (RI) strains of mice. We first tested two previously mapped QTL with well-defined genomic regions; We then tested additional four studies with known QTL regions; and finally we examined the reliability of QTL in 38 sets of data which are produced from relatively large numbers of RI strains, derived from C57BL/6J (B6) X DBA/2J (D2), known as BXD RI mouse strains; 2) studies with RI strains of rats and plants; and 3) studies using F2 populations in mice, rats and plants. In these cases, our method identified the reliability of mapped QTL and localized the candidate genes into the defined genomic regions. Our data also suggests that LRS score produced by permutation tests does not necessarily confirm the reliability of the QTL. Number of strains are not the reliable indicators for the accuracy of QTL either. Our strategy determines the reliability and accuracy of the genomic region of a QTL without any additional experimental study such as congenic breeding. PMID:27203862

  4. Self-Confirmation and Ascertainment of the Candidate Genomic Regions of Complex Trait Loci – A None-Experimental Solution

    Science.gov (United States)

    Wang, Lishi; Jiao, Yan; Wang, Yongjun; Zhang, Mengchen; Gu, Weikuan

    2016-01-01

    Over the past half century, thousands of quantitative trait loci (QTL) have been identified by using animal models and plant populations. However, the none-reliability and imprecision of the genomic regions of these loci have remained the major hurdle for the identification of the causal genes for the correspondent traits. We used a none-experimental strategy of strain number reduction for testing accuracy and ascertainment of the candidate region for QTL. We tested the strategy in over 400 analyses with data from 47 studies. These studies include: 1) studies with recombinant inbred (RI) strains of mice. We first tested two previously mapped QTL with well-defined genomic regions; We then tested additional four studies with known QTL regions; and finally we examined the reliability of QTL in 38 sets of data which are produced from relatively large numbers of RI strains, derived from C57BL/6J (B6) X DBA/2J (D2), known as BXD RI mouse strains; 2) studies with RI strains of rats and plants; and 3) studies using F2 populations in mice, rats and plants. In these cases, our method identified the reliability of mapped QTL and localized the candidate genes into the defined genomic regions. Our data also suggests that LRS score produced by permutation tests does not necessarily confirm the reliability of the QTL. Number of strains are not the reliable indicators for the accuracy of QTL either. Our strategy determines the reliability and accuracy of the genomic region of a QTL without any additional experimental study such as congenic breeding. PMID:27203862

  5. QTL analysis for eating quality-related traits in an F2:3 population derived from waxy corn × sweet corn cross.

    Science.gov (United States)

    Park, Ki Jin; Sa, Kyu Jin; Koh, Hee-Jong; Lee, Ju Kyong

    2013-09-01

    In order to identify quantitative trait loci (QTL) for the eating quality of waxy corn and sweet corn (Zea mays L.), QTL analysis was conducted on an F2 population derived from a cross between a waxy corn inbred line and a sweet corn inbred line. Ten QTLs for pericarp thickness (PER), amylose content (AMY), dextrose content (DEX) and sucrose content (SUC) were found in the 158 F2 families. Among them, four QTLs, qAMY4 (10.43%), qAMY9 (19.33%), qDEX4 (21.31%) and qSUC4 (30.71%), may be considered as major QTLs. Three of these, qAMY4, qDEX4 and qSUC4, were found to be located within a region flanked by two adjacent SSR markers on chromosome 4 (umc1088 and bnlg1265), making this SSR marker pair a useful selection tool for screening the eating quality traits of AMY, DEX and SUC. The QTL for amylose content was found to be located between markers phi027 and umc1634, raising the possibility of its identity being the Wx1 gene, which encodes a granule-bound amylose synthase. The new QTLs identified by the present study could serve as useful molecular markers for selecting important eating quality traits in subsequent waxy corn breeding studies. PMID:24273428

  6. High-resolution genetic linkage mapping, high-temperature tolerance and growth-related quantitative trait locus (QTL) identification in Marsupenaeus japonicus.

    Science.gov (United States)

    Lu, Xia; Luan, Sheng; Hu, Long Yang; Mao, Yong; Tao, Ye; Zhong, Sheng Ping; Kong, Jie

    2016-06-01

    The Kuruma prawn, Marsupenaeus japonicus, is one of the most promising marine invertebrates in the industry in Asia, Europe and Australia. However, the increasing global temperatures result in considerable economic losses in M. japonicus farming. In the present study, to select genetically improved animals for the sustainable development of the Kuruma prawn industry, a high-resolution genetic linkage map and quantitative trait locus (QTL) identification were performed using the RAD technology. The maternal map contained 5849 SNP markers and spanned 3127.23 cM, with an average marker interval of 0.535 cM. Instead, the paternal map contained 3927 SNP markers and spanned 3326.19 cM, with an average marker interval of 0.847 cM. The consensus map contained 9289 SNP markers and spanned 3610.90 cM, with an average marker interval of 0.388 cM and coverage of 99.06 % of the genome. The markers were grouped into 41 linkage groups in the maps. Significantly, negative correlation was detected between high-temperature tolerance (UTT) and body weight (BW). The QTL mapping revealed 129 significant QTL loci for UTT and four significant QTL loci for BW at the genome-wide significance threshold. Among these QTLs, 129 overlapped with linked SNPs, and the remaining four were located in regions between contiguous SNPs. They explained the total phenotypic variance ranging from 8.9 to 12.4 %. Because of a significantly negative correlation between growth and high-temperature tolerance, we demonstrate that this high-resolution linkage map and QTLs would be useful for further marker-assisted selection in the genetic improvement of M. japonicus. PMID:26965508

  7. Overlapping chromosomal regions for fertility traits and production traits in the Danish Holstein population

    DEFF Research Database (Denmark)

    Höglund, Johanna Karolina; Buitenhuis, A J; Guldbrandtsen, B; Su, G; Thomsen, B; Lund, M S

    2009-01-01

    interest to validate which of the subtraits are affected by the QTL. Phenotypic and marker data were collected from 34 grandsire families from the Danish Holstein population. First, the trait data for "fertility treatments" were separated into their underlying subtraits: uterine infections, antibiotics...... placed in the placenta, and abortions. In addition, retained placenta was selected for analysis because it is related to uterine infections. A genome scan was performed using 416 microsatellite markers for the fertility treatment subtraits and retained placenta, and an additional genome scan for milk...... production traits conditional on the QTL regions for the subtraits and retained placenta was conducted. Second, we selected 24 genomic regions harboring QTL for fertility traits from a previous study. A QTL scan for milk production traits conditional on the selected regions was conducted. We found that 16...

  8. QTL dissection of Lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite.

    Directory of Open Access Journals (Sweden)

    Adrien Zimmer

    Full Text Available Quantitative genetics and QTL mapping are efficient strategies for deciphering the genetic polymorphisms that explain the phenotypic differences of individuals within the same species. Since a decade, this approach has been applied to eukaryotic microbes such as Saccharomyces cerevisiae in order to find natural genetic variations conferring adaptation of individuals to their environment. In this work, a QTL responsible for lag phase duration in the alcoholic fermentation of grape juice was dissected by reciprocal hemizygosity analysis. After invalidating the effect of some candidate genes, a chromosomal translocation affecting the lag phase was brought to light using de novo assembly of parental genomes. This newly described translocation (XV-t-XVI involves the promoter region of ADH1 and the gene SSU1 and confers an increased expression of the sulfite pump during the first hours of alcoholic fermentation. This translocation constitutes another adaptation route of wine yeast to sulfites in addition to the translocation VIII-t-XVI previously described. A population survey of both translocation forms in a panel of domesticated yeast strains suggests that the translocation XV-t-XVI has been empirically selected by human activity.

  9. Prospect of the QTL-qSB-9Tq utilized in molecular breeding program of japonica rice against sheath blight

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The major QTL-qSB-9Tq conferring partial resistance to rice (Oryza sativa L.) sheath blight (Rhizoctonia solani Kühn) has been verified on chromosome 9 of the indica rice cultivar, Teqing. In this study, the prospect of this QTL utilized in molecular breeding program of japonica rice for sheath blight resistance was investigated. Most of the japonica rice cultivars showed lower level of sheath blight resistance than the indica rice cultivars. At the corresponding site of qSB-9Tq, nine typical japonica rice culfivars from different ecological regions or countries proved to possess the susceptible allele(s). Introgression of qSB-9Tq into these cultivars enhanced their resistance level by decreasing sheath blight score of 1.0 (0.5-1.3), which indicated that qSB-9Tq had a large potential in strengthening the resistance of japonica rice to sheath blight. The use of the three molecular markers, which were polymorphic between Teqing and many japonica rice cultivars, promotes the application of qSB-9Tq in a concrete molecular breeding program.

  10. Advanced Backcross QTL Analysis for the Whole Plant Growth Duration Salt Tolerance in Rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    CHAI Lu; LI Zhi-kang; ZHANG Jian; PAN Xiao-biao; ZHANG Fan; ZHENG Tian-qing; ZHAO Xiu-qing; WANG Wen-sheng; Ali Jauhar; XU Jian-long

    2014-01-01

    Salinity is a major factor limiting rice yield in coastal areas of Asia. To facilitate breeding salt tolerant rice varieties, the whole-plant growth duration salt tolerance (ST) was genetically dissected by phenotyping two sets of BC2F5 introgression lines (ILs) for four yield traits under severe natural salt stress and non-stress ifled conditions using SSR markers and the methods of advanced backcross QTL (AB-QTL) analysis and selective introgression. Many QTLs affecting four yield traits under salt stress and non-stress conditions were identiifed, most (>90%) of which were clustered in 13 genomic regions of the rice genome and involved in complex epistasis. Most QTLs affecting yield traits were differentially expressed under salt stress and non-stress conditions. Our results suggested that genetics complementarily provides an adequate explanation for the hidden genetic diversity for ST observed in both IL populations. Some promising Huanghuazhan (HHZ) ILs with favorable donor alleles at multiple QTLs and signiifcantly improved yield traits under salt stress and non-stress conditions were identiifed, providing excellent materials and relevant genetic information for improving rice ST by marker-assisted selection (MAS) or genome selection.

  11. Real-time detection, location, and characterization of rockslides using broadband regional seismic networks

    Science.gov (United States)

    Manconi, Andrea; Picozzi, Matteo; Coviello, Velio; De Santis, Francesca; Elia, Luca

    2016-07-01

    We propose a new real-time approach to detect, locate, and estimate the volume of rockslides by analyzing waveforms acquired from broadband regional seismic networks. The identification of signals generated by rockslides from other sources, such as natural and/or induced earthquakes, is accomplished by exploiting the ratio between local magnitudes (ML) and duration magnitudes (MD). We found that signals associated with rockslides have ML/MD earthquakes ML/MD ≅ 1. In addition, we derived an empirical relationship between MD and rockslide volumes, obtaining a preliminary characterization of rockslide volume within seconds after their occurrence. The key points of this study are presented by testing the hypothesis on a recent rockslide event that occurred in northern Italy. We discuss also the potential evolution of the methodology for early warning and/or rapid response purposes.

  12. Stand structure and dead wood characterization in cork forest of Calabria region (southern Italy

    Directory of Open Access Journals (Sweden)

    Barreca L

    2010-07-01

    Full Text Available The cork forests are one the most interesting forest ecosystems in the Mediterranean area. Their distribution and ecological characteristics have undergone a significant transformation after the significant changes following the development and establishment of agricultural crops. Currently, only a few stands, which survive in hard to reach places, prove the wide spread distribution of this species was also in the recent past. This study describes the stand structure of some cork forests in Calabria region (southern Italy. In order, to characterize the vertical structure Latham index has been applied, while for the description of the horizontal distribution NBSI group indices has been used. Detailed surveys on dead wood were also conducted determining the occurring volume and its decay stage according to the decay classes system proposed by Hunter. The aim of this study is to provide guidelines for sustainable management of cork forests, improving and promoting the structural complexity and functional efficiency of these forest stands.

  13. Characterization of regional atmospheric aerosols over Hungary by PIXE elemental analysis. Appendix 9

    International Nuclear Information System (INIS)

    Earlier PIXE analytical data obtained on rural aerosol samples from Hungary have been extended by the results of further analyses in the frame of the present international Co-ordinated Research Programme. Samples have been collected in three more rural, one suburban and two urban stations. A comparison of the data revealed the distribution of aerosol loading by several trace elements over the country, supported the determination of aerosol budget indicating long-range transport from industrial sources and Saharan dust intrusion. The data show that Hungarian air is moderately polluted by aerosols from regional and faraway sources. Methodological results have been obtained in setting up a new microbeam channel for individual characterization of aerosol particles. (author)

  14. Characterization of airborne particulate matter in the metropolitan region of Belo Horizonte

    International Nuclear Information System (INIS)

    In this work soil samples, iron ore and airborne atmospheric particulate matter (PM) in the Metropolitan Region of Belo Horizonte (MRBH), State of Minas Gerais, Brazil, are investigated with the aim of identifying if the sources of the particulate matter are of natural origin, such as, resuspension of particles from soil, or due to anthropogenic origins from mining and processing of iron ore. Samples were characterized by powder X-ray diffraction, X-ray fluorescence and 57Fe-Moessbauer spectroscopy. The results showed that soil samples studied are rich in quartz and have low contents of iron mainly iron oxide with low crystallinity. The samples of iron ore and PM have high concentration of iron, predominantly well crystallized hematite. 57Fe-Moessbauer spectroscopy confirmed the presence of similar iron oxides in samples of PM and in the samples of iron ore, indicating the anthropogenic origin in the material present in atmosphere of the study area. (author)

  15. Characterization of airborne particulate matter in the metropolitan region of Belo Horizonte

    Energy Technology Data Exchange (ETDEWEB)

    Tavares, Fernanda V.F.; Ardisson, Jose Domingos; Rodrigues, Paulo Cesar H.; Brito, Walter de; Macedo, Waldemar Augusto A.; Jacomino, Vanusa Maria F., E-mail: ferufv@yahoo.com.br [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil)

    2013-07-01

    In this work soil samples, iron ore and airborne atmospheric particulate matter (PM) in the Metropolitan Region of Belo Horizonte (MRBH), State of Minas Gerais, Brazil, are investigated with the aim of identifying if the sources of the particulate matter are of natural origin, such as, resuspension of particles from soil, or due to anthropogenic origins from mining and processing of iron ore. Samples were characterized by powder X-ray diffraction, X-ray fluorescence and {sup 57}Fe-Moessbauer spectroscopy. The results showed that soil samples studied are rich in quartz and have low contents of iron mainly iron oxide with low crystallinity. The samples of iron ore and PM have high concentration of iron, predominantly well crystallized hematite. {sup 57}Fe-Moessbauer spectroscopy confirmed the presence of similar iron oxides in samples of PM and in the samples of iron ore, indicating the anthropogenic origin in the material present in atmosphere of the study area. (author)

  16. Characterization of Baker Fjord region through its heavy metal content on sediments (Central Chilean Patagonia

    Directory of Open Access Journals (Sweden)

    Ramón Ahumada

    2015-07-01

    Full Text Available The spatial distribution of heavy metals content (Ba, Cd, Cu, Pb, Sr and Zn in sediments of the Baker Fjord and surrounding channels in the central region of the Chilean fjords (47°45'S, 48°15'S is analyzed. The aim of the study was characterized the patterns of abundance and distribution of these metals in surface sediments. The area corresponds to a poorly studied zone with low human activity. Distribution patterns would be influenced by rainfall conditions (local erosion, fluvial (continental sediments carried by rivers, glacier (glacier flour and estuarine circulation. Cluster analysis allows differentiation among the sampled sites and group with similar characteristics. Finally, the concentrations found were contrasted with average values of metamorphic rocks and show with some certainty that the values found for calendar for this area and the greatest concentrations are the result of natural enrichment.

  17. Characterizing isotopic variability of primary production and consumers in Great Plains ecosystems during protracted regional drought

    Science.gov (United States)

    Haveles, A. W.; Fox-Dobbs, K.; Talmadge, K. A.; Fetrow, A.; Fox, D. L.

    2012-12-01

    Over the last few years (2010-2012), the Great Plains of the central USA experienced protracted drought conditions, including historically severe drought during Summer, 2011. Drought severity in the region generally decreases with increasing latitude, but episodic drought is a fundamental trait of grassland ecosystems. Documenting above ground energy and nutrient flow with current drought is critical to understanding responses of grassland ecosystems in the region to predicted increased episodicity of rainfall and recurrence of drought due to anthropogenic climate change. Characterization of biogeochemical variability of modern ecosystems at the microhabitat, local landscape, and regional scales is also necessary to interpret biogeochemical records of ancient grasslands based on paleosols and fossil mammals. Here, we characterize three grassland ecosystems that span the drought gradient in the Great Plains (sites in the Texas panhandle, southwest Kansas, and northwest Nebraska). We measured δ13C and δ15N values of plants and consumers to characterize the biogeochemical variability within each ecosystem. Vegetation at each site is a mix of trees, shrubs, herbs, and cool- and warm-growing season grasses (C3 and C4, respectively). Thus, consumers have access to isotopically distinct sources of forage that vary in abundance with microhabitat (e.g., open grassland, shrub thicket, riparian woodland). Observations indicate herbivorous arthropod (grasshoppers and crickets) abundance follows drought severity, with high abundance of many species in Texas, and low abundance of few species in Nebraska. Small mammal (rodents) abundance follows the inverse pattern with 0.8%, 3.2% and 17.2% capture success in Texas, Kansas and Nebraska, respectively. The inverse abundance patterns of consumer groups may result from greater sensitivity of small mammal consumers with high metabolic needs to lower local net primary productivity and forage quality under drought conditions. As a

  18. A Ten Step Protocol and Plan for CCS Site Characterization, Based on an Analysis of the Rocky Mountain Region, USA

    Energy Technology Data Exchange (ETDEWEB)

    McPherson, Brian; Matthews, Vince

    2013-09-15

    This report expresses a Ten-Step Protocol for CO2 Storage Site Characterization, the final outcome of an extensive Site Characterization analysis of the Rocky Mountain region, USA. These ten steps include: (1) regional assessment and data gathering; (2) identification and analysis of appropriate local sites for characterization; (3) public engagement; (4) geologic and geophysical analysis of local site(s); (5) stratigraphic well drilling and coring; (6) core analysis and interpretation with other data; (7) database assembly and static model development; (8) storage capacity assessment; (9) simulation and uncertainty assessment; (10) risk assessment. While the results detailed here are primarily germane to the Rocky Mountain region, the intent of this protocol is to be portable or generally applicable for CO2 storage site characterization.

  19. Molecular characterization of barley 3H semi-dwarf genes.

    Directory of Open Access Journals (Sweden)

    Haobing Li

    Full Text Available The barley chromosome 3H accommodates many semi-dwarfing genes. To characterize these genes, the two-rowed semi-dwarf Chinese barley landrace 'TX9425' was crossed with the Australian barley variety 'Franklin' to generate a doubled haploid (DH population, and major QTLs controlling plant height have been identified in our previous study. The major QTL derived from 'TX9425' was targeted to investigate the allelism of the semi-dwarf gene uzu in barley. Twelve sets of near-isogenic lines and a large NILF2 fine mapping population segregating only for the dwarfing gene from 'TX9425' were developed. The semi-dwarfing gene in 'TX9425' was located within a 2.8 cM region close to the centromere on chromosome 3H by fine mapping. Molecular cloning and sequence analyses showed that the 'TX9425'-derived allele contained a single nucleotide substitution from A to G at position 2612 of the HvBRI1 gene. This was apparently the same mutation as that reported in six-rowed uzu barley. Markers co-segregating with the QTL were developed from the sequence of the HvBRI1 gene and were validated in the 'TX9425'/'Franklin' DH population. The other major dwarfing QTL derived from the Franklin variety was distally located on chromosome 3HL and co-segregated with the sdw1 diagnostic marker hv20ox2. A third dwarfing gene, expressed only in winter-sown trials, was identified and located on chromosome 3HS. The effects and interactions of these dwarfing genes under different growing conditions are discussed. These results improve our understanding of the genetic mechanisms controlling semi-dwarf stature in barley and provide diagnostic markers for the selection of semi-dwarfness in barley breeding programs.

  20. Regional characterization of hydraulic properties of rock using well test data

    International Nuclear Information System (INIS)

    This study was aimed at investigating the possible use of data from the SGU well archive for characterization of the hydraulic properties of the crystalline basement of Sweden at a regional scale. Two areas studied as possible candidates for a radioactive waste repository were selected. The SGU well data and the hydraulic conductivity data evaluated from packer tests in boreholes at the sites were characterized statistically also considering possible spatial dependence. The two types of data were compared and the correlation between the data sets was investigated. This part of the study considered the uppermost 100 m of the packer test data, which is the approximate depth range covered by the SGU data. In a second part of the work the packer test data from the two study areas were analyzed in terms of possible depth trends. The exploratory statistical analyses suggested that the SGU data are useful for estimations of hydrogeological parameters for areas of different geologic settings. The geostatistical analysis provided further understanding of the spatial behaviour of the studied parameters. The analysis of depth dependence indicates that at both sites there is a layer of higher hydraulic conductivity close to the surface. Within these layers, about 200 and 280 m thick, resp., the conductivity decreases with increasing depth. At larger depths however, the decrease with depth is very slow or negligible. It was found that the scatter in the measured hydraulic conductivity data is very large compared to differences between the depth functions tested

  1. Characterization and distribution of metal and nonmetal elements in the Alberta oil sands region of Canada.

    Science.gov (United States)

    Huang, Rongfu; McPhedran, Kerry N; Yang, Lingling; El-Din, Mohamed Gamal

    2016-03-01

    This review covers the characterization and distribution of metals and nonmetals in the Alberta oil sands region (AOSR) of Canada. The development of the oil sands industry has resulted in the release of organic, metal and nonmetal contaminants via air and water to the AOSR. For air, studies have found that atmospheric deposition of metals in the AOSR decreased exponentially with distance from the industrial emission sources. For water, toxic metal concentrations often exceeded safe levels leading to the potential for negative impacts to the receiving aquatic environments. Interestingly, although atmospheric deposition, surface waters, fish tissues, and aquatic bird eggs exhibited increasing level of metals in the AOSR, reported results from river sediments showed no increases over time. This could be attributed to physical and/or chemical dynamics of the river system to transport metals to downstream. The monitoring of the airborne emissions of relevant nonmetals (nitrogen and sulphur species) was also considered over the AOSR. These species were found to be increasing along with the oil sands developments with the resultant depositions contributing to nitrogen and sulphur accumulations resulting in ecosystem acidification and eutrophication impacts. In addition to direct monitoring of metals/nonmetals, tracing of air emissions using isotopes was also discussed. Further investigation and characterization of metals/nonmetals emissions in the AOSR are needed to determine their impacts to the ecosystem and to assess the need for further treatment measures to limit their continued output into the receiving environments. PMID:26766359

  2. Systematically characterizing regions of the First Fermi-LAT SNR Catalog

    CERN Document Server

    de Palma, F; Hewitt, J W; Johannesson, G; Tibaldo, L

    2015-01-01

    While supernova remnants (SNRs) are widely thought to be powerful cosmic-ray accelerators, indirect evidence comes from a small number of well-studied cases. Here we systematically determine the gamma-ray emission detected by the Fermi Large Area Telescope (LAT) from all known Galactic SNRs, disentangling them from the sea of cosmic-ray generated photons in the Galactic plane. Using LAT data we have characterized the 1-100 GeV emission in 279 regions containing SNRs, accounting for systematic uncertainties caused by source confusion and instrumental response. We have also developed a method to explore some systematic effects on SNR properties caused by the modeling of the interstellar emission (IEM). The IEM contributes substantially to gamma-ray emission in the regions where SNRs are located. To explore the systematics we consider different model construction methods, different model input parameters, and independently fit the model components to the gamma-ray data. We will describe this analysis method in d...

