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Sample records for characterize qtl regions

  1. Evolution of the polymorphism at molecular markers in QTL and non-QTL regions in selected chicken lines (Open Access publication

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    Bijma Piter

    2008-11-01

    Full Text Available Abstract We investigated the joint evolution of neutral and selected genomic regions in three chicken lines selected for immune response and in one control line. We compared the evolution of polymorphism of 21 supposedly neutral microsatellite markers versus 30 microsatellite markers located in seven quantitative trait loci (QTL regions. Divergence of lines was observed by factor analysis. Five supposedly neutral markers and 12 markers in theQTL regions showed Fst values greater than 0.15. However, the non-significant difference (P > 0.05 between matrices of genetic distances based on genotypes at supposedly neutral markers on the one hand, and at markers in QTL regions, on the other hand, showed that none of the markers in the QTL regions were influenced by selection. A supposedly neutral marker and a marker located in the QTL region on chromosome 14 showed temporal variations in allele frequencies that could not be explained by drift only. Finally, to confirm thatmarkers located inQTL regions on chromosomes 1, 7 and 14were under the influence of selection, simulations were performed using haplotype dropping along the existing pedigree. In the zone located on chromosome 14, the simulation results confirmed that selection had an effect on the evolution of polymorphism of markers within the zone.

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

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    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…

  3. Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean

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    Puji eLestari

    2013-06-01

    Full Text Available Understanding several modes of duplication contributing on the present genome structure is getting an attention because it could be related to numerous agronomically important traits. Since soybean serves as a rich protein source for animal feeds and human consumption, breeding efforts in soybean have been directed toward enhancing seed protein content. The publicly available soybean sequences and its genomically featured elements facilitate comprehending of quantitative trait loci (QTL for seed protein content in concordance with homeologous regions in soybean genome. Although parts of chromosome (Chr 20 and Chr 10 showed synteny, QTLs for seed protein content present only on Chr 20. Using comparative analysis of gene contents in recently duplicated genomic regions harboring QTL for protein/oil content on Chrs 20 and 10, a total of 27 genes are present in duplicated regions of both chromosomes. Notably, 4 tandem duplicates of the putative homeobox protein 22 (HB22 are present only on Chr 20 and this Medicago truncatula homolog expressed in endosperm at seed filling stage. These tandem duplicates could contribute on the protein/oil QTL of Chr 20. Our study suggests that non-shared gene contents within the duplicated genomic regions might lead to absence/presence of QTL related to protein/oil content.

  4. 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

  5. Investigation of QTL regions on Chromosome 17 for genes associated with meat color in the pig.

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    Fan, B; Glenn, K L; Geiger, B; Mileham, A; Rothschild, M F

    2008-08-01

    Previous studies have uncovered several significant quantitative trait loci (QTL) relevant to meat colour traits mapped at the end of SSC17 in the pig. Furthermore, results released from the porcine genome sequencing project have identified genes underlying the entire QTL regions and can further contribute to mining the region for likely causative genes. Ten protein coding genes or novel transcripts located within the QTL regions were screened for single nucleotide polymorphisms (SNPs). Linkage mapping and association studies were carried out in the ISU Berkshire x Yorkshire (B x Y) pig resource family. The total length of the new SSC17 linkage map was 126.6 cM and additional markers including endothelin 3 (EDN3) and phosphatase and actin regulator 3 (PHACTR3) genes were assigned at positions 119.4 cM and 122.9 cM, respectively. A new QTL peak was noted at approximately 120 cM, close to the EDN3 gene, and for some colour traits QTL exceeded the 5% chromosome-wise significance threshold. The association analyses in the B x Y family showed that the EDN3 BslI and PHACTR3 PstI polymorphisms were strongly associated with the subjective colour score and objective colour reflectance measures in the loin, as well as average drip loss percentage and pH value. The RNPC1 DpnII and CTCFL HpyCH4III polymorphisms were associated with some meat colour traits. No significant association between CBLN4, TFAP2C, and four novel transcripts and meat colour traits were detected. The association analyses conducted in one commercial pig line found that both EDN3 BslI and PHACTR3 PstI polymorphisms were associated with meat colour reflectance traits such as centre loin hue angle and Minolta Lightness score. The present findings suggested that the EDN3 and PHACTR3 genes might have potential effects on meat colour in pigs, and molecular mechanisms of their functions are worth exploring.

  6. 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.

  7. 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

  8. QTL Characterization of Fusarium Head Blight Resistance in CIMMYT Bread Wheat Line Soru#1.

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    Xinyao He

    Full Text Available Fusarium head blight (FHB resistant line Soru#1 was hybridized with the German cultivar Naxos to generate 131 recombinant inbred lines for QTL mapping. The population was phenotyped for FHB and associated traits in spray inoculated experiments in El Batán (Mexico, spawn inoculated experiments in Ås (Norway and point inoculated experiments in Nanjing (China, with two field trials at each location. Genotyping was performed with the Illumina iSelect 90K SNP wheat chip, along with a few SSR and STS markers. A major QTL for FHB after spray and spawn inoculation was detected on 2DLc, explaining 15-22% of the phenotypic variation in different experiments. This QTL remained significant after correction for days to heading (DH and plant height (PH, while another QTL for FHB detected at the Vrn-A1 locus on 5AL almost disappeared after correction for DH and PH. Minor QTL were detected on chromosomes 2AS, 2DL, 4AL, 4DS and 5DL. In point inoculated experiments, QTL on 2DS, 3AS, 4AL and 5AL were identified in single environments. The mechanism of resistance of Soru#1 to FHB was mainly of Type I for resistance to initial infection, conditioned by the major QTL on 2DLc and minor ones that often coincided with QTL for DH, PH and anther extrusion (AE. This indicates that phenological and morphological traits and flowering biology play important roles in resistance/escape of FHB. SNPs tightly linked to resistance QTL, particularly 2DLc, could be utilized in breeding programs to facilitate the transfer and selection of those QTL.

  9. Evolution of the polymorphism at molecular markers in QTL and non-QTL regions in selected chicken lines

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    Loywyck, V.; Bed'hom, B.; Pinard-van der Laan, M.H.; Pitel, F.; Verrier, E.; Bijma, P.

    2008-01-01

    We investigated the joint evolution of neutral and selected genomic regions in three chicken lines selected for immune response and in one control line. We compared the evolution of polymorphism of 21 supposedly neutral microsatellite markers versus 30 microsatellite markers located in seven quantit

  10. Most significant genome regions involved in the control of earliness traits in bread wheat, as revealed by QTL meta-analysis.

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    Hanocq, E; Laperche, A; Jaminon, O; Lainé, A-L; Le Gouis, J

    2007-02-01

    Earliness is one of the most important adaptation traits in plant breeding. Our purpose was to identify the genome regions of bread wheat involved in the control of earliness and its three components: photoperiod sensitivity (PS), vernalization requirement (VR) and intrinsic earliness (IE). A QTL meta-analysis was carried out to examine the replicability of QTL across 13 independent studies and to propose meta-QTL (MQTL). Initial QTL were projected on a recent consensus map (2004). Quality criteria were proposed to assess the reliability of this projection. These criteria were based on the distances between markers in the QTL regions. Chromosomes of groups 2 and 5 had a greater incidence on earliness control as they carry the known, major genes Ppd and Vrn. Other chromosome regions played an intermediate role in earliness control: 4A [heading date (HD) Meta-QTL], 4B (HD MQTL), 2B (VR MQTL) and 5B (IE MQTL). Markers at this four MQTL should prove helpful in marker-assisted selection, to better control earliness.

  11. 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

  12. 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.

  13. Quantitative trait loci (QTL study identifies novel genomic regions associated to Chiari-like malformation in Griffon Bruxellois dogs.

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    Philippe Lemay

    Full Text Available Chiari-like malformation (CM is a developmental abnormality of the craniocervical junction that is common in the Griffon Bruxellois (GB breed with an estimated prevalence of 65%. This disease is characterized by overcrowding of the neural parenchyma at the craniocervical junction and disturbance of cerebrospinal fluid (CSF flow. The most common clinical sign is pain either as a direct consequence of CM or neuropathic pain as a consequence of secondary syringomyelia. The etiology of CM remains unknown but genetic factors play an important role. To investigate the genetic complexity of the disease, a quantitative trait locus (QTL approach was adopted. A total of 14 quantitative skull and atlas measurements were taken and were tested for association to CM. Six traits were found to be associated to CM and were subjected to a whole-genome association study using the Illumina canine high density bead chip in 74 GB dogs (50 affected and 24 controls. Linear and mixed regression analyses identified associated single nucleotide polymorphisms (SNPs on 5 Canis Familiaris Autosomes (CFAs: CFA2, CFA9, CFA12, CFA14 and CFA24. A reconstructed haplotype of 0.53 Mb on CFA2 strongly associated to the height of the cranial fossa (diameter F and an haplotype of 2.5 Mb on CFA14 associated to both the height of the rostral part of the caudal cranial fossa (AE and the height of the brain (FG were significantly associated to CM after 10 000 permutations strengthening their candidacy for this disease (P = 0.0421, P = 0.0094 respectively. The CFA2 QTL harbours the Sall-1 gene which is an excellent candidate since its orthologue in humans is mutated in Townes-Brocks syndrome which has previously been associated to Chiari malformation I. Our study demonstrates the implication of multiple traits in the etiology of CM and has successfully identified two new QTL associated to CM and a potential candidate gene.

  14. Identification of candidate genes and mutations in QTL regions for chicken growth using bioinformatic analysis of NGS and SNP-chip data

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    Muhammad eAhsan

    2013-11-01

    Full Text Available Mapping of chromosomal regions harboring genetic polymorphisms that regulate complex traits is usually followed by a search for the causative mutations underlying the observed effects. This is often a challenging task even after fine mapping, as millions of base pairs including many genes will typically need to be investigated. Thus to trace the causative mutation(s there is a great need for efficient bioinformatic strategies. Here, we searched for genes and mutations regulating growth in the Virginia chicken lines – an experimental population comprising two lines that have been divergently selected for body weight at 56 days for more than 50 generations. Several QTL regions have been mapped in an F2 intercross between the lines, and the regions have subsequently been replicated and fine mapped using an Advanced Intercross Line. We have further analyzed the QTL regions where the largest genetic divergence between the High-Weight selected (HWS and Low-Weight selected (LWS lines was observed. Such regions, covering about 37% of the actual QTL regions, were identified by comparing the allele frequencies of the HWS and LWS lines using both individual 60K SNP chip genotyping of birds and analysis of read proportions from genome resequencing of DNA pools. Based on a combination of criteria including significance of the QTL, allele frequency difference of identified mutations between the selected lines, gene information on relevance for growth, and the predicted functional effects of identified mutations we propose here a subset of candidate mutations of highest priority for further evaluation in functional studies. The candidate mutations were identified within the GCG, IGFBP2, GRB14, CRIM1, FGF16, VEGFR-2, ALG11, EDN1, SNX6 and BIRC7 genes. We believe that the proposed method of combining different types of genomic information increases the probability that the genes underlying the observed QTL effects are represented among the candidate mutations

  15. Replication of long-bone length QTL in the F9-F10 LG,SM advanced intercross.

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    Norgard, Elizabeth A; Jarvis, Joseph P; Roseman, Charles C; Maxwell, Taylor J; Kenney-Hunt, Jane P; Samocha, Kaitlin E; Pletscher, L Susan; Wang, Bing; Fawcett, Gloria L; Leatherwood, Christopher J; Wolf, Jason B; Cheverud, James M

    2009-04-01

    Quantitative trait locus (QTL) mapping techniques are frequently used to identify genomic regions associated with variation in phenotypes of interest. However, the F(2) intercross and congenic strain populations usually employed have limited genetic resolution resulting in relatively large confidence intervals that greatly inhibit functional confirmation of statistical results. Here we use the increased resolution of the combined F(9) and F(10) generations (n = 1455) of the LG,SM advanced intercross to fine-map previously identified QTL associated with the lengths of the humerus, ulna, femur, and tibia. We detected 81 QTL affecting long-bone lengths. Of these, 49 were previously identified in the combined F(2)-F(3) population of this intercross, while 32 represent novel contributors to trait variance. Pleiotropy analysis suggests that most QTL affect three to four long bones or serially homologous limb segments. We also identified 72 epistatic interactions involving 38 QTL and 88 novel regions. This analysis shows that using later generations of an advanced intercross greatly facilitates fine-mapping of confidence intervals, resolving three F(2)-F(3) QTL into multiple linked loci and narrowing confidence intervals of other loci, as well as allowing identification of additional QTL. Further characterization of the biological bases of these QTL will help provide a better understanding of the genetics of small variations in long-bone length.

  16. Identification of genome regions controlling cotyledon, pod wall/seed coat and pod wall resistance to pea weevil through QTL mapping.

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    Aryamanesh, N; Zeng, Y; Byrne, O; Hardie, D C; Al-Subhi, A M; Khan, T; Siddique, K H M; Yan, G

    2013-11-15

    Pea weevil, Bruchus pisorum, is one of the limiting factors for field pea (Pisum sativum) cultivation in the world with pesticide application the only available method for its control. Resistance to pea weevil has been found in an accession of Pisum fulvum but transfer of this resistance to cultivated pea (P. sativum) is limited due to a lack of easy-to-use techniques for screening interspecific breeding populations. To address this problem, an interspecific population was created from a cross between cultivated field pea and P. fulvum (resistance source). Quantitative trait locus (QTL) mapping was performed to discover the regions associated with resistance to cotyledon, pod wall/seed coat and pod wall resistance. Three major QTLs, located on linkage groups LG2, LG4 and LG5 were found for cotyledon resistance explaining approximately 80 % of the phenotypic variation. Two major QTLs were found for pod wall/seed coat resistance on LG2 and LG5 explaining approximately 70 % of the phenotypic variation. Co-linearity of QTLs for cotyledon and pod wall/seed coat resistance suggested that the mechanism of resistance for these two traits might act through the same pathways. Only one QTL was found for pod wall resistance on LG7 explaining approximately 9 % of the phenotypic variation. This is the first report on the development of QTL markers to probe Pisum germplasm for pea weevil resistance genes. These flanking markers will be useful in accelerating the process of screening when breeding for pea weevil resistance.

  17. 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.

  18. Epistatic QTL pairs associated with meat quality and carcass composition traits in a porcine Duroc × Pietrain population

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    Jüngst Heinz

    2010-10-01

    Full Text Available Abstract Background Quantitative trait loci (QTL analyses in pig have revealed numerous individual QTL affecting growth, carcass composition, reproduction and meat quality, indicating a complex genetic architecture. In general, statistical QTL models consider only additive and dominance effects and identification of epistatic effects in livestock is not yet widespread. The aim of this study was to identify and characterize epistatic effects between common and novel QTL regions for carcass composition and meat quality traits in pig. Methods Five hundred and eighty five F2 pigs from a Duroc × Pietrain resource population were genotyped using 131 genetic markers (microsatellites and SNP spread over the 18 pig autosomes. Phenotypic information for 26 carcass composition and meat quality traits was available for all F2 animals. Linkage analysis was performed in a two-step procedure using a maximum likelihood approach implemented in the QxPak program. Results A number of interacting QTL was observed for different traits, leading to the identification of a variety of networks among chromosomal regions throughout the porcine genome. We distinguished 17 epistatic QTL pairs for carcass composition and 39 for meat quality traits. These interacting QTL pairs explained up to 8% of the phenotypic variance. Conclusions Our findings demonstrate the significance of epistasis in pigs. We have revealed evidence for epistatic relationships between different chromosomal regions, confirmed known QTL loci and connected regions reported in other studies. Considering interactions between loci allowed us to identify several novel QTL and trait-specific relationships of loci within and across chromosomes.

  19. Characterization of near-isogenic lines carrying QTL for high spikelet number with the genetic background of an indica rice variety IR64 (Oryza sativa L.).

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    Fujita, Daisuke; Tagle, Analiza G; Ebron, Leodegario A; Fukuta, Yoshimichi; Kobayashi, Nobuya

    2012-03-01

    Total spikelet number per panicle (TSN) is one of the most important traits associated with rice yield potential. This trait was assessed in a set of 334 chromosomal segment introgression lines (ILs: BC(3)-derived lines), developed from new plant type (NPT) varieties as donor parents and having the genetic background of an indica-type rice variety IR64. Among the 334 ILs, five lines which had different donor parents and showed significantly higher TSN than IR64 were used for genetic analysis. Quantitative trait locus (QTL) analysis was conducted using F(2) populations derived from crosses between IR64 and these ILs. As a result, a QTL for high TSN (one from each NPT donor variety) was detected on common region of the long arm of chromosome 4. The effect of the QTL was confirmed by an increase in TSN of five near-isogenic lines (NILs) developed in the present study. The variation in TSN was found among these NILs, attributing to the panicle architecture in the numbers of primary, secondary and tertiary branches. The NILs for TSN and the SSR markers linked to the TSN QTLs are expected to be useful materials for research and breeding to enhance the yield potential of rice varieties.

  20. 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

  1. 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.

  2. QTL Analysis in Tetraploid Cotton

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    QTL analyses were performed in tetraploid cotton.An interspecific F2 population consisting of 69 plants,which was developed from the cross between Gossypium hirsutum L.,cv.Handan 208(characterized as high fiber yield) and G.barbadense L.,cv.Pima 90(characterized as excellent fiber quality),was genotyped with SSR,RAPD,SRAP,and REMAP markers.A 1029-locus linkage map was

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

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    Miyakawa, Misato O; Mikheyev, Alexander S

    2015-11-01

    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 diversity of CSD

  4. 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.

  5. 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...

  6. 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

  7. QTL Analysis in Tetraploid Cotton

    Institute of Scientific and Technical Information of China (English)

    LIN Zhong-xu; HE Dao-hua; WANG Hong-mei

    2008-01-01

    @@ QTL analyses were performed in tetraploid cotton.An interspecific F2population consisting of 69 plants,which was developed from the cross between Gossypium hirsutum L.,cv.Handan 208 (characterized as high fiber yield) and G.barbadense L.,cv.Pima 90 (characterized as excellent fiber quality),was genotyped with SSR,RAPD,SRAP,and REMAP markers.A 1029-1ocus linkage map was constructed covering 5472.3 cM with an average distance of 5.32 cM between two markers.

  8. QTL mapping for Mediterranean corn borer resistance in European flint germplasm using recombinant inbred lines

    Directory of Open Access Journals (Sweden)

    Santiago Rogelio

    2010-03-01

    Full Text Available Abstract Background Ostrinia nubilalis (ECB and Sesamia nonagrioides (MCB are two maize stem borers which cause important losses in temperate maize production, but QTL analyses for corn borer resistance were mostly restricted to ECB resistance and maize materials genetically related (mapping populations derived from B73. Therefore, the objective of this work was to identify and characterize QTLs for MCB resistance and agronomic traits in a RILs population derived from European flint inbreds. Results Three QTLs were detected for stalk tunnel length at bins 1.02, 3.05 and 8.05 which explained 7.5% of the RILs genotypic variance. The QTL at bin 3.05 was co-located to a QTL related to plant height and grain humidity and the QTL at bin 8.05 was located near a QTL related to yield. Conclusions Our results, when compared with results from other authors, suggest the presence of genes involved in cell wall biosynthesis or fortification with effects on resistance to different corn borer species and digestibility for dairy cattle. Particularly, we proposed five candidate genes related to cell wall characteristics which could explain the QTL for stalk tunnelling in the region 3.05. However, the small proportion of genotypic variance explained by the QTLs suggest that there are also many other genes of small effect regulating MCB resistance and we conclude that MAS seems not promising for this trait. Two QTLs detected for stalk tunnelling overlap with QTLs for agronomic traits, indicating the presence of pleitropism or linkage between genes affecting resistance and agronomic traits.

  9. Cartographie fine de qtl de fertilite femelle chez les bovins laitiers franÇais

    OpenAIRE

    Ben Jemaa, Slim

    2009-01-01

    The aim of this thesis was to map finely female fertility (FF) QTL in the three main French dairy cattle breeds Prim'Holstein, Normande and Montbeliarde. The first step consisted in detecting QTL on 78 families in 12 genomic regions. Six FF QTL were found in Prim'Holstein and two in Normande breeds. In the second step of the study, the QTL on bovine chromosomes BTA01, BTA02, BTA03 and BTA21 were mapped on a sub-sample of 41 families and the confidence interval for BTA01 and BTA03 QTL was redu...