  3. Characterization of soils from the Algarve region (Portugal): a multidisciplinary approach for forensic applications.

    Science.gov (United States)

    Guedes, Alexandra; Ribeiro, Helena; Valentim, Bruno; Rodrigues, Andreia; Sant'Ovaia, Helena; Abreu, Ilda; Noronha, Fernando

    2011-06-01

    The Algarve is located at a very short distance from North Africa, in Southern Portugal, and as one of the most touristic regions of Portugal, it is accessible by air, land and sea. It is very susceptible to many illegal activities, such as illegal migration, drug trafficking, kidnapping, and murder, among others. Therefore, an Algarve soils database for forensic purposes is being conducted with the conjunction of geological and palynological methodologies on soils characterization, since this is of fundamental importance to assess reliable evidence on forensic investigations. In this study, the properties of soils from several proximate sites from the Algarve were investigated, namely: (i) colour determined by spectrophotometry; (ii) particle size distribution determined by laser granulometry; (iii) low-field magnetic susceptibility by a susceptibility meter; and (iv) pollen content using a light microscope. Finally, a hierarchical cluster analysis was applied to ascertain the capacity of the different soil properties for discrimination between samples. The study reveals the utility of geobotanical techniques for forensic discrimination of soils. Even though some similarities between some of the samples were found, each one presented a combination of colour, particle size distribution, magnetic susceptibility and pollen features that enable the determination of a fingerprint expected to reveal a specific site for future selection of coastal search areas in the Algarve region. PMID:21605829

  4. Regional scale characterization of the topographic control on soil organic carbon spatial distribution

    Science.gov (United States)

    Stevens, François; Bogaert, Patrick; van Wesemael, Bas

    2013-04-01

    The influence of geomorphology on the spatial distribution of soil organic carbon (SOC) has been studied for a large range of scales and conditions. The larger SOC stocks found in dry valleys and concave footslopes of the Belgian loam belt have been explained jointly by the transfer of sediments along the slope and the reduced decomposition rate of buried organic matter. While erosion effect on SOC has been simulated at the hillslope scale, it is generally not considered in SOC inventories and prediction models at regional scale. However, more precise large scales inventories are demanded by the carbon modelling community. The goal of this paper is to characterize the relative importance of geomorphology on the SOC horizontal and vertical variability across whole agricultural region. The large historic dataset of soil horizons Aardewerk together with 147 recently sampled profiles was exploited for cost efficiency reasons. Mean profiles for different soil properties classes were compared. Various topographic indices were computed from a digital elevation model, and their potential to predict SOC content at different depth was quantified using multiple regression and terrain morphologic classification. Both dataset were able to show differences in mean SOC profile among soil properties classes, but only the new profiles dataset shows a clear relationship between SOC content and topographic indices. The various errors in then historic data set (e.g., positioning errors) may explain these limitations. This study thus brings in evidence the major control of topography on SOC vertical distribution in a region where observed heterogeneities for other commonly involved factors are limited. However, the large amount of unexplained variability still limits the usefulness of SOC content spatial prediction and should be addressed by alternative spatial methods.

  5. Molecular characterization of a human matrix attachment region that improves transgene expression in CHO cells.

    Science.gov (United States)

    Sun, Qiu-Li; Zhao, Chun-Peng; Chen, Shao-Nan; Wang, Li; Wang, Tian-Yun

    2016-05-15

    Chinese hamster ovary (CHO) cells offer many advantages for recombinant gene expression, including proper folding and post-translational modification of the recombinant protein. However, due to positional effects resulting from the neighboring chromatin, transgenes are often expressed at low levels in these cells. While previous studies demonstrated that matrix attachment regions (MARs) can be utilized to increase transgene expression by buffering transgene silencing, the mechanism by which this occurs is poorly understood. We therefore performed a deletion analysis of the human β-globin MAR sequence to characterize the regions that are necessary to enhance transgene expression in CHO cells. Our results indicate that of the six β-globin MAR fragments tested (MAR-1-6; nucleotides 1-540, 420-1020, 900-1500, 1380-1980, 1860-2460, and 2340-2999, respectively), MAR-2, followed by MAR-3, was the most effective region for promoting stable and elevated transgene expression. Meanwhile, bioinformatic analyses demonstrated that these fragments encode a MAR-like motif and several transcription factor binding sites, including special AT-rich binding protein 1 (SATB1), CCAAT-enhancer-binding proteins (C/EBP), CCCTC-binding factor (CTCF), and Glutathione (GSH) binding motifs, indicating that these elements may contribute to the MAR-mediated enhancement of transgene expression. In addition, we found that truncated MAR derivatives yield more stable transgene expression levels than transgenes lacking the MAR. We concluded that the MAR-mediated transcriptional activation of transgenes requires a specific AT-rich sequence, as well as specific transcription factor-binding motifs. PMID:26869318

  6. Characterization of traditional raw materials used in housing construction in Huambo region - Angola

    Science.gov (United States)

    Pedro, Elsa; Duarte, Isabel; Varum, Humberto; Pinho, António; Norman, Antónia

    2016-04-01

    The sustainability of buildings associated to the use of raw earth has motivated the studies and the development of techniques and methods in the context of this type of construction. In the region of Huambo, Angola, these construction techniques are widely used, especially for low-income families who represent the majority of the population. Much of the buildings in Huambo province are built with adobe. Due to the climate in this region, subtropical, hot and humid, with altitudes above 1000 meters and extensive river system, these buildings are particularly vulnerable to the action of water and develop, in many situations, early degradation. The Huambo Province is located in central Angola, has 36 km2 area and approximately 2 million inhabitants. This work aims to evaluate, by conducting in-situ tests, physical and mechanical properties of adobe blocks typically used in the construction of those buildings. The methodology is based on field campaigns where in-situ expeditious tests were performed in soils (smell test, color, touch, brightness, sedimentation, ball, hardness, etc.) and tests on adobes blocks made with traditional procedures, particularly in terms of durability and erodibility (erosion test at Geelong method; evaluation test of wet / dry cycle, applying the New Zealand standards 4297: 1998; 4297: 1998 and 4297: 1999). The results will contribute to the characterization of the geomaterials and methods used in construction with earth in Huambo Province, contributing to the improvement of these sustainable solutions, with a strong presence in this region. The results of this study will also contribute to the proposal of constructive solutions with improved performance characteristics, comfort, safety and durability.

  7. QTL detection by multi-parent linkage mapping in oil palm (Elaeis guineensis Jacq.).

    OpenAIRE

    Billotte, N.; Jourjon, M-Francoise; Marseillac, N.; Berger, A; Flori, A.; Asmady, H.; Adon, B.; Singh, R.; Nouy, B.; Potier, F.; Cheah, S.C.; Rohde, W; Ritter, E; Courtois, B.; Charrier, A.

    2010-01-01

    A quantitative trait locus (QTL) analysis designed for a multi-parent population was carried out and tested in oil palm (Elaeis guineensis Jacq.), which is a diploid cross-fertilising perennial species. A new extension of the MCQTL package was especially designed for crosses between heterozygous parents. The algorithm, which is now available for any allogamous species, was used to perform and compare two types of QTL search for small size families, within-family analysis and across-family ana...

  8. Power of QTL detection by either fixed or random models in half-sib designs

    Directory of Open Access Journals (Sweden)

    Schaeffer Lawrence R

    2005-11-01

    Full Text Available Abstract The aim of this study was to compare the variance component approach for QTL linkage mapping in half-sib designs to the simple regression method. Empirical power was determined by Monte Carlo simulation in granddaughter designs. The factors studied (base values in parentheses included the number of sires (5 and sons per sire (80, ratio of QTL variance to total genetic variance (λ = 0.1, marker spacing (10 cM, and QTL allele frequency (0.5. A single bi-allelic QTL and six equally spaced markers with six alleles each were simulated. Empirical power using the regression method was 0.80, 0.92 and 0.98 for 5, 10, and 20 sires, respectively, versus 0.88, 0.98 and 0.99 using the variance component method. Power was 0.74, 0.80, 0.93, and 0.95 using regression versus 0.77, 0.88, 0.94, and 0.97 using the variance component method for QTL variance ratios (λ of 0.05, 0.1, 0.2, and 0.3, respectively. Power was 0.79, 0.85, 0.80 and 0.87 using regression versus 0.80, 0.86, 0.88, and 0.85 using the variance component method for QTL allele frequencies of 0.1, 0.3, 0.5, and 0.8, respectively. The log10 of type I error profiles were quite flat at close marker spacing (1 cM, confirming the inability to fine-map QTL by linkage analysis in half-sib designs. The variance component method showed slightly more potential than the regression method in QTL mapping.

  9. Strategy for Mapping Quantitative Trait Loci (QTL) by Using Human Metapopulations

    OpenAIRE

    Rudan, I; Campbell, H.; Biloglav, Z.; Carothers, A D; Wright, A F

    2006-01-01

    AIM:To present a novel strategy for mapping quantitative trait loci (QTL), using human metapopulations. The strategy is based on the expectation that in geographic clusters of small and distinct human isolates, a combination of founder effect and genetic drift can dramatically increase population frequency of rare QTL variants with large effect. In such cases, the distribution of QT measurements in an (affected) isolate is expected to deviate from that observed in neighboring isolates.METHODS...

  10. Identification of environmentally stable QTL for resistance against Leptosphaeria maculans in oilseed rape (Brassica napus)

    OpenAIRE

    Huang, Y J; Jestin, C.; Welham, S. J.; King, G. J.; Manzanares-Dauleux, M. J.; Fitt, B. D. L.; Delourme, R

    2015-01-01

    Key message Six stable QTL for resistance against L. maculans (phoma stem canker) have been identified by QTL × environment interaction analysis using data from five winter oilseed rape field experiments. Abstract Phoma stem canker, caused by Leptosphaeria maculans, is a disease of worldwide importance on oilseed rape (Brassica napus). Quantitative trait loci (QTL)-mediated resistance against L. maculans in B. napus is considered to be race non-specific and potentially durable. Identification...

  11. QTL Mapping of Low-Temperature Germination Ability in the Maize IBM Syn4 RIL Population

    OpenAIRE

    Hu, Shuaidong; Lübberstedt, Thomas; Zhao, Guangwu; Lee, Michael

    2016-01-01

    Low temperature is the primary factor to affect maize sowing in early spring. It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage. However, little is known about maize QTL involved in low-temperature germination ability. 243 lines of the intermated B73×Mo17 (IBM) Syn4 recombinant inbred line (RIL) population was used for QTL analysis of low-temperature germination ability. There were significant differences in germination-rela...

  12. QTL ANALYSIS OF FIBER COLOR AND FIBER QUALITY IN NATURALLY GREEN COLORED COTTON (Gossypium hirsutum L.)

    OpenAIRE

    SEMİZER-CUMING, Devrim; ALTAN, Filiz; AKDEMIR, Huseyin; TOSUN, Muzaffer; GUREL, Aynur; Tanyolac, Bahattin

    2015-01-01

    ABSTRACT Improving fiber quality of naturally colored cotton has become more important in recent years due to changes in the spinning technology and consumer demand. The identification of quantitative trait loci (QTL) closely linked to the fiber quality traits can allow marker assisted selection (MAS) which leads us to future’s improved cotton cultivars. In this study, we performed genetic mapping on F2 population of G. hirsutum (Yesil × Nazilli 84) intraspecific cross, and identified QTL for...

  13. Analysis of QTL for resistance to radiation in rice

    International Nuclear Information System (INIS)

    The recombinant inbred line (RIL) population derived from rice variates Zhenshan 97B/Miyang 46 and their genetic linkage maps were used to map QTLs controlling resistant to radiation. The trait was measured by the relative germination rate (RGR) and the relative surviving plant rate (RSPR) after the seeds of each line treated with γ-rays irradiation at two 350 and 550 Gy. The results indicated that the lines treated with γ-irradiation showed different performance in resistance to radiation. Under the treatment of 350 Gy, two QTLs with additive effects were detected, of which qRR (g) 81 was only significant for relative germination rate, and it had the positive additive effects from the male parent, explaining 6.53% of the total phenotypic variations. The qRR(s)2-2 was another significant one for relative surviving plant rate, whose positive effects came from the female parent,explaining 12.81% of the total phenotypic variations. Similarly, 4 QTLs were detected under irradiation dose of 550 Gy, and qRR(g)1-2 and qRR(g)8-2 were detected for relative germination rate, with positive effects coming from female and male parent,respectively,explaining 14.38% of the total variations. qRR(s)5-2 and qRR(s)10 were detected for relative surviving plant rate, with positive effects coming from the male parent, explaining 19.65% of total variations. Under different irradiation dose, 9 pairs of double QTL epistasis effects could be identified in this population. The results suggested that the expression of QTL with resistance to radiation might have relation with the irradiation dose. (authors)

  14. eQTL Regulating Transcript Levels Associated with Diverse Biological Processes in Tomato.

    Science.gov (United States)

    Ranjan, Aashish; Budke, Jessica M; Rowland, Steven D; Chitwood, Daniel H; Kumar, Ravi; Carriedo, Leonela; Ichihashi, Yasunori; Zumstein, Kristina; Maloof, Julin N; Sinha, Neelima R

    2016-09-01

    Variation in gene expression, in addition to sequence polymorphisms, is known to influence developmental, physiological, and metabolic traits in plants. Genetic mapping populations have facilitated identification of expression quantitative trait loci (eQTL), the genetic determinants of variation in gene expression patterns. We used an introgression population developed from the wild desert-adapted Solanum pennellii and domesticated tomato (Solanum lycopersicum) to identify the genetic basis of transcript level variation. We established the effect of each introgression on the transcriptome and identified approximately 7,200 eQTL regulating the steady-state transcript levels of 5,300 genes. Barnes-Hut t-distributed stochastic neighbor embedding clustering identified 42 modules revealing novel associations between transcript level patterns and biological processes. The results showed a complex genetic architecture of global transcript abundance pattern in tomato. Several genetic hot spots regulating a large number of transcript level patterns relating to diverse biological processes such as plant defense and photosynthesis were identified. Important eQTL regulating transcript level patterns were related to leaf number and complexity as well as hypocotyl length. Genes associated with leaf development showed an inverse correlation with photosynthetic gene expression, but eQTL regulating genes associated with leaf development and photosynthesis were dispersed across the genome. This comprehensive eQTL analysis details the influence of these loci on plant phenotypes and will be a valuable community resource for investigations on the genetic effects of eQTL on phenotypic traits in tomato. PMID:27418589

  15. Feasibility of the grandprogeny design for quantitative trait loci (QTL) detection in purebred beef cattle.

    Science.gov (United States)

    Moody, D E; Pomp, D; Buchanan, D S

    1997-04-01

    The grandprogeny design (GPD) was developed for dairy cattle to use existing pedigreed populations for quantitative trait locus (QTL) detection. Marker genotypes of grandsires and sons are determined, and trait phenotypic data from grandprogeny are analyzed. The objective of this study was to investigate the potential application of GPD in purebred beef cattle populations. Pedigree structures of Angus (n = 123,319), Hereford (n = 107,778), Brangus (n = 14,449), and Gelbvieh (n = 8,114) sire evaluation reports were analyzed to identify potentially useful families. Power of QTL detection was calculated for a range of QTL effects (.1 to .5 SD) and two Type I error rates (.01 and .001). Reasonable power (> .75) could be achieved using GPD in Angus and Hereford for QTL having moderate effects (.3 SD) on weaning weight and large effects (.4 to .5 SD) on birth, yearling, and maternal weaning weights by genotyping 500 animals. Existing Gelbvieh and Brangus families useful for GPD were limited, and reasonable power could be expected only for QTL having large effects on weaning or birth weights. Although family structures suitable for GPD exist in purebred beef populations, large amounts of genotyping would be required to achieve reasonable power, and only QTL having moderate to large effects could be expected to be identified. PMID:9110205

  16. QTL mapping for test weight by using F2:3 population in maize

    Indian Academy of Sciences (India)

    Jun-Qiang Ding; Jin-Liang Ma; Chun-Rong Zhang; Hua-Fang Dong; Zhang-Ying Xi; Zong-Liang Xia; Jian-Yu Wu

    2011-04-01

    Test weight is an important trait in maize breeding. Understanding the genetic mechanism of test weight is important for effective selection of maize test weight improvement. In this study, quantitative trait loci (QTL) for maize test weight were identified. In the years 2007 and 2008, a F2:3 population along with the parents Chang7-2 and Zheng58 were planted in Zhengzhou, People’s Republic of China. Significant genotypic variation for maize test weight was observed in both years. Based on the genetic map containing 180 polymorphic SSR markers with an average linkage distance of 11.0 cM, QTL for maize test weight were analysed by mixed-model composite interval mapping. Five QTL, including four QTL with only additive effects, were identified on chromosomes 1, 2, 3, 4 and 5, and together explained 25.2% of the phenotypic variation. Seven pairs of epistatic interactions were also detected, involving 11 loci distributed on chromosomes 1, 2, 3, 4, 5 and 7, respectively, which totally contributed 18.2% of the phenotypic variation. However, no significant QTL × environment (Q×E) interaction and epistasis × environment interaction effects were detected. The results showed that besides the additive QTL, epistatic interactions also formed an important genetic basis for test weight in maize.

  17. Comparative QTL mapping of resistance to sugarcane mosaic virus in maize based on bioinformatics

    Institute of Scientific and Technical Information of China (English)

    Xiangling L(U); Xinhai LI; Chuanxiao XIE; Zhuanfang HAO; Hailian JI; Liyu SHI; Shihuang ZHANG

    2008-01-01

    The development of genomics and bioinfor-matics offers new tools for comparative gene mapping. In this paper, an integrated QTL map for sugarcane mosaic virus (SCMV) resistance in maize was constructed by compiling a total of 81 QTL loci available, using the Genetic Map IBM2 2005 Neighbors as reference. These 81 QTL loci were scattered on 7 chromosomes of maize, and most of them were clustered on chromosomes 3 and 6. By using the method of meta-analysis, we identified one "consensus QTL" on chromosome 3 covering a genetic distance of 6.44 cM, and two on chromosome 6 covering genetic distances of 16 cM and 27.48 cM, respectively. Four positional candidate resistant genes were identified within the "consensus QTL" on chromosome 3 via the strategy of comparative genomics. These results suggest that application of a combination of meta-analysis within a species with sequence homology comparison in a related model plant is an efficient approach to identify the major QTL and its candidate gene(s) for the target traits. The results of this study provide useful information for iden-tifying and cloning the major gene(s) conferring resistance to SCMV in maize.

  18. QTL Detection on Chromosome 6 in Landrace×Lantang Pig Resource Population

    Institute of Scientific and Technical Information of China (English)

    LI Jia-qi; ZHANG Hao; LIU Xiao-hong; GAO Ping; WANG Chong; WU Qiu-hao; ZHANG Xi-quan; CHEN Yao-sheng

    2004-01-01

    A resource population constructed by F2 design with Landrace and Chinese indigenous Lantang pigs was used in this study. Seven microsatellite DNA markers on chromosome 6 and USDA2.6 pig genetic linkage map were used for interval QTL mapping, The results revealed that at the position of 38- 41 cM there was a chromosome-wide highly significant QTL affecting carcass backfat A thickness (P<0.01), which was closely linked with MN007 and the ratio of QTL additive variance to F2 phenotypic variance was 5.90%. At the position of 60-70 cM there were two chromosome-wide significant QTLs affecting carcass lean percentage (P<0.01) and skin and fat percentage (P<0.05), which were closely linked with MN003 and the ratio of QTL additive variance to F2 phenotypic variance were 18.44 and 3.75%, respectively. At the same position, there was a single-point QTL also closely linked with MN003 and highly significantly (P<0.01) affecting carcass lean. In addition, there were two chromosome-wide highly significant (P<0.01) QTLs affecting meat color and marbling, which were closely linked with MN13 at the position of 70-75 cM and the ratio of QTL additive variance to F2 phenotypic variance were 14.05 and 1.77%, respectively.

  19. Characterization of sorption properties of selected soils from Lublin region by using water vapour adsorption method

    Science.gov (United States)

    Skic, Kamil; Boguta, Patrycja; Sokołowska, Zofia

    2016-04-01

    *The studies were carried out within the framework of a research project. The project was financed from funds of National Science Center on the base of decision number DEC-2013/11/D/NZ9/02545 Among many methods proposed to study sorption properties of soils an analysis of adsorption/ desorption isotherm is probably the easiest and most convenient one. It characterizes both quantity and quality of mineral and organic components and also their physical and physicochemical properties. The main aim of this study is comparison of sorption properties of selected Polish soils by using water vapour adsorption method. Samples were taken from the depth of 0-20 cm, from the Lublin region, eastern Poland. Soils were selected on the basis of their different physicochemical properties and were classified as: Haplic Fluvisol, Haplic Chernozem, Mollic Gleysol, Rendzic Phaeozem, Stagnic Luvisol, Haplic Cambisol (WG WRB 2006). Data taken from experimental adsorption isotherms were used to determine parameters of monolayer capacity, specific surface area and the total amount of vapour adsorbed at relative pressure of 0.974. Obtained adsorption and desorption isotherms reviled that adsorbate molecules interacted with the soil particles in different extent. Similar monolayer capacity was observed for Haplic Fluvisol, Haplic Chernozem and Stagnic Luvisol, while for Mollic Gleysol was more than 4 times higher. Mollic Gleysol was also characterized by highest values of specific surface area as well as quantity of adsorbed vapour at relative pressure of 0.974. Higher sorption was caused by presence of soil colloids which contains functional groups of a polar nature (mainly hydroxyls, phenolic and carboxyls). These groups similarly to silicates, oxides, hydratable cations as well as electric charge form adsorption centres for water vapour molecules.

  20. QTL analysis of leaf photosynthesis rate and related physiological traits in Brassica napus

    Institute of Scientific and Technical Information of China (English)

    YAN Xing-ying; QU Cun-min; LI Jia-na; CHEN Li; LIU Lie-zhao

    2015-01-01

    Rapeseed (Brassica napus L.) oil is the crucial source of edible oil in China. In addition, it can become a major renewable and sustainable feedstock for biodiesel production in the future. It is known that photosynthesis products are the primary sources for dry matter accumulation in rapeseed. Therefore, increasing the photosynthetic efifciency is desirable for the raise of rapeseed yield. The objective of the present study was to identify the genetic mechanism of photosynthesis based on the description of relationships between different photosynthetic traits and their quantitative trait loci (QTL) by using a recombinant inbred line (RIL) population with 172 lines. Speciifcal y, correlation analysis in this study showed that internal CO2 concentration has negative correlations with other three physiological traits under two different stages. Total y, 11 and 12 QTLs of the four physiological traits measured at the stages 1 and 2 were detected by using a high-density single nu-cleotidepolymorphism (SNP) markers linkage map with composite interval mapping (CIM), respectively. Three co-localized QTLs on A03 were detected at stage 1 with 5, 5, and 10%of the phenotypic variation, respectively. Other two co-localized QTLs were located on A05 at stage 2, which explained up to 12 and 5%of the phenotypic variation, respectively. The results are beneifcial for our understanding of genetic control of photosynthetic physiological characterizations and improvement of rapeseed yield in the future.

  1. Structural characterization of HIV gp41 with the membrane-proximal external region.

    Science.gov (United States)

    Shi, Wuxian; Bohon, Jen; Han, Dong P; Habte, Habtom; Qin, Yali; Cho, Michael W; Chance, Mark R

    2010-07-30

    Human immunodeficiency virus, type 1 (HIV-1) envelope glycoprotein (gp120/gp41) plays a critical role in virus infection and pathogenesis. Three of the six monoclonal antibodies considered to have broadly neutralizing activities (2F5, 4E10, and Z13e1) bind to the membrane-proximal external region (MPER) of gp41. This makes the MPER a desirable template for developing immunogens that can elicit antibodies with properties similar to these monoclonal antibodies, with a long term goal of developing antigens that could serve as novel HIV vaccines. In order to provide a structural basis for rational antigen design, an MPER construct, HR1-54Q, was generated for x-ray crystallographic and x-ray footprinting studies to provide both high resolution atomic coordinates and verification of the solution state of the antigen, respectively. The crystal structure of HR1-54Q reveals a trimeric, coiled-coil six-helical bundle, which probably represents a postfusion form of gp41. The MPER portion extends from HR2 in continuation of a slightly bent long helix and is relatively flexible. The structures observed for the 2F5 and 4E10 epitopes agree well with existing structural data, and enzyme-linked immunosorbent assays indicate that the antigen binds well to antibodies that recognize the above epitopes. Hydroxyl radical-mediated protein footprinting of the antigen in solution reveals specifically protected and accessible regions consistent with the predictions based on the trimeric structure from the crystallographic data. Overall, the HR1-54Q antigen, as characterized by crystallography and footprinting, represents a postfusion, trimeric form of HIV gp41, and its structure provides a rational basis for gp41 antigen design suitable for HIV vaccine development. PMID:20525690

  2. Structural Characterization of HIV gp41 with the Membrane-proximal External Region*

    Science.gov (United States)

    Shi, Wuxian; Bohon, Jen; Han, Dong P.; Habte, Habtom; Qin, Yali; Cho, Michael W.; Chance, Mark R.

    2010-01-01

    Human immunodeficiency virus, type 1 (HIV-1) envelope glycoprotein (gp120/gp41) plays a critical role in virus infection and pathogenesis. Three of the six monoclonal antibodies considered to have broadly neutralizing activities (2F5, 4E10, and Z13e1) bind to the membrane-proximal external region (MPER) of gp41. This makes the MPER a desirable template for developing immunogens that can elicit antibodies with properties similar to these monoclonal antibodies, with a long term goal of developing antigens that could serve as novel HIV vaccines. In order to provide a structural basis for rational antigen design, an MPER construct, HR1-54Q, was generated for x-ray crystallographic and x-ray footprinting studies to provide both high resolution atomic coordinates and verification of the solution state of the antigen, respectively. The crystal structure of HR1-54Q reveals a trimeric, coiled-coil six-helical bundle, which probably represents a postfusion form of gp41. The MPER portion extends from HR2 in continuation of a slightly bent long helix and is relatively flexible. The structures observed for the 2F5 and 4E10 epitopes agree well with existing structural data, and enzyme-linked immunosorbent assays indicate that the antigen binds well to antibodies that recognize the above epitopes. Hydroxyl radical-mediated protein footprinting of the antigen in solution reveals specifically protected and accessible regions consistent with the predictions based on the trimeric structure from the crystallographic data. Overall, the HR1-54Q antigen, as characterized by crystallography and footprinting, represents a postfusion, trimeric form of HIV gp41, and its structure provides a rational basis for gp41 antigen design suitable for HIV vaccine development. PMID:20525690

  3. Structural Characterization of HIV gp41 with the Membrane-proximal External Region

    Energy Technology Data Exchange (ETDEWEB)

    Shi, W.; Bohon, J; Han, D; Habte, H; Qin, Y; Cho, M; Chance, M

    2010-01-01

    Human immunodeficiency virus, type 1 (HIV-1) envelope glycoprotein (gp120/gp41) plays a critical role in virus infection and pathogenesis. Three of the six monoclonal antibodies considered to have broadly neutralizing activities (2F5, 4E10, and Z13e1) bind to the membrane-proximal external region (MPER) of gp41. This makes the MPER a desirable template for developing immunogens that can elicit antibodies with properties similar to these monoclonal antibodies, with a long term goal of developing antigens that could serve as novel HIV vaccines. In order to provide a structural basis for rational antigen design, an MPER construct, HR1-54Q, was generated for x-ray crystallographic and x-ray footprinting studies to provide both high resolution atomic coordinates and verification of the solution state of the antigen, respectively. The crystal structure of HR1-54Q reveals a trimeric, coiled-coil six-helical bundle, which probably represents a postfusion form of gp41. The MPER portion extends from HR2 in continuation of a slightly bent long helix and is relatively flexible. The structures observed for the 2F5 and 4E10 epitopes agree well with existing structural data, and enzyme-linked immunosorbent assays indicate that the antigen binds well to antibodies that recognize the above epitopes. Hydroxyl radical-mediated protein footprinting of the antigen in solution reveals specifically protected and accessible regions consistent with the predictions based on the trimeric structure from the crystallographic data. Overall, the HR1-54Q antigen, as characterized by crystallography and footprinting, represents a postfusion, trimeric form of HIV gp41, and its structure provides a rational basis for gp41 antigen design suitable for HIV vaccine development.

  4. Characterization of the genomic region containing the Shadow of Prion Protein (SPRN gene in sheep

    Directory of Open Access Journals (Sweden)

    Van Zeveren Alex

    2007-05-01

    Full Text Available Abstract Background TSEs are a group of fatal neurodegenerative diseases occurring in man and animals. They are caused by prions, alternatively folded forms of the endogenous prion protein, encoded by PRNP. Since differences in the sequence of PRNP can not explain all variation in TSE susceptibility, there is growing interest in other genes that might have an influence on this susceptibility. One of these genes is SPRN, a gene coding for a protein showing remarkable similarities with the prion protein. Until now, SPRN has not been described in sheep, a highly relevant species in prion matters. Results In order to characterize the genomic region containing SPRN in sheep, a BAC mini-contig was built, covering approximately 200,000 bp and containing the genes ECHS1, PAOX, MTG1, SPRN, LOC619207, CYP2E1 and at least partially SYCE1. FISH mapping of the two most exterior BAC clones of the contig positioned this contig on Oari22q24. A fragment of 4,544 bp was also sequenced, covering the entire SPRN gene and 1206 bp of the promoter region. In addition, the transcription profile of SPRN in 21 tissues was determined by RT-PCR, showing high levels in cerebrum and cerebellum, and low levels in testis, lymph node, jejunum, ileum, colon and rectum. Conclusion Annotation of a mini-contig including SPRN suggests conserved linkage between Oari22q24 and Hsap10q26. The ovine SPRN sequence, described for the first time, shows a high level of homology with the bovine, and to a lesser extent with the human SPRN sequence. In addition, transcription profiling in sheep reveals main expression of SPRN in brain tissue, as in rat, cow, man and mouse.

  5. Novel QTL at chromosome 6p22 for alcohol consumption: Implications for the genetic liability of alcohol use disorders.

    Science.gov (United States)

    Kos, Mark Z; Glahn, David C; Carless, Melanie A; Olvera, Rene; McKay, D Reese; Quillen, Ellen E; Gelernter, Joel; Chen, Xiang-Ding; Deng, Hong-Wen; Kent, Jack W; Dyer, Thomas D; Göring, Harald H H; Curran, Joanne E; Duggirala, Ravi; Blangero, John; Almasy, Laura

    2014-06-01

    Linkage studies of alcoholism have implicated several chromosome regions, leading to the successful identification of susceptibility genes, including ADH4 and GABRA2 on chromosome 4. Quantitative endophenotypes that are potentially closer to gene action than clinical endpoints offer a means of obtaining more refined linkage signals of genes that predispose alcohol use disorders (AUD). In this study we examine a self-reported measure of the maximum number of drinks consumed in a 24-hr period (abbreviated Max Drinks), a significantly heritable phenotype (h(2)  = 0.32 ± 0.05; P = 4.61 × 10(-14)) with a strong genetic correlation with AUD (ρg  = 0.99 ± 0.13) for the San Antonio Family Study (n = 1,203). Genome-wide SNPs were analyzed using variance components linkage methods in the program SOLAR, revealing a novel, genome-wide significant QTL (LOD = 4.17; P = 5.85 × 10(-6)) for Max Drinks at chromosome 6p22.3, a region with a number of compelling candidate genes implicated in neuronal function and psychiatric illness. Joint analysis of Max Drinks and AUD status shows that the QTL has a significant non-zero effect on diagnosis (P = 4.04 × 10(-3)), accounting for 8.6% of the total variation. Significant SNP associations for Max Drinks were also identified at the linkage region, including one, rs7761213 (P = 2.14 × 10(-4)), obtained for an independent sample of Chinese families. Thus, our study identifies a potential risk locus for AUD at 6p22.3, with significant pleiotropic effects on the heaviness of alcohol consumption that may not be population specific. PMID:24692236

  6. A Major QTL,Ghd8,Plays Pleiotropic Roles in Regulating Grain Productivity,Plant Height and Heading Date in Rice

    Institute of Scientific and Technical Information of China (English)

    Wen-Hao Yan; Yong-Zhong Xing; Qi-Fa Zhang; Peng Wang; Hua-Xia Chen; Hong-Ju Zhou; Qiu-Ping Li; Chong-Rong Wang; Ze-Hong Ding; Yu-Shan Zhang; Si-Bin Yu

    2011-01-01

    Rice yield and heading date are two distinct traits controlled by quantitative trait loci (QTLs). The dissection of molecular mechanisms underlying rice yield traits is important for developing high-yielding rice varieties. Here,we report the cloning and characterization of Ghd8,a major QTL with pleiotropic effects on grain yield,heading date,and plant height. Two sets of near isogenic line populations were developed for the cloning of Ghd8. Ghd8 was narrowed down to a 20-kb region containing two putative genes,of which one encodes the OsHAP3 subunit of a CCAAT-box binding protein (HAP complex);this gene was regarded as the Ghd8 candidate. A complementary test confirmed the identity and pleiotropic effects of the gene;interestingly,the genetic effect of Ghd8 was dependent on its genetic background. By regulating Ehd1,RFT1,and Hd3a,Ghd8 delayed flowering under long-day conditions,but promoted flowering under short-day conditions. Ghd8 up-regulated M0C1,a key gene controlling tillering and branching;this increased the number of tillers,primary and secondary branches,thus producing 50% more grains per plant. The ectopic expression of Ghd8 in Arabidopsis caused early flowering by 10 d-a situation similar to the one observed by its homolog AtHAP3b. When compared to wild-type under long-day conditions;these findings indicate the conserved function of Ghd8 and AtHAP3b in flowering in Arabidopsis. Our results demonstrated the important roles of Ghd8 in rice yield formation and flowering,as well as its opposite functions in flowering between rice and Arabidopsis under long-day conditions.

  7. CHARACTERIZATION AND CLASSIFICATION OF FLOODPLAIN SOILS IN THE PORTO ALEGRE METROPOLITAN REGION, RS, BRAZIL

    Directory of Open Access Journals (Sweden)

    Luís de França da Silva Neto

    2015-10-01

    Full Text Available ABSTRACTIn the Porto Alegre metropolitan region (PAMR there are a significant proportion of floodplain soils, mainly Planosols and Gleysols, in relation to upland soils. This study aimed to evaluate the morphological, chemical and physical characteristics, and to classify floodplain soils in the PAMR. Six soil profiles were evaluated under different sedimentary lithologies and drainage classes, and samples were collected for chemical and physical analyzes. Two orders of mineral soils (Planosols and Gleysols and one order of organic soil (Organosols were identified. The soils were moderately deep to deep and stratified. In mineral soils hue ranged between 7.5YR and 2.5Y, with the occurrence of Bg, Btg or Cg gley horizons, while in organic soil the colors were neutral. Sand and silt were the predominant particle sizes according to the origin sedimentary deposits. The organic carbon content was negatively related to soil density and positively related to soil specific surface area and with soil cation exchange capacity. Soil chemical characterization showed expressive variation in bases, aluminum and sodium saturation. Ki index and Fe(CBD/Fe(H2SO4 ratio indicated a low soil weathering degree. The different sedimentary lithologies and the soil hydromorphism degree were the main factors related to differences in morphological, physical and chemical characteristics of soils in the PAMR.

  8. PCR amplification and characterization of the intergenic spacer region of the ribosomal DNA in Pyrenophora graminea.

    Science.gov (United States)

    Pecchia, S; Mercatelli, E; Vannacci, G

    1998-09-01

    Successful amplification of the whole intergenic spacer region of the nuclear ribosomal repeat (IGS) in Pyrenophora graminea was obtained with a PCR-based assay. Single amplification products showed length differences. Depending on the length of the IGS-PCR product, ca. 3.8 or 4.4 kb, two groups of isolates could be identified. The RFLP patterns of isolates obtained with the 6-base cutting enzymes Apal, BglII, DraI, EcoRV, HindIII and SacI were similar within each group and different between the two groups. Restriction patterns of IGS-PCR products digested with the 4-base cutting enzyme AluI were polymorphic among isolates in spite of their IGS-PCR product length. In order to characterize the long and short IGS-PCR products the restriction map is shown. The long product shows an additional HindIII site and a BglII site that is lacking in the short product. However, the latter shows a SacI site that is not present in the long IGS-PCR product. Therefore, the described PCR-RFLP analysis of the IGS appears to be a useful tool to resolve genetic variation between P. graminea isolates. PMID:9741081

  9. Characterizing regulated reservoirs dynamics in regional to global scale hydrologic models

    Science.gov (United States)

    Beighley, E.; Yoon, Y.; Lee, H.; Pavelsky, T.; Allen, G. H.

    2015-12-01

    Lakes and reservoirs are widely used for water supply and flood control resulting in regulated release of outflows that are nonconcurrent with inflows. In hydrologic modeling applications, accounting for the regulated behavior of reservoirs distributed throughout a river system poses a significant challenge because detailed reservoir operation rules or strategies can be difficult or not possible to obtain. Building on this problem, this study addresses the science questions: Can we model reservoir water storage changes and outlet discharges based on satellite measurements of river water surface elevation and inundated area, and How does repeat cycle, mission duration and measurement uncertainty impact our ability to characterize reservoir behavior? A modeling framework suitable for regional to global applications and based on the forthcoming Surface Water and Ocean Topography (SWOT) satellite mission is presented. Although our framework can be combined with data assimilation techniques for real-time flood forecasting, our goal is to represent reservoir storage patterns in large-scale hydrologic models for simulating: (i) impacts of future climate and/or land cover conditions on water resources, and (ii) synthetic storm events (e.g., 100-yr flood) or event catalogs for flood hazard and risk assessments. In-situ and remotely sensed reservoir dynamics are presented for select locations in the Mississippi River Basin and used in the Hillslope River Routing (HRR) hydrologic model to simulate downstream flow dynamics.

  10. Characterization of the irradiation parameters in the IFMIF high flux test region

    Science.gov (United States)

    Daum, E.; Wilson, P. P. H.; Fischer, U.; Ehrlich, K.

    1998-10-01

    The purpose of the international fusion materials irradiation facility (IFMIF) is to provide typical D-T fusion irradiation conditions for future material testing and material development. In order to demonstrate the suitability of IFMIF for irradiation experiments a comprehensive characterization of the neutronics of the high flux test region (HFTR) has been carried out. For Fe, the neutron flux density was found to range between 4 × 10 14 and 10 15 n/s cm 2 which corresponds to 20-55 DPA/FPY in a maximum volume of 550 ± 180 cm 3. Gas production rates were calculated and a H/DPA ratio of 35-50 appm/DPA and a He/DPA ratio of 10-12 appm/DPA were found, which are very similar to those of a DEMO D-T fusion reactor. Additionally, an analysis of the primary knock-on spectra has been performed and a displacement damage characteristic in IFMIF almost ideal to the first wall of DEMO was found. IFMIF therefore provides an adequate environment for the simulation of D-T fusion reactor irradiation conditions.

  11. Characterization of the irradiation parameters in the IFMIF high flux test region

    International Nuclear Information System (INIS)

    The purpose of the international fusion materials irradiation facility (IFMIF) is to provide typical D-T fusion irradiation conditions for future material testing and material development. In order to demonstrate the suitability of IFMIF for irradiation experiments a comprehensive characterization of the neutronics of the high flux test region (HFTR) has been carried out. For Fe, the neutron flux density was found to range between 4 x 1014 and 1015 n/s cm2 which corresponds to 20-55 DPA/FPY in a maximum volume of 550 ± 180 cm3. Gas production rates were calculated and a H/DPA ratio of 35-50 appm/DPA and a He/DPA ratio of 10-12 appm/DPA were found, which are very similar to those of a DEMO D-T fusion reactor. Additionally, an analysis of the primary knock-on spectra has been performed and a displacement damage characteristic in IFMIF almost ideal to the first wall of DEMO was found. IFMIF therefore provides an adequate environment for the simulation of D-T fusion reactor irradiation conditions. (orig.)

  12. Application of PIXE to the characterization of vitreous dacites from archaeolgical sites in the Atacama region in northern Chile

    International Nuclear Information System (INIS)

    Geochemical characterization studies using PIXE were carried out on 21 vitreous dacite artifacts from early formative archaeological sites in the Atacama region, in northern Chile, and on 13 samples taken from two potential volcanic sources located within the region. Performing statistical analyses it was possible to obtain elemental concentration patterns for the archaeological samples of this material and match some of these artifacts with the geological source samples

  13. Application of PIXE to the characterization of vitreous dacites from archaeolgical sites in the Atacama region in northern Chile

    Energy Technology Data Exchange (ETDEWEB)

    Morales, J.R.; Cancino, S. [Departamento de Fisica, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Nunoa, Santiago 1 (Chile); Miranda, P. [Departamento de Fisica, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Nunoa, Santiago 1 (Chile)], E-mail: pjmirand@gmail.com; Dinator, M.I. [Departamento de Fisica, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Nunoa, Santiago 1 (Chile); Seelenfreund, A. [Universidad Academia de Humanismo Cristiano, Condell 343, Providencia, Santiago (Chile)

    2007-11-15

    Geochemical characterization studies using PIXE were carried out on 21 vitreous dacite artifacts from early formative archaeological sites in the Atacama region, in northern Chile, and on 13 samples taken from two potential volcanic sources located within the region. Performing statistical analyses it was possible to obtain elemental concentration patterns for the archaeological samples of this material and match some of these artifacts with the geological source samples.

  14. A mixed model QTL analysis for sugarcane multiple-harvest-location trial data.

    Science.gov (United States)

    Pastina, M M; Malosetti, M; Gazaffi, R; Mollinari, M; Margarido, G R A; Oliveira, K M; Pinto, L R; Souza, A P; van Eeuwijk, F A; Garcia, A A F

    2012-03-01

    Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane. PMID:22159754

  15. Plant DB link - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods Plant DB link Da... Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  16. Application of non-parametric bootstrap methods to estimate confidence intervals for QTL location in a beef cattle QTL experimental population.

    Science.gov (United States)

    Jongjoo, Kim; Davis, Scott K; Taylor, Jeremy F

    2002-06-01

    Empirical confidence intervals (CIs) for the estimated quantitative trait locus (QTL) location from selective and non-selective non-parametric bootstrap resampling methods were compared for a genome scan involving an Angus x Brahman reciprocal fullsib backcross population. Genetic maps, based on 357 microsatellite markers, were constructed for 29 chromosomes using CRI-MAP V2.4. Twelve growth, carcass composition and beef quality traits (n = 527-602) were analysed to detect QTLs utilizing (composite) interval mapping approaches. CIs were investigated for 28 likelihood ratio test statistic (LRT) profiles for the one QTL per chromosome model. The CIs from the non-selective bootstrap method were largest (87 7 cM average or 79-2% coverage of test chromosomes). The Selective II procedure produced the smallest CI size (42.3 cM average). However, CI sizes from the Selective II procedure were more variable than those produced by the two LOD drop method. CI ranges from the Selective II procedure were also asymmetrical (relative to the most likely QTL position) due to the bias caused by the tendency for the estimated QTL position to be at a marker position in the bootstrap samples and due to monotonicity and asymmetry of the LRT curve in the original sample. PMID:12220133

  17. Partial genetic characterization of Stearoyl Coa-Desaturase´s structural region in Bubalus bubalis

    Directory of Open Access Journals (Sweden)

    R.B. Thomazine

    2010-02-01

    Full Text Available Conjugated Linoleic Acids (CLAs comprise a family of positional and geometric isomers of linoleic acid. The main form of CLA, cis-9, trans-11-C18:2 show positive effects in cancer prevention and treatment. The major dietary sources of these fatty acids are derived from ruminant animals, in particular dairy products. In these animals, the endogenous synthesis mainly occurs in mammary gland by the action of enzyme Stearoyl CoA Desaturase (SCD. Different levels of expression and activity of SCD in mammary gland can explain partially the variation of CLA levels in fat milk. Considering a great fat concentration in bubaline milk and the benefit of a high and positive correlation between fat milk and CLA production, this study was carried on with the intention of sequencing and characterizing part of the gene that codifies SCD in buffaloes. Genomic DNA was extracted from blood samples of lactating bubaline which begins to the breed Murrah. After the (acho que nao precisa desse the extractions, PCR (Polymerase Chain Reaction reactions were made by using primers Z43D1 and E143F1. The fragments obtained in PCR were cloned into “T” vectors and transformed in competent cells DH10B line. After this, three samples of each fragment were sequenced from 5’ and 3’ extremities using a BigDye kit in an automatic sequencer. Sequences were edited in a consensus of each fragment and were submitted to BLAST-n / NCBI for similarity comparisions among other species. The sequence obtained with Z43D1 primers shows 938 bp enclosing exons 1 and 2 and intron 1. The primers E143F1 show 70 bp corresponding to exon 3 of bubaline SCD gene. Similarities were obtained between 85% and 97% among bubaline sequences and sequences of SCD gene described in human, mouse, rat, swine, bovine, caprine and ovine species. This study has permitted the identification and partial characterization of SCD codifing region in Bubalus bubalis specie.

  18. Regional hydrogeochemical groundwater characterization and Natural Arsenic occurrence in Upper Valtellina Valley (Central Italian Alps, Italy)

    Science.gov (United States)

    Pena Reyes, Fredy; Crosta, Giovanni B.; Frattini, Paolo; Basiricò, Stefano

    2015-04-01

    The aim of the research is the characterization of the alpine Upper Valtellina Valley (central Italian Alps, 800 km2) aquifers by means of hydrogeological, hydrogeochemical, As speciation, isotopic and whole-rock analyses. In particular, the main focus of the study was the understanding of the processes responsible for As release and mobilization into the groundwater. Historical chemical data from springs, wells, lakes, rivers and public fountains were collected from the Lombardy Region Health Agency (ASL) and implemented into a geodatabase. The available groundwater chemistry analyses (3050) from five municipalities (Bormio, Livigno, Valdidentro, Valdisotto and Valfurva) cover a relatively long time span between 1996 and 2011. Moreover, samples across the entire study area and covering one full hydrologic year 2012-2013 were collected during four different campaigns (June 2012, October 2012, May 2013, and September 2013) and analyzed . During these campaigns, water samples have been collected from both cold springs and thermal springs. The hydrogeochemistry of aquifers and superficial waters through the hydrologic year, and the long-term regional As distribution and time variability were analyzed. Although the studied springs belong to different catchments with different hydrochemical and lithological conditions, they present some typical characteristics: (1) the water types are dominated by dissolution of the main ions Ca - Mg and SO4-HCO3; (2) the Cl concentration is always very low, and poorly correlated with other ions; (3) the circulation time obtained from isotopic data ranges between 5 and 10 years for thermal springs and it is lower than 2 years for cold springs; (4) the average yearly temperatures (about 12°C for cold springs, and between 18°C and 42° for thermal springs) are nearly constant through the year; (5) dominant oxidizing environments have been observed for most of the cold springs and also for the thermal springs; (6) anthropogenic

  19. Cultivation and Characterization of Cynara Cardunculus for Solid Biofuels Production in the Mediterranean Region

    Directory of Open Access Journals (Sweden)

    Nicholas G. Danalatos

    2008-07-01

    Full Text Available Technical specifications of solid biofuels are continuously improved towards the development and promotion of their market. Efforts in the Greek market are limited, mainly due to the climate particularity of the region, which hinders the growth of suitable biofuels. Taking also into account the increased oil prices and the high inputs required to grow most annual crops in Greece, cardoon (Cynara cardunculus L. is now considered the most important and promising sources for solid biofuel production in Greece in the immediate future. The reason is that cardoon is a perennial crop of Mediterranean origin, well adapted to the xerothermic conditions of southern Europe, which can be utilized particularly for solid biofuel production. This is due to its minimum production cost, as this perennial weed may perform high biomass productivity on most soils with modest or without any inputs of irrigation and agrochemicals. Within this framework, the present research work is focused on the planning and analysis of different land use scenarios involving this specific energy crop and the combustion behaviour characterization for the solid products. Such land use scenarios are based on quantitative estimates of the crop’s production potential under specific soil-climatic conditions as well as the inputs required for its realization in comparison to existing conventional crops. Concerning its decomposition behaviour, devolatilisation and char combustion tests were performed in a non-isothermal thermogravimetric analyser (TA Q600. A kinetic analysis was applied and accrued results were compared with data already available for other lignocellulosic materials. The thermogravimetric analysis showed that the decomposition process of cardoon follows the degradation of other lignocellulosic fuels, meeting high burnout rates. This research work concludes that Cynara cardunculus, under certain circumstances, can be used as a solid biofuel of acceptable quality.