  10. QTL Information Table: 432 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available DHL CT9993-5-10-1-M IR62266-42-6-2 B CDO20 pha Nguyen, T.T., Klueva, N., Chamareck, V., Aarti, A., Magpanta...y, G., Millena, A.C., Pathan, M.S., and Nguyen, H.T. (2004). Saturation mapping of QTL regions and identific

  11. QTL Information Table: 435 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Interval DHL CT9993-5-10-1-M IR62266-42-6-2 A RG9 pha Nguyen, T.T., Klueva, N., Chamareck, V., Aarti, A., Ma...gpantay, G., Millena, A.C., Pathan, M.S., and Nguyen, H.T. (2004). Saturation mapping of QTL regions and ide

  12. QTL Information Table: 434 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available C)Interval DHL CT9993-5-10-1-M IR62266-42-6-2 A RG9 pha Nguyen, T.T., Klueva, N., Chamareck, V., Aarti, A., ...Magpantay, G., Millena, A.C., Pathan, M.S., and Nguyen, H.T. (2004). Saturation mapping of QTL regions and i

  13. QTL Information Table: 433 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available erval DHL CT9993-5-10-1-M IR62266-42-6-2 A RG257 R1261 pha Nguyen, T.T., Klueva, N., Chamareck, V., Aarti, A...., Magpantay, G., Millena, A.C., Pathan, M.S., and Nguyen, H.T. (2004). Saturation mapping of QTL regions an

  14. QTL Information Table: 430 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available DHL CT9993-5-10-1-M IR62266-42-6-2 B RG140 pha Nguyen, T.T., Klueva, N., Chamareck, V., Aarti, A., Magpantay..., G., Millena, A.C., Pathan, M.S., and Nguyen, H.T. (2004). Saturation mapping of QTL regions and identifica

  15. QTL Information Table: 431 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available al DHL CT9993-5-10-1-M IR62266-42-6-2 A C711 pha Nguyen, T.T., Klueva, N., Chamareck, V., Aarti, A., Magpant...ay, G., Millena, A.C., Pathan, M.S., and Nguyen, H.T. (2004). Saturation mapping of QTL regions and identifi

  16. Characterization of the Main Effects, Epistatic Effects and Their Environmental Interactions of QTL on the Genetic Basis of Plant Height and Heading Date in Rice

    Institute of Scientific and Technical Information of China (English)

    JIANG Gong-hao; XU Cai-guo; LI Xiang-hua; HE Yu-qing

    2005-01-01

    Main-effect QTL, epistatic effects and their interactions with environment are important genetic components of quantitative traits. In this study, we analyzed the QTL, epistatic effects and QTL by environment interactions (QE) underlying plant height and heading date, using a doubled-haploid (DH) population consisting of 190 lines from the cross between an indica parent Zhenshan 97 and a japonica parent Wuyujing 2, and tested in two-year replicated field trials. A genetic linkage map with 179 SSR (simple sequence repeat) marker loci was constructed. A mixed linear model approach was applied to detect QTL, digenic interactions and QEs for the two traits. In total, 20 main-effect QTLs, 9 digenic interactions involving 18 loci, and 5 QTL by environment interactions were found to be responsible for the two traits. No interactions were detected between the digenic interaction and environment. The amounts of variations explained by QTLs of main effect were 53.9% for plant height and 57.8% for heading date, larger than that explained by epistasis and QEs. However,the epistasis and QE interactions sometimes accounted for a significant part of phenotypic variation and should not be disregarded.

  17. A gene-based high-resolution comparative radiation hybrid map as a framework for genome sequence assembly of a bovine chromosome 6 region associated with QTL for growth, body composition, and milk performance traits

    Directory of Open Access Journals (Sweden)

    Laurent Pascal

    2006-03-01

    Full Text Available Abstract Background A number of different quantitative trait loci (QTL for various phenotypic traits, including milk production, functional, and conformation traits in dairy cattle as well as growth and body composition traits in meat cattle, have been mapped consistently in the middle region of bovine chromosome 6 (BTA6. Dense genetic and physical maps and, ultimately, a fully annotated genome sequence as well as their mutual connections are required to efficiently identify genes and gene variants responsible for genetic variation of phenotypic traits. A comprehensive high-resolution gene-rich map linking densely spaced bovine markers and genes to the annotated human genome sequence is required as a framework to facilitate this approach for the region on BTA6 carrying the QTL. Results Therefore, we constructed a high-resolution radiation hybrid (RH map for the QTL containing chromosomal region of BTA6. This new RH map with a total of 234 loci including 115 genes and ESTs displays a substantial increase in loci density compared to existing physical BTA6 maps. Screening the available bovine genome sequence resources, a total of 73 loci could be assigned to sequence contigs, which were already identified as specific for BTA6. For 43 loci, corresponding sequence contigs, which were not yet placed on the bovine genome assembly, were identified. In addition, the improved potential of this high-resolution RH map for BTA6 with respect to comparative mapping was demonstrated. Mapping a large number of genes on BTA6 and cross-referencing them with map locations in corresponding syntenic multi-species chromosome segments (human, mouse, rat, dog, chicken achieved a refined accurate alignment of conserved segments and evolutionary breakpoints across the species included. Conclusion The gene-anchored high-resolution RH map (1 locus/300 kb for the targeted region of BTA6 presented here will provide a valuable platform to guide high-quality assembling and

  18. 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.

  19. 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.

  20. Identification of unconditional and conditional QTL for oil, protein and starch content in maize

    Institute of Scientific and Technical Information of China (English)

    Yuqiu; Guo; Xiaohong; Yang; Subhash; Chander; Jianbing; Yan; Jun; Zhang; Tongming; Song; Jiansheng; Li

    2013-01-01

    Oil, protein and starch are key chemical components of maize kernels. A population of 245 recombinant inbred lines(RILs) derived from a cross between a high-oil inbred line, By804, and a regular inbred line, B73, was used to dissect the genetic interrelationships among oil, starch and protein content at the individual QTL level by unconditional and conditional QTL mapping. Combined phenotypic data over two years with a genetic linkage map constructed using 236 markers, nine, five and eight unconditional QTL were detected for oil, protein and starch content, respectively. Some QTL for oil, protein and starch content were clustered in the same genomic regions and the direction of their effects was consistent with the sign of their correlation. In conditional QTL mapping, 37(29/8) unconditional QTL were not detected or showed reduced effects, four QTL demonstrated similar effects under unconditional and conditional QTL mapping, and 17 additional QTL were identified by conditional QTL mapping. These results imply that there is a strong genetic relationship among oil, protein and starch content in maize kernels. The information generated in the present investigation could be helpful in marker-assisted breeding for maize varieties with desirable kernel quality traits.

  1. 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

    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 co...

  2. QTL mapping designs for aquaculture.

    NARCIS (Netherlands)

    Massault, C.; Bovenhuis, H.; Haley, C.S.; Koning, de D.J.

    2008-01-01

    Rapid development of genomics technology is providing new opportunities for genetic studies, including QTL mapping, in many aquaculture species. This paper investigates the strengths and limitations of QTL mapping designs for fish and shellfish under three different controlled breeding schemes. For

  3. 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.

  4. 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.

  5. Advances in QTL Mapping in Pigs

    Directory of Open Access Journals (Sweden)

    Max F. Rothschild, Zhi-liang Hu, Zhihua Jiang

    2007-01-01

    Full Text Available Over the past 15 years advances in the porcine genetic linkage map and discovery of useful candidate genes have led to valuable gene and trait information being discovered. Early use of exotic breed crosses and now commercial breed crosses for quantitative trait loci (QTL scans and candidate gene analyses have led to 110 publications which have identified 1,675 QTL. Additionally, these studies continue to identify genes associated with economically important traits such as growth rate, leanness, feed intake, meat quality, litter size, and disease resistance. A well developed QTL database called PigQTLdb is now as a valuable tool for summarizing and pinpointing in silico regions of interest to researchers. The commercial pig industry is actively incorporating these markers in marker-assisted selection along with traditional performance information to improve traits of economic performance. The long awaited sequencing efforts are also now beginning to provide sequence available for both comparative genomics and large scale single nucleotide polymorphism (SNP association studies. While these advances are all positive, development of useful new trait families and measurement of new or underlying traits still limits future discoveries. A review of these developments is presented.

  6. Fine mapping of multiple QTL using combined linkage and linkage disequilibrium mapping – A comparison of single QTL and multi QTL methods

    Directory of Open Access Journals (Sweden)

    Meuwissen Theo HE

    2007-04-01

    Full Text Available Abstract Two previously described QTL mapping methods, which combine linkage analysis (LA and linkage disequilibrium analysis (LD, were compared for their ability to detect and map multiple QTL. The methods were tested on five different simulated data sets in which the exact QTL positions were known. Every simulated data set contained two QTL, but the distances between these QTL were varied from 15 to 150 cM. The results show that the single QTL mapping method (LDLA gave good results as long as the distance between the QTL was large (> 90 cM. When the distance between the QTL was reduced, the single QTL method had problems positioning the two QTL and tended to position only one QTL, i.e. a "ghost" QTL, in between the two real QTL positions. The multi QTL mapping method (MP-LDLA gave good results for all evaluated distances between the QTL. For the large distances between the QTL (> 90 cM the single QTL method more often positioned the QTL in the correct marker bracket, but considering the broader likelihood peaks of the single point method it could be argued that the multi QTL method was more precise. Since the distances were reduced the multi QTL method was clearly more accurate than the single QTL method. The two methods combine well, and together provide a good tool to position single or multiple QTL in practical situations, where the number of QTL and their positions are unknown.

  7. Meta-analysis of QTL involved in silage quality of maize and comparison with the position of candidate genes.

    Science.gov (United States)

    Truntzler, M; Barrière, Y; Sawkins, M C; Lespinasse, D; Betran, J; Charcosset, A; Moreau, L

    2010-11-01

    A meta-analysis of quantitative trait loci (QTL) associated with plant digestibility and cell wall composition in maize was carried out using results from 11 different mapping experiments. Statistical methods implemented in "MetaQTL" software were used to build a consensus map, project QTL positions and perform meta-analysis. Fifty-nine QTL for traits associated with digestibility and 150 QTL for traits associated with cell wall composition were included in the analysis. We identified 26 and 42 metaQTL for digestibility and cell wall composition traits, respectively. Fifteen metaQTL with confidence interval (CI) smaller than 10 cM were identified. As expected from trait correlations, 42% of metaQTL for digestibility displayed overlapping CIs with metaQTL for cell wall composition traits. Coincidences were particularly strong on chromosomes 1 and 3. In a second step, 356 genes selected from the MAIZEWALL database as candidates for the cell wall biosynthesis pathway were positioned on our consensus map. Colocalizations between candidate genes and metaQTL positions appeared globally significant based on χ(2) tests. This study contributed in identifying key chromosomal regions involved in silage quality and potentially associated genes for most of these regions. These genes deserve further investigation, in particular through association mapping.

  8. 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.

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

    NARCIS (Netherlands)

    Lawrenson, K.; Li, Q.; Kar, S.; Seo, J.H.; Tyrer, J.; Spindler, T.J.; Lee, J. van der; Chen, Y; Karst, A.; Drapkin, R.; Aben, K.K.H.; Anton-Culver, H.; Antonenkova, N.; Baker, H.; Bandera, E.V.; Bean, Y.; Beckmann, M.W.; Berchuck, A.; Bisogna, M.; Bjorge, L.; Bogdanova, N.; Brinton, L.A.; Brooks-Wilson, A.; Bruinsma, F.; Butzow, R.; Campbell, I.G.; Carty, K.; Chang-Claude, J.; Chenevix-Trench, G.; Chen, A; Chen, Z.; Cook, L.S.; Cramer, D.W; Cunningham, J.M.; Cybulski, C.; Dansonka-Mieszkowska, A.; Dennis, J.; Dicks, E.; Doherty, J.A.; Dork, T.; Bois, A. du; Durst, M.; Eccles, D.; Easton, D.T.; Edwards, R.P.; Eilber, U.; Ekici, A.B.; Fasching, P.A.; Fridley, B.L.; Gao, Y.T.; Gentry-Maharaj, A.; Giles, G.G.; Glasspool, R.; Goode, E.L.; Goodman, M.T.; Grownwald, J.; Harrington, P.; Harter, P.; Hasmad, H.N.; Hein, A.; Heitz, F.; Hildebrandt, M.A.; Hillemanns, P.; Hogdall, E.; Hogdall, C.; Hosono, S.; Iversen, E.S.; Jakubowska, A.; James, P.; Jensen, A.; Ji, B.T.; Karlan, B.Y.; Kjaer, S. Kruger; Kelemen, L.E.; Kellar, M.; Kelley, J.L.; Kiemeney, L.A.; Krakstad, C.; Kupryjanczyk, J.; Lambrechts, D.; Lambrechts, S.; Le, N.D.; Lee, A.W.; Lele, S.; Leminen, A.; Lester, J.; Levine, D.A.; Liang, D.; Lissowska, J.; Lu, K.; Lubinski, J.; Lundvall, L.; Massuger, L.F.; Matsuo, K.; McGuire, V.; McLaughlin, J.R.; Nevanlinna, H.; McNeish, I.; Menon, U.; Modugno, F.

    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 associat

  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)Int... G. (2007). A Large-Effect QTL for Grain Yield under Reproductive-Stage Drought Stress in Upland Rice. Crop

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

    Directory of Open Access Journals (Sweden)

    Dhananjay Dhokane

    Full Text Available 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.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.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 report that the wheat

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

    Institute of Scientific and Technical Information of China (English)

    YUE; Genhua; (岳根华); Petra; Beeckmann; Gerhard; Moser; Elisabeth; Müller; Hans; Bartenschlager; Stanislav; Cepica; Jaroslav; Schroffel; Antonin; Stratil; Hermann; Geldermann

    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.

  13. Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL.

    Science.gov (United States)

    Cavanagh, Colin R; Jonas, Elisabeth; Hobbs, Matthew; Thomson, Peter C; Tammen, Imke; Raadsma, Herman W

    2010-09-16

    An (Awassi × Merino) × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL) for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1) and 3.5 (cohort 2) years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3), 15 significant (LOD ≥ 2), and 11 suggestive QTL (1.7 ≤ LOD < 2) were detected on eleven chromosomes. Regression analysis confirmed 28 of these QTL and an additional 17 suggestive (P < 0.1) and two significant (P < 0.05) QTL were identified using this method. QTL with pleiotropic effects for two or more tissues were identified on chromosomes 1, 6, 10, 14, 16 and 23. No tissue-specific QTL were identified.A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.

  14. Multiple Breed Validation of Five QTL Affecting Mastitis Resistance

    DEFF Research Database (Denmark)

    Vilkki, Johanna; Dolezal, Marlies A; Sahana, Goutam;

    (on BTA3, BTA6, BTA8, BTA19, and BTA27) agreed across the breeds, but no identical associated SNPs were detected. Higher power (imputation to bigger population samples) will be needed to confirm results. On BTA6 the results indicate several QTL within a 5 Mb region. The results provide a basis...

  15. 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.

  16. 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.

  17. Fusarium head blight resistance QTL in the spring wheat cross Kenyon/86ISMN 2137

    Directory of Open Access Journals (Sweden)

    Curt A McCartney

    2016-10-01

    Full Text Available Fusarium head blight (FHB, caused by Fusarium graminearum, is a very important disease of wheat globally. Damage caused by F. graminearum includes reduced grain yield, reduced grain functional quality, and results in the presence of the trichothecene mycotoxin deoxynivalenol in Fusarium-damaged kernels. The development of FHB resistant wheat cultivars is an important component of integrated management. The objective of this study was to identify QTL for FHB resistance in a recombinant inbred line (RIL population of the spring wheat cross Kenyon/86ISMN 2137. Kenyon is a Canadian spring wheat, while 86ISMN 2137 is an unrelated spring wheat. The RIL population was evaluated for FHB resistance in six FHB nurseries. Nine additive effect QTL for FHB resistance were identified, six from Kenyon and three from 86ISMN 2137. Rht8 and Ppd-D1a co-located with two FHB resistance QTL on chromosome arm 2DS. A major QTL for FHB resistance from Kenyon (QFhb.crc-7D was identified on chromosome 7D. The QTL QFhb.crc-2D.4 from Kenyon mapped to the same region as a FHB resistance QTL from Wuhan-1 on chromosome arm 2DL. This result was unexpected since Kenyon does not share common ancestry with Wuhan-1. Other FHB resistance QTL on chromosomes 4A, 4D, and 5B also mapped to known locations of FHB resistance. Four digenic epistatic interactions were detected for FHB resistance, which involved eight QTL. None of these QTL were significant based upon additive effect QTL analysis. This study provides insight into the genetic basis of native FHB resistance in Canadian spring wheat.

  18. 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.

  19. QTL for the thermotolerance effect of heat hardening, knowckdown resistance to heat and chill-coma recovery in an intercontinental set of recombinant inbred lines of Drosophila melanogaster

    DEFF Research Database (Denmark)

    Norry, Fabian M.; Scannapieco, Alejandra C.; Sambucetti, Pablo;

    2008-01-01

    The thermotolerance effect of heat hardening (also called short-term acclimation), knockdown resistance to high temperature (KRHT) with and without heat hardening and chill-coma recovery (CCR) are important phenotypes of thermal adaptation in insects and other organisms. Drosophila melanogaster......-hardened and nonhardened RIL. Composite interval mapping revealed a more complex genetic architecture for KRHT without heat-hardening than for KRHT in heat-hardened insects. Five quantitative trait loci (QTL) were found for KRHT, but only two of them were significant after heat hardening. KRHT and CCR showed trade...... decreased by heat hardening. We discuss candidate loci for each QTL. One HHE-QTL was found in the region of small heat-shock protein genes. However, HHE-QTL explained only a small fraction of the phenotypic variance. Most heat-resistance QTL did not colocalize with CCR-QTL. Large-effect QTL for CCR and KRHT...

  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. 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.

  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. Characterizing Site Hydrology (Region 10, Seattle, WA)

    Science.gov (United States)

    Hydrogeology is the foundation of subsurface site characterization for evaluations of monitored natural attenuation (MNA). Three case studies are presented. Examples of the potentially detrimental effects of drilling additives on ground-water samples from monitoring wells are d...

  4. 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

    2016-06-07

    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.

  5. 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...

  6. 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

    a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link this with information on published QTL. The starting point is a set...... of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH) 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 provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link...

  7. 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.

  8. 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.

  9. 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...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 ...

  10. 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 W.... 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 ...

  11. QTL Information Table: 734 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qtl12.1 Resistance or Tolerance Drought tolerance Flowering delay SSR C)Interval F3...). 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: 730 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qtl12.1 Resistance or Tolerance Drought tolerance Harvest index SSR C)Interval F3 W... 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: 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. ...

  14. QTL Information Table: 73 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available GS3 Morphological trait Seed small grain, CAPS A)Physical BC3F2 Minghui 63 Chuan 7 ...hang, Q. (2006). GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in

  15. Fine mapping and replication of QTL in outbred chicken advanced intercross lines

    Directory of Open Access Journals (Sweden)

    Andersson Leif

    2011-01-01

    Full Text Available Abstract Background Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F2 populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL, the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL are produced by repeated intercrossing of F2 animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature. Methods We have produced a nine-generation AIL pedigree (n = 1529 from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F2 population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight. Results Five of the nine QTL detected with the original F2 population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL. Conclusions Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that

  16. QTL mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower

    Science.gov (United States)

    Whitney, Kenneth D.; Broman, Karl W.; Kane, Nolan C.; Hovick, Stephen M.; Randell, Rebecca A.; Rieseberg, Loren H.

    2014-01-01

    The wild North American sunflowers Helianthus annuus and H. debilis are participants in one of the earliest identified examples of adaptive trait introgression, and the exchange is hypothesized to have triggered a range expansion in H. annuus. However, the genetic basis of the adaptive exchange has not been examined. Here, we combine quantitative trait locus (QTL) mapping with field measurements of fitness to identify candidate H. debilis QTL alleles likely to have introgressed into H. annuus to form the natural hybrid lineage H. a. texanus. Two 500-individual BC1 mapping populations were grown in central Texas, genotyped for 384 SNP markers, and then phenotyped in the field for two fitness and 22 herbivore resistance, ecophysiological, phenological, and architectural traits. We identified a total of 110 QTL, including at least one QTL for 22 of the 24 traits. Over 75% of traits exhibited at least one H. debilis QTL allele that would shift the trait in the direction of the wild hybrid H. a. texanus. We identified three chromosomal regions where H. debilis alleles increased both female and male components of fitness; these regions are expected to be strongly favored in the wild. QTL for a number of other ecophysiological, phenological, and architectural traits co-localized with these three regions and are candidates for the actual traits driving adaptive shifts. G × E interactions played a modest role, with 17% of the QTL showing potentially divergent phenotypic effects between the two field sites. The candidate adaptive chromosomal regions identified here serve as explicit hypotheses for how the genetic architecture of the hybrid lineage came into existence. PMID:25522096

  17. Linkage relationships among multiple QTL for horticultural traits and late blight (P. infestans) resistance on chromosome 5 introgressed from wild tomato Solanum habrochaites.

    Science.gov (United States)

    Haggard, J Erron; Johnson, Emily B; St Clair, Dina A

    2013-12-09

    When the allele of a wild species at a quantitative trait locus (QTL) conferring a desirable trait is introduced into cultivated species, undesirable effects on other traits may occur. These negative phenotypic effects may result from the presence of wild alleles at other closely linked loci that are transferred along with the desired QTL allele (i.e., linkage drag) and/or from pleiotropic effects of the desired allele. Previously, a QTL for resistance to Phytophthora infestans on chromosome 5 of Solanum habrochaites was mapped and introgressed into cultivated tomato (S. lycopersicum). Near-isogenic lines (NILs) were generated and used for fine-mapping of this resistance QTL, which revealed coincident or linked QTL with undesirable effects on yield, maturity, fruit size, and plant architecture traits. Subsequent higher-resolution mapping with chromosome 5 sub-NILs revealed the presence of multiple P. infestans resistance QTL within this 12.3 cM region. In our present study, these sub-NILs were also evaluated for 17 horticultural traits, including yield, maturity, fruit size and shape, fruit quality, and plant architecture traits in replicated field experiments over the course of two years. Each previously detected single horticultural trait QTL fractionated into two or more QTL. A total of 41 QTL were detected across all traits, with ∼30% exhibiting significant QTL × environment interactions. Colocation of QTL for multiple traits suggests either pleiotropy or tightly linked genes control these traits. The complex genetic architecture of horticultural and P. infestans resistance trait QTL within this S. habrochaites region of chromosome 5 presents challenges and opportunities for breeding efforts in cultivated tomato.

  18. Mapping Quantitative Trait Loci (QTL in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL

    Directory of Open Access Journals (Sweden)

    Thomson Peter C

    2010-09-01

    Full Text Available Abstract An (Awassi × Merino × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1 and 3.5 (cohort 2 years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3, 15 significant (LOD ≥ 2, and 11 suggestive QTL (1.7 ≤ LOD P P A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.

  19. Quantitative Trait Loci (QTL Analysis for Production Traits of Birth Weight and Weight 360 days in Backcross Sheep

    Directory of Open Access Journals (Sweden)

    ENDANG TRI MARGAWATI

    2006-03-01

    Full Text Available Four half-sib families (n = 382 consisting predominantly of ITT x Merino x Merino backcross progeny, including some F2 progeny were used to analyze QTL for two production traits (Birth weight = BW1 and Body weight at 360 days = BW360. The study exploited differences in weight performance between the Merino and ITT sheep. A total of 141 informative microsatellite markers were used in a genome-wide scan covering the 26 autosomal sheep chromosomes. QTL analysis was conducted online using QTL Express. This study reports the effect of QTL for birth weight on Chromosomes 5 (p < 0.05 at 112cM (0cM-128cM. Location of candidate genes for birth weight was predicted at the region of flanking markers MCM527-BMS1247. A QTL for BW360 days existed on Chromosome 18 (p < 0.01 at 104cM (25.0-125cM. Location of candidate genes related to production traits for body weight 360 days was predicted at the segment of flanking markers of CSSM018-TMR1. Only the QTL on Chromosome 18 retained significance (p < 0.01 under experiment-wide significance testing. This QTL region is being examined for candidate genes by investigating to the homologous human chromosomal segments.

  20. Genetic, physiological, and gene expression analyses reveal that multiple QTL enhance yield of rice mega-variety IR64 under drought.

    Directory of Open Access Journals (Sweden)

    B P Mallikarjuna Swamy

    Full Text Available BACKGROUND: Rice (Oryza sativa L. is a highly drought sensitive crop, and most semi dwarf rice varieties suffer severe yield losses from reproductive stage drought stress. The genetic complexity of drought tolerance has deterred the identification of agronomically relevant quantitative trait loci (QTL that can be deployed to improve rice yield under drought in rice. Convergent evidence from physiological characterization, genetic mapping, and multi-location field evaluation was used to address this challenge. METHODOLOGY/PRINCIPAL FINDINGS: Two pairs of backcross inbred lines (BILs from a cross between drought-tolerant donor Aday Sel and high-yielding but drought-susceptible rice variety IR64 were produced. From six BC4F3 mapping populations produced by crossing the +QTL BILs with the -QTL BILs and IR64, four major-effect QTL--one each on chromosomes 2, 4, 9, and 10--were identified. Meta-analysis of transcriptome data from the +QTL/-QTL BILs identified differentially expressed genes (DEGs significantly associated with QTL on chromosomes 2, 4, 9, and 10. Physiological characterization of BILs showed increased water uptake ability under drought. The enrichment of DEGs associated with root traits points to differential regulation of root development and function as contributing to drought tolerance in these BILs. BC4F3-derived lines with the QTL conferred yield advantages of 528 to 1875 kg ha⁻¹ over IR64 under reproductive-stage drought stress in the targeted ecosystems of South Asia. CONCLUSIONS/SIGNIFICANCE: Given the importance of rice in daily food consumption and the popularity of IR64, the BC4F3 lines with multiple QTL could provide higher livelihood security to farmers in drought-prone environments. Candidate genes were shortlisted for further characterization to confirm their role in drought tolerance. Differential yield advantages of different combinations of the four QTL reported here indicate that future research should include

  1. QTL Mapping of Kernel Number-Related Traits and Validation of One Major QTL for Ear Length in Maize.

    Science.gov (United States)

    Huo, Dongao; Ning, Qiang; Shen, Xiaomeng; Liu, Lei; Zhang, Zuxin

    2016-01-01

    The kernel number is a grain yield component and an important maize breeding goal. Ear length, kernel number per row and ear row number are highly correlated with the kernel number per ear, which eventually determines the ear weight and grain yield. In this study, two sets of F2:3 families developed from two bi-parental crosses sharing one inbred line were used to identify quantitative trait loci (QTL) for four kernel number-related traits: ear length, kernel number per row, ear row number and ear weight. A total of 39 QTLs for the four traits were identified in the two populations. The phenotypic variance explained by a single QTL ranged from 0.4% to 29.5%. Additionally, 14 overlapping QTLs formed 5 QTL clusters on chromosomes 1, 4, 5, 7, and 10. Intriguingly, six QTLs for ear length and kernel number per row overlapped in a region on chromosome 1. This region was designated qEL1.10 and was validated as being simultaneously responsible for ear length, kernel number per row and ear weight in a near isogenic line-derived population, suggesting that qEL1.10 was a pleiotropic QTL with large effects. Furthermore, the performance of hybrids generated by crossing 6 elite inbred lines with two near isogenic lines at qEL1.10 showed the breeding value of qEL1.10 for the improvement of the kernel number and grain yield of maize hybrids. This study provides a basis for further fine mapping, molecular marker-aided breeding and functional studies of kernel number-related traits in maize.

  2. An empirical method for establishing positional confidence intervals tailored for composite interval mapping of QTL.

    Directory of Open Access Journals (Sweden)

    Andrew Crossett

    Full Text Available BACKGROUND: Improved genetic resolution and availability of sequenced genomes have made positional cloning of moderate-effect QTL realistic in several systems, emphasizing the need for precise and accurate derivation of positional confidence intervals (CIs for QTL. Support interval (SI methods based on the shape of the QTL likelihood curve have proven adequate for standard interval mapping, but have not been shown to be appropriate for use with composite interval mapping (CIM, which is one of the most commonly used QTL mapping methods. RESULTS: Based on a non-parametric confidence interval (NPCI method designed for use with the Haley-Knott regression method for mapping QTL, a CIM-specific method (CIM-NPCI was developed to appropriately account for the selection of background markers during analysis of bootstrap-resampled data sets. Coverage probabilities and interval widths resulting from use of the NPCI, SI, and CIM-NPCI methods were compared in a series of simulations analyzed via CIM, wherein four genetic effects were simulated in chromosomal regions with distinct marker densities while heritability was fixed at 0.6 for a population of 200 isolines. CIM-NPCIs consistently capture the simulated QTL across these conditions while slightly narrower SIs and NPCIs fail at unacceptably high rates, especially in genomic regions where marker density is high, which is increasingly common for real studies. The effects of a known CIM bias toward locating QTL peaks at markers were also investigated for each marker density case. Evaluation of sub-simulations that varied according to the positions of simulated effects relative to the nearest markers showed that the CIM-NPCI method overcomes this bias, offering an explanation for the improved coverage probabilities when marker densities are high. CONCLUSIONS: Extensive simulation studies herein demonstrate that the QTL confidence interval methods typically used to positionally evaluate CIM results can be

  3. pain2: A neuropathic pain QTL identified on rat chromosome 2.

    Science.gov (United States)

    Nissenbaum, Jonathan; Shpigler, Hagai; Pisanté, Anne; DelCanho, Sonia; Minert, Anne; Seltzer, Ze'ev; Devor, Marshall; Darvasi, Ariel

    2008-03-01

    We aimed to locate a chronic pain-associated QTL in the rat (Rattus norvegicus) based on previous findings of a QTL (pain1) on chromosome 15 of the mouse (Mus musculus). The work was based on rat selection lines HA (high autotomy) and LA (low autotomy) which show a contrasting pain phenotype in response to nerve injury in the neuroma model of neuropathic pain. An F(2) segregating population was generated from HA and LA animals. Phenotyped F(2) rats were genotyped on chromosome 7 and chromosome 2, regions that share a partial homology with mouse chromosome 15. Our interval mapping analysis revealed a LOD score value of 3.63 (corresponding to p=0.005 after correcting for multiple testing using permutations) on rat chromosome 2, which is suggestive of the presence of a QTL affecting the predisposition to neuropathic pain. This QTL was mapped to the 14-26cM interval of chromosome 2. Interestingly, this region is syntenic to mouse chromosome 13, rather than to the region of mouse chromosome 15 that contains pain1. This chromosomal position indicates that it is possibly a new QTL, and hence we name it pain2. Further work is needed to replicate and to uncover the underlying gene(s) in both species.

  4. Quantitative trait locus (QTL mapping reveals a role for unstudied genes in Aspergillus virulence.

    Directory of Open Access Journals (Sweden)

    Julian K Christians

    Full Text Available Infections caused by the fungus Aspergillus are a major cause of morbidity and mortality in immunocompromised populations. To identify genes required for virulence that could be used as targets for novel treatments, we mapped quantitative trait loci (QTL affecting virulence in the progeny of a cross between two strains of A. nidulans (FGSC strains A4 and A91. We genotyped 61 progeny at 739 single nucleotide polymorphisms (SNP spread throughout the genome, and constructed a linkage map that was largely consistent with the genomic sequence, with the exception of one potential inversion of ∼527 kb on Chromosome V. The estimated genome size was 3705 cM and the average intermarker spacing was 5.0 cM. The average ratio of physical distance to genetic distance was 8.1 kb/cM, which is similar to previous estimates, and variation in recombination rate was significantly positively correlated with GC content, a pattern seen in other taxa. To map QTL affecting virulence, we measured the ability of each progeny strain to kill model hosts, larvae of the wax moth Galleria mellonella. We detected three QTL affecting in vivo virulence that were distinct from QTL affecting in vitro growth, and mapped the virulence QTL to regions containing 7-24 genes, excluding genes with no sequence variation between the parental strains and genes with only synonymous SNPs. None of the genes in our QTL target regions have been previously associated with virulence in Aspergillus, and almost half of these genes are currently annotated as "hypothetical". This study is the first to map QTL affecting the virulence of a fungal pathogen in an animal host, and our results illustrate the power of this approach to identify a short list of unknown genes for further investigation.

  5. Genetic background effects on QTL and QTL × environment interaction for yield and its component traits as revealed by reciprocal introgression lines in rice

    Institute of Scientific and Technical Information of China (English)

    Xiaoqian; Wang; Yunlong; Pang; Jian; Zhang; Qiang; Zhang; Yonghong; Tao; Bo; Feng; Tianqing; Zheng; Jianlong; Xu; Zhikang; Li

    2014-01-01

    QTLs for quantitative traits are influenced by genetic background(GB) and environment.Identification of QTL with GB independency and environmental stability is prerequisite for effective marker-assisted selection(MAS). In this study, QTLs and QTL × environment interactions affecting grain yield per plant(GY) and its component traits, filled grain number per panicle(FGN), panicle number per plant(PN) and 1000-grain weight(TGW) across six environments were dissected using two sets of reciprocal introgression lines(ILs) derived from the cross Lemont × Teqing and SNP genotypic data. ANOVA indicated that the differences among genotypes and environments within each set of ILs were highly significant for all traits. A total of 72 distinct QTLs for GY and its component traits including 15 for GY, 25 for FGN, 18 for PN, and 29 for TGW were detected over the six environments. Most QTLs(87.4%) showed significant QTL × environment interactions(QEIs) and appeared to be more or less environment-specific. Among 72 QTLs, 15(20.8%) QTLs and 12(16.7%) QEIs were commonly identified in both backgrounds, indicating QTL especially QEI for yield and its component traits had strong GB effects. Four QTL regions affecting GY and its component traits, including S1269707–S4288071, S16661497–S17511092, and S35861863–S36341768 on chromosome 3, and S4134205–S7643153 on chromosome 5, were detected in both backgrounds and coincided with cloned genes for yield-related traits. These regions can be the targeted in rice breeding for high yield potential through MAS. Application of QTL main effects and their environmental interaction effects in MAS was discussed in detail.

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. QTL Information Table: 453 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Source activity spikelet fertility RFLP C)Interval RIL Zhenshan...ison of QTL detection for yield traits using F2 and recombinant inbred lines in rice. Rice Genetics Newsletter 17, 49-51. ...

  12. QTL Information Table: 997 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qPTD-2 Morphological trait Panicle/flower peduncle top diameter RFLP C)Interval DHL...02). QTL analysis of rice peduncle vascular bundle system and panicle traits. Acta Bot Sinica 44, 301-306 ...

  13. 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 ...

  14. 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 ...

  15. 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 ...

  16. QTL Information Table: 692 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available , N., Takagi, K., Ichikawa, N., Maruoka, M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture and Its Ecological Significance in Asian Wild Rice. Breeding Science 57, 7-16. ...

  17. QTL Information Table: 841 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available gs. TAG Theoretical and Applied Genetics 102, 793-800. http://dx.doi.org/10.1007/s001220000467 ... ... function map: QTL analysis and comparison between QTLs and expressed sequence ta

  18. 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.

  19. Genome-wide linkage analysis of QTL for growth and body composition employing the PorcineSNP60 BeadChip

    Directory of Open Access Journals (Sweden)

    Fernández Ana I

    2012-05-01

    Full Text Available Abstract Background The traditional strategy to map QTL is to use linkage analysis employing a limited number of markers. These analyses report wide QTL confidence intervals, making very difficult to identify the gene and polymorphisms underlying the QTL effects. The arrival of genome-wide panels of SNPs makes available thousands of markers increasing the information content and therefore the likelihood of detecting and fine mapping QTL regions. The aims of the current study are to confirm previous QTL regions for growth and body composition traits in different generations of an Iberian x Landrace intercross (IBMAP and especially identify new ones with narrow confidence intervals by employing the PorcineSNP60 BeadChip in linkage analyses. Results Three generations (F3, Backcross 1 and Backcross 2 of the IBMAP and their related animals were genotyped with PorcineSNP60 BeadChip. A total of 8,417 SNPs equidistantly distributed across autosomes were selected after filtering by quality, position and frequency to perform the QTL scan. The joint and separate analyses of the different IBMAP generations allowed confirming QTL regions previously identified in chromosomes 4 and 6 as well as new ones mainly for backfat thickness in chromosomes 4, 5, 11, 14 and 17 and shoulder weight in chromosomes 1, 2, 9 and 13; and many other to the chromosome-wide signification level. In addition, most of the detected QTLs displayed narrow confidence intervals, making easier the selection of positional candidate genes. Conclusions The use of higher density of markers has allowed to confirm results obtained in previous QTL scans carried out with microsatellites. Moreover several new QTL regions have been now identified in regions probably not covered by markers in previous scans, most of these QTLs displayed narrow confidence intervals. Finally, prominent putative biological and positional candidate genes underlying those QTL effects are listed based on recent porcine

  20. Texas Barrier Islands Region ecological characterization: environmental synthesis papers

    Energy Technology Data Exchange (ETDEWEB)

    Shew, D.M.; Baumann, R.H.; Fritts, T.H.; Dunn, L.S.

    1981-09-01

    This report is a synthesis of selected environmental literature for the Texas Barrier Islands Region and is a part of the Texas Barrier Islands Region Ecological Characterization Study. The Texas Barrier Islands Region is defined to include the coastal counties and extends 64 km inland and offshore to the State-Federal demarcation. These papers deal with six drainage basins along the Texas coast: Galveston, Matagorda-Brazos, San Antonio, Copano-Aransas, Corpus Christi and Laguna Madre; as well as the marine system offshore. The papers address the geology, climate, hydrology and hydrography, and the biology of each basin.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. Mapping QTL for Traits Associated with Resistance to Ferrous Iron Toxicity in Rice (Oryza sativa L.),Using japonica Chromosome Segment Substitution Lines%利用粳稻染色体片段置换系群体检测水稻抗亚铁毒胁迫有关性状QTL

    Institute of Scientific and Technical Information of China (English)

    万建林; 翟虎渠; 万建民; 安井秀; 吉村淳

    2003-01-01

    A mapping population of 66 japonica chromosome segment substitution lines (CSSLs) in indica genetic background,derived from a cross between a japonica variety Asominori and an indica variety IR24 by the single-seed descent,backcrossing and marker-assisted selection,was used to detect quantitative trait loci (QTLs) for leaf bronzing index (LBI),stem dry weight (SDW),plant height (PH),root length (RL) and root dry weight (RDW) under Fe2+ stress condition in rice.Two parents and 66 japonica CSSLs were phenotyped for the traits by growing them in Fe2+ toxicity nutrient solution.A total of fourteen QTLs were detected on chromosome 3,6,7,9,11 and 12,respectively,with LOD of QTLs ranging from 2.72 to 6.63.Three QTLs controlling LBI were located at the region of C515~XNpb279,R2638~C1263 and G1465~C950 on chromosome 3,9 and 11,their contributions to whole variation were 16.45%,11.16% and 28.02%,respectively.Comparing with the other mapping results,the QTL for LBI located at the region of C515~XNpb279 on chromosome 3 was identical with the QTL for chlorophyll content on a rice function map.The results indicated that ferrous iron toxicity of rice is characterized by bronzing spots on the lower leaves,which spread over the whole leaves,causing the lower leaves to turn dark gray and to product chlorophyll catabolites or derivatives which reduce cytotoxicity of some heavy metals,such as ferrous iron.Futhermore,the QTL for LBI,SDW and RDW located at the region of G1465~C950 on chromosome 11 is a major QTL.Whether the QTL for SDW ,PH,RL and RDW at the region of XNpb386~XNpb342 on chromosome 6 is associated with resistance to ferrous iron toxicity need further studies.Our goal is to identify breeding materials for resistance to Fe2+ toxicity through marker-assisted selection based on the detected markers.%潜育性水稻田广泛分布于中国、斯里兰卡、印度、印度尼西亚、塞拉里昂、利比亚、尼日利亚、哥伦比亚和菲律宾等国,其

  8. Dynamic QTL analysis for fruit lycopene content and total soluble solid content in a Solanum lycopersicum x S. pimpinellifolium cross.

    Science.gov (United States)

    Sun, Y D; Liang, Y; Wu, J M; Li, Y Z; Cui, X; Qin, L

    2012-10-11

    Fruit lycopene content and total soluble solid content are important factors determining fruit quality of tomatoes; however, the dynamic quantitative trait loci (QTL) controlling lycopene and soluble solid content have not been well studied. We mapped the chromosomal regions controlling these traits in different periods in F(2:3) families derived from a cross between the domestic and wild tomato species Solanum lycopersicum and S. pimpinellifolium. Fifteen QTLs for lycopene and soluble solid content and other related traits analyzed at three different fruit ripening stages were detected with a composite interval mapping method. These QTLs explained 7-33% of the individual phenotypic variation. QTLs detected in the color-changing period were different from those detected in the other two periods. On chromosome 1, the soluble solid content QTL was located in the same region during the color-changing and full-ripe periods. On chromosome 4, the same QTL for lycopene content was found during the color-changing and full-ripe periods. The QTL for lycopene content on chromosome 4 co-located with the QTL for soluble solid content during the full-ripe period. Co-location of lycopene content QTL and soluble solid content QTLs may be due to pleiotropic effects of a single gene or a cluster of genes via physiological relationships among traits. On chromosome 9, the same two QTLs for lycopene content at two different fruit ripening periods may reflect genes controlling lycopene content that are always expressed in tomato fruit development.

  9. Mapping QTL for drought stress-induced premature senescence and maturity in cowpea [Vigna unguiculata (L.) Walp.].

    Science.gov (United States)

    Muchero, Wellington; Ehlers, Jeffrey D; Close, Timothy J; Roberts, Philip A

    2009-03-01

    Cowpea is an important crop for subsistence farmers in arid regions of Africa, Asia, and South America. Efforts to develop cultivars with improved productivity under drought conditions are constrained by lack of molecular markers associated with drought tolerance. Here, we report the mapping of 12 quantitative trait loci (QTL) associated with seedling drought tolerance and maturity in a cowpea recombinant inbred (RIL) population. One hundred and twenty-seven F(8) RILs developed from a cross between IT93K503-1 and CB46 were screened with 62 EcoR1 and Mse1 primer combinations to generate 306 amplified fragment length polymorphisms for use in genetic linkage mapping. The same population was phenotyped for maintenance of stem greenness (stg) and recovery dry weight (rdw) after drought stress in six greenhouse experiments. In field experiments conducted over 3 years, visual ratings and dry weights were used to phenotype drought stress-induced premature senescence in the RIL population. Kruskall-Wallis and multiple-QTL model mapping analysis were used to identify QTL associated with drought response phenotypes. Observed QTL were highly reproducible between stg and rdw under greenhouse conditions. Field studies confirmed all ten drought-response QTL observed under greenhouse conditions. Regions harboring drought-related QTL were observed on linkage groups 1, 2, 3, 5, 6, 7, 9, and 10 accounting for between 4.7 and 24.2% of the phenotypic variance (R(2)). Further, two QTL for maturity (R(2) = 14.4-28.9% and R(2) = 11.7-25.2%) mapped on linkage groups 7 and 8 separately from drought-related QTL. These results provide a platform for identification of genetic determinants of seedling drought tolerance in cowpea.

  10. 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.

  11. 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℃ 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(28QTL) 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 qVI4 b and qGE3 a 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.

  12. Regulatory variation at glypican-3 underlies a major growth QTL in mice.

    Directory of Open Access Journals (Sweden)

    Fiona Oliver

    2005-05-01

    Full Text Available The genetic basis of variation in complex traits remains poorly understood, and few genes underlying variation have been identified. Previous work identified a quantitative trait locus (QTL responsible for much of the response to selection on growth in mice, effecting a change in body mass of approximately 20%. By fine-mapping, we have resolved the location of this QTL to a 660-kb region containing only two genes of known function, Gpc3 and Gpc4, and two other putative genes of unknown function. There are no non-synonymous polymorphisms in any of these genes, indicating that the QTL affects gene regulation. Mice carrying the high-growth QTL allele have approximately 15% lower Gpc3 mRNA expression in kidney and liver, whereas expression differences at Gpc4 are non-significant. Expression profiles of the two other genes within the region are inconsistent with a factor responsible for a general effect on growth. Polymorphisms in the 3' untranslated region of Gpc3 are strong candidates for the causal sequence variation. Gpc3 loss-of-function mutations in humans and mice cause overgrowth and developmental abnormalities. However, no deleterious side-effects were detected in our mice, indicating that genes involved in Mendelian diseases also contribute to complex trait variation. Furthermore, these findings show that small changes in gene expression can have substantial phenotypic effects.