  20. Cultivation and characterization of Cynara Cardunculus for solid biofuels production in the Mediterranean region.

    Science.gov (United States)

    Grammelis, Panagiotis; Malliopoulou, Anastasia; Basinas, Panagiotis; Danalatos, Nicholas G

    2008-06-01

    Technical specifications of solid biofuels are continuously improved towards the development and promotion of their market. Efforts in the Greek market are limited, mainly due to the climate particularity of the region, which hinders the growth of suitable biofuels. Taking also into account the increased oil prices and the high inputs required to grow most annual crops in Greece, cardoon (Cynara cardunculus L.) is now considered the most important and promising sources for solid biofuel production in Greece in the immediate future. The reason is that cardoon is a perennial crop of Mediterranean origin, well adapted to the xerothermic conditions of southern Europe, which can be utilized particularly for solid biofuel production. This is due to its minimum production cost, as this perennial weed may perform high biomass productivity on most soils with modest or without any inputs of irrigation and agrochemicals. Within this framework, the present research work is focused on the planning and analysis of different land use scenarios involving this specific energy crop and the combustion behaviour characterization for the solid products. Such land use scenarios are based on quantitative estimates of the crop'sproduction potential under specific soil-climatic conditions as well as the inputs required for its realization in comparison to existing conventional crops. Concerning its decomposition behaviour, devolatilisation and char combustion tests were performed in a non-isothermal thermogravimetric analyser (TA Q600). A kinetic analysis was applied and accrued results were compared with data already available for other lignocellulosic materials. The thermogravimetric analysis showed that the decomposition process of cardoon follows the degradation of other lignocellulosic fuels, meeting high burnout rates. This research work concludes that Cynara cardunculus, under certain circumstances, can be used as a solid biofuel of acceptable quality. PMID:19325802

  1. Domestic water uses: Characterization of daily cycles in the north region of Portugal

    International Nuclear Information System (INIS)

    Nowadays, there is an increasing discussion among specialists about water use efficiency and the best measures to improve it. In Portugal, there have been a few attempts to expand the implementation of in situ water reuse projects. However, there is a lack of information about indoor water uses and how they are influenced by sociodemographic characteristics. There are several studies that investigate per capita global water usage, but the partitioning of this volume per domestic device and daily cycles is yet unknown. Identified as one of the key questions in sustainable building design, the water end-use is of primary importance to the design of hydraulic networks in buildings. In order to overcome this lack, a quantitative characterization of daily water uses for each domestic device was performed, based on a weekly monitoring program in fifty-two different dwellings in the northern region of Portugal (Vila Real, Valpaços and Oporto). For forty of them, each water usage of different domestic devices of each dwelling was recorded. At the same time, the remaining twelve dwellings were also monitored in order to register the volume of water consumed in each utilization of each domestic device. This paper presents the results of this complete monitoring program, using collected data to establish indoor water use patterns for each domestic device, aiming to support a more realistic approach to residential water use. The daily cycles in the different cities, where the monitoring program was performed, are also presented, in order to evaluate possible influences of sociodemographic characteristics. - Highlights: • This paper presents a method to find out the pattern of water use in dwellings. • The number of uses per person a day, by domestic device, is presented. • The volume spent per type of use by domestic device is presented. • The daily cycles per domestic device are presented. • Sociodemographic characteristics seem to affect the daily cycles

  2. Domestic water uses: Characterization of daily cycles in the north region of Portugal

    Energy Technology Data Exchange (ETDEWEB)

    Matos, Cristina, E-mail: crismato@utad.pt [ECT, University of Trás-os-Montes e Alto Douro (UTAD), Apartado 1013, 5001801 Vila Real (Portugal); Teixeira, Carlos A. [CITAB, University of Trás-os-Montes e Alto Douro, Apartado 1013, 5001-801 Vila Real Portugal (Portugal); Duarte, A.A.L.S. [Civil Engineering Department, University of Minho, Campus de Gualtar, 4710-057 Braga (Portugal); Bentes, I. [ECT, University of Trás-os-Montes e Alto Douro (UTAD), Apartado 1013, 5001801 Vila Real (Portugal)

    2013-08-01

    Nowadays, there is an increasing discussion among specialists about water use efficiency and the best measures to improve it. In Portugal, there have been a few attempts to expand the implementation of in situ water reuse projects. However, there is a lack of information about indoor water uses and how they are influenced by sociodemographic characteristics. There are several studies that investigate per capita global water usage, but the partitioning of this volume per domestic device and daily cycles is yet unknown. Identified as one of the key questions in sustainable building design, the water end-use is of primary importance to the design of hydraulic networks in buildings. In order to overcome this lack, a quantitative characterization of daily water uses for each domestic device was performed, based on a weekly monitoring program in fifty-two different dwellings in the northern region of Portugal (Vila Real, Valpaços and Oporto). For forty of them, each water usage of different domestic devices of each dwelling was recorded. At the same time, the remaining twelve dwellings were also monitored in order to register the volume of water consumed in each utilization of each domestic device. This paper presents the results of this complete monitoring program, using collected data to establish indoor water use patterns for each domestic device, aiming to support a more realistic approach to residential water use. The daily cycles in the different cities, where the monitoring program was performed, are also presented, in order to evaluate possible influences of sociodemographic characteristics. - Highlights: • This paper presents a method to find out the pattern of water use in dwellings. • The number of uses per person a day, by domestic device, is presented. • The volume spent per type of use by domestic device is presented. • The daily cycles per domestic device are presented. • Sociodemographic characteristics seem to affect the daily cycles.

  3. Learning of speckle statistics for in vivo and noninvasive characterization of cutaneous wound regions using laser speckle contrast imaging.

    Science.gov (United States)

    Basak, Kausik; Dey, Goutam; Mahadevappa, Manjunatha; Mandal, Mahitosh; Sheet, Debdoot; Dutta, Pranab Kumar

    2016-09-01

    Laser speckle contrast imaging (LSCI) provides a noninvasive and cost effective solution for in vivo monitoring of blood flow. So far, most of the researches consider changes in speckle pattern (i.e. correlation time of speckle intensity fluctuation), account for relative change in blood flow during abnormal conditions. This paper introduces an application of LSCI for monitoring wound progression and characterization of cutaneous wound regions on mice model. Speckle images are captured on a tumor wound region at mice leg in periodic interval. Initially, raw speckle images are converted to their corresponding contrast images. Functional characterization begins with first segmenting the affected area using k-means clustering, taking wavelet energies in a local region as feature set. In the next stage, different regions in wound bed are clustered based on progressive and non-progressive nature of tissue properties. Changes in contrast due to heterogeneity in tissue structure and functionality are modeled using LSCI speckle statistics. Final characterization is achieved through supervised learning of these speckle statistics using support vector machine. On cross evaluation with mice model experiment, the proposed approach classifies the progressive and non-progressive wound regions with an average sensitivity of 96.18%, 97.62% and average specificity of 97.24%, 96.42% respectively. The clinical information yield with this approach is validated with the conventional immunohistochemistry result of wound to justify the ability of LSCI for in vivo, noninvasive and periodic assessment of wounds. PMID:27131831

  4. QTL Mapping of Low-Temperature Germination Ability in the Maize IBM Syn4 RIL Population.

    Science.gov (United States)

    Hu, Shuaidong; Lübberstedt, Thomas; Zhao, Guangwu; Lee, Michael

    2016-01-01

    Low temperature is the primary factor to affect maize sowing in early spring. It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage. However, little is known about maize QTL involved in low-temperature germination ability. 243 lines of the intermated B73×Mo17 (IBM) Syn4 recombinant inbred line (RIL) population was used for QTL analysis of low-temperature germination ability. There were significant differences in germination-related traits under both conditions of low temperature (12°C/16h, 18°C/8h) and optimum temperature (28°C/24h) between the parental lines. Only three QTL were identified for controlling optimum-temperature germination rate. Six QTL controlling low-temperature germination rate were detected on chromosome 4, 5, 6, 7 and 9, and contribution rate of single QTL explained between 3.39%~11.29%. In addition, six QTL controlling low-temperature primary root length were detected in chromosome 4, 5, 6, and 9, and the contribution rate of single QTL explained between 3.96%~8.41%. Four pairs of QTL were located at the same chromosome position and together controlled germination rate and primary root length under low temperature condition. The nearest markers apart from the corresponding QTL (only 0.01 cM) were umc1303 (265.1 cM) on chromosome 4, umc1 (246.4 cM) on chromosome 5, umc62 (459.1 cM) on chromosome 6, bnl14.28a (477.4 cM) on chromosome 9, respectively. A total of 3155 candidate genes were extracted from nine separate intervals based on the Maize Genetics and Genomics Database (http://www.maizegdb.org). Five candidate genes were selected for analysis as candidates putatively affecting seed germination and seedling growth at low temperature. The results provided a basis for further fine mapping, molecular marker assisted breeding and functional study of cold-tolerance at the stage of seed germination in maize. PMID:27031623

  5. QTL Mapping of Low-Temperature Germination Ability in the Maize IBM Syn4 RIL Population.

    Directory of Open Access Journals (Sweden)

    Shuaidong Hu

    Full Text Available Low temperature is the primary factor to affect maize sowing in early spring. It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage. However, little is known about maize QTL involved in low-temperature germination ability. 243 lines of the intermated B73×Mo17 (IBM Syn4 recombinant inbred line (RIL population was used for QTL analysis of low-temperature germination ability. There were significant differences in germination-related traits under both conditions of low temperature (12°C/16h, 18°C/8h and optimum temperature (28°C/24h between the parental lines. Only three QTL were identified for controlling optimum-temperature germination rate. Six QTL controlling low-temperature germination rate were detected on chromosome 4, 5, 6, 7 and 9, and contribution rate of single QTL explained between 3.39%~11.29%. In addition, six QTL controlling low-temperature primary root length were detected in chromosome 4, 5, 6, and 9, and the contribution rate of single QTL explained between 3.96%~8.41%. Four pairs of QTL were located at the same chromosome position and together controlled germination rate and primary root length under low temperature condition. The nearest markers apart from the corresponding QTL (only 0.01 cM were umc1303 (265.1 cM on chromosome 4, umc1 (246.4 cM on chromosome 5, umc62 (459.1 cM on chromosome 6, bnl14.28a (477.4 cM on chromosome 9, respectively. A total of 3155 candidate genes were extracted from nine separate intervals based on the Maize Genetics and Genomics Database (http://www.maizegdb.org. Five candidate genes were selected for analysis as candidates putatively affecting seed germination and seedling growth at low temperature. The results provided a basis for further fine mapping, molecular marker assisted breeding and functional study of cold-tolerance at the stage of seed germination in maize.

  6. An efficient hierarchical generalized linear mixed model for mapping QTL of ordinal traits in crop cultivars.

    Directory of Open Access Journals (Sweden)

    Jian-Ying Feng

    Full Text Available Many important phenotypic traits in plants are ordinal. However, relatively little is known about the methodologies for ordinal trait association studies. In this study, we proposed a hierarchical generalized linear mixed model for mapping quantitative trait locus (QTL of ordinal traits in crop cultivars. In this model, all the main-effect QTL and QTL-by-environment interaction were treated as random, while population mean, environmental effect and population structure were fixed. In the estimation of parameters, the pseudo data normal approximation of likelihood function and empirical Bayes approach were adopted. A series of Monte Carlo simulation experiments were performed to confirm the reliability of new method. The result showed that new method works well with satisfactory statistical power and precision. The new method was also adopted to dissect the genetic basis of soybean alkaline-salt tolerance in 257 soybean cultivars obtained, by stratified random sampling, from 6 geographic ecotypes in China. As a result, 6 main-effect QTL and 3 QTL-by-environment interactions were identified.

  7. License - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods License License ...stered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods © Satoshi Tabata (Kazusa D...Update History of This Database Site Policy | Contact Us License - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  8. Genetic analysis of arsenic accumulation in maize using QTL mapping.

    Science.gov (United States)

    Fu, Zhongjun; Li, Weihua; Xing, Xiaolong; Xu, Mengmeng; Liu, Xiaoyang; Li, Haochuan; Xue, Yadong; Liu, Zonghua; Tang, Jihua

    2016-01-01

    Arsenic (As) is a toxic heavy metal that can accumulate in crops and poses a threat to human health. The genetic mechanism of As accumulation is unclear. Herein, we used quantitative trait locus (QTL) mapping to unravel the genetic basis of As accumulation in a maize recombinant inbred line population derived from the Chinese crossbred variety Yuyu22. The kernels had the lowest As content among the different maize tissues, followed by the axes, stems, bracts and leaves. Fourteen QTLs were identified at each location. Some of these QTLs were identified in different environments and were also detected by joint analysis. Compared with the B73 RefGen v2 reference genome, the distributions and effects of some QTLs were closely linked to those of QTLs detected in a previous study; the QTLs were likely in strong linkage disequilibrium. Our findings could be used to help maintain maize production to satisfy the demand for edible corn and to decrease the As content in As-contaminated soil through the selection and breeding of As pollution-safe cultivars. PMID:26880701

  9. QTL mapping and correlation analysis for 1000-grain weight and percentage of grains with chalkiness in rice

    Indian Academy of Sciences (India)

    Jian-Min Bian; Huan Shi; Cui-Juan Li; Chang-Lan Zhu; Qiu-Ying Yu; Xiao-Song Peng; Jun-Ru Fu; Xiao-Peng He; Xiao-Rong Chen; Li-Fang Hu; Lin-Juan Ouyang; Hao-Hua He

    2013-08-01

    The study of 1000-grain weight (TGW) and percentage of grains with chalkiness (PGWC) is very important in rice. In this study, a set of introgression lines (ILs), derived from Sasanishiki/Habataki with Sasanishiki as the recurrent parent, were used to detect correlations and quantitative trait loci (QTL) on TGW and PGWC in two different environments. Phenotypic correlation analysis showed that there was no significant correlation between TGW and PGWC in both environments, which indicated that the linkage of TGW and PGWC traits could be broken via suitable population. A total of 20 QTL were detected in both environments, nine QTL for 1000-paddy-grain weight (PTGW), five QTL for 1000-brown-grain weight (BTGW) and six QTL for percentage of grains with chalkiness (PGWC). Moreover, five QTL, qPTGW3, qPTGW8.2, qPTGW11.1 for PTGW and qPGWC1.1, qPGWC1.2 for PGWC, were stably expressed in both environments. Phenotypic values were significantly different ($P \\lt 0.01$) between the introgression lines carrying these five QTL alleles and the genetic background parent, Sasanishiki. The introgression lines carrying these QTL also represent a useful genetic resource in the context of rice yield and quality improvement via a design-breeding approach.

  10. Application of the BovineSNP50 assay for QTL mapping and prediction of genetic merit in Holstein cattle

    Science.gov (United States)

    The previous fifteen years have produced numerous QTL mapping experiments aimed at the identification of causal or linked polymorphisms for use in marker assisted selection programs to increase the rate of genetic gain in livestock species. To date, very few causal mutations for QTL have been ident...

  11. QTL analysis of ICA Bunsi-derived resistance to white mold in a pinto x navy bean cross

    Science.gov (United States)

    Breeding for genetic resistance to white mold [Sclerotinia sclerotiorum (Lib.) de Bary] in dry bean (Phaseolus vulgaris L.) is difficult because of low heritability. To facilitate breeding, researchers have sought to identify QTL underpinning genetic resistance to white mold. We identified two QTL ...

  12. Characterization of the regional variability of flood regimes within the Omo-Gibe River Basin, Ethiopia

    Science.gov (United States)

    Yared, Adanech; Demissie, Solomon S.; Sivapalan, Murugesu; Viglione, Alberto; MacAlister, Charlotte

    2014-05-01

    Hydrological variability and seasonality is one of the Ethiopia's primary water resource management challenges. Variability is most obviously manifest in endemic, devastating droughts and floods. While the level of flooding is quite often extremely high and destroys human beings and property, in many cases flooding is of vital importance because the community benefits from flood recession agriculture. This is the case of the lower Omo plain whose agriculture is based on the regularity of the inundations due to flooding of the Omo Gibe River. The big flood in 2006, which caused death for more than 300 people and 2000 cattle, poses a dilemma. Flooding must be controlled and regulated in a way that the damages are reduced as much as possible but the flooding-related benefits are not lost. To this aim, characterization and understanding of hydrological variability of the Omo Gibe River basin is fundamental. The goal of this work is to extract the maximal amount of information on the hydrological variability and specially on the flooding regime from the few data available in the region. Because most of the basin is ungauged, hydrological information is reconstructed using the data from 9 gauged catchments. A daily water balance model has been developed, calibrated and validated for 9 gauged catchments and, subsequently, the parameters have been correlated to catchment characteristics in order to establish a functional relationship that allows to apply the model to ungauged catchments. Daily streamflow has been predicted for 15 ungauged catchments, which are assumed to comprehensively represent the hydrological variability of the Omo-Gibe River Basin. Even though both northern and southern catchments are affected by a strong seasonality of precipitation, with most of the rain falling in less than 3 months, most of the northern catchments are humid, while in the southern part of the Omo-Gibe River basin, the catchments are either humid, dry sub humid, semiarid or arid. As

  13. Mapping of QTL for resistance to powdery mildew and resistance gene analogues in perennial ryegrass

    DEFF Research Database (Denmark)

    Schejbel, B; Jensen, L B; Asp, T; Xing, Y; Lübberstedt, T

    2008-01-01

    The objective of this study was to map resistance gene analogues (RGA) and quantitative trait loci (QTL) for powdery mildew resistance in perennial ryegrass (Lolium perenne L.). The mapping population consisted of 184 F2 genotypes produced from a cross between one genotype of a synthetic perennial...... the heritability was 71.7%. In total, two QTL for powdery mildew resistance were identified, and mapped to linkage groups (LG) LG3 and LG7. Individually, these QTL explained between 7.5% and 22.1% of the total phenotypic variation. Six RGA and three laccases were mapped to LG2, LG3, LG4, LG5 and LG7...

  14. Simultaneous estimation of QTL effects and positions when using genotype data with errors

    Indian Academy of Sciences (India)

    Liang Tong; Weijun Ma; Haidong Liu; Chaofeng Yuan; Ying Zhou

    2015-03-01

    Accurate genetic data are important prerequisite of performing genetic linkage test or association test. Currently, most analytical methods assume that the observed genotypes are correct. However, due to the constraint at the technical level, most of the genetic data that people used so far contain errors. In this paper, we considered the problem of QTL mapping based on biological data with genotyping errors. By analysing all possible genotypes of each individual in framework of multiple-interval mapping, we proposed an algorithm of inferring all model parameters through the expectation-maximization (EM) algorithm and discussed the hypothesis testing of the existence of QTL. We carried out extensive simulation studies to assess the proposed method. Simulation results showed that the new method outperforms the method that does not take the genotyping errors into account, and therefore it can decrease the impact of genotyping errors on QTL mapping. The proposed method was also applied to analyse a real barley dataset.

  15. Resistance to Downy Mildew in Lettuce 'La Brillante' is Conferred by Dm50 Gene and Multiple QTL.

    Science.gov (United States)

    Simko, Ivan; Ochoa, Oswaldo E; Pel, Mathieu A; Tsuchida, Cayla; Font I Forcada, Carolina; Hayes, Ryan J; Truco, Maria-Jose; Antonise, Rudie; Galeano, Carlos H; Michelmore, Richard W

    2015-09-01

    Many cultivars of lettuce (Lactuca sativa L.) are susceptible to downy mildew, a nearly globally ubiquitous disease caused by Bremia lactucae. We previously determined that Batavia type cultivar 'La Brillante' has a high level of field resistance to the disease in California. Testing of a mapping population developed from a cross between 'Salinas 88' and La Brillante in multiple field and laboratory experiments revealed that at least five loci conferred resistance in La Brillante. The presence of a new dominant resistance gene (designated Dm50) that confers complete resistance to specific isolates was detected in laboratory tests of seedlings inoculated with multiple diverse isolates. Dm50 is located in the major resistance cluster on linkage group 2 that contains at least eight major, dominant Dm genes conferring resistance to downy mildew. However, this Dm gene is ineffective against the isolates of B. lactucae prevalent in the field in California and the Netherlands. A quantitative trait locus (QTL) located at the Dm50 chromosomal region (qDM2.2) was detected, though, when the amount of disease was evaluated a month before plants reached harvest maturity. Four additional QTL for resistance to B. lactucae were identified on linkage groups 4 (qDM4.1 and qDM4.2), 7 (qDM7.1), and 9 (qDM9.2). The largest effect was associated with qDM7.1 (up to 32.9% of the total phenotypic variance) that determined resistance in multiple field experiments. Markers identified in the present study will facilitate introduction of these resistance loci into commercial cultivars of lettuce. PMID:25915441

  16. Identification of genetic loci associated with fire blight resistance in Malus through combined use of QTL and association mapping.

    Science.gov (United States)

    Khan, M Awais; Zhao, Youfu Frank; Korban, Schuyler S

    2013-07-01

    Fire blight, incited by the enterobacterium Erwinia amylovora, is a destructive disease of Rosaceae, particularly of apples and pears. There are reports on the molecular mechanisms underlying E. amylovora pathogenesis and how the host activates its resistance mechanism. The host's resistance mechanism is quantitatively controlled, although some major genes might also be involved. Thus far, quantitative trait loci (QTL) mapping and differential expression studies have been used to elucidate those genes and/or genomic regions underlying quantitative resistance present in the apple genome. In this study, an effort is undertaken to dissect the genetic basis of fire blight resistance in apple using both QTL and genome-wide association mapping. On the basis of an F1 pedigree of 'Coop 16' × 'Coop 17' and a genome-wide association study (GWAS) mapping population of Malus accessions (species, old and new cultivars and selections), new QTLs and associations have been identified. A total of three QTLs for resistance to fire blight, with above 95% significant logarithm of odds threshold value of 2.5, have been identified on linkage groups (LGs) 02, 06, and 15 of the apple genome with phenotypic variation explained values of 14.7, 20.1 and 17.4, respectively. Although elevated P-values with signals for marker-trait associations are observed for some LGs, these are not found to be significant. However, a total of 34 significant associations, with P-values ≥0.02, have been detected including 8 for lesion length at 7 days following inoculation (PL1), 14 for lesion length at 14 days following inoculation (PL2), and 12 for shoot length. PMID:23627651

  17. High-throughput phenotyping to detect drought tolerance QTL in wild barley introgression lines.

    Directory of Open Access Journals (Sweden)

    Nora Honsdorf

    Full Text Available Drought is one of the most severe stresses, endangering crop yields worldwide. In order to select drought tolerant genotypes, access to exotic germplasm and efficient phenotyping protocols are needed. In this study the high-throughput phenotyping platform "The Plant Accelerator", Adelaide, Australia, was used to screen a set of 47 juvenile (six week old wild barley introgression lines (S42ILs for drought stress responses. The kinetics of growth development was evaluated under early drought stress and well watered treatments. High correlation (r=0.98 between image based biomass estimates and actual biomass was demonstrated, and the suitability of the system to accurately and non-destructively estimate biomass was validated. Subsequently, quantitative trait loci (QTL were located, which contributed to the genetic control of growth under drought stress. In total, 44 QTL for eleven out of 14 investigated traits were mapped, which for example controlled growth rate and water use efficiency. The correspondence of those QTL with QTL previously identified in field trials is shown. For instance, six out of eight QTL controlling plant height were also found in previous field and glasshouse studies with the same introgression lines. This indicates that phenotyping juvenile plants may assist in predicting adult plant performance. In addition, favorable wild barley alleles for growth and biomass parameters were detected, for instance, a QTL that increased biomass by approximately 36%. In particular, introgression line S42IL-121 revealed improved growth under drought stress compared to the control Scarlett. The introgression line showed a similar behavior in previous field experiments, indicating that S42IL-121 may be an attractive donor for breeding of drought tolerant barley cultivars.

  18. High-throughput phenotyping to detect drought tolerance QTL in wild barley introgression lines

    KAUST Repository

    Honsdorf, Nora

    2014-05-13

    Drought is one of the most severe stresses, endangering crop yields worldwide. In order to select drought tolerant genotypes, access to exotic germplasm and efficient phenotyping protocols are needed. In this study the high-throughput phenotyping platform "The Plant Accelerator", Adelaide, Australia, was used to screen a set of 47 juvenile (six week old) wild barley introgression lines (S42ILs) for drought stress responses. The kinetics of growth development was evaluated under early drought stress and well watered treatments. High correlation (r = 0.98) between image based biomass estimates and actual biomass was demonstrated, and the suitability of the system to accurately and non-destructively estimate biomass was validated. Subsequently, quantitative trait loci (QTL) were located, which contributed to the genetic control of growth under drought stress. In total, 44 QTL for eleven out of 14 investigated traits were mapped, which for example controlled growth rate and water use efficiency. The correspondence of those QTL with QTL previously identified in field trials is shown. For instance, six out of eight QTL controlling plant height were also found in previous field and glasshouse studies with the same introgression lines. This indicates that phenotyping juvenile plants may assist in predicting adult plant performance. In addition, favorable wild barley alleles for growth and biomass parameters were detected, for instance, a QTL that increased biomass by approximately 36%. In particular, introgression line S42IL-121 revealed improved growth under drought stress compared to the control Scarlett. The introgression line showed a similar behavior in previous field experiments, indicating that S42IL-121 may be an attractive donor for breeding of drought tolerant barley cultivars. © 2014 Honsdorf et al.