  13. QTL Mapping for Quality Traits of Chinese Dry Noodle

    Institute of Scientific and Technical Information of China (English)

    ZHAO Jing-lan; CHEN Min-sheng; MA Yan-ming; LI Rui-jun; REN Yong-pan; SUN Qing-quan; LI Si-shen

    2009-01-01

    The QTLs for quality traits of Chinese dry noodle(CDN)were mapped based on a population of recombinant inbred lines(RILs)derived from the cross between two Chinese winter wheat varieties,Chuan 35050 and Shannong 483.Sensory quality traits of CDN were tested according to the standard of Ministry of Commerce of P.R.China(SB/T10137-93),and the textural property traits were detected using a texture analyser(TA.XTplus).We have obtained 8 putative QTLs for 6 sensory quality traits and 2 QTLs for textural property of CDN with a single QTL explainning 4.07-75.67% of phenotypic variations on chromosomes 1A,1D,3D,4A,and 6D.A duster of 3 QTLs for palate,elasticity and smoothness of CDN was found near the Glu-D1 locus on chromosome 1D with high contributions.The increasing effect come from Chuan 35050,and the relationship between the QTLs were positive.On chromosome 4A,co-location QTLs for stickiness and total score were detected in the region of Xwmc420-Xswes620-Xswes615.Their contributions were high and the increasing effects come from Shannong 483.A taste QTL QStas.sdau-4A.1 was obtained in Xsrap18-Xswes624c-Xissr25b-Xissr23b on chromosome 4A with the highest contribution of 75.67%.This QTL was a major gene and the increasing effects come from Shannong 483.

  14. 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.

  15. Characterization of 3'-untranslated region of the mouse GDNF gene

    Directory of Open Access Journals (Sweden)

    Oh-hashi Kentaro

    2012-01-01

    Full Text Available Abstract Background Glial cell line-derived neurotrophic factor (GDNF is a potent survival factor for many cell types, and its expression is widespread both within and outside of the nervous system. The regulation of GDNF expression has been extensively investigated but is not fully understood. Results Using a luciferase reporter assay, we identified the role of the 3'-untranslated region (3'-UTR of the mouse GDNF gene in the regulation of gene expression. We focused on a well-conserved A- and T-rich region (approximately 200 bp in length, which is located approximately 1000 bp downstream of the stop codon in exon 4 of the gene and contains three typical AU-rich elements (AREs, AUUUA. Interestingly, these AREs are well conserved in several GDNF genes. By testing reporter constructs containing various regions and lengths of the 3'-UTR fused to the end of the luciferase gene, we demonstrated that the ARE-induced decrease in luciferase activity correlates with the attenuation of the mRNA stability. Furthermore, we found that several regions around the AREs in the 3'-UTR suppressed the luciferase activity. Moreover, the expression level of the GDNF protein was negligible in C6 glioma cells transfected with the ARE-containing GDNF expression vector. Conclusions Our study is the first characterization of the possible role of AREs and other suppressive regions in the 3'-UTR in regulating the amounts of GDNF mRNA in C6 cells.

  16. QTL map meets population genomics: an application to rice.

    Directory of Open Access Journals (Sweden)

    Jeffrey A Fawcett

    Full Text Available Genes involved in the transition from wild to cultivated crop species should be of great agronomic importance. Population genomic approaches utilizing genome resequencing data have been recently applied for this purpose, although it only reports a large list of candidate genes with no biological information. Here, by resequencing more than 30 genomes altogether of wild rice Oryza rufipogon and cultivated rice O. sativa, we identified a number of regions with clear footprints of selection during the domestication process. We then focused on identifying candidate domestication genes in these regions by utilizing the wealth of QTL information in rice. We were able to identify a number of interesting candidates such as transcription factors that should control key domestication traits such as shattering, awn length, and seed dormancy. Other candidates include those that might have been related to the improvement of grain quality and those that might have been involved in the local adaptation to dry conditions and colder environments. Our study shows that population genomic approaches and QTL mapping information can be used together to identify genes that might be of agronomic importance.

  17. Characterization of recombination in the HLA class II region

    Energy Technology Data Exchange (ETDEWEB)

    Cullen, M.; Carrington, M. [National Cancer Institute, Frederick, MD (United States); Noble, J. [Roche Molecular Systems, Almeda, CA (United States)] [and others

    1997-02-01

    Studies of linkage disequilibrium across the HLA class II region have been useful in predicting where recombination is most likely to occur. The strong associations between genes within the 85-kb region from DQB1 to DRB1 are consistent with low frequency of recombination in this segment of DNA. Conversely, a lack of association between alleles of TAP1 and TAP2 ({approximately}15 kb) has been observed, suggesting that recombination occurs here with relatively high frequency. Much of the HLA class II region has now been sequenced, providing the tools to undertake detailed analysis of recombination. Twenty-seven families containing one or two recombinant chromosomes within the 500-kb interval between the DPB1 and DRB1 genes were used to determine patterns of recombination across this region. SSCP analysis and microsatellite typing yielded identification of 127 novel polymorphic markers distributed throughout the class II region, allowing refinement of the site of crossover in 30 class II recombinant chromosomes. The three regions where recombination was observed most frequently are as follows: the 45-kb interval between HLA-DNA and RING3 (11 cases), the 50-kb interval between DQB3 and DQB1 (6 cases), and an 8.8-kb segment of the TAP2 gene (3 cases). Six of the 10 remaining recombinants await further characterization, pending identification of additional informative markers, while four recombinants were localized to other intervals (outliers). Analysis of association between markers flanking HLA-DNA to RING3 (45 kb), as well as TAP1 to TAP2 (15 kb), by use of independent CEPH haplotypes indicated little or no linkage disequilibrium, supporting the familial recombination data. A notable sequence motif located within a region associated with increased rates of recombination consisted of a (TGGA){sub 12} tandem repeat within the TAP2 gene. 74 refs., 3 figs., 2 tabs.

  18. Advances on methods for mapping QTL in plant

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yuan-Ming

    2006-01-01

    Advances on methods for mapping quantitative trait loci (QTL) are firstly summarized.Then, some new methods, including mapping multiple QTL, fine mapping of QTL, and mapping QTL for dynamic traits, are mainly described. Finally, some future prospects are proposed, including how to dig novel genes in the germplasm resource, map expression QTL (eQTL) by the use of all markers,phenotypes and micro-array data, identify QTL using genetic mating designs and detect viability loci. The purpose is to direct plant geneticists to choose a suitable method in the inheritance analysis of quantitative trait and in search of novel genes in germplasm resource so that more potential genetic information can be uncovered.

  19. Statistical properties of interval mapping methods on quantitative trait loci location: impact on QTL/eQTL analyses

    Directory of Open Access Journals (Sweden)

    Wang Xiaoqiang

    2012-04-01

    Full Text Available Abstract Background Quantitative trait loci (QTL detection on a huge amount of phenotypes, like eQTL detection on transcriptomic data, can be dramatically impaired by the statistical properties of interval mapping methods. One of these major outcomes is the high number of QTL detected at marker locations. The present study aims at identifying and specifying the sources of this bias, in particular in the case of analysis of data issued from outbred populations. Analytical developments were carried out in a backcross situation in order to specify the bias and to propose an algorithm to control it. The outbred population context was studied through simulated data sets in a wide range of situations. The likelihood ratio test was firstly analyzed under the "one QTL" hypothesis in a backcross population. Designs of sib families were then simulated and analyzed using the QTL Map software. On the basis of the theoretical results in backcross, parameters such as the population size, the density of the genetic map, the QTL effect and the true location of the QTL, were taken into account under the "no QTL" and the "one QTL" hypotheses. A combination of two non parametric tests - the Kolmogorov-Smirnov test and the Mann-Whitney-Wilcoxon test - was used in order to identify the parameters that affected the bias and to specify how much they influenced the estimation of QTL location. Results A theoretical expression of the bias of the estimated QTL location was obtained for a backcross type population. We demonstrated a common source of bias under the "no QTL" and the "one QTL" hypotheses and qualified the possible influence of several parameters. Simulation studies confirmed that the bias exists in outbred populations under both the hypotheses of "no QTL" and "one QTL" on a linkage group. The QTL location was systematically closer to marker locations than expected, particularly in the case of low QTL effect, small population size or low density of markers, i

  20. Characterization of microsatellite loci in the SLA class I region.

    Science.gov (United States)

    Chung, Hoyoung; McClure, Matthew Charles

    2011-04-01

    Microsatellite (MS) markers in the SLA-1 region were characterized via sequencing analysis with BAC clones generated from the National Institute of Health miniature pigs (MIPs). A total of 16 BAC clones were sequenced producing 15,228 shotgun reads, corresponding to 11.2 X sequencing coverage, that were used to construct a contig of 12.18 Mb in length. MS markers were compared with previously deposited GenBank sequences to verify the existence of 423 potential MS candidate markers in the SLA-1 region. Evaluation of these polymorphisms confirmed 59 markers in MIPs, and the combined data including sequences from GenBank revealed 155 polymorphic MS markers. MS markers identified from this analysis can be used to provide an alternative method to direct typing for determining an individual's SLA-1 haplotype.

  1. 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. ...

  2. 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. ...

  3. QTL Information Table: 917 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available RIL Nekken-1 IR36 RM5586 RM3916 RM3839 pha Ochiai, K., Uemura, S., Shimizu, A., Okumoto, Y., and Matoh, T. (...2008). Boron toxicity in rice (Oryza sativa L.). I. Quantitative trait locus (QTL) analysis of tolerance to boron toxicity. Theor Appl Genet 117, 125-133. ...

  4. QTL Information Table: 887 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available nd Yashima, S. (1998). Identification of QTL for salt tolerance in rice via molecular markers. . Chin. J. Rice Sci. 12, 72-78 ... ...segregated RIL Tesanai 2 CB A RG716 pha Lin, H.X., Yanagihara, S., Zhuang, J.Y., Senboku, T., Zheng, K.L., a

  5. QTL Information Table: 380 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available C)Interval RIL IR64 O. rufipogon (Acc 106424) B RG28 RM223 pha Nguyen, B.D., Brar, D.S., Bui, B.C., Nguyen,... T.V., Pham, L.N., and Nguyen, H.T. (2003). Identification and mapping of the QTL for aluminum tolerance int

  6. QTL Information Table: 381 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available re C)Interval RIL IR64 O. rufipogon (Acc 106424) B RG28 RM223 pha Nguyen, B.D., Brar, D.S., Bui, B.C., Nguye...n, T.V., Pham, L.N., and Nguyen, H.T. (2003). Identification and mapping of the QTL for aluminum tolerance i

  7. 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. ...

  8. 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

  9. 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

  10. QTL Information Table: 1041 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available yashi, H., Hirayama, M., Ohta, H., Nemoto, H., Kato, H., Ando, I., Ohtsubo, K., rsquo, ichi, Yano, M., and Imbe, T. (2007). QTL Detec...tion for Eating Quality Including Glossiness, Stickiness, Taste and Hardness of Cooked Rice. Breeding Science 57, 231-242. ...

  11. QTL Information Table: 1039 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available yashi, H., Hirayama, M., Ohta, H., Nemoto, H., Kato, H., Ando, I., Ohtsubo, K., rsquo, ichi, Yano, M., and Imbe, T. (2007). QTL Detec...tion for Eating Quality Including Glossiness, Stickiness, Taste and Hardness of Cooked Rice. Breeding Science 57, 231-242. ...

  12. QTL Information Table: 929 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available val RIL Bala Azucena B RZ2 G1465 C189 pha Price, A.H., Steele, K.A., Moore, B.J., Barraclough, P.P., and Clark, L.J. (2000). A combin...ed RFLP and AFLP linkage map of upland rice ( Oryza sativa L.) used to identify QTL

  13. 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

  14. 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

  15. 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

  16. 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. ...

  17. 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. ...

  18. 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. ...

  19. QTL Information Table: 752 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qGW3 Morphological trait Seed Grain width Mixture C)Interval F2 98SQ1496 Koshihikari 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. ...

  20. QTL Information Table: 626 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Shoot/Seedling Mesocotyl-length RFLP d)Co-segregated F2 Labelle Black Gora B RZ403 rgn Redofia, E.D., and Mackill, D.J. (1994). Identification and internal mapping of seedling vigor QTL's in rice. Rice Genetics Newsletter 11, 124-126. ...

  1. QTL Information Table: 210 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Seed Grain yield RFLP C)Interval RIL Zhenshan 97B Milyang 46 RG...138 RZ398 pha Zhuang, J.Y., Fan, Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2001). Comparison of the detection of QTL for yield trai

  2. QTL Information Table: 181 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Glu6 Physiological trait Eating quality glutelin subunit polypeptides A)Physical OS...JNBa0083F15 pha Xu, J.C., Li, J.Z., Zheng, X.W., Zou, L.X., and Zhu, L.H. (2001). QTL mapping of the root traits in rice seedling. Yi Chuan Xue Bao 28, 433-438. ...

  3. QTL Information Table: 321 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qCR-3 Physiological trait Source activity chlorophyll a/b ratio RFLP C)Interval RIL... Kinmaze DV85 B C25 R518 rgn Hu, M.L., Wang, C.M., Yang, Q.H., Zhai, H.Q., and Wan, J.M. (2004). QTL analysis for trait

  4. 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 C...711 G103 pha Xu, J.C., Li, J.Z., Zheng, X.W., Zou, L.X., and Zhu, L.H. (2001). QTL mapping of the root traits in rice seedling. Yi Chuan Xue Bao 28, 433-438. ...

  5. 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 RG...138 RZ398 rgn Zhuang, J.Y., Fan, Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Comparison of QTL detection for yield trait

  6. QTL Information Table: 322 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qCC-1 Physiological trait Source activity chlorophyll content of leaf RFLP C)Interv...al RIL Kinmaze DV85 B C122 R1012 rgn Hu, M.L., Wang, C.M., Yang, Q.H., Zhai, H.Q., and Wan, J.M. (2004). QTL analysis for trait

  7. 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...detection of QTL for yield traits in different generations of a rice cross using two mapping approaches. Yi Chuan Xue Bao 28, 458-464. ...

  8. 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 rgn Zhuang, J.Y., Fan, Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Comparison of QTL detection for yield trait

  9. QTL Information Table: 839 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available siological and agronomic characters on a rice function map: QTL analysis and compar...maru, K., Yano, M., Aoki, N., Ono, K., Hirose, T., Lin, S.Y., Monna, L., Sasaki, T., and Ohsugi, R. (2001). Toward the mapping of phy

  10. QTL Information Table: 823 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Resistance or Tolerance Other soil stress tolerance Plant height (Low N level, Soil... QTL × N-level interaction for plant height in rice (Oriza Sativa L.). Plant and Soil 236, 237-242. http://dx.doi.org/10.1023/A:1012787510201 ...

  11. QTL Information Table: 820 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Resistance or Tolerance Other soil stress tolerance Plant height (High N level, Soi...QTL × N-level interaction for plant height in rice (Oriza Sativa L.). Plant and Soil 236, 237-242. http://dx.doi.org/10.1023/A:1012787510201 ...

  12. QTL Information Table: 819 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Resistance or Tolerance Other soil stress tolerance Plant height (High N level, Soi.... QTL × N-level interaction for plant height in rice (Oriza Sativa L.). Plant and Soil 236, 237-242. http://dx.doi.org/10.1023/A:1012787510201 ...

  13. QTL Information Table: 360 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available H.C., McLaren, G., and Khush, G.S. (2003). Identification of QTL for growth- and ...Zheng, K.L., Liu, G.F., Wang, G.C., Sidhu, J.S., Srivantaneeyakul, S., Singh, V.P., Bagali, P.G., Prasanna,

  14. 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.

  15. 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.

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

    Directory of Open Access Journals (Sweden)

    Jennifer DeWoody

    Full Text Available 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

  17. 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

  18. 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.

  19. Data-driven assessment of eQTL mapping methods

    Directory of Open Access Journals (Sweden)

    Schughart Klaus

    2010-09-01

    Full Text Available Abstract Background The analysis of expression quantitative trait loci (eQTL is a potentially powerful way to detect transcriptional regulatory relationships at the genomic scale. However, eQTL data sets often go underexploited because legacy QTL methods are used to map the relationship between the expression trait and genotype. Often these methods are inappropriate for complex traits such as gene expression, particularly in the case of epistasis. Results Here we compare legacy QTL mapping methods with several modern multi-locus methods and evaluate their ability to produce eQTL that agree with independent external data in a systematic way. We found that the modern multi-locus methods (Random Forests, sparse partial least squares, lasso, and elastic net clearly outperformed the legacy QTL methods (Haley-Knott regression and composite interval mapping in terms of biological relevance of the mapped eQTL. In particular, we found that our new approach, based on Random Forests, showed superior performance among the multi-locus methods. Conclusions Benchmarks based on the recapitulation of experimental findings provide valuable insight when selecting the appropriate eQTL mapping method. Our battery of tests suggests that Random Forests map eQTL that are more likely to be validated by independent data, when compared to competing multi-locus and legacy eQTL mapping methods.

  20. 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

  1. 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.

  2. A genome scan for QTL affecting resistance to Haemonchus contortus in sheep.

    Science.gov (United States)

    Sallé, G; Jacquiet, P; Gruner, L; Cortet, J; Sauvé, C; Prévot, F; Grisez, C; Bergeaud, J P; Schibler, L; Tircazes, A; François, D; Pery, C; Bouvier, F; Thouly, J C; Brunel, J C; Legarra, A; Elsen, J M; Bouix, J; Rupp, R; Moreno, C R

    2012-12-01

    Gastrointestinal nematodes are one of the main health issues in sheep breeding. To identify loci affecting the resistance to Haemonchus contortus, a genome scan was carried out using 1,275 Romane × Martinik Black Belly backcross lambs. The entire population was challenged with Haemonchus contortus in 2 consecutive experimental infections, and fecal egg counts (FEC) and packed cell volumes were measured. A subgroup of 332 lambs with extreme FEC was necropsied to determine the total worm burden, length of female worms, sex ratio in the worm population, abomasal pH, and serum and mucosal G immunoglobulins (IgG) responses. Pepsinogen concentration was measured in another subset of 229 lambs. For QTL detection, 160 microsatellite markers were used as well as the Illumina OvineSNP50 BeadChip that provided 42,469 SNP markers after quality control. Linkage, association, and joint linkage and association analyses were performed with the QTLMAP software. Linkage disequilibrium (LD) was estimated within each pure breed, and association analyses were carried out either considering or not the breed origin of the haplotypes. Four QTL regions on sheep chromosomes (OAR)5, 12, 13, and 21 were identified as key players among many other QTL with small to moderate effects. A QTL on OAR21 affecting pepsinogen concentration exactly matched the pepsinogen (PGA5) locus. A 10-Mbp region affecting FEC after the 1st and 2nd infections was found on OAR12. The SNP markers outperformed microsatellites in the linkage analysis. Taking advantage of the LD helped to refine the locations of the QTL mapped on OAR5 and 13.

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

    Directory of Open Access Journals (Sweden)

    Riccardo Rinaldi

    2016-07-01

    Full Text Available 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

  4. QTL Information Table - Q-TARO | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ct character Category of object character Character Character Marker Type of marker...ta item Description id ID number of QTL QTL/Gene Name of QTL Major category Major category of quantitative character Category of obje

  5. QTL Information Table: 40 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available OSJNBb0074M06 RMw357 RMw353 C80 C1677 pha Wan, X.Y., Wan, J.M., Jiang, L., Wang, J.K., Zhai, H.Q., Weng, J.F., Wang,... H.L., Lei, C.L., Wang, J.L., Zhang, X., Cheng, Z.J., and Guo, X.P. (2006). QTL analysis for rice gr

  6. QTL Information Table: 677 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Gw2 Morphological trait Seed Grain weight Mixture A)Physical F2 WY3 Fengaizhan-1 AP005004 W024 W004 pha Song, X.J., Huang, W., Shi, M., Zhu, M.Z., and Lin, H.X. (2007). A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39, 623-630. ...

  7. 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 RG653 RG433 pha Xu, J.C., Li, J.Z., Zheng, X.W., Zou, L.X., and Zhu, L.H. (2001). QTL mapping of the root traits in rice seedling. Yi Chuan Xue Bao 28, 433-438. ...

  8. 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...... of milk production in the Czech Fleckvieh cattle....... 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...

  9. 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.

  10. 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...

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

    Science.gov (United States)

    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 illustrating the polygenic nature of these traits. QTLs for multiple traits co-localized and we identified eight hotspots for quantitative trait loci (QTL) of seed weight, seed germination, and root and shoot lengths. A QTL hotspot for seed germination on A02 mapped at the B. rapa Flowering Locus C (BrFLC2). Another hotspot on A05 with salt stress specific QTLs co-located with the B. rapa Fatty acid desaturase 2 (BrFAD2) locus. Epistatic interactions were observed between QTL hotspots for seed germination on A02 and A10 and with a salt tolerance QTL on A05. These results contribute to the understanding of the genetics of seed quality and seeding vigor in B. rapa and can offer tools for Brassica breeding.

  12. Integrating QTL mapping and transcriptomics identifies candidate genes underlying QTLs associated with soybean tolerance to low-phosphorus stress.