  19. Morphological characterization of the nasopalatine region in human fetuses and its association to pathologies

    OpenAIRE

    Saulo Gabriel Moreira FALCI; Verli, Flaviana Dornela; CONSOLARO, Alberto; Cassio Roberto Rocha dos SANTOS

    2013-01-01

    The nasopalatine region is composed of structures such as the vomeronasal organ and nasopalatine duct. The nasopalatine duct may provide the communication of the mouth to the nasal cavity in human fetuses and can be obliterated in an adult human. Knowledge on the development of the nasopalatine region and nasopalatine duct in humans is necessary for understanding the morphology and etiopathogenesis of lesions that occur in this region. Objective The aim of the present study was...

  20. Identification of QTL genes for BMD variation using both linkage and gene-based association approaches

    OpenAIRE

    Li, Gloria Hoi-Yee; Cheung, Ching-Lung; Xiao, Su-Mei; Lau, Kam-Shing; Gao, Yi; Bow, Cora H.; Huang, Qing-Yang; Sham, Pak-Chung; Kung, Annie Wai-Chee

    2011-01-01

    Low bone mineral density (BMD) is a risk factor for osteoporotic fracture with a high heritability. Previous large scale linkage study in Northern Chinese has identified four significant quantitative trait loci (QTL) for BMD variation on chromosome 2q24, 5q21, 7p21 and 13q21. We performed a replication study of these four QTL in 1,459 Southern Chinese from 306 pedigrees. Successful replication was observed on chromosome 5q21 for femoral neck BMD with a LOD score of 1.38 (nominal p value = 0.0...

  1. A Statistical Framework for eQTL Mapping Using RNA-seq Data

    OpenAIRE

    Sun, Wei

    2011-01-01

    RNA-seq may replace gene expression microarrays in the near future. Using RNA-seq, the expression of a gene can be estimated using the total number of sequence reads mapped to that gene, known as the Total Read Count (TReC). Traditional eQTL mapping methods, such as linear regression, can be applied to TReC measurements after they are properly normalized. In this paper, we show that eQTL mapping, by directly modeling TReC using discrete distributions, has higher statistical power than the two...

  2. Identification of QTL for dorso-caudal chronic pleuritis in 12 crossbred porcine families

    DEFF Research Database (Denmark)

    Gregersen, V R; Sørensen, K K; Christensen, O F;

    2010-01-01

    loci (QTL) or markers associated with the prevalence of CP should be identified. In this study, 7470 pigs from crosses between 12 Danish Duroc boars and 604 sows (Danish Landrace × Danish Large White) were evaluated for CP located on the dorso-caudal part of the lungs. Quantitative trait loci were...... within families, the odds-ratio of having CP was approximately twice as high for the unfavourable allele compared to the favourable one. These QTL and closely linked markers show promise for the development of gene-specific markers associated with a reduced incidence of CP located on the dorso-caudal...

  3. Detection of two major grain yield QTL in bread wheat (Triticum aestivum L.) under heat, drought and high yield potential environments.

    Science.gov (United States)

    Bennett, Dion; Reynolds, Matthew; Mullan, Daniel; Izanloo, Ali; Kuchel, Haydn; Langridge, Peter; Schnurbusch, Thorsten

    2012-11-01

    A large proportion of the worlds' wheat growing regions suffers water and/or heat stress at some stage during the crop growth cycle. With few exceptions, there has been no utilisation of managed environments to screen mapping populations under repeatable abiotic stress conditions, such as the facilities developed by the International Wheat and Maize Improvement Centre (CIMMYT). Through careful management of irrigation and sowing date over three consecutive seasons, repeatable heat, drought and high yield potential conditions were imposed on the RAC875/Kukri doubled haploid population to identify genetic loci for grain yield, yield components and key morpho-physiological traits under these conditions. Two of the detected quantitative trait loci (QTL) were located on chromosome 3B and had a large effect on canopy temperature and grain yield, accounting for up to 22 % of the variance for these traits. The locus on chromosome arm 3BL was detected under all three treatments but had its largest effect under the heat stress conditions, with the RAC875 allele increasing grain yield by 131 kg ha(-1) (or phenotypically, 7 % of treatment average). Only two of the eight yield QTL detected in the current study (including linkage groups 3A, 3D, 4D 5B and 7A) were previously detected in the RAC875/Kukri doubled haploid population; and there were also different yield components driving grain yield. A number of discussion points are raised to understand differences between the Mexican and southern Australian production environments and explain the lack of correlation between the datasets. The two key QTL detected on chromosome 3B in the present study are candidates for further genetic dissection and development of molecular markers. PMID:22772727

  4. Fine mapping of Msv1, a major QTL for resistance to Maize Streak Virus leads to development of production markers for breeding pipelines.

    Science.gov (United States)

    Nair, Sudha K; Babu, Raman; Magorokosho, Cosmos; Mahuku, George; Semagn, Kassa; Beyene, Yoseph; Das, Biswanath; Makumbi, Dan; Lava Kumar, P; Olsen, Michael; Boddupalli, Prasanna M

    2015-09-01

    Msv1 , the major QTL for MSV resistance was delimited to an interval of 0.87 cM on chromosome 1 at 87 Mb and production markers with high prediction accuracy were developed. Maize streak virus (MSV) disease is a devastating disease in the Sub-Saharan Africa (SSA), which causes significant yield loss in maize. Resistance to MSV has previously been mapped to a major QTL (Msv1) on chromosome 1 that is germplasm and environment independent and to several minor loci elsewhere in the genome. In this study, Msv1 was fine-mapped through QTL isogenic recombinant strategy using a large F 2 population of CML206 × CML312 to an interval of 0.87 cM on chromosome 1. Genome-wide association study was conducted in the DTMA (Drought Tolerant Maize for Africa)-Association mapping panel with 278 tropical/sub-tropical breeding lines from CIMMYT using the high-density genotyping-by-sequencing (GBS) markers. This study identified 19 SNPs in the region between 82 and 93 Mb on chromosome 1(B73 RefGen_V2) at a P trend regression identified a haplotype block significantly associated with response to MSV. Three SNPs in this haplotype block at 87 Mb on chromosome 1 had an accuracy of 0.94 in predicting the disease reaction in a collection of breeding lines with known responses to MSV infection. In two biparental populations, selection for resistant Msv1 haplotype demonstrated a reduction of 1.03-1.39 units on a rating scale of 1-5, compared to the susceptible haplotype. High-throughput KASP assays have been developed for these three SNPs to enable routine marker screening in the breeding pipeline for MSV resistance. PMID:26081946

  5. Genome-wide association studies identifies seven major regions responsible for iron deficiency chlorosis in soybean (Glycine max.

    Directory of Open Access Journals (Sweden)

    Sujan Mamidi

    Full Text Available Iron deficiency chlorosis (IDC is a yield limiting problem in soybean (Glycine max (L. Merr production regions with calcareous soils. Genome-wide association study (GWAS was performed using a high density SNP map to discover significant markers, QTL and candidate genes associated with IDC trait variation. A stepwise regression model included eight markers after considering LD between markers, and identified seven major effect QTL on seven chromosomes. Twelve candidate genes known to be associated with iron metabolism mapped near these QTL supporting the polygenic nature of IDC. A non-synonymous substitution with the highest significance in a major QTL region suggests soybean orthologs of FRE1 on Gm03 is a major gene responsible for trait variation. NAS3, a gene that encodes the enzyme nicotianamine synthase which synthesizes the iron chelator nicotianamine also maps to the same QTL region. Disease resistant genes also map to the major QTL, supporting the hypothesis that pathogens compete with the plant for Fe and increase iron deficiency. The markers and the allelic combinations identified here can be further used for marker assisted selection.

  6. Characterization of Pseudomonas Species Isolated from the Rhizosphere of Plants Grown in Serozem Soil, Semi-Arid Region of Uzbekistan

    OpenAIRE

    Dilfuza Egamberdiyeva

    2005-01-01

    Collections of native Pseudomonas spp. are kept at the NCAM of Uzbekistan. Some of those organisms were isolated from the rhizosphere of cotton, wheat, corn, melon, alfalfa, and tomato grown in field locations within a semi-arid region of Uzbekistan. Strains used for this study were Pseudomonas alcaligenes, P. aurantiaca, P. aureofaciens, P. denitrificans, P. mendocina, P. rathonis, and P. stutzeri. Some of the pseudomonads have been characterized in this report. These strains produced enzyme...

  7. Neosols, relict paleosols, and alterites in the Transmexican Volcanic Belt, Morelos state: Characterization and regional spatial distribution

    OpenAIRE

    Jorge Enrique Gama Castro; David Flores Román; Elizabeth Solleiro Rebolledo; Carolina Jasso Castañeda; Ernestina Vallejo Gómez; Ana María Rocha Torrallardona; José Luis Villalpando González

    2004-01-01

    Investigations concerning the pedological linkages between modern soils and paleosequences, as well as the research regarding their spatial distribution and variability dynamics along the landscape are unfortunately very scarce. Both studies can provide, in a geochronological scale, a very useful paradigm to decipher the present and past biotic and abiotic environmental conditions that prevailed in many regions of the world. The aim of this paper is: (1) to characterize the environment as wel...

  8. Mapping and introgression of QTL for yield and related traits in two backcross populations derived from Oryza sativa cv. Swarna and two accessions of O. nivara

    Indian Academy of Sciences (India)

    B. P. Mallikarjuna Swamy; K. Kaladhar; G. Ashok Reddy; B. C. Viraktamath; N. Sarla

    2014-12-01

    Advanced backcross QTL (AB-QTL) analysis was carried out in two Oryza nivara-derived BC2F2 populations. For nine traits, we identified 28 QTL in population 1 and 26 QTL in population 2. The two most significant yield-enhancing QTL, yldp9.1 and yldp2.1 showed an additive effect of 16 and 7 g per plant in population 1, while yld2.1 and yld11.1 showed an additive effect of 11 and 10 g per plant in population 2. At least one O. nivara-derived QTL with a phenotypic variance of >15% was detected for seven traits in population 1 and three traits in population 2. The O. nivara-derived QTL ph1.1, nt12.1, nsp1.1, nfg1.1, bm11.1, yld2.1 and yld11.1 were conserved at the same chromosomal locations in both populations. Two major QTL clusters were detected at the marker intervals RM488–RM431 and RM6–RM535 on chromosomes 1 and 2, respectively. The colocation of O. nivara-derived yield QTL with yield meta-QTL on chromosomes 1, 2 and 9 indicates their accuracy and consistency. The major-effect QTL reported in this study are useful for marker-assisted breeding and are also suitable for further fine mapping and candidate gene identification.

  9. QTL identification of grain protein concentration and its genetic correlation with starch concentration and grain weight using two populations in maize (Zea mays L.)

    Indian Academy of Sciences (India)

    Yuling Li; Yanzhao Wang; Mengguan Wei; Xuehui Li; Jiafeng Fu

    2009-04-01

    Protein is one of the three main storage chemical components in maize grains, and is negatively correlated with starch concentration (SC). Our objective was to analyse the influence of genetic backgrounds on QTL detection for protein concentration (PC) and to reveal the molecular genetic associations between PC and both SC and grain weight (GWP). Two hundred and eighty-four (Pop1) and 265 (Pop2) F2:3 families were developed from two crosses between one high-oil maize inbred GY220 and two normal maize inbreds 8984 and 8622 respectively, and were genotyped with 185 and 173 pairs of SSR markers. PC, SC and GWP were evaluated under two environments. Composite interval mapping (CIM) and multiple interval mapping (MIM) methods were used to detect single-trait QTL for PC, and multiple-trait QTL for PC with both SC and GWP. No common QTL were shared between the two populations for their four and one PC QTL. Common QTL with opposite signs of effects for PC and SC/GWP were detected on three marker intervals at bins 6.07–6.08, 8.03 and 8.03–8.04. Multiple-traits QTL mapping showed that tightly-linked QTL, pleiotropic QTL and QTL having effects with opposite directions for PC and SC/GWP were all observed in Pop1, while all QTL reflected opposite effects in Pop2.

  10. Mapping main, epistatic and sex-specific QTL for body composition in a chicken population divergently selected for low or high growth rate

    Directory of Open Access Journals (Sweden)

    Vignal Alain

    2010-02-01

    Full Text Available Abstract Background Delineating the genetic basis of body composition is important to agriculture and medicine. In addition, the incorporation of gene-gene interactions in the statistical model provides further insight into the genetic factors that underlie body composition traits. We used Bayesian model selection to comprehensively map main, epistatic and sex-specific QTL in an F2 reciprocal intercross between two chicken lines divergently selected for high or low growth rate. Results We identified 17 QTL with main effects across 13 chromosomes and several sex-specific and sex-antagonistic QTL for breast meat yield, thigh + drumstick yield and abdominal fatness. Different sets of QTL were found for both breast muscles [Pectoralis (P major and P. minor], which suggests that they could be controlled by different regulatory mechanisms. Significant interactions of QTL by sex allowed detection of sex-specific and sex-antagonistic QTL for body composition and abdominal fat. We found several female-specific P. major QTL and sex-antagonistic P. minor and abdominal fatness QTL. Also, several QTL on different chromosomes interact with each other to affect body composition and abdominal fatness. Conclusions The detection of main effects, epistasis and sex-dimorphic QTL suggest complex genetic regulation of somatic growth. An understanding of such regulatory mechanisms is key to mapping specific genes that underlie QTL controlling somatic growth in an avian model.

  11. 通过构建单染色体片段代换系验证水稻细菌性条斑病抗性QTL qBlsr3d%Verification of QTL qBlsr3d Conferring Resistance to Bacterial Leaf Streak in Rice by Constructing SSSL

    Institute of Scientific and Technical Information of China (English)

    曹金良; 陈志伟; 林德塨; 吴为人; 谢小芳

    2014-01-01

    单染色体片段代换系是QTL精细定位的理想材料。水稻对细菌性条斑病的抗性属于典型的数量抗性。本研究以课题组构建的携有多个细条病抗性QTL (qBlsr3d, qBlsr5a和qBlsr5b)的近等基因系H359R为供体亲本,以感病品种H359为受体亲本,通过杂交,多次回交和自交,并结合分子标记辅助选择,成功构建了仅携有QTL qBlsr3d的单染色体片段代换系,命名为H359-BLSR3D。进一步通过分子标记定位分析表明:渗入区段位于第3号染色体分子标记3DSSR3和3DSSR12之间,物理距离约为1250 kb。田间接种鉴定表明:H359-BLSR3D与感病亲本H359间的细条病抗性差异显著,结果证明了抗性QTL qBlsr3d的真实存在。H359-BLSR3D将为QTL qBlsr3d的精细定位和最终克隆奠定基础。%Chromosome segment substitution line (CSSL) is an ideal material for fine mapping of QTL. Bacterial leaf steak (BLS) resistance in rice is quantitatively inherited. In the present study, using near-isogenic lines H359R with multi-resistant QTLs (qBlsr3d, qBlsr5a, qBlsr5b) as the donor parent (constructed by our group previous) and H359 as the recurrent parent, by cross, back-cross, self-cross and marker-based selection, single segment substitution line (SSSL) with qBlsr3d was developed. Further mapping showed that:the target fragment is located within a 1 250 kb region between markers 3DSSR3 and 3DSSR12 on chromosome 3. Inoculation experiment showed that the resistrance was statistically significant between H359-BLSR3D and H359, the result testify that QTL qBlsr3d is truly exsit. H359-BLSR3D would provide the basis for QTL qBlsr3d fine mapping and its final cloning.

  12. Naturally occurring clay nanoparticles in Latosols of Brazil central region: detection and characterization

    Science.gov (United States)

    Dominika Dybowska, Agnieszka; Luciene Maltoni, Katia; Piella, Jordi; Najorka, Jens; Puntes, Victor; Valsami-Jones, Eugenia

    2015-04-01

    Stability and reactivity of minerals change as a particle size function, which makes mineral nanoparticles (defined here as mineral nanoparticles contribute to many biogeochemical processes, however much remains to be learnt about these materials, their size dependent behavior and environmental significance. Advances in analytical, imaging and spectroscopic techniques made it now possible to study such particles; however we still have limited knowledge of their chemical, structural and morphological identity and reactivity, in particular in soils. The aim of this research was to characterize the naturally occurring nanoparticles in three soils from Brazil central region. The samples were collected in the A horizon, treated with H2O2 to remove organic material, dispersed in ultrasonic bath and wet sieved (53 µm) to remove the sand fraction. The clay fraction was collected by siphoning the supernatant, conditioned in 1000 ml cylinder, according to the Stock's law. This fraction was further processed by re-suspension in water, sonication and repeated centrifugation, to separate the fraction smaller than 100nm. This material, called here the soil "nanofraction", was analyzed using a range of techniques: 1) nanoparticle size/morphology and crystallinity with Transmission Electron Microscopy (TEM operateing in scanning (HAADF-STEM) and High Resolution (HRTEM) mode), 2) size distribution in water with Dynamic Light Scattering (DLS) and surface charge estimated from electrophoretic mobility measurements 3) crystal phase and crystallite size with X-ray Diffraction (XRD) 4) Chemical composition by quantitative analysis of elements (e.g., Si, Fe, Al, Ti) and their spatial distribution with HRTEM/EDS elemental mappings. The nanofraction had an average hydrodynamic particle diameter ranging from 83 to 92nm with a low polydispersity index of 0.13-0.17 and was found highly stable in aqueous suspension (no change in average particle size up to several months of storage). Particle

  13. Characterization of temperature profiles in the outer region of RFX-mod

    International Nuclear Information System (INIS)

    The onset of helical states has been shown to strongly affect the transport properties and the plasma performance of both the core region (|R − R0|/a ≲ 0.5) and the plasma edge (|R − R0|/a ≳ 0.95) in the RFX-mod reversed field pinch experiment. Both regions have been widely investigated and a strong effort is still dedicated to deepening the comprehension of the phenomena affecting them. Conversely, the region bounded between the plasma core and the plasma edge (0.6 ≲ |R − R0|/a ≲ 0.95) has been poorly analyzed, despite the large plasma volume enclosed in this domain. Improvements in RFX-mod global plasma performance are thus closely linked to the identification of the physical mechanisms occurring in this region, referred to as the outer region. A specifically conceived method of analysis, which gathers together data from a Thomson scattering system and two edge temperature diagnostics, allows the study of the entire temperature profile of RFX-mod. A statistical analysis performed on a large discharge database shows that the temperature profile in the central region of the plasma column is mainly established by the plasma current and the degree of stochasticity of the magnetic field. On the other hand, the temperature profile in the outer plasma region is found to vary with electron density and plasma equilibrium. (paper)

  14. CHARACTERIZATION OF PRECIPITATION EXTREMES AND TRENDS IN TWO REGIONS OF NORTH AFRICA

    Directory of Open Access Journals (Sweden)

    ZEINEDDINE N.

    2015-03-01

    Full Text Available To identify extreme precipitation, we use the “Standardized Precipitation Index” (SPI method designed to determine periods of climatic drought. This research attempts to assess the synchronization of cycles of precipitation and trends in two regions of the Mediterranean basin, the Soummam Valley (north - east of Algeria and the Cap Bon which forming a peninsula in north-east Tunisia. The results show a severe climate drought observed in these regions from the late eighties and a rainfall return observed at end of the series ( but more confirmed in the Cap Bon region.

  15. QTL Analysis of Forage Quantity and Quality-Related Traits of Barley

    Directory of Open Access Journals (Sweden)

    M Naghavi

    2009-04-01

    Full Text Available In order to map the genomic regions affecting barley forage quantity and quality, two experiments were conducted with 72 doubled haploid lines and their two parents (‘Steptoe’ and ‘Morex’, at the Research Farms of the Faculty of Crop and Animal Sciences, University College of Agriculture and Natural Resources, University of Tehran and Agriculture and Natural Resources Research Station of Sistan, in 2007. The experiments were arranged in a randomized complete block design with two replications. Each plot consisted of six rows that were 3m in length and spaced 25cm apart. QTL analysis was conducted by Composite interval mapping (CIM method separately for each trait in each location. The main effect of genotype was high significant for all the studied traits. Transgressive segregation in both directions (positive and negative was observed for all the studied traits. There was a negative relationship between forage qualityrelated with quantity-related traits. Thirty-three QTLs controlling different studied traits were identified. Phenotypic variance explained by these QTLs varies from 7.07 to 39.04%. Highest LOD scores were obtained for the leaf to stem ratio on chromosome 2H. QTLs of forage quality (total digestible nutrient, dry organic matter digestibility, leaf to stem ratio, seed to forage ratio and number of tiller per plant and quantity (plant height, forage wet and dry matter indexes were found on chromosomes 1H, 2H, 3H, 4H, 5H, 6H and 7H. Most of mapped QTLs appear to be fairly stable between locations and can become candidates for marker-assisted selection.

  16. Mapping quantitative trait loci (QTL) in sheep. II. Meta-assembly and identification of novel QTL for milk production traits in sheep

    OpenAIRE

    Lam Mary K; Hobbs Matthew; McGill David; Jonas Elisabeth; Raadsma Herman W; Thomson Peter C

    2009-01-01

    Abstract An (Awassi × Merino) × Merino backcross family of 172 ewes was used to map quantitative trait loci (QTL) for different milk production traits on a framework map of 200 loci across all autosomes. From five previously proposed mathematical models describing lactation curves, the Wood model was considered the most appropriate due to its simplicity and its ability to determine ovine lactation curve characteristics. Derived milk traits for milk, fat, protein and lactose yield, as well as ...

  17. Socio-economic characterization of olive groves in a region in the south of Portugal

    OpenAIRE

    Freitas, Maria de Belém; Simão, B. N. J.; Neves, M. A. R.; Lucas, M. R. V.

    2007-01-01

    Serpa and Moura region, in the South of Portugal, have important agricultural potential as well as important agricultural resources that can and should be used and developed, in spite of economic and social depression signs reinforced by demographic difficulties that can lead to desertification in some areas. The main farms' Technical-Economic Orientation (TEO) is olives production, to produce olive oil, since this region has excellent conditions for the activity development. Some mobilizatio...

  18. Coal and energy: a southern perspective. Regional characterization report for the National Coal Utilization Assessment

    Energy Technology Data Exchange (ETDEWEB)

    Boercker, F. D.; Davis, R. M.; Goff, F. G.; Olson, J. S.; Parzyck, D. C.

    1977-08-01

    This publication is the first of several reports to be produced for the National Coal Utilization Assessment, a program sponsored by the Assistant Administrator for Environment and Safety through the Division of Technology Overview of ERDA. The purpose of the report is to present the state and regional perspective on energy-related issues, especially those concerning coal production and utilization for 12 southern states. This report compiles information on the present status of: (1) state government infrastructure that deals with energy problems; (2) the balance between energy consumption and energy production; (3) the distribution of proved reserves of various mineral energy resources; (4) the major characteristics of the population; (5) the important features of the environment; and (6) the major constraints to increased coal production and utilization as perceived by the states and regional agencies. Many energy-related characteristics described vary significantly from state to state within the region. Regional and national generalizations obscure these important local variations. The report provides the state and regional perspective on energy issues so that these issues may be considered objectively and incorporated into the National Coal Utilization Assessment. This Assessment is designed to provide useful outputs for national, regional, and local energy planners.

  19. Genic SNP markers and legume synteny reveal candidate genes underlying QTL for Macrophomina phaseolina resistance and maturity in cowpea [Vigna unguiculata (L Walp.