    Science.gov (United States)

    Zhang, Dan; Zhang, Hengyou; Chu, Shanshan; Li, Hongyan; Chi, Yingjun; Triebwasser-Freese, Daniella; Lv, Haiyan; Yu, Deyue

    2017-01-01

    Soybean is a high phosphorus (P) demand species that is sensitive to low-P stress. Although many quantitative trait loci (QTL) for P efficiency have been identified in soybean, but few of these have been cloned and agriculturally applied mainly due to various limitations on identifying suitable P efficiency candidate genes. Here, we combined QTL mapping, transcriptome profiling, and plant transformation to identify candidate genes underlying QTLs associated with low-P tolerance and response mechanisms to low-P stress in soybean. By performing QTL linkage mapping using 152 recombinant inbred lines (RILs) that were derived from a cross between a P-efficient variety, Nannong 94-156, and P-sensitive Bogao, we identified four major QTLs underlying P efficiency. Within these four QTL regions, 34/81 candidate genes in roots/leaves were identified using comparative transcriptome analysis between two transgressive RILs, low-P tolerant genotype B20 and sensitive B18. A total of 22 phosphatase family genes were up-regulated significantly under low-P condition in B20. Overexpression of an acid phosphatase candidate gene, GmACP2, in soybean hairy roots increased P efficiency by 15.43-24.54 % compared with that in controls. Our results suggest that integrating QTL mapping and transcriptome profiling could be useful for rapidly identifying candidate genes underlying complex traits, and phosphatase-encoding genes, such as GmACP2, play important roles involving in low-P stress tolerance in soybean.

  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. Identification of loci governing eight agronomic traits using a GBS-GWAS approach and validation by QTL mapping in soya bean.

    Science.gov (United States)

    Sonah, Humira; O'Donoughue, Louise; Cober, Elroy; Rajcan, Istvan; Belzile, François

    2015-02-01

    Soya bean is a major source of edible oil and protein for human consumption as well as animal feed. Understanding the genetic basis of different traits in soya bean will provide important insights for improving breeding strategies for this crop. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of agronomic traits in soya bean. A genotyping-by-sequencing (GBS) approach was used to provide dense genome-wide marker coverage (>47,000 SNPs) for a panel of 304 short-season soya bean lines. A subset of 139 lines, representative of the diversity among these, was characterized phenotypically for eight traits under six environments (3 sites × 2 years). Marker coverage proved sufficient to ensure highly significant associations between the genes known to control simple traits (flower, hilum and pubescence colour) and flanking SNPs. Between one and eight genomic loci associated with more complex traits (maturity, plant height, seed weight, seed oil and protein) were also identified. Importantly, most of these GWAS loci were located within genomic regions identified by previously reported quantitative trait locus (QTL) for these traits. In some cases, the reported QTLs were also successfully validated by additional QTL mapping in a biparental population. This study demonstrates that integrating GBS and GWAS can be used as a powerful complementary approach to classical biparental mapping for dissecting complex traits in soya bean.

  15. Genome-wide QTL mapping for three traits related to teat number in a White Duroc × Erhualian pig resource population

    Directory of Open Access Journals (Sweden)

    Ai Huashui

    2009-02-01

    Full Text Available Abstract Background Teat number is an important fertility trait for pig production, reflecting the mothering ability of sows. It is also a discrete and often canalized trait presenting bilateral symmetry with minor differences between the two sides, providing a potential power to evaluate fluctuating asymmetry and developmental instability. The knowledge of its genetic control is still limited. In this study, a genome-wide scan was performed with 183 microsatellites covering the pig genome to identify quantitative trait loci (QTL for three traits related to teat number including the total teat number (TTN, the teat number at the left (LTN and right (RTN sides in a large scale White Duroc × Erhualian resource population. Results A sex-average linkage map with a total length of 2350.3 cM and an average marker interval of 12.84 cM was constructed. Eleven genome-wide significant QTL for TTN were detected on 8 autosomes including pig chromosomes (SSC 1, 3, 4, 5, 6, 7, 8 and 12. Six suggestive QTL for this trait were detected on SSC6, 9, 13, 14 and 16. Eight chromosomal regions each on SSC1, 3, 4, 5, 6, 7, 8 and 12 showed significant associations with LTN. These regions were also evidenced as significant QTL for RTN except for those on SSC6 and SSC8. The most significant QTL for the 3 traits were all located on SSC7. Erhualian alleles at most of the identified QTL had positive additive effects except for three QTL on SSC1 and SSC7, at which White Duroc alleles increased teat numbers. On SSC1, 6, 9, 13 and 16, significant dominance effects were observed on TTN, and predominant imprinting effect on TTN was only detected on SSC12. Conclusion The results not only confirmed the QTL regions from previous experiments, but also identified five new QTL for the total teat number in swine. Minor differences between the QTL regions responsible for LTN and RTN were validated. Further fine mapping should be focused on consistently identified regions with small

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

    NARCIS (Netherlands)

    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 gard

  17. GWAS analysis of QTL for enteric septicemia of catfish and their involved genes suggest evolutionary conservation of a molecular mechanism of disease resistance.

    Science.gov (United States)

    Zhou, Tao; Liu, Shikai; Geng, Xin; Jin, Yulin; Jiang, Chen; Bao, Lisui; Yao, Jun; Zhang, Yu; Zhang, Jiaren; Sun, Luyang; Wang, Xiaozhu; Li, Ning; Tan, Suxu; Liu, Zhanjiang

    2017-02-01

    Disease problems cause major economic losses for the aquaculture industries. In catfish, enteric septicemia of catfish (ESC), caused by the bacterial pathogen Edwardsiella ictaluri, is the leading disease problem, causing tens of millions of dollars of annual economic losses. In this study, we conducted a genome-wide association study to determine quantitative trait loci (QTL) for resistance against ESC using an interspecific hybrid system. Five hundred fish were used in the analysis and 192 phenotypic extremes were used for genotyping with the catfish 250K SNP arrays. A genomic region on linkage group (LG) 1 was found significantly associated with ESC disease resistance. In addition, two suggestively associated QTL for ESC resistance were identified on LG 12 and LG 16. The nlrc3 duplicates were identified within all the three QTL, suggesting their importance in association with the QTL. Within the significant QTL on LG 1, 16 genes with known functions in immunity were identified. Of particular interest is the nck1 gene nearby the most significantly associated SNP. Nck1 was known to function as an adaptor to facilitating the pathogenesis of enteropathogenic Escherichia coli (EPEC) in humans. E. ictaluri and EPEC pathogens belong to the same bacterial family and share many common characteristics. The fact that nck1 is mapped in the QTL and that it was significantly upregulated in channel catfish intestine after ESC challenge suggested its candidacy of being involved in resistance/susceptibility of ESC.

  18. Dissection of Genetic Effects of Quantitative Trait Loci(QTL) in Transgenic Cotton

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    When alien DNA inserts into cotton genome in multi-copy manner,several QTL in cotton genome are disrupted,which are called dQTL in this study.Transgenic mutant line is near-isogenic to its recipient which is divergent for the dQTL from remaining QTL.So,a set of data from a transgenic

  19. 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.

  20. 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.

  1. Joint QTL mapping and gene expression analysis identify positional candidate genes influencing pork quality traits

    Science.gov (United States)

    González-Prendes, Rayner; Quintanilla, Raquel; Cánovas, Angela; Manunza, Arianna; Figueiredo Cardoso, Tainã; Jordana, Jordi; Noguera, José Luis; Pena, Ramona N.; Amills, Marcel

    2017-01-01

    Meat quality traits have an increasing importance in the pig industry because of their strong impact on consumer acceptance. Herewith, we have combined phenotypic and microarray expression data to map loci with potential effects on five meat quality traits recorded in the longissimus dorsi (LD) and gluteus medius (GM) muscles of 350 Duroc pigs, i.e. pH at 24 hours post-mortem (pH24), electric conductivity (CE) and muscle redness (a*), lightness (L*) and yellowness (b*). We have found significant genome-wide associations for CE of LD on SSC4 (~104 Mb), SSC5 (~15 Mb) and SSC13 (~137 Mb), while several additional regions were significantly associated with meat quality traits at the chromosome-wide level. There was a low positional concordance between the associations found for LD and GM traits, a feature that reflects the existence of differences in the genetic determinism of meat quality phenotypes in these two muscles. The performance of an eQTL search for SNPs mapping to the regions associated with meat quality traits demonstrated that the GM a* SSC3 and pH24 SSC17 QTL display positional concordance with cis-eQTL regulating the expression of several genes with a potential role on muscle metabolism. PMID:28054563

  2. A major QTL introgressed from wild Lycopersicon hirsutum confers chilling tolerance to cultivated tomato (Lycopersicon esculentum).

    Science.gov (United States)

    John Goodstal, F; Kohler, Glenn R; Randall, Leslie B; Bloom, Arnold J; St Clair, Dina A

    2005-09-01

    Many plants of tropical or subtropical origin, such as tomato, suffer damage under chilling temperatures (under 10 degrees C but above 0 degrees C). An earlier study identified several quantitative trait loci (QTLs) for shoot turgor maintenance (stm) under root chilling in an interspecific backcross population derived from crossing chilling-susceptible cultivated tomato (Lycopersicon esculentum) and chilling-tolerant wild L. hirsutum. The QTL with the greatest phenotypic effect on stm was located in a 28 cM region on chromosome 9 (designated stm 9), and enhanced chilling-tolerance was conferred by the presence of the Lycopersicon hirsutum allele at this QTL. Here, near-isogenic lines (NILs) were used to verify the effect of stm 9, and recombinant sub-NILs were used to fine map its position. Replicated experiments were performed with NILs and sub-NILs in a refrigerated hydroponic tank in the greenhouse. Sub-NIL data was analyzed using least square means separations, marker-genotype mean t-tests, and composite interval mapping. A dominant QTL controlling shoot turgor maintenance under root chilling was confirmed on chromosome 9 using both NILs and sub-NILs. Furthermore, sub-NILs permitted localization of stm 9 to a 2.7 cM interval within the original 28 cM QTL region. If the presence of the L. hirsutum allele at stm 9 also confers chilling-tolerance in L. esculentum plants grown under field conditions, it has the potential to expand the geographic areas in which cultivated tomato can be grown for commercial production.

  3. High-resolution mapping of a major effect QTL from wild tomato Solanum habrochaites that influences water relations under root chilling.

    Science.gov (United States)

    Arms, Erin M; Bloom, Arnold J; St Clair, Dina A

    2015-09-01

    QTL stm9 controlling rapid-onset water stress tolerance in S. habrochaites was high-resolution mapped to a chromosome 9 region that contains genes associated with abiotic stress tolerances. Wild tomato (Solanum habrochaites) exhibits tolerance to abiotic stresses, including drought and chilling. Root chilling (6 °C) induces rapid-onset water stress by impeding water movement from roots to shoots. S. habrochaites responds to such changes by closing stomata and maintaining shoot turgor, while cultivated tomato (S. lycopersicum) fails to close stomata and wilts. This response (shoot turgor maintenance under root chilling) is controlled by a major QTL (designated stm9) on chromosome 9, which was previously fine-mapped to a 2.7-cM region. Recombinant sub-near-isogenic lines for chromosome 9 were marker-selected, phenotyped for shoot turgor maintenance under root chilling in two sets of replicated experiments (Fall and Spring), and the data were used to high-resolution map QTL stm9 to a 0.32-cM region. QTL mapping revealed a single QTL that was coincident for both the Spring and Fall datasets, suggesting that the gene or genes contributing to shoot turgor maintenance under root chilling reside within the marker interval H9-T1673. In the S. lycopersicum reference genome sequence, this chromosome 9 region is gene-rich and contains representatives of gene families that have been associated with abiotic stress tolerance.

  4. Genetic mapping of two QTL from the wild tomato Solanum pimpinellifolium L. controlling resistance against two-spotted spider mite (Tetranychus urticae Koch).

    Science.gov (United States)

    Salinas, María; Capel, Carmen; Alba, Juan Manuel; Mora, Blanca; Cuartero, Jesús; Fernández-Muñoz, Rafael; Lozano, Rafael; Capel, Juan

    2013-01-01

    A novel source of resistance to two-spotted spider mite (Tetranychus urticae Koch) was found in Solanum pimpinellifolium L. accession TO-937 and thereby a potential source of desirable traits that could be introduced into new tomato varieties. This resistance was found to be controlled by a major locus modulated by minor loci of unknown location in the genome of this wild tomato. We first applied a bulked segregant analysis (BSA) approach in an F(4) population as a method for rapidly identifying a genomic region of 17 cM on chromosome 2, flanked by two simple sequence repeat markers, harboring Rtu2.1, one of the major QTL involved in the spider mite resistance. A population of 169 recombinant inbred lines was also evaluated for spider mite infestation and a highly saturated genetic map was developed from this population. QTL mapping corroborated that chromosome 2 harbored the Rtu2.1 QTL in the same region that our previous BSA findings pointed out, but an even more robust QTL was found in the telomeric region of this chromosome. This QTL, we termed Rtu2.2, had a LOD score of 15.43 and accounted for more than 30% of the variance of two-spotted spider mite resistance. Several candidate genes involved in trichome formation, synthesis of trichomes exudates and plant defense signaling have been sequenced. However, either the lack of polymorphisms between the parental lines or their map position, away from the QTL, led to their rejection as candidate genes responsible for the two-spotted spider mite resistance. The Rtu2 QTL not only serve as a valuable target for marker-assisted selection of new spider mite-resistant tomato varieties, but also as a starting point for a better understanding of the molecular genetic functions underlying the resistance to this pest.

  5. 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.

  6. 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.

  7. Advanced technologies for genomic analysis in farm animals and its application for QTL mapping.

    Science.gov (United States)

    Hu, Xiaoxiang; Gao, Yu; Feng, Chungang; Liu, Qiuyue; Wang, Xiaobo; Du, Zhuo; Wang, Qingsong; Li, Ning

    2009-06-01

    Rapid progress in farm animal breeding has been made in the last few decades. Advanced technologies for genomic analysis in molecular genetics have led to the identification of genes or markers associated with genes that affect economic traits. Molecular markers, large-insert libraries and RH panels have been used to build the genetic linkage maps, physical maps and comparative maps in different farm animals. Moreover, EST sequencing, genome sequencing and SNPs maps are helping us to understand how genomes function in various organisms and further areas will be studied by DNA microarray technologies and proteomics methods. Because most economically important traits in farm animals are controlled by multiple genes and the environment, the main goal of genome research in farm animals is to map and characterize genes determining QTL. There are two main strategies to identify trait loci, candidate gene association tests and genome scan approaches. In recent years, some new concepts, such as RNAi, miRNA and eQTL, have been introduced into farm animal research, especially for QTL mapping and finding QTN. Several genes that influence important traits have already been identified or are close to being identified, and some of them have been applied in farm animal breeding programs by marker-assisted selection.

  8. A Bayesian partition method for detecting pleiotropic and epistatic eQTL modules.

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    2010-01-01

    Full Text Available Studies of the relationship between DNA variation and gene expression variation, often referred to as "expression quantitative trait loci (eQTL mapping", have been conducted in many species and resulted in many significant findings. Because of the large number of genes and genetic markers in such analyses, it is extremely challenging to discover how a small number of eQTLs interact with each other to affect mRNA expression levels for a set of co-regulated genes. We present a Bayesian method to facilitate the task, in which co-expressed genes mapped to a common set of markers are treated as a module characterized by latent indicator variables. A Markov chain Monte Carlo algorithm is designed to search simultaneously for the module genes and their linked markers. We show by simulations that this method is more powerful for detecting true eQTLs and their target genes than traditional QTL mapping methods. We applied the procedure to a data set consisting of gene expression and genotypes for 112 segregants of S. cerevisiae. Our method identified modules containing genes mapped to previously reported eQTL hot spots, and dissected these large eQTL hot spots into several modules corresponding to possibly different biological functions or primary and secondary responses to regulatory perturbations. In addition, we identified nine modules associated with pairs of eQTLs, of which two have been previously reported. We demonstrated that one of the novel modules containing many daughter-cell expressed genes is regulated by AMN1 and BPH1. In conclusion, the Bayesian partition method which simultaneously considers all traits and all markers is more powerful for detecting both pleiotropic and epistatic effects based on both simulated and empirical data.

  9. 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 [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGDBj Registered...Policy | Contact Us QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  10. 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

  11. A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection.

    Directory of Open Access Journals (Sweden)

    George Nicholson

    2011-09-01

    Full Text Available We have performed a metabolite quantitative trait locus (mQTL study of the (1H nuclear magnetic resonance spectroscopy ((1H NMR metabolome in humans, building on recent targeted knowledge of genetic drivers of metabolic regulation. Urine and plasma samples were collected from two cohorts of individuals of European descent, with one cohort comprised of female twins donating samples longitudinally. Sample metabolite concentrations were quantified by (1H NMR and tested for association with genome-wide single-nucleotide polymorphisms (SNPs. Four metabolites' concentrations exhibited significant, replicable association with SNP variation (8.6×10(-11region (hence we report a total of three implicated genomic regions. Two of the three hit regions lie within haplotype blocks (at 2p13.1 and 10q24.2 that carry the genetic signature of strong, recent, positive selection in European populations. Genes NAT8 and PYROXD2, both with relatively uncharacterized functional roles, are good candidates for mediating the corresponding mQTL associations. The study's longitudinal twin design allowed detailed variance-components analysis of the sources of population variation in metabolite levels. The mQTLs explained 40%-64% of biological population variation in the corresponding metabolites' concentrations. These effect sizes are stronger than those reported in a recent, targeted mQTL study of metabolites in serum using the targeted-metabolomics Biocrates platform. By re-analysing our plasma samples using the Biocrates platform, we replicated the mQTL findings of the previous study and discovered a previously uncharacterized yet substantial familial component of variation in metabolite levels in addition to the heritability contribution from

  12. A major QTL controls susceptibility to spinal curvature in the curveback guppy

    Directory of Open Access Journals (Sweden)

    Dreyer Christine

    2011-01-01

    Full Text Available Abstract Background Understanding the genetic basis of heritable spinal curvature would benefit medicine and aquaculture. Heritable spinal curvature among otherwise healthy children (i.e. Idiopathic Scoliosis and Scheuermann kyphosis accounts for more than 80% of all spinal curvatures and imposes a substantial healthcare cost through bracing, hospitalizations, surgery, and chronic back pain. In aquaculture, the prevalence of heritable spinal curvature can reach as high as 80% of a stock, and thus imposes a substantial cost through production losses. The genetic basis of heritable spinal curvature is unknown and so the objective of this work is to identify quantitative trait loci (QTL affecting heritable spinal curvature in the curveback guppy. Prior work with curveback has demonstrated phenotypic parallels to human idiopathic-type scoliosis, suggesting shared biological pathways for the deformity. Results A major effect QTL that acts in a recessive manner and accounts for curve susceptibility was detected in an initial mapping cross on LG 14. In a second cross, we confirmed this susceptibility locus and fine mapped it to a 5 cM region that explains 82.6% of the total phenotypic variance. Conclusions We identify a major QTL that controls susceptibility to curvature. This locus contains over 100 genes, including MTNR1B, a candidate gene for human idiopathic scoliosis. The identification of genes associated with heritable spinal curvature in the curveback guppy has the potential to elucidate the biological basis of spinal curvature among humans and economically important teleosts.

  13. Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses

    Directory of Open Access Journals (Sweden)

    Lionikas Arimantas

    2012-11-01

    Full Text Available Abstract Background We have recently identified a number of Quantitative Trait Loci (QTL contributing to the 2-fold muscle weight difference between the LG/J and SM/J mouse strains and refined their confidence intervals. To facilitate nomination of the candidate genes responsible for these differences we examined the transcriptome of the tibialis anterior (TA muscle of each strain by RNA-Seq. Results 13,726 genes were expressed in mouse skeletal muscle. Intersection of a set of 1061 differentially expressed transcripts with a mouse muscle Bayesian Network identified a coherent set of differentially expressed genes that we term the LG/J and SM/J Regulatory Network (LSRN. The integration of the QTL, transcriptome and the network analyses identified eight key drivers of the LSRN (Kdr, Plbd1, Mgp, Fah, Prss23, 2310014F06Rik, Grtp1, Stk10 residing within five QTL regions, which were either polymorphic or differentially expressed between the two strains and are strong candidates for quantitative trait genes (QTGs underlying muscle mass. The insight gained from network analysis including the ability to make testable predictions is illustrated by annotating the LSRN with knowledge-based signatures and showing that the SM/J state of the network corresponds to a more oxidative state. We validated this prediction by NADH tetrazolium reductase staining in the TA muscle revealing higher oxidative potential of the SM/J compared to the LG/J strain (p Conclusion Thus, integration of fine resolution QTL mapping, RNA-Seq transcriptome information and mouse muscle Bayesian Network analysis provides a novel and unbiased strategy for nomination of muscle QTGs.

  14. Molecular characterization of chikungunya virus from three regions of Cameroon

    Institute of Scientific and Technical Information of China (English)

    Demanou Maurice; Sadeuh-Mba Serge Alain; Vanhecke Christophe; Ndikweti Rene; Kouna Tsala Irene; Inais Nsizoa Marthe; Njouom Richard

    2015-01-01

    Dear Editor,Chikungunya virus(CHIKV),a single-stranded RNA virus that belongs to the genus Alphavirus,family Togaviridae,is transmitted by mosquitoes of the genus Aedes(Diptera:Culicidae),predominantly Aedes aegypti and A.albopictus(Staples et al.,2014).CHIKV infection is most often characterized by fever,headache,

  15. Characterization of the promoter region of the mouse Xist gene.

    Science.gov (United States)

    Pillet, N; Bonny, C; Schorderet, D F

    1995-01-01

    The mouse Xist gene is expressed exclusively from the inactive X chromosome and may be implicated in initiating X inactivation. To better understand the mechanisms underlying the control of Xist expression, we investigated the upstream regulatory region of the mouse Xist promoter. A 1.2-kb upstream region of the Xist gene was sequenced and promoter activity was studied by chloramphenicol acetyltransferase (CAT) assays after transfection in murine XX and XY cell lines. The region analyzed (-1157 to +917 showed no in vitro sex-specific promoter activity. However, a minimal constitutional promoter was assigned to a region from -81 to +1, and a cis element from -41 to -15 regulates promoter activity. We showed that a nuclear factor binds to an element located at -30 to -25 (TTAAAG). A second sequence at -41 to -15 does not act as an enhancer and is unable to confer transcriptional activity to the Xist gene on its own. A third region from -82 to -41 is needed for correct expression. Deletion of the segment -441 to -231 is associated with an increase in CAT activity and may represent a silencer element. Images Fig. 3 PMID:8618932

  16. Oenoclimatic Characterization on the Viticultural Regions and Centers from Romania

    Directory of Open Access Journals (Sweden)

    Aurel POPA

    2010-12-01

    Full Text Available The concept of oenoclimatic signifies the asset of a region able to allow the organized growth vine. One or many kinds of wine or wine distillations might be thus obtained. Their composition fulfils all the lawful conditions bearing them an origin denomination. Organoleptic features stand for it. This paper relies upon the study of: chemical composition and microbiological parameters, the Romanian traditions, the beverages behaviour and awarded prizes. A specific taxonomy of the Romanian viticultural regions, with their distinctive assets, is therefore drawn.