    Directory of Open Access Journals (Sweden)

    Ehlers Jeffrey D

    2011-01-01

    Full Text Available Abstract Background Macrophomina phaseolina is an emerging and devastating fungal pathogen that causes significant losses in crop production under high temperatures and drought stress. An increasing number of disease incidence reports highlight the wide prevalence of the pathogen around the world and its contribution toward crop yield suppression. In cowpea [Vigna unguiculata (L Walp.], limited sources of low-level host resistance have been identified, the genetic basis of which is unknown. In this study we report on the identification of strong sources of host resistance to M. phaseolina and the genetic mapping of putative resistance loci on a cowpea genetic map comprised of gene-derived single nucleotide polymorphisms (SNPs and amplified fragment length polymorphisms (AFLPs. Results Nine quantitative trait loci (QTLs, accounting for between 6.1 and 40.0% of the phenotypic variance (R2, were identified using plant mortality data taken over three years in field experiments and disease severity scores taken from two greenhouse experiments. Based on annotated genic SNPs as well as synteny with soybean (Glycine max and Medicago truncatula, candidate resistance genes were found within mapped QTL intervals. QTL Mac-2 explained the largest percent R2 and was identified in three field and one greenhouse experiments where the QTL peak co-located with a SNP marker derived from a pectin esterase inhibitor encoding gene. Maturity effects on the expression of resistance were indicated by the co-location of Mac-6 and Mac-7 QTLs with maturity-related senescence QTLs Mat-2 and Mat-1, respectively. Homologs of the ELF4 and FLK flowering genes were found in corresponding syntenic soybean regions. Only three Macrophomina resistance QTLs co-located with delayed drought-induced premature senescence QTLs previously mapped in the same population, suggesting that largely different genetic mechanisms mediate cowpea response to drought stress and Macrophomina infection

  20. Use of the EM algorithm to detect QTL affecting multiple-traits in an across half-sib family analysis

    Directory of Open Access Journals (Sweden)

    McLachlan GM

    2005-01-01

    Full Text Available Abstract QTL detection experiments in livestock species commonly use the half-sib design. Each male is mated to a number of females, each female producing a limited number of progeny. Analysis consists of attempting to detect associations between phenotype and genotype measured on the progeny. When family sizes are limiting experimenters may wish to incorporate as much information as possible into a single analysis. However, combining information across sires is problematic because of incomplete linkage disequilibrium between the markers and the QTL in the population. This study describes formulæ for obtaining MLEs via the expectation maximization (EM algorithm for use in a multiple-trait, multiple-family analysis. A model specifying a QTL with only two alleles, and a common within sire error variance is assumed. Compared to single-family analyses, power can be improved up to fourfold with multi-family analyses. The accuracy and precision of QTL location estimates are also substantially improved. With small family sizes, the multi-family, multi-trait analyses reduce substantially, but not totally remove, biases in QTL effect estimates. In situations where multiple QTL alleles are segregating the multi-family analysis will average out the effects of the different QTL alleles.

  1. Study of the possibilities of using nuclear methods for characterizing the surface region of glasses

    International Nuclear Information System (INIS)

    Following a review of the different methods used for the analysis of surfaces, we give a detailed description of charged particle elastic backscattering and the experimental devices. We then apply this method to the study of the lixiviation of borosilicate glasses in aqueous media and to the characterization of two heavy elements, cerium and thorium and their possible interaction in simple borosilicates

  2. Characterization of Dermanyssus gallinae (Acarina: Dermanissydae) by sequence analysis of the ribosomal internal transcribed spacer regions.

    Science.gov (United States)

    Potenza, L; Cafiero, M A; Camarda, A; La Salandra, G; Cucchiarini, L; Dachà, M

    2009-10-01

    In the present work mites previously identified as Dermanyssus gallinae De Geer (Acari, Mesostigmata) using morphological keys were investigated by molecular tools. The complete internal transcribed spacer 1 (ITS1), 5.8S ribosomal DNA, and ITS2 region of the ribosomal DNA from mites were amplified and sequenced to examine the level of sequence variations and to explore the feasibility of using this region in the identification of this mite. Conserved primers located at the 3'end of 18S and at the 5'start of 28S rRNA genes were used first, and amplified fragments were sequenced. Sequence analyses showed no variation in 5.8S and ITS2 region while slight intraspecific variations involving substitutions as well as deletions concentrated in the ITS1 region. Based on the sequence analyses a nested PCR of the ITS2 region followed by RFLP analyses has been set up in the attempt to provide a rapid molecular diagnostic tool of D. gallinae. PMID:19214768

  3. QTL with dominance effect affecting residual feed intake on BTA6

    Science.gov (United States)

    Residual feed intake (RFI) is a measure of feed efficiency and therefore an economically relevant trait. A genome-wide scan for quantitative trait loci (QTL) affecting RFI in beef cattle was conducted. Approximately equally spaced microsatellite markers (n = 229) spanned the 29 bovine autosomes. Tw...

  4. Association analyses of four genes within QTL for meat quality on q arm of SSC2

    Czech Academy of Sciences Publication Activity Database

    Čepica, Stanislav; Óvilo, C.; Masopust, Martin; Knoll, Aleš; Fernández, A.; López, A.; Rohrer, G. A.; Nonneman, D.

    Edinburgh : International Society for Animal Getics, 2010. s. 111-111. [32nd Conference of the International Society for Animal Genetics. 26.07.2010 - 30.07.2010, Edinburgh] R&D Projects: GA ČR GAP502/10/1216 Institutional research plan: CEZ:AV0Z50450515 Keywords : meat quality * QTL * IMF Subject RIV: GI - Animal Husbandry ; Breeding

  5. High Resolution QTL Maps Of 31 Traits in Contemporary U.S. Holstein Cows

    Science.gov (United States)

    High-resolution QTL maps of 1586 SNPs affecting 31 dairy traits (top 100 effects per trait)were constructed based on a genome-wide association analysis of 1,654 contemporary U.S. Holstein cows genotyped with 45,878 SNPs. The 31 traits include net merit and its 8 compnent traits, 4 calving traits, an...

  6. Freezing tolerance-associated QTL in the Brundage × Coda wheat recombinant inbred line population

    Science.gov (United States)

    Freezing tolerance is an essential trait for winter wheat (Triticum aestivum L.) cultivars. A genetic analysis of a Brundage × Coda winter wheat recombinant inbred line (RIL) mapping population was undertaken to identify quantitative trait loci (QTL) associated with freezing tolerance. Five- to six...

  7. Genome scan for parent-of-origin QTL effects on bovine growth and carcass traits

    NARCIS (Netherlands)

    Imumorin, I.G.; Kim, B.; Li, Y.; Koning, de D.J.; Arendonk, van J.A.M.; Donato, S.

    2011-01-01

    Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We ident

  8. Zero-inflated Poisson regression models for QTL mapping applied to tick-resistance in a Gyr × Holstein F2 population.

    Science.gov (United States)

    Silva, Fabyano Fonseca; Tunin, Karen P; Rosa, Guilherme J M; da Silva, Marcos V B; Azevedo, Ana Luisa Souza; da Silva Verneque, Rui; Machado, Marco Antonio; Packer, Irineu Umberto

    2011-10-01

    Now a days, an important and interesting alternative in the control of tick-infestation in cattle is to select resistant animals, and identify the respective quantitative trait loci (QTLs) and DNA markers, for posterior use in breeding programs. The number of ticks/animal is characterized as a discrete-counting trait, which could potentially follow Poisson distribution. However, in the case of an excess of zeros, due to the occurrence of several noninfected animals, zero-inflated Poisson and generalized zero-inflated distribution (GZIP) may provide a better description of the data. Thus, the objective here was to compare through simulation, Poisson and ZIP models (simple and generalized) with classical approaches, for QTL mapping with counting phenotypes under different scenarios, and to apply these approaches to a QTL study of tick resistance in an F2 cattle (Gyr × Holstein) population. It was concluded that, when working with zero-inflated data, it is recommendable to use the generalized and simple ZIP model for analysis. On the other hand, when working with data with zeros, but not zero-inflated, the Poisson model or a data-transformation-approach, such as square-root or Box-Cox transformation, are applicable. PMID:22215960

  9. Zero-inflated Poisson regression models for QTL mapping applied to tick-resistance in a Gyr x Holstein F2 population

    Directory of Open Access Journals (Sweden)

    Fabyano Fonseca Silva

    2011-01-01

    Full Text Available Nowadays, an important and interesting alternative in the control of tick-infestation in cattle is to select resistant animals, and identify the respective quantitative trait loci (QTLs and DNA markers, for posterior use in breeding programs. The number of ticks/animal is characterized as a discrete-counting trait, which could potentially follow Poisson distribution. However, in the case of an excess of zeros, due to the occurrence of several noninfected animals, zero-inflated Poisson and generalized zero-inflated distribution (GZIP may provide a better description of the data. Thus, the objective here was to compare through simulation, Poisson and ZIP models (simple and generalized with classical approaches, for QTL mapping with counting phenotypes under different scenarios, and to apply these approaches to a QTL study of tick resistance in an F2 cattle (Gyr x Holstein population. It was concluded that, when working with zero-inflated data, it is recommendable to use the generalized and simple ZIP model for analysis. On the other hand, when working with data with zeros, but not zero-inflated, the Poisson model or a data-transformation-approach, such as square-root or Box-Cox transformation, are applicable.

  10. Comparative mapping reveals similar linkage of functional genes to QTL of yield-related traits between Brassica napus and Oryza sativa

    Indian Academy of Sciences (India)

    Fupeng Li; Chaozhi Ma; Qingfang Chen; Touming Liu; Jinxiong Shen; Jinxing Tu; Yongzhong Xing; Tingdong Fu

    2012-08-01

    Oryza sativa and Brassica napus—two important crops for food and oil, respectively—share high seed yield as a common breeding goal. As a model plant, O. sativa genomics have been intensively investigated and its agronomic traits have been advanced. In the present study, we used the available information on O. sativa to conduct comparative mapping between O. sativa and B. napus, with the aim of advancing research on seed-yield and yield-related traits in B. napus. Firstly, functional markers (from 55 differentially expressed genes between a hybrid and its parents) were used to detect B. napus genes that co-localized with yield-related traits in an F2∶3 population. Referring to publicly available sequences of 55 B. napus genes, 53 homologous O. sativa genes were subsequently detected by screening, and their chromosomal locations were determined using silico mapping. Comparative location of yield-related QTL between the two species showed that a total of 37 O. sativa and B. napus homologues were located in similar yield-related QTL between species. Our results indicate that homologous genes between O. sativa and B. napus may have consistent function and control similar traits, which may be helpful for agronomic gene characterization in B. napus based on what is known in O. sativa.

  11. Characterization of residual biomass from the Arequipa region for the production of biofuels

    Directory of Open Access Journals (Sweden)

    María Laura Stronguiló Leturia

    2015-12-01

    Full Text Available The aim of this work is to select residual biomass from the Arequipa Region for the production of biofuels (biodiesel, bioethanol and biogas. In each case, the initial point is a matrix based on products with residual biomass available in the region, from the agricultural and livestock sectors, information that was obtained from the regional Management of Agriculture web site. Specific factors of the resudue that will be used as raw material for each biofuel production would be considered for the selection process. For the production of biodiesel it is necessary to start from the oil extracted from oilseeds. Regarding obtaining bioethanol, it requires that the residual biomass has high percent of cellulose. With regard to the generation of biogas, we will use animal droppings. Finally, the raw materials selected are: squash and avocado seeds for biodiesel, rice chaff and deseeded corncob for bioethanol and cow and sheep droppings for biogas

  12. Morphological characterization of the nasopalatine region in human fetuses and its association to pathologies

    Directory of Open Access Journals (Sweden)

    Saulo Gabriel Moreira FALCI

    2013-06-01

    Full Text Available The nasopalatine region is composed of structures such as the vomeronasal organ and nasopalatine duct. The nasopalatine duct may provide the communication of the mouth to the nasal cavity in human fetuses and can be obliterated in an adult human. Knowledge on the development of the nasopalatine region and nasopalatine duct in humans is necessary for understanding the morphology and etiopathogenesis of lesions that occur in this region. Objective The aim of the present study was to describe the morphological aspects of the nasopalatine region in human fetuses and correlate these aspects with the development of pathologies in this region. Material and Methods Five human fetuses with no facial or palatine abnormalities were used for the acquisition of specimens from the nasopalatine region. After demineralization, the specimens were histologically processed. Histological cuts were stained with methylene blue to orient the cutting plane and hematoxylin-eosin for the descriptive histological analysis. Results The age of the fetuses was 8.00, 8.25, 9.00 and 9.25 weeks, and it was not possible to determine the age in the last one. The incisive canal was observed in all specimens as an opening delimited laterally by the periosteum and connecting oral and nasal cavity. The nasopalatine duct is an epithelial structure with the greatest morphological variation, with either unilateral or bilateral occurrence and total patent, partial patent and islet forms. The vomeronasal organ is a bilateral epithelized structure located alongside the nasal septum above the incisive canal in all the fetuses. Conclusions The incisive canal, nasopalatine duct and vomeronasal organ are distinct anatomic structures. The development of nasopalatine duct cysts may occur in all forms of the nasopalatine duct.

  13. A genome scan revealed significant associations of growth traits with a major QTL and GHR2 in tilapia

    OpenAIRE

    Feng Liu; Fei Sun; Jun Hong Xia; Jian Li; Gui Hong Fu; Grace Lin; Rong Jian Tu; Zi Yi Wan; Delia Quek; Gen Hua Yue

    2014-01-01

    Growth is an important trait in animal breeding. However, the genetic effects underpinning fish growth variability are still poorly understood. QTL mapping and analysis of candidate genes are effective methods to address this issue. We conducted a genome-wide QTL analysis for growth in tilapia. A total of 10, 7 and 8 significant QTLs were identified for body weight, total length and standard length at 140 dph, respectively. The majority of these QTLs were sex-specific. One major QTL for growt...

  14. Characterization of ISR region and development of a PCR assay for rapid detection of the fish pathogen Tenacibaculum soleae.

    Science.gov (United States)

    López, Jose R; Hamman-Khalifa, Abdel M; Navas, José I; de la Herran, Roberto

    2011-11-01

    The aims of this work were to characterize the 16S-23S internal spacer region of the fish pathogen Tenacibaculum soleae and to develop a PCR assay for its identification and detection. All T. soleae strains tested displayed a single internal spacer region class, containing tRNA(I) (le) and tRNA(A) (la) genes; nevertheless, a considerable intraspecific heterogeneity was observed. However, this region proved to be useful for differentiation of T. soleae from related and non-related species. Species-specific primers were designed targeting the 16S rRNA gene and the internal spacer region region, yielding a 1555-bp fragment. Detection limit was of 1 pg DNA per reaction (< 30 bacterial cells) when using pure cultures. The detection level in the presence of DNA from fish or other bacteria was lower; however, 10 pg were detected at a target/background ratio of 1 : 10(5) . The PCR assay proved to be more sensitive than agar cultivation for the detection of T. soleae from naturally diseased fish, offering a useful tool for diagnosis and for understanding the epidemiology of this pathogen. PMID:22092820

  15. Assembly and characterization of the MHC class I region of the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis).

    Science.gov (United States)

    Ruan, Rui; Wan, Xiao-Ling; Zheng, Yang; Zheng, Jin-Song; Wang, Ding

    2016-01-01

    The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis; YFP) is the sole freshwater subspecies of N. asiaeorientalis and is now critically endangered. Major histocompatibility complex (MHC) is a family of highly polymorphic genes that play an important immunological role in antigen presentation in the vertebrates. Currently, however, little is known about MHC region in the genome of the YFP, which hampers conservation genetics and evolutionary ecology study using MHC genes. In this work, a nucleotide sequence of 774,811 bp covering the YFP MHC class I region was obtained by screening a YFP bacterial artificial chromosome (BAC) library, followed by sequencing and assembly of positive BAC clones. A total of 45 genes were successfully annotated, of which four were MHC class I genes. There are high similarities among the four YFP MHC class I genes (>94%). Divergence in the coding region of the four YFP MHC class I genes is mainly localized to exons 2 and 3, which encode the antigen-binding sites of MHC class I genes. Additionally, comparison of the MHC structure in YFP to those of cattle, sheep, and pig showed that MHC class I genes are located in genome regions with regard to the conserved genes, and the YFP contains the fewest MHC class I genes among these species. This is the first report characterizing a cetacean MHC class I region and describing its organization, which would be valuable for further investigation of adaptation in natural populations of the YFP and other cetaceans. PMID:26585324

  16. Characterization of mesostasis regions in lunar basalts: Understanding late-stage melt evolution and its influence on apatite formation

    Science.gov (United States)

    Potts, Nicola J.; TartèSe, Romain; Anand, Mahesh; Westrenen, Wim; Griffiths, Alexandra A.; Barrett, Thomas J.; Franchi, Ian A.

    2016-07-01

    Recent studies geared toward understanding the volatile abundances of the lunar interior have focused on the volatile-bearing accessory mineral apatite. Translating measurements of volatile abundances in lunar apatite into the volatile inventory of the silicate melts from which they crystallized, and ultimately of the mantle source regions of lunar magmas, however, has proved more difficult than initially thought. In this contribution, we report a detailed characterization of mesostasis regions in four Apollo mare basalts (10044, 12064, 15058, and 70035) in order to ascertain the compositions of the melts from which apatite crystallized. The texture, modal mineralogy, and reconstructed bulk composition of these mesostasis regions vary greatly within and between samples. There is no clear relationship between bulk-rock basaltic composition and that of bulk-mesostasis regions, indicating that bulk-rock composition may have little influence on mesostasis compositions. The development of individual melt pockets, combined with the occurrence of silicate liquid immiscibility, exerts greater control on the composition and texture of mesostasis regions. In general, the reconstructed late-stage lunar melts have roughly andesitic to dacitic compositions with low alkali contents, displaying much higher SiO2 abundances than the bulk compositions of their host magmatic rocks. Relevant partition coefficients for apatite-melt volatile partitioning under lunar conditions should, therefore, be derived from experiments conducted using intermediate compositions instead of compositions representing mare basalts.

  17. Cloning and characterization of the 5'-flanking region of the Ehox gene

    International Nuclear Information System (INIS)

    The paired-like homeobox-containing gene Ehox plays a role in embryonic stem cell differentiation and is highly expressed in the developing placenta and thymus. To understand the mechanisms of regulation of Ehox gene expression, the 5'-flanking region of the Ehox gene was isolated from a mouse BAC library. 5'-RACE analysis revealed a single transcriptional start site 130 nucleotides upstream of the translation initiation codon. Transient transfection with a luciferase reporter gene under the control of serially deleted 5'-flanking sequences revealed that the nt -84 to -68 region contained a positive cis-acting element for efficient expression of the Ehox gene. Mutational analysis of this region and oligonucleotide competition in the electrophoretic mobility shift assay revealed the presence of a CCAAT box, which is a target for transcription nuclear factor Y (NFY). NFY is essential for positive gene regulation. No tissue-specific enhancer was identified in the 1.9-kb 5'-flanking region of the Ehox gene. Ehox is expressed during the early stages of embryo development, specifically in Brain at 9.5 dpc, as well as during the late stages of embryo development. These results suggest that NFY is an essential regulatory factor for Ehox transcriptional activity, which is important for the post-implantation stage of the developing embryo

  18. North Central Regional geologic characterization report. Volume 2. Plates. Final report

    International Nuclear Information System (INIS)

    Volume 8(2) contains the following maps: Geologic map of the Lake Superior Region (Minnesota, Wisconsin, and northern Michigan); Index Map; Overburden Thickness; Faults and Ground Acceleration; Rock and Mineral Resources; Ground Water Basins and Potential Major Discharge Zones; and Ground Water Resource Potential

  19. Airborne in situ characterization of dry aerosol optical properties in a multisource influenced marine region

    OpenAIRE

    Targino, Admir C.; Noone, Kevin J.; Öström, Elisabeth

    2011-01-01

    In situ data from the 2nd Aerosol Characterization Experiment (ACE-2) were used to describe the aerosol opticalproperties in a marine environment perturbed by continental sources, such as the outflow of European aerosol and dustoutbreaks from North Africa. The data consist of airborne measurements made with an integrating nephelometer andabsorption photometer.The cases investigated in theACE-2 experiment included vertical profiles flown in dusty, polluted and clean airmasses.While it was poss...

  20. Characterization of Maize Producing Households in Drought Prone Regions of Eastern Africa

    OpenAIRE

    Erenstein, Olaf; Kassie, Girma Tesfahun; Langyintuo, Augustine S.; Mwangi, Wilfred

    2011-01-01

    Agriculture in eastern Africa is predominantly rainfed and maize is a major food crop,primarily produced for home consumption and the market by small-scale family farms. The study characterized farm households in the drought prone maize growing areas of eastern Africa synthesizing data from parallel household surveys in Ethiopia, Kenya, Uganda and Tanzania. The study provides a comparative analysis of the farm households’ assets, livelihood strategies and crop management practices, with an em...

  1. Process-based characterization of evapotranspiration sources over the North American monsoon region

    Science.gov (United States)

    Bohn, Theodore J.; Vivoni, Enrique R.

    2016-01-01

    Evapotranspiration (ET) is a poorly constrained flux in the North American monsoon (NAM) region, leading to potential errors in land-atmosphere feedbacks. We quantified the spatiotemporal variations of ET using the Variable Infiltration Capacity (VIC) model, modified to account for soil evaporation (Esoil), irrigated agriculture, and the variability of land surface properties derived from the Moderate Resolution Imaging Spectroradiometer during 2000-2012. Simulated ET patterns were compared to field observations at 59 eddy covariance towers, water balance estimates in nine basins, and six available gridded ET products. The modified VIC model performed well at eddy covariance towers representing the natural and agricultural land covers in the region. Simulations revealed that major sources of ET were forested mountain areas during the summer season and irrigated croplands at peak times of growth in the winter and summer, accounting for 22% and 9% of the annual ET, respectively. Over the NAM region, Esoil was the largest component (60%) of annual ET, followed by plant transpiration (T, 32%) and evaporation of canopy interception (8%). Esoil and T displayed different relationships with P in natural land covers, with Esoil tending to peak earlier than T by up to 1 month, while only a weak correlation between ET and P was found in irrigated croplands. Based on the model performance, the VIC-based estimates are the most realistic to date for this region. Furthermore, spatiotemporal patterns reveal new information on the magnitudes, locations, and timing of ET in the North American monsoon region with implications on land-atmosphere feedbacks.

  2. Karyotype characterization, constitutive heterochromatin and nucleolus organizer regions of Paranaita opima (Coleoptera, Chrysomelidae, Alticinae

    Directory of Open Access Journals (Sweden)

    Mara Cristina de Almeida

    2006-01-01

    Full Text Available Species of the subtribe Oedionychina not only have a highly uniform diploid number of 2n = 22 (20+X+y but have the karyotypic peculiarity of possessing extremely large sex chromosomes. We analyzed Paranaita opima embryos and gonadal cells to determine their diploid number, chromosomal morphology, type of sex determination system, constitutive heterochromatin pattern and which chromosomes bear nucleolus organizer regions (NORs. The diploid number of P. opima was 2n = 22 (20+XY/XX with all chromosomes being metacentric. Chromosome pair 6 showed an interstitial secondary constriction on the short arm. The C-banding technique revealed centromeric constitutive heterochromatin in all chromosomes, which, in pair 6, extended up to the secondary constriction of the short arm, additional C-bands also being present on the Y chromosome. Silver nitrate nucleolar organizer region (Ag-NOR staining showed NORs on the secondary constriction of pair 6. Fluorochrome analysis with chromomycin A3 (CMA3, 4'-6-diamidino-2-phenylindole (DAPI and the distamycin A (DA counterstain showed that the short arm of chromosome pair 6 exhibited a GC-rich block extending from the proximal to the median region, including part of the secondary constriction. The same techniques also showed AT-rich blocks at the centromeric region of all chromosomes and at the terminal region of the short arm of pair 6. The basic karyotype characteristics and C band pattern of P. opima are similar to those described for other species in the subtribe Oedionychina. The pattern of autosomal NORs observed in P. opima corresponds to that registered in the majority of the Chrysomelidae species.