  17. 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.

  18. Improving Drought Tolerance of Rice by Designed QTL Pyramiding

    Institute of Scientific and Technical Information of China (English)

    Z.K. Li; Y. Sun; L.H. Zhu; D. Dwivedi; Y.M. Gao; T.Q. Zheng; R. Lafitte; J.L. Xu; D. Mackill; B.Y. Fu; J.Domingo

    2007-01-01

    @@ Drought is the most important factor limiting rice yields in the rainfed areas of Asia. To overcome the problem, we developed a new strategy 'designed QTL pyramiding' to more efficiently develop drought tolerant (DT)rice cultivars.

  19. 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)

  20. Probabilistic Tracklet Characterization and Prioritization Using Admissible Regions

    Science.gov (United States)

    2014-09-01

    of deter- mining the potential threat of the object and obtaining further measurements. The solution to this problem is confounded in scenarios with...association and track initiation tasks. Well before their use in data association for asteroids and SOs, admissible regions have been used in stochastic...logic resource management.14 Milani et al.15 first proposed using ARs to assist in the optical detection and discrimination of asteroids . This work is

  1. Genetic control of soybean seed oil: I. QTL and genes associated with seed oil concentration in RIL populations derived from crossing moderately high-oil parents.

    Science.gov (United States)

    Eskandari, Mehrzad; Cober, Elroy R; Rajcan, Istvan

    2013-02-01

    Soybean seed is a major source of oil for human consumption worldwide and the main renewable feedstock for biodiesel production in North America. Increasing seed oil concentration in soybean [Glycine max (L.) Merrill] with no or minimal impact on protein concentration could be accelerated by exploiting quantitative trait loci (QTL) or gene-specific markers. Oil concentration in soybean is a polygenic trait regulated by many genes with mostly small effects and which is negatively associated with protein concentration. The objectives of this study were to discover and validate oil QTL in two recombinant inbred line (RIL) populations derived from crosses between three moderately high-oil soybean cultivars, OAC Wallace, OAC Glencoe, and RCAT Angora. The RIL populations were grown across several environments over 2 years in Ontario, Canada. In a population of 203 F(3:6) RILs from a cross of OAC Wallace and OAC Glencoe, a total of 11 genomic regions on nine different chromosomes were identified as associated with oil concentration using multiple QTL mapping and single-factor ANOVA. The percentage of the phenotypic variation accounted for by each QTL ranged from 4 to 11 %. Of the five QTL that were tested in a population of 211 F(3:5) RILs from the cross RCAT Angora × OAC Wallace, a "trait-based" bidirectional selective genotyping analysis validated four QTL (80 %). In addition, a total of seven two-way epistatic interactions were identified for oil concentration in this study. The QTL and epistatic interactions identified in this study could be used in marker-assisted introgression aimed at pyramiding high-oil alleles in soybean cultivars to increase oil concentration for biodiesel as well as edible oil applications.

  2. [Characterizations of InP in terahertz region].

    Science.gov (United States)

    Zhang, Cai-Hong; Wang, Yuan-Yuan; Ma, Jin-Long; Jin, Biao-Bing; Xu, Wei-Wei; Kang, Lin; Chen, Jian; Wu, Pei-Heng

    2009-08-01

    Terahertz time-domain spectroscopy (THz-TDS), which directly measures the THz wave's temporal electric field, can give the amplitude and phase of the THz wave pulse simultaneously. THz-TDS is attracting more attention among scientists. InP with short carrier average collision time and low effective mass is growing up as one of the best photoconductive materials for emitting and detecting THz waves. An n-type InP of 0.35 omega x cm was characterized over the range from 0.2 to 4 THz at room temperature in the present paper with THz time-domain spectroscopy, which was placed in a closed box purged with dry nitrogen gas. Some THz optical properties, such as complex refractive index, dielectric constant, and conductivity, were extracted, based on more exact iterative method with new initial function. Drude model was also applied for simulation, which fitted well with the experimental results. Finally, the carrier average collision time, density and mobility of the InP were also characterized.

  3. Molecular characterization of a strong candidate region for schizophrenia

    Energy Technology Data Exchange (ETDEWEB)

    Karayiorgou, M. [MIT, Cambridge, MA (United States)]|[Fred Hutchinson Cancer Research Center, Seattle, WA (United States); Housman, D.E. [MIT, Cambridge, MA (United States); Morrow, B. [Albert Einstein College of Medicine, Bronx, NY (United States)] [and others

    1994-09-01

    Two lines of evidence point to a region on chromosome 22 as potentially involved in the etiology of schizophrenia: First, our own linkage data and second, observations that a greater than expected number of cases with the VCF (velo-cardio-facial) syndrome, a developmental syndrome due to microdeletions of the same genetic region, develop psychotic illness during adolescence. On the molecular genetic level, we are testing the hypothesis that the partial phenotypic overlap between schizophrenia and VCF may be due to overlapping genetic abnormalities. To that end, we have generated somatic cell hybrids from an initial group of nine VCF patients over the age of 15 who underwent psychiatric evaluation. Three were assigned a DSM-III-R diagnosis of schizophrenia. Several hybrid cell lines were generated from each patient carrying either the deleted chromosome, or the intact chromosome, or both. We have analyzed these hybrids and the extent of their chromosome 22 deletions with 41 markers so far (21 polymorphic microsatellite markers and 20 STSs). One of these markers is COMT (catechol-O-methyltransferase) that could be considered a candidate for schizophrenia. We are searching for potential molecular genetic differences between the subgroup of VCF patients that do develop schizophrenia and the subgroup that do not. Our initial efforts concentrate on the possibility of correlation between the extent of the deletion and the schizophrenic phenotype. Results from our analysis so far will be presented. Our goal is to narrow and define more accurately the region potentially involved in the etiology of schizophrenia and successfully identify any gene(s) that may play a role.

  4. 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

  5. Toward Regional Characterizations of the Oceanic Internal Wavefield

    CERN Document Server

    Polzin, Kurt L

    2010-01-01

    Many major oceanographic internal wave observational programs of the last 4 decades are reanalyzed in order to characterize variability of the deep ocean internal wavefield. The observations are discussed in the context of the universal spectral model proposed by Garrett and Munk. The Garrett and Munk model is a good description of wintertime conditions at Site-D on the continental rise north of the Gulf Stream. Elsewhere and at other times, significant deviations in terms of amplitude, separability of the 2-D vertical wavenumber - frequency spectrum, and departure from the model's functional form are noted. Subtle geographic patterns are apparent in deviations from the high frequency and high vertical wavenumber power laws of the Garrett and Munk spectrum. Moreover, such deviations tend to co-vary: whiter frequency spectra are partnered with redder vertical wavenumber spectra. Attempts are made to interpret the variability in terms of the interplay between generation, propagation and nonlinearity using a sta...

  6. Structural Characterization of Core Region in Erwinia amylovora Lipopolysaccharide.

    Science.gov (United States)

    Casillo, Angela; Ziaco, Marcello; Lindner, Buko; Merino, Susana; Mendoza-Barberá, Elena; Tomás, Juan M; Corsaro, Maria Michela

    2017-03-04

    Erwinia amylovora (E. amylovora) is the first bacterial plant pathogen described and demonstrated to cause fire blight, a devastating plant disease affecting a wide range of species including a wide variety of Rosaceae. In this study, we reported the lipopolysaccharide (LPS) core structure from E. amylovora strain CFBP1430, the first one for an E. amylovora highly pathogenic strain. The chemical characterization was performed on the mutants waaL (lacking only the O-antigen LPS with a complete LPS-core), wabH and wabG (outer-LPS core mutants). The LPSs were isolated from dry cells and analyzed by means of chemical and spectroscopic methods. In particular, they were subjected to a mild acid hydrolysis and/or a hydrazinolysis and investigated in detail by one and two dimensional Nuclear Magnetic Resonance (NMR) spectroscopy and ElectroSpray Ionization Fourier Transform-Ion Cyclotron Resonance (ESI FT-ICR) mass spectrometry.

  7. Structural Characterization of Core Region in Erwinia amylovora Lipopolysaccharide

    Directory of Open Access Journals (Sweden)

    Angela Casillo

    2017-03-01

    Full Text Available Erwinia amylovora (E. amylovora is the first bacterial plant pathogen described and demonstrated to cause fire blight, a devastating plant disease affecting a wide range of species including a wide variety of Rosaceae. In this study, we reported the lipopolysaccharide (LPS core structure from E. amylovora strain CFBP1430, the first one for an E. amylovora highly pathogenic strain. The chemical characterization was performed on the mutants waaL (lacking only the O-antigen LPS with a complete LPS-core, wabH and wabG (outer-LPS core mutants. The LPSs were isolated from dry cells and analyzed by means of chemical and spectroscopic methods. In particular, they were subjected to a mild acid hydrolysis and/or a hydrazinolysis and investigated in detail by one and two dimensional Nuclear Magnetic Resonance (NMR spectroscopy and ElectroSpray Ionization Fourier Transform-Ion Cyclotron Resonance (ESI FT-ICR mass spectrometry.

  8. Structural Characterization of Core Region in Erwinia amylovora Lipopolysaccharide

    Science.gov (United States)

    Casillo, Angela; Ziaco, Marcello; Lindner, Buko; Merino, Susana; Mendoza-Barberá, Elena; Tomás, Juan M.; Corsaro, Maria Michela

    2017-01-01

    Erwinia amylovora (E. amylovora) is the first bacterial plant pathogen described and demonstrated to cause fire blight, a devastating plant disease affecting a wide range of species including a wide variety of Rosaceae. In this study, we reported the lipopolysaccharide (LPS) core structure from E. amylovora strain CFBP1430, the first one for an E. amylovora highly pathogenic strain. The chemical characterization was performed on the mutants waaL (lacking only the O-antigen LPS with a complete LPS-core), wabH and wabG (outer-LPS core mutants). The LPSs were isolated from dry cells and analyzed by means of chemical and spectroscopic methods. In particular, they were subjected to a mild acid hydrolysis and/or a hydrazinolysis and investigated in detail by one and two dimensional Nuclear Magnetic Resonance (NMR) spectroscopy and ElectroSpray Ionization Fourier Transform-Ion Cyclotron Resonance (ESI FT-ICR) mass spectrometry. PMID:28273861

  9. 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.

  10. 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.

  11. QTL mapping of agronomic waterlogging tolerance using recombinant inbred lines derived from tropical maize (Zea mays L) germplasm.

    Science.gov (United States)

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

    2015-01-01

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

  12. Characterization of the bovine pseudoautosomal region and comparison with sheep, goat, and other mammalian pseudoautosomal regions.

    Science.gov (United States)

    Das, P J; Chowdhary, B P; Raudsepp, T

    2009-01-01

    The pseudoautosomal region (PAR) is a small region of sequence homology between mammalian X and Y chromosomes and is needed for sex chromosome segregation in male meiosis. The region, though studied as yet in only a few species, shows considerable variation in size and gene content. We have constructed a medium-density gene map for the cattle PAR and the adjacent X-specific region by isolating and mapping 18 BAC clones which contain 20 PAR- and 5 X-specific genes. One BAC clone containing TBL1XY and GPR143 spanned the recently demarcated bovine pseudoautosomal boundary (PAB). Comparing the gene map of cattle PAR with the high-resolution maps of human, horse, and dog PAR allowed to estimate that the size of cattle PAR is approximately 5-9 Mb. BAC end sequence analysis showed that there is a gradient of decreasing GC content from PARter towards the PAB which is consistent with findings in human, mouse, and horse. The 20 PAR- and 5 X-specific cattle genes were mapped also in goat and sheep, showing that PAR in the 3 species is similar in size, gene content, and gene order. For the first time the PAB was determined in goat sex chromosomes. Comparison of cattle, goat, and sheep PAR with homologous regions on human and horse X chromosomes showed a high degree of linkage conservation between all species. However, the most terminal human, horse, and dog PAR gene, PLCXD1, is X-specific in ruminants. Since the human/horse linkage group containing PLCXD1 is of ancestral origin, the location of PLCXD1 can be considered as a de novo event in ruminant sex chromosome evolution. The gene map of the cattle PAR adds to our knowledge about the comparative organization and evolution of the eutherian PAR and aids the sequencing, sequence assembly, and annotation of the terminal region of BTAXq.

  13. Genetic characterization of Phytophthora nicotianae by the analysis of polymorphic regions of the mitochondrial DNA.

    Science.gov (United States)

    A new method based on the analysis of mitochondrial intergenic regions characterized by intraspecific variation in DNA sequences was developed and applied to the study of the plant pathogen Phytophthora nicotianae. Two regions flanked by genes trny and rns and trnw and cox2 were identified by compa...

  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. 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.

  16. 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

  17. Blood cis-eQTL analysis fails to identify novel association signals among sub-threshold candidates from genome-wide association studies in restless legs syndrome.

    Directory of Open Access Journals (Sweden)

    Eva C Schulte

    Full Text Available Restless legs syndrome (RLS is a common neurologic disorder characterized by nightly dysesthesias affecting the legs primarily during periods of rest and relieved by movement. RLS is a complex genetic disease and susceptibility factors in six genomic regions have been identified by means of genome-wide association studies (GWAS. For some complex genetic traits, expression quantitative trait loci (eQTLs are enriched among trait-associated single nucleotide polymorphisms (SNPs. With the aim of identifying new genetic susceptibility factors for RLS, we assessed the 332 best-associated SNPs from the genome-wide phase of the to date largest RLS GWAS for cis-eQTL effects in peripheral blood from individuals of European descent. In 740 individuals belonging to the KORA general population cohort, 52 cis-eQTLs with pnominal<10(-3 were identified, while in 976 individuals belonging to the SHIP-TREND general population study 53 cis-eQTLs with pnominal<10(-3 were present. 23 of these cis-eQTLs overlapped between the two cohorts. Subsequently, the twelve of the 23 cis-eQTL SNPs, which were not located at an already published RLS-associated locus, were tested for association in 2449 RLS cases and 1462 controls. The top SNP, located in the DET1 gene, was nominally significant (p<0.05 but did not withstand correction for multiple testing (p = 0.42. Although a similar approach has been used successfully with regard to other complex diseases, we were unable to identify new genetic susceptibility factor for RLS by adding this novel level of functional assessment to RLS GWAS data.

  18. Blood cis-eQTL Analysis Fails to Identify Novel Association Signals among Sub-Threshold Candidates from Genome-Wide Association Studies in Restless Legs Syndrome

    Science.gov (United States)

    Schulte, Eva C.; Schramm, Katharina; Schurmann, Claudia; Lichtner, Peter; Herder, Christian; Roden, Michael; Gieger, Christian; Peters, Annette; Trenkwalder, Claudia; Högl, Birgit; Frauscher, Birgit; Berger, Klaus; Fietze, Ingo; Gross, Nadine; Stiasny-Kolster, Karin; Oertel, Wolfgang; Bachmann, Cornelius G.; Paulus, Walter; Zimprich, Alexander; Völzke, Henry; Schminke, Ulf; Nauck, Matthias; Illig, Thomas; Meitinger, Thomas; Müller-Myhsok, Bertram; Prokisch, Holger; Winkelmann, Juliane

    2014-01-01

    Restless legs syndrome (RLS) is a common neurologic disorder characterized by nightly dysesthesias affecting the legs primarily during periods of rest and relieved by movement. RLS is a complex genetic disease and susceptibility factors in six genomic regions have been identified by means of genome-wide association studies (GWAS). For some complex genetic traits, expression quantitative trait loci (eQTLs) are enriched among trait-associated single nucleotide polymorphisms (SNPs). With the aim of identifying new genetic susceptibility factors for RLS, we assessed the 332 best-associated SNPs from the genome-wide phase of the to date largest RLS GWAS for cis-eQTL effects in peripheral blood from individuals of European descent. In 740 individuals belonging to the KORA general population cohort, 52 cis-eQTLs with pnominal<10−3 were identified, while in 976 individuals belonging to the SHIP-TREND general population study 53 cis-eQTLs with pnominal<10−3 were present. 23 of these cis-eQTLs overlapped between the two cohorts. Subsequently, the twelve of the 23 cis-eQTL SNPs, which were not located at an already published RLS-associated locus, were tested for association in 2449 RLS cases and 1462 controls. The top SNP, located in the DET1 gene, was nominally significant (p<0.05) but did not withstand correction for multiple testing (p = 0.42). Although a similar approach has been used successfully with regard to other complex diseases, we were unable to identify new genetic susceptibility factor for RLS by adding this novel level of functional assessment to RLS GWAS data. PMID:24875634

  19. Robust Linear Models for Cis-eQTL Analysis.

    Directory of Open Access Journals (Sweden)

    Mattias Rantalainen

    Full Text Available Expression Quantitative Trait Loci (eQTL analysis enables characterisation of functional genetic variation influencing expression levels of individual genes. In outbread populations, including humans, eQTLs are commonly analysed using the conventional linear model, adjusting for relevant covariates, assuming an allelic dosage model and a Gaussian error term. However, gene expression data generally have noise that induces heavy-tailed errors relative to the Gaussian distribution and often include atypical observations, or outliers. Such departures from modelling assumptions can lead to an increased rate of type II errors (false negatives, and to some extent also type I errors (false positives. Careful model checking can reduce the risk of type-I errors but often not type II errors, since it is generally too time-consuming to carefully check all models with a non-significant effect in large-scale and genome-wide studies. Here we propose the application of a robust linear model for eQTL analysis to reduce adverse effects of deviations from the assumption of Gaussian residuals. We present results from a simulation study as well as results from the analysis of real eQTL data sets. Our findings suggest that in many situations robust models have the potential to provide more reliable eQTL results compared to conventional linear models, particularly in respect to reducing type II errors due to non-Gaussian noise. Post-genomic data, such as that generated in genome-wide eQTL studies, are often noisy and frequently contain atypical observations. Robust statistical models have the potential to provide more reliable results and increased statistical power under non-Gaussian conditions. The results presented here suggest that robust models should be considered routinely alongside other commonly used methodologies for eQTL analysis.

  20. Joint QTL analyses for partial resistance to Phytophthora sojae using six nested inbred populations with heterogeneous conditions

    Science.gov (United States)

    Partial resistance to Phytophthora sojae in soybean is controlled by multiple quantitative trait loci (QTL). With traditional QTL mapping approaches, power to detect these QTL, frequently of small effect, can be limited by population size. Joint linkage QTL analysis of nested recombinant inbred li...

  1. QTL Analysis for Plant Height with Molecular Markers in Maize

    Institute of Scientific and Technical Information of China (English)

    YAN Jian-bing; TANG Hua; HUANG Yi-qin; SHI Yong-gang; ZHENG Yong-lian; LI Jian-sheng

    2003-01-01

    Plant height has become one of important agronomic traits with the increase of planting densityrecently and the rapid developments of molecular markers have provided powerful tools to localize importantagronomic QTL at the genomic level. The purposes of this investigation are to map plant height QTL with mo-lecular markers and to analyze their genetic effects in maize. An F2:3 population from an elite combination(Zong3 × 87-1) was utilized for evaluating plant height in two locations, Wuhan and Xiangfan, with a ran-domized complete block design. The mapping population included 266 F2:3 family lines. A genetic linkagemap, containing 150 SSR and 24 RFLP markers, was constructed, spanning a total of 2 531.6 cm with an av-erage interval of 14.5 cm. Totally 10 QTL affecting plant height were mapped on six different chromosomeswith the composite interval mapping. Seven of 10 QTL were detected in two locations. The contributions tophenotypic variations for the single QTL varied between 5.3 and 17.1%. Additive, partial dominance, domi-nance, and overdominance actions existed among all detected QTL affecting plant heights. A large number ofdigenic interactions for plant height were detected by two-way analyses of variance. 107 and 98 two-locus com-binations were found to be significant at a 0.01 probability level in two locations respectively. 23 of them weresimultaneously detected in both locations. They accounted for phenotypic variations of 4.5 -11%. It was no-ticed that a locus, umc1122, had digenic interactive effects with other four different loci for plant height,which distributed on three chromosomes. A few of plant height QTL was involved in significant digenic inter-actions, but most significant interactions occurred between markers that are not adjacent to mapped QTL.These results demonstrated that epistatic interactions might play an equal importance role as the single-locuseffects in determining plant height of maize.

  2. 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.

  3. 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).

  4. 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.

  5. Inheritance studies of apple scab resistance and identification of Rvi14, a new major gene that acts together with other broad-spectrum QTL.