  3. QTL Mapping for Drought Tolerance at Stages of Germination and Seedling in Wheat (Triticum aestivum L.)Using a DH Population

    Institute of Scientific and Technical Information of China (English)

    HAO Zhuan-fang; CHANG Xiao-ping; GUO Xiao-jian; JING Rui-lian; LI Run-zhi; JIA Ji-zeng

    2003-01-01

    Drought is a major constraint in many wheat(Triticum aestivum L.) production regions. Quantitative trait loci (QTLs) conditioning drought tolerance at stages of germination and seedling in wheat were identified in a double haploid (DH) population derived from the cross, Hanxuan10×Lumai14, using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. Interval mapping analysis revealed that QTLs for drought tolerance at germination stage were located on chromosomes 1B, 2B, 5A, 6B, 7A and 7B, respectively, and the most effective QTL was mapped on chromosome 2B, explaining 27.2% of phenotypic variance. The QTLs for drought tolerance at seedling stage were located on 1B, 3B and 7B, respectively, and the most effective QTL was mapped on chromosome 3B, explaining 21.6% of phenotypic variance. Their positions were different from those of QTLs conferring drought tolerance at germination stage, indicating that drought tolerance at germination stage and seedling stage was controlled by different loci. Most of the identified QTLs explained 18% or more of phenotypic variance for drought tolerance at germination and seedling stage, and would be useful in future for marker assisted selection programs and cultivar improvement.

  4. Integration of disease association and eQTL data using a Bayesian colocalisation approach highlights six candidate causal genes in immune-mediated diseases.

    Science.gov (United States)

    Guo, Hui; Fortune, Mary D; Burren, Oliver S; Schofield, Ellen; Todd, John A; Wallace, Chris

    2015-06-15

    The genes and cells that mediate genetic associations identified through genome-wide association studies (GWAS) are only partially understood. Several studies that have investigated the genetic regulation of gene expression have shown that disease-associated variants are over-represented amongst expression quantitative trait loci (eQTL) variants. Evidence for colocalisation of eQTL and disease causal variants can suggest causal genes and cells for these genetic associations. Here, we used colocalisation analysis to investigate whether 595 genetic associations to ten immune-mediated diseases are consistent with a causal variant that regulates, in cis, gene expression in resting B cells, and in resting and stimulated monocytes. Previously published candidate causal genes were over-represented amongst genes exhibiting colocalisation (odds ratio > 1.5), and we identified evidence for colocalisation (posterior odds > 5) between cis eQTLs in at least one cell type and at least one disease for six genes: ADAM15, RGS1, CARD9, LTBR, CTSH and SYNGR1. We identified cell-specific effects, such as for CTSH, the expression of which in monocytes, but not in B cells, may mediate type 1 diabetes and narcolepsy associations in the chromosome 15q25.1 region. Our results demonstrate the utility of integrating genetic studies of disease and gene expression for highlighting causal genes and cell types. PMID:25743184

  5. Correlation and QTL Analyses for Photosynthetic Traits in Maize%玉米光合性状的相关性及 QTL 分析

    Institute of Scientific and Technical Information of China (English)

    余婷婷; 刘朝显; 梅秀鹏; 王久光; 王国强; 蔡一林

    2015-01-01

    In order to explore the correlation and genetic mechanism of maize photosynthetic traits ,two F2 populations (Y and R) with different genetic backgrounds were used to identify correlation and QTLs for 10 photosynthetic traits ,which included chlorophyll‐a content ,chlorophyll‐b content ,total chlorophyll content ,net photosynthetic rate ,stomata conductance ,intercellular CO2 concentration ,transpiration rate and some others .The correlation between two of chlorophyll‐a content ,chlorophyll‐b content and total chlorophyll content in different periods was non‐significant in population Y ,and was highly significant in population R .The correlation between other traits of the two populations was highly consistent .In the same growth period of the plants ,total chlorophyll content was in highly significant correlation with chlo‐rophyll‐a content and chlorophyll‐b content ,highly significant correlation was also detected between net photosynthetic rate and stomata conductance ,between net photosynthetic rate and transpiration rate ,and between stomata conductance and transpiration rate ,stomata conductance was moderately correlated with intercellular CO2 concentration ,and chlorophyll content was weakly correlated with net photosynthetic rate ,stomata conductance ,intercellular CO2 concentration and transpiration rate .In population Y ,1 QTL was detected for chlorophyll‐a content (FCa) ,chlorophyll‐b content (FCb) and total chlorophyll content (FCt) each ,at the five‐leaf stage .All these QTLs were located in umc2391‐mmc0371 on chromosome 4 and each explained 8.65% to 9.87% of the phenotypic variance .And other three QTLs were detected at the milk stage ,one for chlorophyll‐a content ,one for chlorophyll‐b content and one for total chlorophyll content .They were located in mmc0501‐bnlg1451 on chromosome 10 and explained 6.77 to 6.93% of the phenotypic variance each .Six QTLs were detected at the pollination stage ,one for net photosynthetic

  6. Source characterization of selected North Caspian events from the relative excitation of regional phases. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Niazi, M.

    1981-11-01

    Seismograms of seven recent events (presumed underground nuclear explosions) which occurred during 1976-1979 in the North Caspian Sea region of the western Soviet Kazakh are compared at regional distances for their relative source excitation characteristics. The body wave magnitude estimates of these events range from 5.1 to 6.0. The data consist of analog and digital records collected at stations ranging in instrumental sophistication from temporary sites with single component smoke drum capability to those of SRO, ASRO and array (ILPA) configurations with digitally recorded down-hole observations. The amplitude and frequency measurements of the analog seismograms for the first arrival and the peak amplitude of P coda as well as for the clear S wave signals recorded for different events at the same station are compared.

  7. OLFACTOMETRIC CHARACTERIZATION OF TAMÂIOASA ROMÂNEASCĂ WINE COME FROM DIFFERENT WINE REGIONS

    Directory of Open Access Journals (Sweden)

    Luminiţa VIŞAN

    2015-10-01

    Full Text Available The work refers to the analysis of aroma compounds identified in Tamaioasa Romanian wines from 2 distinct Romanian wine-growing areas: vineyard Stefanesti-Arges and Pietroasa, watching, and in particular the variation of flavorings depending on the region of origin. Gas chromatographic method coupled with mass Spectrometry were identified 6 esters, 3 higher alcohols, 1 aromatic alcohol, 2 terpenes, 1 lactone, 1 acid and 1 aldehyde. The high concentration of ethyl acetate, ethyl butanoate, isoamyl alcohol were identified; flavor specific Tamaioasa Romanian wine is given by 1-Į-terpineol, terpenic alcohol has been identified in this wine in large quantities. Research has shown that wine-growing region influence the organoleptic characteristics of wine and aromatic content of their wines, so the wines can be very quickly recognized when tasting.

  8. Impact of land cover characterization on regional climate modeling over West Africa

    Science.gov (United States)

    Sylla, Mouhamadou Bamba; Pal, Jeremy S.; Wang, Guiling L.; Lawrence, Peter J.

    2016-01-01

    The impact of high resolution modern vegetation cover on the West African climate is examined using the International Centre for Theoretical Physics Regional Climate Model implementing the NCAR Community Land Model. Two high resolution 25 km long-term simulations driven by the output from a coarser 50-km resolution simulation are performed for the period 1998-2010. One high resolution simulation uses an earlier and coarser-resolution version of plant functional type distribution and leaf area index, while the other uses a more recent, higher-quality, and finer-resolution version of the data. The results indicate that the new land cover distribution substantially alters the distribution of temperature with warming in Central Nigeria, northern Gulf of Guinea and part of the Sahel due to the replacement of C4 grass with corn; and cooling along the coastlines of the Gulf of Guinea and in Central Africa due to the replacement of C4 grass with tropical broadleaf evergreen trees. Changes in latent heat flux appear to be largely responsible for these temperature changes with a net decrease (increase) in regions of warming (cooling). The improved land cover distribution also results in a wetter monsoon season. The presence of corn tends to favor larger precipitation amounts via more intense events, while the presence of tropical broadleaf evergreen trees tends to favor the occurrence of both more intense and more frequent events. The wetter conditions appear to be sustained via (1) an enhanced soil moisture feedback; and (2) elevated moisture transport due to increased low-level convergence in regions south of 10N where the most substantial land cover differences are present. Overall the changes induced by the improved vegetation cover improve, to some extent, the performance of the high resolution regional climate model in simulating the main West African summer monsoon features.

  9. Cultivation and Characterization of Cynara Cardunculus for Solid Biofuels Production in the Mediterranean Region

    OpenAIRE

    Nicholas G. Danalatos; Panagiotis Basinas; Anastasia Malliopoulou; Panagiotis Grammelis

    2008-01-01

    Technical specifications of solid biofuels are continuously improved towards the development and promotion of their market. Efforts in the Greek market are limited, mainly due to the climate particularity of the region, which hinders the growth of suitable biofuels. Taking also into account the increased oil prices and the high inputs required to grow most annual crops in Greece, cardoon (Cynara cardunculus L.) is now considered the most important and promising sources for solid biofuel produ...

  10. Molecular characterization of hepatitis C virus core region in moroccan intravenous drug users.

    Science.gov (United States)

    Trimbitas, Roxana-Delia; Fayssel, Naouar; Serghini, Fatima-Zahra; Wakrim, Lahcen; Khyatti, Meriem; Essalhi, Mohammed; Bellefquih, Abdelkrim Meziane; Benani, Abdelouaheb

    2016-08-01

    Intravenous drug users (IDUs) represent a highly-infected reservoir for Hepatitis C virus (HCV) worldwide, harboring some of the most elevated prevalences and majority of the epidemic in developed nations. Studies aimed at sequencing regions of the viral genome uncovered amino acid mutations, some of which have been implicated in resistance to standard of care pegylated interferon/Ribavirin double therapy. Using the nested PCR method on the Core region of HCV strains in Moroccan IDUs living in the Tangier region this study sought to identify genotype-specific amino acid mutations, followed by Phylogenetic methods in order to compare them with international strains so as to identify sequences of highest homology. Genotyping was confirmed and recombination events excluded by line-probe assay. Italy was found most homologous for genotypes 1a and 3a, Iran for genotype 1a and Egypt for genotype 4a. Amino Acid Mutation analysis revealed the following novel genotype 3a-specific mutations: N16I, L36V, T49A, P71S, T75S, and T110N. The outcome of this work describes the HCV genetic heterogeneity in high-risk intravenous drug users, and it gives clues to the global migratory flow of genotypes as they cross geographical boundaries between various IDU populations and identifies "signature" amino acid mutations traceable to HCV genotype 3a. Identification of key amino acid positions in the HCV Core region with higher rates of mutations paves the way for eventual clinical trials seeking to establish a link between these recurrent mutations and response to standard of care Interferon and Ribavirin antiviral therapy. J. Med. Virol. 88:1376-1383, 2016. © 2016 Wiley Periodicals, Inc. PMID:26754854

  11. Characterization of the ''three-phonon'' region of sup 1 sup 0 sup 0 Ru

    CERN Document Server

    Genilloud, L L; Corminboeuf, F; Garrett, P E; Hannant, C D; Jolie, J; Warr, N; Yates, S W

    2001-01-01

    Lifetimes of excited states in sup 1 sup 0 sup 0 Ru were determined from Doppler-shift attenuation measurements following the sup 1 sup 0 sup 0 Ru(n, n sup 'gamma) reaction. Absolute transition rates or limits thereon were extracted for states in the three-phonon region and were compared with an interacting boson model description of this nucleus. Intruder states were identified, and a candidate for the 2 sup + mixed-symmetry state is suggested.

  12. Characterization of the Helicoverpa assulta nucleopolyhedrovirus genome and sequence analysis of the polyhedrin gene region

    Indian Academy of Sciences (India)

    Soo-Dong Woo; Jae Young Choi; Yeon Ho Je; Byung Rae Jin

    2006-09-01

    A local strain of Helicoverpa assulta nucleopolyhedrovirus (HasNPV) was isolated from infected H. assulta larvae in Korea. Restriction endonuclease fragment analysis, using 4 restriction enzymes, estimated that the total genome size of HasNPV is about 138 kb. A degenerate polymerase chain reaction (PCR) primer set for the polyhedrin gene successfully amplified the partial polyhedrin gene of HasNPV. The sequencing results showed that the about 430 bp PCR product was a fragment of the corresponding polyhedrin gene. Using HasNPV partial predicted polyhedrin to probe the Southern blots, we identified the location of the polyhedrin gene within the 6 kb EcoRI, 15 kb NcoI, 20 kb XhoI, 17 kb BglII and 3 kb ClaI fragments, respectively. The 3 kb ClaI fragment was cloned and the nucleotide sequences of the polyhedrin coding region and its flaking regions were determined. Nucleotide sequence analysis indicated the presence of an open reading frame of 735 nucleotides which could encode 245 amino acids with a predicted molecular mass of 29 kDa. The nucleotide sequences within the coding region of HasNPV polyhedrin shared 73.7% identity with the polyhedrin gene from Autographa californica NPV but were most closely related to Helicoverpa and Heliothis species NPVs with over 99% sequence identity.

  13. Spitzer and Herschel multiwavelength characterization of the dust content of evolved HII regions

    CERN Document Server

    Paladini, R; Veneziani, M; Noriega-Crespo, A; Anderson, L D; Piacentini, F; Goncalves, D Pinheiro; Paradis, D; Tibbs, C T; Bernard, J -P; Natoli, P

    2012-01-01

    We have analyzed a uniform sample of 16 evolved HII regions located in a 2 deg X 2 deg Galactic field centered at (l,b) = (30 deg, 0 deg) and observed as part of the Herschel Hi-GAL survey. The evolutionary stage of these HII regions was established using ancillary radio continuum data. By combining Hi-GAL PACS (70 micron, 160 micron) and SPIRE (250 micron, 350 micron and 500 micron) measurements with MIPSGAL 24 micron data, we built Spectral Energy Distributions (SEDs) of the sources and showed that a 2-component grey-body model is a good representation of the data. In particular, wavelengths > 70 micron appear to trace a cold dust component, for which we estimated an equilibrium temperature of the Big Grains (BGs) in the range 20 - 30 K, while for lambda < 70 micron, the data indicated the presence of a warm dust component at temperatures of the order of 50 - 90 K. This analysis also revealed that dust is present in the interior of HII regions, although likely not in a large amount. In addition, the data...

  14. Paenibacillus larvae 16S-23S rDNA intergenic transcribed spacer (ITS) regions: DNA fingerprinting and characterization.

    Science.gov (United States)

    Dingman, Douglas W

    2012-07-01

    Paenibacillus larvae is the causative agent of American foulbrood in honey bee (Apis mellifera) larvae. PCR amplification of the 16S-23S ribosomal DNA (rDNA) intergenic transcribed spacer (ITS) regions, and agarose gel electrophoresis of the amplified DNA, was performed using genomic DNA collected from 134 P. larvae strains isolated in Connecticut, six Northern Regional Research Laboratory stock strains, four strains isolated in Argentina, and one strain isolated in Chile. Following electrophoresis of amplified DNA, all isolates exhibited a common migratory profile (i.e., ITS-PCR fingerprint pattern) of six DNA bands. This profile represented a unique ITS-PCR DNA fingerprint that was useful as a fast, simple, and accurate procedure for identification of P. larvae. Digestion of ITS-PCR amplified DNA, using mung bean nuclease prior to electrophoresis, characterized only three of the six electrophoresis bands as homoduplex DNA and indicating three true ITS regions. These three ITS regions, DNA migratory band sizes of 915, 1010, and 1474 bp, signify a minimum of three types of rrn operons within P. larvae. DNA sequence analysis of ITS region DNA, using P. larvae NRRL B-3553, identified the 3' terminal nucleotides of the 16S rRNA gene, 5' terminal nucleotides of the 23S rRNA gene, and the complete DNA sequences of the 5S rRNA, tRNA(ala), and tRNA(ile) genes. Gene organization within the three rrn operon types was 16S-23S, 16S-tRNA(ala)-23S, and l6S-5S-tRNA(ile)-tRNA(ala)-23S and these operons were named rrnA, rrnF, and rrnG, respectively. The 23S rRNA gene was shown by I-CeuI digestion and pulsed-field gel electrophoresis of genomic DNA to be present as seven copies. This was suggestive of seven rrn operon copies within the P. larvae genome. Investigation of the 16S-23S rDNA regions of this bacterium has aided the development of a diagnostic procedure and has helped genomic mapping investigations via characterization of the ITS regions. PMID:22510214

  15. Characterizing chemical transport of ozone and fine particles in the Great Lakes region

    Science.gov (United States)

    Spak, Scott N.

    This dissertation presents a science framework relevant to evaluating impacts of land use policy scenarios, energy technologies, and climate on urban and regional air quality. Emerging from collaboration with urban planners, this work provides a means for employing atmospheric chemical transport modeling to understand environmental ramifications of long-term, spatially disaggregated changes in population and automobile emissions at the census tract level, and to assess the sensitivity of these changes to densification strategies. Toward these goals, the framework is used to evaluate model skill in resolving contemporary characteristics of ozone (O3) and speciated fine particles (PM2.5) in the Great Lakes region of North America, and to quantitatively explore meteorological processes that bring about observed features of these pollutants in the region. The Great Lakes were chosen due to a population concentrated in sprawling metropolitan areas, consistently high and widespread pollutant burdens, and seasonal effects of the lakes on the atmosphere. In annual simulation at 36 km resolution, the Community Multiscale Air Quality model is evaluated using speciated PM2.5 measurements taken at regulatory monitoring networks orientated to sample urban, rural, and remote areas. Performance relative to ad-hoc regional modeling goals and prior studies is average to excellent for most species throughout the year. Both pollution episodes and seasonality are captured. The Great Lakes affect pollution seasonality: strong winds advect aerosols around the deep marine boundary layer to lower surface PM2.5 in fall and winter, while O3 over the lakes is enhanced throughout the year, driven by temperature in the cool seasons and lake breeze circulation in spring and summer. Simulations confirm observational evidence that rural and small-city sources are responsible for most regional PM2.5. Sensitivities to urban and rural reductions are of comparable magnitude on a percentage basis

  16. Resequencing at ≥40-Fold Depth of the Parental Genomes of a Solanum lycopersicum × S. pimpinellifolium Recombinant Inbred Line Population and Characterization of Frame-Shift InDels That Are Highly Likely to Perturb Protein Function

    Science.gov (United States)

    Kevei, Zoltan; King, Robert C.; Mohareb, Fady; Sergeant, Martin J.; Awan, Sajjad Z.; Thompson, Andrew J.

    2015-01-01

    A recombinant in-bred line population derived from a cross between Solanum lycopersicum var. cerasiforme (E9) and S. pimpinellifolium (L5) has been used extensively to discover quantitative trait loci (QTL), including those that act via rootstock genotype, however, high-resolution single-nucleotide polymorphism genotyping data for this population are not yet publically available. Next-generation resequencing of parental lines allows the vast majority of polymorphisms to be characterized and used to progress from QTL to causative gene. We sequenced E9 and L5 genomes to 40- and 44-fold depth, respectively, and reads were mapped to the reference Heinz 1706 genome. In L5 there were three clear regions on chromosome 1, chromosome 4, and chromosome 8 with increased rates of polymorphism. Two other regions were highly polymorphic when we compared Heinz 1706 with both E9 and L5 on chromosome 1 and chromosome 10, suggesting that the reference sequence contains a divergent introgression in these locations. We also identified a region on chromosome 4 consistent with an introgression from S. pimpinellifolium into Heinz 1706. A large dataset of polymorphisms for the use in fine-mapping QTL in a specific tomato recombinant in-bred line population was created, including a high density of InDels validated as simple size-based polymerase chain reaction markers. By careful filtering and interpreting the SnpEff prediction tool, we have created a list of genes that are predicted to have highly perturbed protein functions in the E9 and L5 parental lines. PMID:25809074

  17. Characterization of tsunamigenic earthquake in Java region based on seismic wave calculation

    International Nuclear Information System (INIS)

    This study is to characterize the source mechanism of tsunamigenic earthquake based on seismic wave calculation. The source parameter used are the ratio (Θ) between the radiated seismic energy (E) and seismic moment (Mo), moment magnitude (MW), rupture duration (To) and focal mechanism. These determine the types of tsunamigenic earthquake and tsunami earthquake. We calculate the formula using the teleseismic wave signal processing with the initial phase of P wave with bandpass filter 0.001 Hz to 5 Hz. The amount of station is 84 broadband seismometer with far distance of 30° to 90°. The 2 June 1994 Banyuwangi earthquake with MW=7.8 and the 17 July 2006 Pangandaran earthquake with MW=7.7 include the criteria as a tsunami earthquake which distributed about ratio Θ=−6.1, long rupture duration To>100 s and high tsunami H>7 m. The 2 September 2009 Tasikmalaya earthquake with MW=7.2, Θ=−5.1 and To=27 s which characterized as a small tsunamigenic earthquake

  18. Identification and Characterization of Performance Limiting Regions in Poly-Si Wafers Used for PV Cells: Preprint

    International Nuclear Information System (INIS)

    As demand for silicon photovoltaic (PV) material increases, so does the need for cost-effective feedstock and production methods that will allow enhanced penetration of silicon PV into the total energy market. The focus on cost minimization for production of polycrystalline silicon (poly-Si) PV has led to relaxed feedstock purity requirements, which has also introduced undesirable characteristics into cast poly-Si PV wafers. To produce cells with the highest possible conversion efficiencies, it is crucial to understand how reduced purity requirements and defects that are introduced through the casting process can impair minority carrier properties in poly-Si PV cells. This is only possible by using multiple characterization techniques that give macro-scale information (such as the spatial distribution of performance-limiting regions), as well as micro and nano-scale information about the structural and chemical nature of such performance-limiting regions. This study demonstrates the usefulness of combining multiple techniques to analyze performance-limiting regions in the poly-Si wafers that are used for PV cells. This is done by first identifying performance-limiting regions using macro-scale techniques including photoluminescence (PL) imaging, microwave photoconductive decay (uPCD), and reflectometry, then using smaller-scale techniques such as scanning electron microscopy (SEM), electron backscattered diffraction (EBSD), laser ablation inductively coupled mass spectrometry (LA-ICP-MS), cathodoluminescence (CL), and transmission electron microscopy (TEM) to understand the nature of such regions. This analysis shows that structural defects as well as metallic impurities are present in performance-limiting regions, which together act to decrease conversion efficiencies in poly-Si PV cells.

  19. Characterization of genetic deletions in Becker muscular dystrophy using monoclonal antibodies against a deletion-prone region of dystrophin

    Energy Technology Data Exchange (ETDEWEB)

    Thanh, L.T.; Man, Nguyen Thi; Morris, G.E. [Wales Institute, Clwyd (United Kingdom)] [and others

    1995-08-28

    We have produced a new panel of 20 monoclonal antibodies (mAbs) against a region of the dystrophin protein corresponding to a deletion-prone region of the Duchenne muscular dystrophy gene (exons 45-50). We show that immunohistochemistry or Western blotting with these {open_quotes}exon-specific{close_quotes} mAbs can provide a valuable addition to Southern blotting or PCR methods for the accurate identification of genetic deletions in Becker muscular dystrophy patients. The antibodies were mapped to the following exons: exon 45 (2 mAbs), exon 46 (6), exon 47 (1), exons 47/48 (4), exons 48-50 (6), and exon 50 (1). PCR amplification of single exons or groups of exons was used both to produce specific dystrophin immunogens and to map the mAbs obtained. PCR-mediated mutagenesis was also used to identify regions of dystrophin important for mAb binding. Because the mAbs can be used to characterize the dystrophin produced by individual muscle fibres, they will also be useful for studying {open_quotes}revertant{close_quotes} fibres in Duchenne muscle and for monitoring the results of myoblast therapy trials in MD patients with deletions in this region of the dystrophin gene. 27 refs., 7 figs., 3 tabs.

  20. The comparative analysis based on maize integrated QTL map and meta-analysis of plant height QTLs

    Institute of Scientific and Technical Information of China (English)

    WANG Yi; YAO Ji; ZHANG Zhengfeng; ZHENG Yonglian

    2006-01-01

    1201 published maize QTLs conferring for 68 traits were collected and imported into local CMap software to construct an integrated QTL map, which can be used for marker-mining, QTL localization, gene cloning and marker-assisted selection. The maize integrated QTL map showed that maize QTLs for various traits usually clustered in all chromosomes. 22 plant height QTLs of maize were co-linear with 64 plant height QTLs of rice, 43 grain yield QTLs of maize were co-liner with 7 grain yield QTLs of rice. 127 plant height QTLs of maize were refined by means of "overview" analysis. At last, 40 "real" QTLs were identifed. A substantial number of candidate quantitative trait genes for plant height of maize were found. These results established an important bioinformatics platform for extracting most of maize QTL information.