    Science.gov (United States)

    Soufflet-Freslon, V; Gianfranceschi, L; Patocchi, A; Durel, C-E

    2008-08-01

    Scab, caused by the fungal pathogen Venturia inaequalis, is the most common disease of cultivated apple (Malus xdomestica). The fungal races 6 and 7 have now overcome the major resistance gene Vf, which is widely used in apple breeding programmes. New breeding strategies to achieve durable resistance are thus necessary. The aim of this study was to determine the genetic basis of quantitative resistance of the apple cultivar 'Dülmener Rosenapfel', known to be scab resistant under different environmental conditions. An F1 progeny derived from the cross between the susceptible cultivar 'Gala' and 'Dülmener Rosenapfel' was tested in a greenhouse with a multi-isolate inoculum of V. inaequalis. Rvi14, a new major gene that conditions a chlorotic-type reaction, was mapped on linkage group (LG) 6 in a genomic region not known to be involved in disease resistance. A further three quantitative trait loci (QTL) for resistance were identified. One co-localized with Rvi14 on LG6, whereas the remaining two were detected on LG11 and LG17, in genomic regions already reported to carry broad-spectrum QTL in other genetic backgrounds. Since a selective genotyping approach was used to detect QTL, an expectation-maximization (EM) computation was used to estimate the corrected QTL contributions to phenotypic variation and was validated by entire progeny genotyping.

  6. Influence of outliers on QTL mapping for complex traits

    Institute of Scientific and Technical Information of China (English)

    Yousaf HAYAT; Jian YANG; Hai-ming XU; Jun ZHU

    2008-01-01

    A method was proposed for the detection of outliers and influential observations in the framework of a mixed linear model, prior to the quantitative trait locus (QTL) mapping analysis. We investigated the impact of outliers on QTL mapping for complex traits in a mouse BXD population, and observed that the dropping of outliers could provide the evidence of additional QTL and epistatic loci affecting the 1 stBrain-OB and the 2ndBrain-OB in a cross of the abovementioned population. The results could also reveal a remarkable increase in estimating heritabilities of QTL in the absence of outliers. In addition, simulations were conducted to investigate the detection powers and false discovery rates (FDRs) of QTLs in the presence and absence of outliers. The results suggested that the presence of a small proportion of outliers could increase the FDR and hence decrease the detection power of QTLs. A drastic increase could be obtained in the estimates of standard errors for position, additive and additivex environment interaction effects of QTLs in the presence of outliers.

  7. Bayesian multi-QTL mapping for growth curve parameters

    DEFF Research Database (Denmark)

    Heuven, Henri C M; Janss, Luc L G

    2010-01-01

    . The locations of the QTLs for separate parameters were very close in some cases and probably caused the genetic correlation observed between ASYM and XMID and SCAL respectively. None of the QTL appeared on chromosome five. Conclusions Repeated observations on individuals were affected by at least nine QTLs...

  8. Development of Sequence Characterized Amplified Region (SCAR) Primers for the Detection of Resistance to Sporisorium reiliana in Maize

    Institute of Scientific and Technical Information of China (English)

    SHI Hong-liang; LI Xin-hai; ZHANG De-gui; XIE Chuan-xiao; HAO Zhuan-fang; LI Ming-shun; PAN Guang-tang; ZHANG Shi-huang

    2009-01-01

    Head smut of maize (Zea mays L.), which was caused by Sporisorium reiliana, occurred in most of the maize growing areas of the world. The purpose of this study was to develop SCAR markers for map-based cloning of resistance genes and MAS. Two sets of BC3 progenies, one (BC3Q) derived from the cross Qi319 (resistance)x Huangzao 4 (susceptible),the other (BC3M) from Mol 7 (resistance)x Huangzao 4 (susceptible), were generated. Huangzao 4 was the recurrent parent in both progenies. A combination of BSA (bulked segregant analysis) with AFLP (amplified fragment length polymorphism) method was applied to map the genes involving the resistance to S. Reiliana, and corresponding resistant and susceptible bulks and their parental lines were used for screening polymorphic AFLP primer pairs. One fragment of P13M61-152 was converted into SCAR (sequence charactered amplified fragment) marker S130. The marker was mapped at chromosome bin 2.09, the interval of a major QTL region previously reported to contribute to S. Reiliana resistance.Furthermore, S130 was highly associated with resistance to S. Reiliana, and could be useful for marker-assisted selection and facilitate map-based cloning of resistance genes.

  9. Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries).

    Science.gov (United States)

    Beraldi, Dario; McRae, Allan F; Gratten, Jacob; Pilkington, Jill G; Slate, Jon; Visscher, Peter M; Pemberton, Josephine M

    2007-01-01

    A genome-wide scan was performed to detect quantitative trait loci (QTL) for resistance to gastrointestinal parasites and ectoparasitic keds segregating in the free-living Soay sheep population on St. Kilda (UK). The mapping panel consisted of a single pedigree of 882 individuals of which 588 were genotyped. The Soay linkage map used for the scans comprised 251 markers covering the whole genome at average spacing of 15cM. The traits here investigated were the strongyle faecal egg count (FEC), the coccidia faecal oocyst count (FOC) and a count of keds (Melophagus ovinus). QTL mapping was performed by means of variance component analysis so that the genetic parameters of the study traits were also estimated and compared with previous studies in Soay and domestic sheep. Strongyle FEC and coccidia FOC showed moderate heritability (h(2)=0.26 and 0.22, respectively) in lambs but low heritability in adults (h(2)scans were performed for the traits with moderate heritability and two genomic regions reached the level of suggestive linkage for coccidia FOC in lambs (logarithm of the odds=2.68 and 2.21 on chromosomes 3 and X, respectively). We believe this is the first study to report a QTL search for parasite resistance in a free-living animal population and therefore may represent a useful reference for similar studies aimed at understanding the genetics of host-parasite co-evolution in the wild.

  10. 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.

  11. 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.

  12. The mouse QTL map helps interpret human genome-wide association studies for HDL cholesterol.

    Science.gov (United States)

    Leduc, Magalie S; Lyons, Malcolm; Darvishi, Katayoon; Walsh, Kenneth; Sheehan, Susan; Amend, Sarah; Cox, Allison; Orho-Melander, Marju; Kathiresan, Sekar; Paigen, Beverly; Korstanje, Ron

    2011-06-01

    Genome-wide association (GWA) studies represent a powerful strategy for identifying susceptibility genes for complex diseases in human populations but results must be confirmed and replicated. Because of the close homology between mouse and human genomes, the mouse can be used to add evidence to genes suggested by human studies. We used the mouse quantitative trait loci (QTL) map to interpret results from a GWA study for genes associated with plasma HDL cholesterol levels. We first positioned single nucleotide polymorphisms (SNPs) from a human GWA study on the genomic map for mouse HDL QTL. We then used mouse bioinformatics, sequencing, and expression studies to add evidence for one well-known HDL gene (Abca1) and three newly identified genes (Galnt2, Wwox, and Cdh13), thus supporting the results of the human study. For GWA peaks that occur in human haplotype blocks with multiple genes, we examined the homologous regions in the mouse to prioritize the genes using expression, sequencing, and bioinformatics from the mouse model, showing that some genes were unlikely candidates and adding evidence for candidate genes Mvk and Mmab in one haplotype block and Fads1 and Fads2 in the second haplotype block. Our study highlights the value of mouse genetics for evaluating genes found in human GWA studies.

  13. QTL mapping of soybean oil content for marker-assisted selection in plant breeding program.

    Science.gov (United States)

    Leite, D C; Pinheiro, J B; Campos, J B; Di Mauro, A O; Unêda-Trevisoli, S H

    2016-03-18

    The present study was undertaken to detect and map the quantitative trait loci (QTL) related to soybean oil content. We used 244 progenies derived from a bi-parental cross of the Lineage 69 (from Universidade Estadual Paulista "Júlio de Mesquita Filho"/Faculdade de Ciências Agrárias e Veterinárias - Breeding Program) and Tucunaré cultivar. A total of 358 simple sequence repeat (SSR; microsatellite) markers were used to investigate the polymorphism between the parental lines, and for the polymorphic lines all the F2 individuals were tested. Evaluation of the oil content and phenotype was performed with the aid of a Tango equipment by near infra-red reflectance spectroscopy, using single F2 seeds and F2:3 progenies, in triplicate. The data were analyzed by QTL Cartographer program for 56 SSR polymorphic markers. Two oil-content related QTLs were detected on K and H linkage groups. The total phenotypic variation explained by QTLs ranged from 7.8 to 46.75% for oil content. New QTLs were identified for the oil content in addition to those previously identified in other studies. The results reported in this study show that regions different from those already known could be involved in the genetic control of soybean oil content.

  14. QTL mapping under truncation selection in homozygous lines derived from biparental crosses.

    Science.gov (United States)

    Melchinger, Albrecht E; Orsini, Elena; Schön, Chris C

    2012-02-01

    In plant breeding, a large number of progenies that will be discarded later in the breeding process must be phenotyped and marker genotyped for conducting QTL analysis. In many cases, phenotypic preselection of lines could be useful. However, in QTL analyses even moderate preselection can have a significant effect on the power of QTL detection and estimation of effects of the target traits. In this study, we provide exact formulas for quantifying the change of allele frequencies within marker classes, expectations of marker contrasts and the variance of the marker contrasts under truncation selection, for the general case of two QTL affecting the target trait and a correlated trait. We focused on homozygous lines derived at random from biparental crosses. The effects of linkage between the marker and the QTL under selection as well as the effect of selection on a correlated trait can be quantified with the given formulas. Theoretical results clearly show that depending on the magnitude of QTL effects, high selection intensities can lead to a dramatic reduction in power of QTL detection and that approximations based on the infinitesimal model deviate substantially from exact solutions. The presented formulas are valuable for choosing appropriate selection intensity when performing QTL mapping experiments on the data on phenotypically preselected traits and enable the calculation and bias correction of the effects of QTL under selection. Application of our theory to experimental data revealed that selection-induced bias of QTL effects can be successfully corrected.

  15. 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.

  16. Mendelizing all components of a pyramid of three yield QTL in tomato

    Directory of Open Access Journals (Sweden)

    Amit eGur

    2015-12-01

    Full Text Available Molecular markers allowed breeders to Mendelize quantitative trait loci (QTL providing another demonstration that quantitative traits are governed by the same principles as single qualitative genes. This research extends the QTL analysis to two and three QTL and tests our ability to Mendelize an oligogenic trait. In tomato, agricultural yield is determined by the weight of the fruits harvested per unit area and the total soluble solids (% Brix–sugars and acids. The current study explores the segregation of multiple independent yield-related QTL that were identified and mapped using introgression lines (IL of Solanum pennellii in cultivated processing tomato (Solanum lycopersicum. We screened 45 different double and triple IL-QTL combinations for agricultural yield, to identify QTL pyramids that behaved in an additive manner and were suitable substrate for Mendelizing an oligogenic trait. A pyramid of three independent QTL that significantly improved Brix*Yield (BXY - the soluble solids output per unit area compared to M82 was selected. In the progenies of the tri-hybrid we bred using markers a nearly isogenic 'immortalized F2'. While the common mode of QTL-QTL interactions across the 45 IL-QTLs combinations was less than additive, the three QTLs in the selected triple-stack performed in an additive manner which made it an exceptional material for breeding. This study demonstrates that using the phenotypic effect of all 27 possible QTL-alleles combinations it is possible to make reliable predictions about the genotypes that will maximize the yield.

  17. 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.

  18. Resistance to Soil-borne cereal mosaic virus in durum wheat is controlled by a major QTL on chromosome arm 2BS and minor loci.

    Science.gov (United States)

    Maccaferri, Marco; Ratti, Claudio; Rubies-Autonell, Concepcion; Vallega, Victor; Demontis, Andrea; Stefanelli, Sandra; Tuberosa, Roberto; Sanguineti, Maria Corinna

    2011-08-01

    Soil-borne cereal mosaic (SBCM) is a viral disease, which seriously affects hexaploid as well as tetraploid wheat crops in Europe. In durum wheat (Triticum durum Desf.), the elite germplasm is characterized by a wide range of responses to SBCMV, from susceptibility to almost complete resistance. In this study, the genetic analysis of SBCMV resistance was carried out using a population of 181 durum wheat recombinant inbred lines (RILs) obtained from Meridiano (resistant) × Claudio (moderately susceptible), which were profiled with SSR and DArT markers. The RILs were characterized for SBCMV response in the field under severe and uniform SBCMV infection during 2007 and 2008. A wide range of disease reactions (as estimated by symptom severity and DAS-ELISA) was observed. A large portion of the variability for SBCMV response was explained by a major QTL (QSbm.ubo-2BS) located in the distal telomeric region of chromosome 2BS near the marker triplet Xbarc35-Xwmc661-Xgwm210, with R(2) values ranging from 51.6 to 91.6%. The favorable allele was contributed by Meridiano. Several QTLs with minor effects on SBCMV response were also detected. Consistently with the observed transgressive segregation, the resistance alleles at minor QTLs were contributed by both parents. The presence and effects of QSbm.ubo-2BS were validated through association mapping in a panel of 111 elite durum wheat accessions.

  19. A QTL on chromosome 6A in bread wheat (Triticum aestivum) is associated with longer coleoptiles, greater seedling vigour and final plant height.

    Science.gov (United States)

    Spielmeyer, W; Hyles, J; Joaquim, P; Azanza, F; Bonnett, D; Ellis, M E; Moore, C; Richards, R A

    2007-06-01

    Wheat crops with greater early vigour shade the soil surface more rapidly and reduce water loss. Evaporative losses affect water-use efficiency particularly in drier regions where most of the rainfall occurs early in the growing season before canopy closure. Greater seedling leaf area and longer coleoptiles are major determinants of increased vigour and better crop establishment. A previously developed high vigour breeding line 'Vigour 18' was used to establish a large recombinant inbred family and framework map to identify a QTL on chromosome 6A that accounted for up to 8% of the variation for coleoptile length, 14% of seedling leaf width and was associated with increased plant height. The SSR marker NW3106, nearest to the 6A QTL, was also associated with greater leaf width in a breeding population that was also derived from a cross involving the high vigour donor line 'Vigour18'. The association between the NW3106 marker and coleoptile length was validated in a second breeding population which was developed using an unrelated long coleoptile donor line. The 'Vigour18' allele of the QTL on chromosome 6A promoted coleoptile length and leaf width during early plant growth but was also associated with increased plant height at maturity. Markers linked to the QTL are being used to increase the frequency of increased vigour and long coleoptile alleles in early generations of breeding populations.

  20. QTL underlying iron and zinc toxicity tolerances at seedling stage revealed by two sets of reciprocal introgression populations of rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    Huan Liu

    2016-08-01

    Full Text Available Iron and zinc are two trace elements that are essential for rice. But they are toxic at higher concentrations, leading to severe rice yield losses especially in acid soils and inland valleys. In this study, two reciprocal introgression line (IL populations sharing the same parents were used with high-density SNP bin markers to identify QTL tolerant to iron and zinc toxicities. The results indicated that the japonica variety 02,428 had stronger tolerance to iron and zinc toxicities than the indica variety Minghui 63. Nine and ten QTL contributing to iron and zinc toxicity tolerances, respectively, were identified in the two IL populations. The favorable alleles of most QTL came from 02,428. Among them, qFRRDW2, qZRRDW3, and qFRSDW11 appeared to be independent of genetic background. The region C11S49–C11S60 on chromosome 11 harbored QTL affecting multiple iron and zinc toxicity tolerance-related traits, indicating partial genetic overlap between the two toxicity tolerances. Our results provide essential information and materials for developing excellent rice cultivars with iron and/or zinc tolerance by marker-assisted selection (MAS.

  1. TaWRKY70 transcription factor in wheat QTL-2DL regulates downstream metabolite biosynthetic genes to resist Fusarium graminearum infection spread within spike

    Science.gov (United States)

    Kage, Udaykumar; Yogendra, Kalenahalli N.; Kushalappa, Ajjamada C.

    2017-01-01

    A semi-comprehensive metabolomics was used to identify the candidate metabolites and genes to decipher mechanisms of resistance in wheat near-isogenic lines (NILs) containing QTL-2DL against Fusarium graminearum (Fg). Metabolites, with high fold-change in abundance, belonging to hydroxycinnamic acid amides (HCAAs): such as coumaroylagmatine, coumaroylputrescine and Fatty acids: phosphatidic acids (PAs) were identified as resistance related induced (RRI) metabolites in rachis of resistant NIL (NIL-R), inoculated with Fg. A WRKY like transcription factor (TF) was identified within the QTL-2DL region, along with three resistance genes that biosynthesized RRI metabolites. Sequencing and in-silico analysis of WRKY confirmed it to be wheat TaWRKY70. Quantitative real time-PCR studies showed a higher expression of TaWRKY70 in NIL-R as compared to NIL-S after Fg inoculation. Further, the functional validation of TaWRKY70 based on virus induced gene silencing (VIGS) in NIL-R, not only confirmed an increased fungal biomass but also decreased expressions of downstream resistance genes: TaACT, TaDGK and TaGLI1, along with decreased abundances of RRI metabolites biosynthesized by them. Among more than 200 FHB resistance QTL identified in wheat, this is the first QTL from which a TF was identified, and its downstream target genes as well as the FHB resistance functions were deciphered. PMID:28198421

  2. fw 2.2:a major QTL controlling fruit weight is common to both red- and green-fruited tomato species.

    Science.gov (United States)

    Alpert, K B; Grandillo, S; Tanksley, S D

    1995-11-01

    We have shown that a major QTL for fruit weight (fw2.2) maps to the same position on chromosome 2 in the green-fruited wild tomato species, Lycopersicon pennellii and in the red-fruited wild tomato species, L. pimpinellifolium. An introgression line F2 derived from L. esculentum (tomato) x L. pennellii and a backcross 1 (BC1) population derived from L. esculentum x L. pimpinellifolium both place fw2.2 near TG91 and TG167 on chromosome 2 of the tomato highdensity linkage map. fw2.2 accounts for 30% and 47% of the total phenotypic variance in the L. pimpinellifolium and L. pennellii populations, respectively, indicating that this is a major QTL controlling fruit weight in both species. Partial dominance (d/a of 0.44) was observed for the L. pennellii allele of fw 2.2 as compared with the L. esculentum allele. A QTL with very similar phenotypic affects and gene action has also been identified and mapped to the same chromosomal region in other wild tomato accessions: L. cheesmanii and L. pimpinellifolium. Together, these data suggest that fw2.2 represents an orthologous QTL (i.e., derived by speciation as opposed to duplication) common to most, if not all, wild tomato species. High-resolution mapping may ultimately lead to the cloning of this key locus controlling fruit development in tomato.

  3. Identification of QTL for UV-protective eye area pigmentation in cattle by progeny phenotyping and genome-wide association analysis.

    Directory of Open Access Journals (Sweden)

    Hubert Pausch

    Full Text Available Pigmentation patterns allow for the differentiation of cattle breeds. A dominantly inherited white head is characteristic for animals of the Fleckvieh (FV breed. However, a minority of the FV animals exhibits peculiar pigmentation surrounding the eyes (ambilateral circumocular pigmentation, ACOP. In areas where animals are exposed to increased solar ultraviolet radiation, ACOP is associated with a reduced susceptibility to bovine ocular squamous cell carcinoma (BOSCC, eye cancer. Eye cancer is the most prevalent malignant tumour affecting cattle. Selection for animals with ACOP rapidly reduces the incidence of BOSCC. To identify quantitative trait loci (QTL underlying ACOP, we performed a genome-wide association study using 658,385 single nucleotide polymorphisms (SNPs. The study population consisted of 3579 bulls of the FV breed with a total of 320,186 progeny with phenotypes for ACOP. The proportion of progeny with ACOP was used as a quantitative trait with high heritability (h(2 = 0.79. A variance component based approach to account for population stratification uncovered twelve QTL regions on seven chromosomes. The identified QTL point to MCM6, PAX3, ERBB3, KITLG, LEF1, DKK2, KIT, CRIM1, ATRN, GSDMC, MITF and NBEAL2 as underlying genes for eye area pigmentation in cattle. The twelve QTL regions explain 44.96% of the phenotypic variance of the proportion of daughters with ACOP. The chromosomes harbouring significantly associated SNPs account for 54.13% of the phenotypic variance, while another 19.51% of the phenotypic variance is attributable to chromosomes without identified QTL. Thus, the missing heritability amounts to 7% only. Our results support a polygenic inheritance pattern of ACOP in cattle and provide the basis for efficient genomic selection of animals that are less susceptible to serious eye diseases.

  4. 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.

    Science.gov (United States)

    Zou, Zhongwei; Ishida, Masahiko; Li, Feng; Kakizaki, Tomohiro; Suzuki, Sho; Kitashiba, Hiroyasu; Nishio, Takeshi

    2013-01-01

    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.

  5. Dense seismic networks as a tool to characterize active faulting in regions of slow deformation

    Science.gov (United States)

    Custódio, Susana; Arroucau, Pierre; Carrilho, Fernando; Cesca, Simone; Dias, Nuno; Matos, Catarina; Vales, Dina

    2016-04-01

    The theory of plate tectonics states that the relative motion between lithospheric plates is accommodated at plate boundaries, where earthquakes occur on long faults. However, earthquakes with a wide range of magnitudes also occur both off plate boundaries, in intra-plate settings, and along discontinuous, diffuse plate boundaries. These settings are characterized by low rates of lithospheric deformation. A fundamental limitation in the study of slowly deforming regions is the lack of high-quality observations. In these regions, earthquake catalogs have traditionally displayed diffuse seismicity patterns. The location, geometry and activity rate of faults - all basic parameters for understanding fault dynamics - are usually poorly known. The dense seismic networks deployed in the last years around the world have opened new windows in observational seismology. Although high-magnitude earthquakes are rare in regions of slow deformation, low-magnitude earthquakes are well observable on the time-scale of these deployments. In this presentation, we will show how data from dense seismic deployments can be used to characterize faulting in regions of slow deformation. In particular, we will present the case study of western Iberia, a region undergoing low-rate deformation and which has generated some of the largest earthquakes in Europe, both intraplate (mainland) and interplate (offshore). The methods that we employ include automated earthquake detection methods to lower the completeness magnitude of catalogs, earthquake relocations, focal mechanisms patterns, waveform similarity and clustering analysis.