  1. High field FT-ICR mass spectrometry for molecular characterization of snow board from Moscow regions.

    Science.gov (United States)

    Mazur, Dmitry M; Harir, Mourad; Schmitt-Kopplin, Philippe; Polyakova, Olga V; Lebedev, Albert T

    2016-07-01

    High field Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry analysis of eight snow samples from Moscow city allowed us to identify more than 2000 various elemental compositions corresponding to regional air pollutants. The hierarchical cluster analysis (HCA) of the data showed good concordance of three main groups of samples with the main wind directions. The North-West group (A1) is represented by several homologous CHOS series of aliphatic organic aerosols. They may form as a result of enhanced photochemical reactions including oxidation of hydrocarbons with sulfonations due to higher amount of SO2 emissions in the atmosphere in this region. Group A2, corresponding to the South-East part of Moscow, contains large amount of oxidized hydrocarbons of different sources that may form during oxidation in atmosphere. These hydrocarbons appear correlated to emissions from traffic, neighboring oil refinery, and power plants. Another family of compounds specific for this region involves CHNO substances formed during oxidation processes including NOx and NO3 radical since emissions of NOx are higher in this part of the city. Group A3 is rich in CHO type of compounds with high H/C and low O/C ratios, which is characteristic of oxidized hydrocarbon-like organic aerosol. CHNO types of compounds in A3 group are probably nitro derivatives of condensed hydrocarbons such as PAH. This non-targeted profiling revealed site specific distribution of pollutants and gives a chance to develop new strategies in air quality control and further studies of Moscow environment. PMID:26994789

  2. Uncorrelated Track Classification, Characterization, & Prioritization using Admissible Regions and Bayesian Inference

    Science.gov (United States)

    Holzinger, M.

    2014-09-01

    This paper introduces and discusses a method to rigorously classify and prioritize UCTs using Bayesian inference and admissible regions. A detailed derivation and discussion of the methodology is given, followed by a generalized definition of prioritization parameters. Several example prioritization parameters including `time left to detect,' 'zero-effort miss,' and `effective albedo-area' are motivated and given. A number of illustrative applications with optical UCTs are examined to demonstrate information that can be extracted from each observation. Finally, the information extracted from each UCT is then compared and approaches to observation prioritization discussed.

  3. Characterizing Daytime GHZ Scintillation at Equatorial Regions Using Gnss Radio Occultation Measurements

    Science.gov (United States)

    Seif, A.; Zhang, K.; Tsunoda, R. T.; Abdullah, M.; Carter, B. A.; Norman, R.; Wu, S.

    2015-12-01

    Ionospheric scintillation of radio waves can behave differently at different locations with a strong diurnal dependence; particularly in the equatorial regions. Ionospheric scintillations at gigahertz (GHz) frequencies have been observed during both daytime and nighttime. It is believed that daytime scintillation is associated with blanketing sporadic E (Esb), whereas nighttime scintillation is attributed to F layer irregularities. Scintillation events associated with Esbduring daytime are of our primary interest. Recent studies show that in the ionosphere, electron density profiles from Global Navigation Satellite System (GNSS) Radio Occultation (RO) provide valuable information to help better understand the physics of the ionosphere. In particular, GNSS RO observations of GHz scintillation in the proximity of the E-layer have been interpreted as being caused by sporadic E. In this paper the characteristics of daytime scintillations at 1.5 GHz recorded simultaneously from two stations (i) Universiti Kebangsaan Malaysia (UKM) (2.55°N, 101.461°E; dip latitude 5.78°S), and (ii) Langkawi (6.19°N, 99.51°E; dip latitude 1.90°S) during November and December 2010 are analyzed. The characteristics of daytime GHz scintillation and its relationship with E region irregularities at equatorial regions are investigated. Ground-based scintillation and Total Electron Content (TEC) data recorded by the GSV4004 receivers were utilized in combination with the amplitude scintillation measurements in terms of GPS C/A code SNR fluctuations during a ground-based GPS and space-borne GNSS RO experiment at the two equatorial stations. Scintillation activity was found to be more prominent at UKM. Moreover, strong scintillation with the S4 index exceeding 0.6 has only been observed at UKM, while at Langkawi the scintillation intensity (S4 index) did not exceed 0.3. Signal-to-noise measurements obtained from GNSS RO indicate that daytime scintillations are very likely caused by Esb. Our

  4. Characterization of ceramic product of the Apodi region in Rio Grande do Norte, Brazil

    International Nuclear Information System (INIS)

    Due to the great precariousness of information on ceramics products, as the brick of Rio Grande do Norte state, the purpose of this work was to analyze the physical and mechanical characteristics of ceramic bricks for construction manufactured in Assu region of the state. Therefore, samples were collected in cities belonging to different potters poles. The bricks were subjected to several tests: visual, absorption, suction, compressive strength, dimensions and flatness deviation from the square. According to ABNT standard, the products need some improvement in quality

  5. Characterization of Moringa oleifera seed oil from drought and irrigated regions of Punjab, Pakistan

    Directory of Open Access Journals (Sweden)

    Rashid, Umer

    2006-06-01

    Full Text Available The aim of the present study was to investigate the composition of M.oleifera seed oil from drought and irrigated regions of Pakistan. The hexane-extracted oil content of M.oleifera seeds harvested from one drought (Layyah and two irrigated regions (Rahim Yar Khan, Jhang of Punjab, Pakistan was found to be 30.36 and 35.26, 38.37% respectively. Results of physical and chemical parameters of the extracted oils were as follows: iodine value, 65.86 and 70.50, 67.86; refractive index (40°C, 1.4570 and 1.4582,1.4581; density (24°C, 0.9059 and 0.9069, 0.9002 mg mL-1; saponification value,  181.1 and 183.7, 183.1; unsaponifaiable matter, 0.84 and 0.85, 0.97%; acidity (as oleic acid 0.28 and 0.35, 0.33%.The induction period (Rancimat 20L/h, 120 °C of the M.oleifera oil from the drought region was significantly higher (9.63 h as compared with those of irrigated regions (8.74, 8.33 h. Specific extinctions at 232 and 270 nm were 1.92 and 1.98, 1.68; 1.02 and 0.97, 0.75 respectively. The overall contents of tocopherols (α, γ and δ, which did not differ significantly in the Moringa oils from both regions ranged from 95.85-103.80, 80.26-86.56 and 55.75-64.55 mg kg-1 respectively. Fatty acid profiles of the M.oleifera oils from drought and irrigated regions of Punjab consisted in a high level of oleic acid (up to 72.68 and 75.55, 74.66 % followed by palmitic and behenic acid (up to 9.26 and 8.76, 9.20 and 5.46 and 3.72, 4.53 % respectively. Results of various physical and chemical parameters of the investigated M.oleifera seed oils revealed that drought is one of the most visible factors that have amplified the induction period and C22:0 content of the oils and reduced seed weight, oil yield, iodine value and C18:1 content.La intención del presente estudio ha sido la de investigar la composición del aceite obtenido de la semilla de M. oleifera cultivada en regiones de secano y de regadío Paquistaní. El contenido de aceite extraído de estas semillas

  6. Genetic characterization of DNA region containing the trh and ure genes of Vibrio parahaemolyticus.

    Science.gov (United States)

    Park, K S; Iida, T; Yamaichi, Y; Oyagi, T; Yamamoto, K; Honda, T

    2000-10-01

    We have demonstrated that possession of the gene for thermostable direct hemolysin-related hemolysin (trh) coincides with the presence of the urease gene among clinical Vibrio parahaemolyticus strains and that the location of the two genes are in close proximity on the chromosome. Here, we cloned and sequenced the 15,754-bp DNA region containing the trh gene and the gene cluster for urease production from the chromosome of clinical V. parahaemolyticus (TH3996). We found 16 open reading frames (ORFs) and a lower G+C content (41%) compared with the total genome of this bacterium (46 to 47%). The ure cluster consisted of eight genes, namely, ureDABCEFG and ureR. ureR was located 5.2 kb upstream of the other seven genes in the opposite direction. The genetic organization and sequences of the ure genes resembled those found in Proteus mirabilis. Between ureR and the other ure genes, there were five ORFs, which are homologous with the nickel transport operon (nik) of Escherichia coli. We disrupted each of the ureR, ureC, and nikD genes in TH3996 by homologous recombination and analyzed the phenotype of the mutants. In the presence of urea these mutant strains had dramatically less urease activity than the strain they were derived from. Disruption of ureR, nikD, or ureC, however, had no effect on TRH production. The DNA region containing the trh, nik, and ure genes was found in only trh-positive strains and not in Kanagawa phenomenon-positive and environmental V. parahaemolyticus strains. At the end of the region, an insertion sequence-like element existed. These results suggest that the DNA region was introduced into V. parahaemolyticus in the past through a mechanism mediated by insertion sequences. This is the first reported case that the genes for an ATP-binding cassette-type nickel transport system, which may play a role in nickel transport through bacterial cytoplasmic membrane, are located adjacent to the ure cluster on the genome of an organism. PMID:10992480

  7. Characterization of intracellular regions in the human serotonin transporter for phosphorylation sites

    DEFF Research Database (Denmark)

    Sørensen, Lena; Strømgaard, Kristian; Kristensen, Anders S

    2014-01-01

    /dephosphorylation during transporter regulation by multiple pathways. In particular, activation and/or inhibition of kinases including PKC, PKG, p38MAPK, and CaMKII modulate SERT function and trafficking. The molecular mechanisms by which kinase activity is linked to SERT regulation are poorly understood, including the...... identity of specific phosphorylated residues. To elucidate SERT phosphorylation sites, we have generated peptides corresponding to the entire intracellular region of human SERT and performed in vitro phosphorylation assays with a panel of kinases suggested to be involved in SERT regulation or for which...

  8. Genetic variation, linkage mapping of QTL and correlation studies for yield, root, and agronomic traits for aerobic adaptation

    OpenAIRE

    Sandhu, Nitika; Jain, Sunita; Kumar, Arvind; Mehla, Balwant Singh; Jain, Rajinder

    2013-01-01

    Background Water scarcity and drought have seriously threatened traditional rice cultivation practices in several parts of the world, including India. Aerobic rice that uses significantly less water than traditional flooded systems has emerged as a promising water-saving technology. The identification of QTL conferring improved aerobic adaptation may facilitate the development of high-yielding aerobic rice varieties. In this study, experiments were conducted for mapping QTL for yield, root-re...

  9. 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.

  10. A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer

    OpenAIRE

    Wang, Chun Ming; Bai, Zhi Yi; He, Xiao Ping; Lin, Grace; Xia, Jun Hong; Sun, Fei; Lo, Loong Chueng; Feng, Felicia; Zhu, Ze Yuan; Yue, Gen Hua

    2011-01-01

    Background High density linkage maps are essential for comparative analysis of synteny, fine mapping of quantitative trait loci (QTL), searching for candidate genes and facilitating genome sequence assembly. However, in most foodfish species, marker density is still low. We previously reported a first generation linkage map with 240 DNA markers and its application to preliminarily map QTL for growth traits in Asian seabass (Lates calcarifer). Here, we report a high-resolution linkage map with...

  11. Biomechanical testing and material characterization for the rat large intestine: regional dependence of material parameters

    International Nuclear Information System (INIS)

    The function of the large bowel is to absorb water from the remaining indigestible food matter and subsequently pass useless waste material from the body, but there has been only a small amount of data in the literature on its biomechanical characteristics that would facilitate our understanding of its transport function. Our study aims to fill this gap by affording comprehensive inflation/extension data of intestinal segments from distinct areas, spanning a physiologically relevant deformation range (100–130% axial stretches and 0–15 mmHg lumen pressures). These data were characterized by the Fung-type exponential model in the thick-walled setting, showing reasonable agreement, i.e. root-mean-square error ∼30%. Based on optimized material parameters, i.e. a1

  12. Characterization of cosmic rays and direction dependence in the Polar Region up to 88 km altitude

    Science.gov (United States)

    Zábori, Balázs; Hirn, Attila; Deme, Sándor; Apáthy, István; Pázmándi, Tamás

    2016-02-01

    Aims: The sounding rocket experiment REM-RED was developed to operate on board the REXUS-17 rocket in order to measure the intensity of cosmic rays. The experiment was launched from the ESRANGE Space Center (68 °N, 21 °E) on the 17th of March 2015 at the beginning of the most intense geomagnetic storm within the preceding 10 years. The experiment provided the opportunity to measure the intensity of cosmic rays in the Polar Region up to an altitude of 88 km above sea level. Methods: The experiment employed Geiger-Müller (GM) counters oriented with their axes perpendicular to each other in order to measure the cosmic ray intensity during the flight of the rocket. This measurement setup allowed performing direction-sensitive measurements as well. During the ascent phase the rocket was spinning and hence stabilized along its longitudinal axis looking close to the zenith direction. This phase of the flight was used for studying the direction dependence of the charged particle component of the cosmic rays. Results: In comparison with earlier, similar rocket experiments performed with GM tubes at lower geomagnetic latitudes, significantly higher cosmic radiation flux was measured above 50 km. A non-isotropic behavior was found below 50 km and described in detail for the first time in the Polar Region. This behavior is in good agreement with the results of the TECHDOSE experiment that used the same type of GM tubes on board the BEXUS-14 stratospheric balloon.

  13. PHENOTIPIC AND GENOTIPIC CHARACTERIZATION OF SALMONELLA SPP ISOLATED FROM MOLLUSCAN SHELLFISH IN MARCHE REGION

    Directory of Open Access Journals (Sweden)

    S. Fisichella

    2009-06-01

    Full Text Available Salmonella enterica is a major epidemic cause of gastrointestinal infection worldwide. Although the animal host is believed to be the primary habitat of this specie, Salmonella is frequently isolated from water sources and it has been identified in marine environments. In this study the incidence of serotypes of Salmonella in the coastal water of the Italian region of Marche on the Adriatic Sea was evaluated. A total of 3985 samples of molluscan shellfish were analyzed during routine surveillance activity for a period of five years (2002-2007 and 0,95% of the samples were found contaminated with Salmonella. The most prevalent serotypes were Seftenberg (23.5%, Typhimurium (14,7% and Enteritidis (11.8% respectively. Pulsed-field electrophoresis and phage typing were used to determine possible genetic relationship (relatedness between S. Enteritidis strains isolated from bivalve mollusc and those isolated from human cases, animals and foods in Region of Marche. Three isolates from mollusc shellfish, 7 from sporadic human infection and 4 from poultry farms were confirmed as phagetype PT2 and PFGE profile XB0002. These results suggest a molecular fingerprinting relationship among shellfish, human and animal isolates, which could be considered as preliminary evidence of human infections associated with poultry production industry.

  14. Characterization of cosmic rays and direction dependence in the Polar Region up to 88 km altitude

    Directory of Open Access Journals (Sweden)

    Zábori Balázs

    2016-01-01

    Full Text Available Aims: The sounding rocket experiment REM-RED was developed to operate on board the REXUS-17 rocket in order to measure the intensity of cosmic rays. The experiment was launched from the ESRANGE Space Center (68 °N, 21 °E on the 17th of March 2015 at the beginning of the most intense geomagnetic storm within the preceding 10 years. The experiment provided the opportunity to measure the intensity of cosmic rays in the Polar Region up to an altitude of 88 km above sea level. Methods: The experiment employed Geiger-Müller (GM counters oriented with their axes perpendicular to each other in order to measure the cosmic ray intensity during the flight of the rocket. This measurement setup allowed performing direction-sensitive measurements as well. During the ascent phase the rocket was spinning and hence stabilized along its longitudinal axis looking close to the zenith direction. This phase of the flight was used for studying the direction dependence of the charged particle component of the cosmic rays. Results: In comparison with earlier, similar rocket experiments performed with GM tubes at lower geomagnetic latitudes, significantly higher cosmic radiation flux was measured above 50 km. A non-isotropic behavior was found below 50 km and described in detail for the first time in the Polar Region. This behavior is in good agreement with the results of the TECHDOSE experiment that used the same type of GM tubes on board the BEXUS-14 stratospheric balloon.

  15. Characterization and calibration of compact array spectrometers in the ultraviolet spectral region

    International Nuclear Information System (INIS)

    Array-based spectrometers, with their compact size, low weight, low cost, and fast measurement time, are now frequently used in place of both conventional single-channel scanning monochromators, and broadband meters. Their rapid measurement capability makes them an attractive option for routine solar UV spectral measurements, where shortterm variability in signal is a challenge. However, compactness, portability, low cost and high speed are achieved at the expense of the spectrometer's optical and electronic performance. Thus such spectrometers are more prone to measurement error from environmental changes, and more prone to other intrinsic sources of error such as stray light and detector non-linearity, which significantly affect solar UV measurements, than a scanning monochromator. The effects of stray light and non-linearity can be reduced either by improved optical and detector design or by a detailed spectrometer characterization. We present in this paper our investigation of the performance of three different commercial array spectrometers: two mini-spectrometers, and a more elaborate array spectrometer with an on-board image amplifier device. These were tested for a subset of performance parameters: their wavelength accuracy and stability, electronic linearity, responsivity linearity, stray light sensitivity, and mechanical stability and repeatability. With all three spectrometers we found that these parameters, particularly but not limited to stray light, had a significant impact on the measurement of the incoming optical radiation. This meant that, without characterization, the instruments would be unable to accurately measure the UV component of any source with significant visible radiation. We discuss various simple and low-cost solutions for improving the performance of these instruments, and providing a rigorous calibration using a straightforward set-up including optical filters and the quasi-monochromatic light from a double monochromator.

  16. NMR Characterization and Membrane Interactions of the Loop Region of Kindlin-3 F1 Subdomain

    Science.gov (United States)

    Chua, Geok-Lin; Tan, Suet-Mien; Bhattacharjya, Surajit

    2016-01-01

    Kindlins-1,2 and 3 are FERM domain-containing cytosolic proteins involved in the activation and regulation of integrin-mediated cell adhesion. Apart from binding to integrin β cytosolic tails, kindlins and the well characterized integrin-activator talin bind membrane phospholipids. The ubiquitin-like F1 sub-domain of the FERM domain of talin contains a short loop that binds to the lipid membrane. By contrast, the F1 sub-domain of kindlins contains a long loop demonstrated binding to the membrane. Here, we report structural characterization and lipid interactions of the 83-residue F1 loop of kindlin-3 using NMR and optical spectroscopy methods. NMR studies demonstrated that the F1 loop of kindlin-3 is globally unfolded but stretches of residues assuming transient helical conformations could be detected in aqueous solution. We mapped membrane binding interactions of the F1 loop with small unilamellar vesicles (SUVs) containing either zwitterionic lipids or negatively charged lipids using 15N-1H HSQC titrations. These experiments revealed that the F1 loop of kindlin-3 preferentially interacted with the negatively charged SUVs employing almost all of the residues. By contrast, only fewer residues appeared to be interacted with SUVs containing neutral lipids. Further, CD and NMR data suggested stabilization of helical conformations and predominant resonance perturbations of the F1 loop in detergent containing solutions. Conformations of an isolated N-terminal peptide fragment, or EK21, of the F1 loop, containing a poly-Lys sequence motif, important for membrane interactions, were also investigated in detergent solutions. EK21 adopted a rather extended or β-type conformations in complex with negatively charged SDS micelles. To our knowledge, this is the first report describing the conformations and residue-specific interactions of kindlin F1 loop with lipids. These data therefore provide important insights into the interactions of kindlin FERM domain with membrane

  17. Identification of QTL with effects on fatty acid composition of meat in a Charolais x Holstein cross population.

    Science.gov (United States)

    Gutiérrez-Gil, B; Wiener, P; Richardson, R I; Wood, J D; Williams, J L

    2010-08-01

    A whole-genome scan was carried out to detect quantitative trait loci (QTL) influencing beef fatty acid composition using a CharolaisxHolstein population established using a balanced F2 and Backcross breeding design. The phenotypes considered in this study included a total of 24 fatty acid related traits determined in loin muscle samples of the 235 second-generation cross-bred bull calves of the herd. The QTL regression analysis performed, based on 165 microsatellite markers distributed across the 29 bovine autosomes, identified 34 QTL with F-ratios exceeding the 5% chromosome-wide significance threshold. Three of these QTL, one located on chromosome 1 (for the content on linoleic acid, C18:2n-6) and two on chromosome 10 (for the content of gamma-linoleic DPA-docosapentaenoic and DPA-docosapentaenoic, C20:3n-6 and C22:5n-3), also exceeded the 5% genome-wide significance level. A follow-up analysis correcting for intramuscular fat content showed that some of the QTL detected initially (e.g. those localised on chromosome 22) were influenced by fat deposition differences between the founder breeds. The coincident location of some of the linkage associations identified and QTL previously reported for beef fatty acid composition and other meat quality traits, in the same or other cattle populations, provides supporting evidence for the results reported here. PMID:20416790

  18. Cross-Characterization of Aerosol Properties from Multiple Spaceborne Sensors Facilitated by Regional Ground-Based Observations

    Science.gov (United States)

    Petrenko, Maksym; Ichoku, Charles; Leptoukh, Gregory

    2010-01-01

    Aerosol observations from space have become a standard source for retrieval of aerosol properties on both regional and global scales. Indeed, the large number of currently operational spaceborne sensors provides for unprecedented access to the most complete set of complimentary aerosol measurements ever to be available. Nonetheless, this resource remains under-utilized, largely due to the discrepancies and differences existing between the sensors and their aerosol products. To characterize the inconsistencies and bridge the gap that exists between the sensors, we have designed and implemented an online Multi-sensor Aerosol Products Sampling System (MAPSS) that facilitates the joint sampling of aerosol data from multiple sensors. MAPSS consistently samples aerosol products from multiple spaceborne sensors using a unified spatial and temporal resolution, where each dataset is sampled over Aerosol Robotic Network (AERONET) locations together with coincident AERONET data samples. In this way, MAPSS enables a direct cross-characterization and data integration between aerosol products from multiple sensors. Moreover, the well-characterized co-located ground-based AERONET data provides the basis for the integrated validation of these products.

  19. Characterization of the blob generation region and blobby transport in a stellarator

    Science.gov (United States)

    Fuchert, G.; Birkenmeier, G.; Ramisch, M.; Stroth, U.

    2016-05-01

    Filaments of increased pressure (‘blobs’) in the scrape-off layer of toroidally confined magnetized plasmas are studied in the context of fusion research due to their relevance for confinement and wall safety. Analytical models in simple toroidal magnetic field geometries have proven useful to get a quantitative understanding of blob dynamics in tokamaks. However, their direct applicability to the more complicated stellarator geometry is far less studied. The experiments presented here show that in the stellarator TJ-K blobs are field-aligned structures occurring in scrape-off layer regions of negative mean normal curvature, which is in agreement with common blob models. Furthermore, it is shown that in TJ-K, in accordance with findings from tokamaks, blobs account for a significant fraction of the turbulent scrape-off layer transport of the order of several tens of percent.

  20. Characterizing droughts under current and future climates in the Jordan River region

    Directory of Open Access Journals (Sweden)

    T. Törnros

    2013-05-01

    Full Text Available The Standardized Precipitation Index (SPI was applied in order to address the characteristics of current and future agricultural droughts in the Jordan River region located in the southeastern Mediterranean area. In the first step, the SPI was applied on spatially interpolated monthly precipitation data at multiple timescales, i.e. accumulated precipitation was considered over a number of timescales, for example: 1, 3, and 6 months. To investigate the performance of the drought index, correlation analyses were conducted with the Normalized Difference Vegetation Index (NDVI obtained from remote sensing. The results show that the 6 month SPI best explains the inter-annual variation of the NDVI. Hence, a timescale of 6 months is the most appropriate when addressing agricultural drought in the semi-arid region. In the second step, the 6 month SPI was applied to three climate projections based on the IPCC emission scenario A1B. When comparing the period 2031–2060 with 1961–1990, it is shown that the mean drought duration is projected to increase. Furthermore, the droughts are expected to become more severe because the frequency of severe and extreme droughts is projected to increase and the frequency of moderate drought is projected to decrease. To address the impact of drought on the agricultural sector, the irrigation water demand during drought was simulated with a hydrological model on a spatial resolution of 1 km. A large increase in the demand for irrigation water was simulated, showing that the agricultural sector is expected to become even more vulnerable to drought in the future.