  6. On the characterization of the regions of feasible trajectories in the workspace of parallel manipulators

    CERN Document Server

    Chablat, Damien

    2009-01-01

    It was shown recently that parallel manipulators with several inverse kinematic solutions have the ability to avoid parallel singularities [Chablat 1998a] and self-collisions [Chablat 1998b] by choosing appropriate joint configurations for the legs. In effect, depending on the joint configurations of the legs, a given configuration of the end-effector may or may not be free of singularity and collision. Characterization of the collision/singularity-free workspace is useful but may be insufficient since two configurations can be accessible without collisions nor singularities but it may not exist a feasible trajectory between them. The goal of this paper is to define the maximal regions of the workspace where it is possible to execute trajectories. Twodifferent families of regions are defined : 1. those regions where the end-effector can move between any set of points, and 2. the regions where any continuous path can be tracked. These regions are characterized from the notion of aspects and free-aspects recent...

  7. 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...

  8. 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.

  9. 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.

  10. 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...... 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...

  11. Dissection of Genetic Effects of Quantitative Trait Loci (QTL) in Transgenic Cotton

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yong-shan

    2008-01-01

    @@ When alien DNA inserts into cotton genome in multi-copy manner,several QTL in cotton genome are disrupted,which are called dQTL in this study.Transgenic mutant line is near-isogenic to its recipient which is divergent for the dQTL from remaining QTL.So,a set of data from a transgenic QTL mutant line produced by Agrobacterium-mediated transformation,30074,its recipient,their F1 hybrids between them,and three elite lines were analyzed under a modified additive-dominance model with genotype by environment interactions in three different environments to dissect the genetic effects due to dQTL from the whole genome based genetic effects.

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

    Energy Technology Data Exchange (ETDEWEB)

    Darboux, M.; Dinten, J.M.; Nicolas, E.

    1996-12-31

    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). 4 refs.

  13. Cell Specific eQTL Analysis without Sorting Cells.

    Directory of Open Access Journals (Sweden)

    Harm-Jan Westra

    2015-05-01

    Full Text Available The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE meta-analysis on data from 5,683 samples to infer the cell type specificity of whole blood cis-eQTLs. We demonstrate that this method is able to predict neutrophil and lymphocyte specific cis-eQTLs and replicate these predictions in independent cell-type specific datasets. Finally, we show that SNPs associated with Crohn's disease preferentially affect gene expression within neutrophils, including the archetypal NOD2 locus.

  14. 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.

  15. Regional Characterization of Metropolitan Areas in Japan for Strong Ground Motion Evaluation

    Science.gov (United States)

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

    2002-12-01

    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 Headquarters for Earthquake Research Promotion, was formed to oversee appropriate research in the earth sciences and civil engineering. This agency distributes research funds of \\$130 million per year. Projects include these topics: 1) Densification of seismic and GPS networks, 2) Paleoseismological investigation of major active faults, 3) Research on the geometry and physical properties of basins under the cities, 4) Probablistic strong ground motion estimation, and 5) Regional characterization of faults and physical parameters. Regional Characterization Study A long-term goal is to produce map of reliable estimations of strong ground motion. This requires accurate determination of: Source, Propagation path, Near surface and Ground motion response.A new five year project starts this year to characterize the "source" and "propagation path" in the Kanto (Tokyo) region and Kinki (Osaka) region. The proximity of the Pacific and Philippine Sea subducting plates requires study of the relationship between earthquakes and regional tectonics. This projects 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 Reconstruction of source fault and velocity models allow for more realistic 3D EQ wave simulations. All of these information will be synthesized and provided to communities involved in probablistic hazards analysis, risk assessment and societal response. In 2002, we have started to deploy seismic profiling lines in the Boso Peninsula (112 km) and the Sagami bay area( 75 km) to image the subducting Philippine Sea plate

  16. 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. ...

  17. 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

  18. 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.

  19. 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.

  20. A General Method for QTL Mapping in Multiple Related Populations Derived from Multiple Parents

    Institute of Scientific and Technical Information of China (English)

    AO Yan; HU Zhi-qiu; TANG Zai-xiang; WANG Xue-feng; XU Chen-wu

    2009-01-01

    It's well known that incorporating some existing populations derived from multiple parents may improve QTL mapping and QTL-based breeding programs. However, no general maximum likelihood method has been available for this strategy. Based on the QTL mapping in multiple related populations derived from two parents, a maximum likelihood estimation method was proposed, which can incorporate several populations derived from three or more parents and also can be used to handle different mating designs. Taking a circle design as an example, we conducted simulation studies to study the effect of QTL heritability and sample size upon the proposed method. The results showed that under the same heritability, enhanced power of QTL detection and more precise and accurate estimation of parameters could be obtained when three F2 populations were jointly analyzed, compared with the joint analysis of any two F2 populations. Higher heritability, especially with larger sample sizes, would increase the ability of QTL detection and improve the estimation of parameters. Potential advantages of the method are as follows: firstly, the existing results of QTL mapping in single population can be compared and integrated with each other with the proposed method, therefore the ability of QTL detection and precision of QTL mapping can be improved. Secondly, owing to multiple alleles in multiple parents, the method can exploit gene resource more adequately, which will lay an important genetic groundwork for plant improvement.

  1. Isolation and functional characterization of a novel seed-specific promoter region from peanut.

    Science.gov (United States)

    Sunkara, Sowmini; Bhatnagar-Mathur, Pooja; Sharma, Kiran Kumar

    2014-01-01

    The importance of using tissue-specific promoters in the genetic transformation of plants has been emphasized increasingly. Here, we report the isolation of a novel seed-specific promoter region from peanut and its validation in Arabidopsis and tobacco seeds. The reported promoter region referred to as groundnut seed promoter (GSP) confers seed-specific expression in heterologous systems, which include putative promoter regions of the peanut (Arachis hypogaea L.) gene 8A4R19G1. This region was isolated, sequenced, and characterized using gel shift assays. Tobacco transgenics obtained using binary vectors carrying uidA reporter gene driven by GSP and/or cauliflower mosaic virus 35S promoters were confirmed through polymerase chain reaction (PCR), RT-PCR, and computational analysis of motifs which revealed the presence of TATA, CAAT boxes, and ATG signals. This seed-specific promoter region successfully targeted the reporter uidA gene to seed tissues in both Arabidopsis and tobacco model systems, where its expression was confirmed by histochemical analysis of the transgenic seeds. This promoter region is routinely being used in the genetic engineering studies in legumes aimed at targeting novel transgenes to the seeds, especially those involved in micronutrient enhancement, fungal resistance, and molecular pharming.

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

    Science.gov (United States)

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

    1984-03-01

    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 1D1119. However, no homology was detected between pTAR DNA and several Ti plasmids or several other small cryptic plasmids in many A. tumefaciens strains. A recombinant plasmid containing the origin of replication and stability maintenance region of pTAR was compatible with pTiC58, pTi15955, and pTi119 and incompatible with pAg119. A new compatibility group, Inc Ag-1, is discussed.

  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. A multi-marker model for detecting chromosomal segments displaying QTL activity

    Energy Technology Data Exchange (ETDEWEB)

    Rodolphe, F.; Lefort, M. (INRA Centre de Recherches de Jouy en Josas (France))

    1993-08-01

    A statistical method is presented for detecting quantitative trait loci (QTLs), based on the linear model. Unlike methods able to detect a few well separated QTLs and to estimate their effects and positions, this method considers the genome as a whole and enables the detection of chromosomal segments involved in the differences between two homozygous lines, and their backcross, doubled haploid, or F[sub 2] progenies, for a quantitative trait. Genetic markers must be codominant, but missing markers are accepted, provided they are missing independently from the experiment. Asymptotic properties, which are of practical use, are developed. This method does not rely on strong genetic hypotheses, and thus does not permit any precise genetic analysis of the trait under study, but it does assess which regions of the genome are involved, whatever the complexity of the genetic determinism (number, effects and interactions among QTLs). Simultaneous use of several methods, including this one, should lead to better efficiency in QTL detection.

  5. Genetic dissection of milk yield traits and mastitis resistance QTL on chromosome 20 in dairy cattle

    DEFF Research Database (Denmark)

    Kadri, Naveen Kumar; Guldbrandtsen, Bernt; Lund, Mogens Sandø;

    2015-01-01

    but not the former situation, undesirable genetic correlation could potentially be broken by selecting animals that have favorable variants for both traits. First, we performed a within-breed association study using a haplotype-based method in Danish Holstein cattle (HOL). Next, we analyzed Nordic Red dairy cattle...... (RDC) and Danish Jersey cattle (JER) with the goal of determining whether these QTL identified in Holsteins were segregating across breeds. Genotypes for 12,566 animals (5,966 HOL, 5,458 RDC, and 1,142 JER) were determined by using the Illumina Bovine SNP50 BeadChip (50k), which identifies 1,568 single...... nucleotide polymorphisms (SNP) on BTA20. Data were combined, phased, and clustered into haplotype states, followed by within- and across-breed haplotype-based association analyses using a linear mixed model. Association signals for both CM and MY peaked in the 26 to 40 Mb region on BTA20 in HOL. Single...

  6. Polymorphism in the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs.

    Directory of Open Access Journals (Sweden)

    Jordi Corominas

    Full Text Available BACKGROUND: The ELOVL fatty acid elongase 6 (ELOVL6, the only elongase related to de novo lipogenesis, catalyzes the rate-limiting step in the elongation cycle by controlling the fatty acid balance in mammals. It is located on pig chromosome 8 (SSC8 in a region where a QTL affecting palmitic, and palmitoleic acid composition was previously detected, using an Iberian x Landrace intercross. The main goal of this work was to fine-map the QTL and to evaluate the ELOVL6 gene as a positional candidate gene affecting the percentages of palmitic and palmitoleic fatty acids in pigs. METHODOLOGY AND PRINCIPAL FINDINGS: The combination of a haplotype-based approach and single-marker analysis allowed us to identify the main, associated interval for the QTL, in which the ELOVL6 gene was identified and selected as a positional candidate gene. A polymorphism in the promoter region of ELOVL6, ELOVL6:c.-533C>T, was highly associated with the percentage of palmitic and palmitoleic acids in muscle and backfat. Significant differences in ELOVL6 gene expression were observed in backfat when animals were classified by the ELOVL6:c.-533C>T genotype. Accordingly, animals carrying the allele associated with a decrease in ELOVL6 gene expression presented an increase in C16:0 and C16:1(n-7 fatty acid content and a decrease of elongation activity ratios in muscle and backfat. Furthermore, a SNP genome-wide association study with ELOVL6 relative expression levels in backfat showed the strongest effect on the SSC8 region in which the ELOVL6 gene is located. Finally, different potential genomic regions associated with ELOVL6 gene expression were also identified by GWAS in liver and muscle, suggesting a differential tissue regulation of the ELOVL6 gene. CONCLUSIONS AND SIGNIFICANCE: Our results suggest ELOVL6 as a potential causal gene for the QTL analyzed and, subsequently, for controlling the overall balance of fatty acid composition in pigs.

  7. 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. ...

  8. 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. ...

  9. 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

  10. 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.

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

    Science.gov (United States)

    Catarious, David M; Baydush, Alan H; Floyd, Carey E

    2006-11-01

    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

  12. 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

  13. Genome analysis methods - 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 [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGDBj Registered...ear Year of genome analysis Sequencing method Sequencing method Read counts Read counts Covered genome region Covered...otation method Number of predicted genes Number of predicted genes Genome database Genome database informati... License Update History of This Database Site Policy | Contact Us Genome analysis... methods - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  14. 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...

  15. QTL Information Table: 788 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSHT-4 Morphological trait Panicle/flower shattering Mixture C)Interval RIL Pei-Khu... W1944(O. rufipogon Griff.) CDO244 RG214 pha Cai, H.W., and Morishima, H. (2000). Genomic regions affecting seed shatter

  16. QTL Information Table: 702 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available SR C)Interval RIL Lemont Teqing A RM148 RM85 pha Huang, Z., Yu, T., Su, L., Yu, S.B., Zhang, Z.H., and Zhu, Y.G. (2004). Identificati...on of chromosome regions associated with seedling vigor in rice. Yi Chuan Xue Bao 31, 596-603. ...

  17. QTL Information Table: 703 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available SR C)Interval RIL Lemont Teqing A RM263 RM221 pha Huang, Z., Yu, T., Su, L., Yu, S.B., Zhang, Z.H., and Zhu, Y.G. (2004). Identificat...ion of chromosome regions associated with seedling vigor in rice. Yi Chuan Xue Bao 31, 596-603. ...

  18. QTL Information Table: 1026 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available ht resistance in rice: comparative mapping within and across species. TAG Theoretical and Applied Genetics 103, 19-29. http://dx.doi.org/10.1007/s001220000534 ... ...Nguyen, H.T. (2001). Locating genomic regions associated with components of droug

  19. QTL Information Table: 1024 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available parative mapping within and across species. TAG Theoretical and Applied Genetics 103, 19-29. http://dx.doi.org/10.1007/s001220000534 ... ...guyen, H.T. (2001). Locating genomic regions associated with components of drought resistance in rice: com

  20. QTL Information Table: 30 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qUVR-10 Resistance or Tolerance Other stress resistance ultraviolet-B (UVB) resista... and Yano, M. (2004). Delimitation of the chromosomal region for a quantitative trait locus, qUVR- 10, conferring resistance to ultra...violet-B radiation in rice (Oryza sativa L.). Theor Appl Genet 108, 385-391. ...

  1. QTL Information Table: 876 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available QSbr3a Resistance or Tolerance Sheath blight resistance sheath blight response rati...ngs (SBRs) RFLP C)Interval F4 Lemont Teqing B RG348 RG944 pha Li, Z., Pinson, S.R.M., Marchetti, M.A., Stans...el, J.W., and Park, W.D. (1995). Characterization of quantitative trait loci (QTLs) in cultivated rice contributing to field resistan

  2. 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.

  3. 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.

  4. QTL analyses on genotype-specific component traits in a crop simulation model for capsicum annuum L.

    NARCIS (Netherlands)

    Wubs, A.M.; Heuvelink, E.; Dieleman, J.A.; Magan, J.J.; Palloix, A.; Eeuwijk, van F.A.

    2012-01-01

    Abstract: QTL for a complex trait like yield tend to be unstable across environments and show QTL by environment interaction. Direct improvement of complex traits by selecting on QTL is therefore difficult. For improvement of complex traits, crop growth models can be useful, as such models can disse

  5. 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

  6. 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...

  7. Characterization of copy number variation in genomic regions containing STR loci using array comparative genomic hybridization.

    Science.gov (United States)

    Repnikova, Elena A; Rosenfeld, Jill A; Bailes, Andrea; Weber, Cecilia; Erdman, Linda; McKinney, Aimee; Ramsey, Sarah; Hashimoto, Sayaka; Lamb Thrush, Devon; Astbury, Caroline; Reshmi, Shalini C; Shaffer, Lisa G; Gastier-Foster, Julie M; Pyatt, Robert E

    2013-09-01

    Short tandem repeat (STR) loci are commonly used in forensic casework, familial analysis for human identification, and for monitoring hematopoietic cell engraftment after bone marrow transplant. Unexpected genetic variation leading to sequence and length differences in STR loci can complicate STR typing, and presents challenges in casework interpretation. Copy number variation (CNV) is a relatively recently identified form of genetic variation consisting of genomic regions present at variable copy numbers within an individual compared to a reference genome. Large scale population studies have demonstrated that likely all individuals carry multiple regions with CNV of 1kb in size or greater in their genome. To date, no study correlating genomic regions containing STR loci with CNV has been conducted. In this study, we analyzed results from 32,850 samples sent for clinical array comparative genomic hybridization (CGH) analysis for the presence of CNV at regions containing the 13 CODIS (Combined DNA Index System) STR, and the Amelogenin X (AMELX) and Amelogenin Y (AMELY) loci. Thirty-two individuals with CNV involving STR loci on chromosomes 2, 4, 7, 11, 12, 13, 16, and 21, and twelve with CNV involving the AMELX/AMELY loci were identified. These results were correlated with data from publicly available databases housing information on CNV identified in normal populations and additional clinical cases. These collective results demonstrate the presence of CNV in regions containing 9 of the 13 CODIS STR and AMELX/Y loci. Further characterization of STR profiles within regions of CNV, additional cataloging of these variants in multiple populations, and contributing such examples to the public domain will provide valuable information for reliable use of these loci.

  8. SPITZER AND HERSCHEL MULTIWAVELENGTH CHARACTERIZATION OF THE DUST CONTENT OF EVOLVED H II REGIONS

    Energy Technology Data Exchange (ETDEWEB)

    Paladini, R. [NASA Herschel Science Center, California Institute of Technology, 1200, East California Boulevard, Pasadena, CA 91125 (United States); Umana, G. [INAF-Osservatorio Astrofisico di Catania, Via S. Sofia 78, I-95123 Catania (Italy); Veneziani, M.; Noriega-Crespo, A. [Infrared Processing and Analysis Center, California Institute of Technology, 1200, East California Boulevard, Pasadena, CA 91125 (United States); Anderson, L. D. [Department of Physics, West Virginia University, Morgantown, WV 26506 (United States); Piacentini, F. [Dipartimento di Fisica, Universita di Roma La Sapienza, I-00185 Roma (Italy); Pinheiro Goncalves, D. [Department of Astronomy and Astrophysics, University of Toronto 50 George Street, Toronto, ON M5S 3H4 (Canada); Paradis, D.; Bernard, J.-P. [Centre d' Etude Spatiale des Rayonnements, 9 Avenue du Colonel Roche, F-31028 Toulouse Cedex 4 (France); Tibbs, C. T. [Spitzer Science Center, California Institute of Technology, 1200, East California Boulevard, Pasadena, CA 91125 (United States); Natoli, P., E-mail: paladini@ipac.caltech.edu [Istituto Nazionale di Fisica Nucleare, Sezione Ferrara, I-44100 Ferrara (Italy)

    2012-12-01

    We have analyzed a uniform sample of 16 evolved H II regions located in a 2 Degree-Sign Multiplication-Sign 2 Degree-Sign Galactic field centered at (l,b) = (30 Degree-Sign , 0 Degree-Sign ) and observed as part of the Herschel Hi-GAL survey. The evolutionary stage of these H II regions was established using ancillary radio-continuum data. By combining Hi-GAL PACS (70 {mu}m, 160 {mu}m) and SPIRE (250 {mu}m, 350 {mu}m, and 500 {mu}m) measurements with MIPSGAL 24 {mu}m data, we built spectral energy distributions of the sources and showed that a two-component gray-body model is a good representation of the data. In particular, wavelengths >70 {mu}m 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 {mu}m, the data indicate 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 H II regions, although likely not in a large amount. In addition, the data seem to corroborate the hypothesis that the main mechanism responsible for the (partial) depletion of dust in H II regions is radiation-pressure-driven drift. In this framework, we speculated that the 24 {mu}m emission that spatially correlates with ionized gas might be associated with either very small grain or BG replenishment, as recently proposed for the case of wind-blown bubbles. Finally, we found that evolved H II regions are characterized by distinctive far-IR and submillimeter colors, which can be used as diagnostics for their identification in unresolved Galactic and extragalactic regions.

  9. Molecular structural and functional characterization of STAT1 gene regulatory region in teleost Channa argus.

    Science.gov (United States)

    Jia, Weizhang; Zhou, Xiuxia

    2010-05-15

    The transcription factor STAT1 is involved in signal transduction of type I and II interferons (IFNs). However, the molecular characteristics of the STAT1 regulatory region still remain to be elucidated in teleosts. In the present study, the complete cDNA and the regulatory region of the STAT1 gene were isolated from snakehead (Channa argus). More than 2.4kb 5'-flanking region of STAT1 shares the regulatory elements of IFN-stimulated response element (ISRE) and IFN-gamma activation site (GAS). Consensus ISRE and GAS were located from -373 to -361 and -716 to -724 in the promoter region, respectively. Moreover, it is noticeable that the crucial elements of ISRE (+698 to +710) and GAS (+294 and +301) are present in the first intron of snakehead STAT1. Comparisons of six vertebrate STAT1 5'-flanking regions all present the common sequence characteristics of IFN-induced gene promoter, which include ISRE, GAS and Sp1 sites. In order to further characterize the snakehead STAT1 regulatory region, six reporter constructs of snakehead STAT1 promoter and first intron were generated to examine the specificity to human interferon-gamma (hIFN-gamma). Only those constructs containing the ISRE element showed notable reporter activity after stimulation of Hela cells with hIFN-gamma. However, sequential deletions of putative transcription factor binding sites indicated that GAS elements have little effect on the promoter and intronic activity in response to hIFN-gamma. Taken together, these results suggest that the regulatory mechanisms of IFN-signalling appear to be mediated in a similar manner in fish and mammals.

  10. 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.

  11. Expression QTL modules as functional components underlying higher-order phenotypes.

    Directory of Open Access Journals (Sweden)

    Lei Bao

    Full Text Available Systems genetics studies often involve the mapping of numerous regulatory relations between genetic loci and expression traits. These regulatory relations form a bipartite network consisting of genetic loci and expression phenotypes. Modular network organizations may arise from the pleiotropic and polygenic regulation of gene expression. Here we analyzed the expression QTL (eQTL networks derived from expression genetic data of yeast and mouse liver and found 65 and 98 modules respectively. Computer simulation result showed that such modules rarely occurred in randomized networks with the same number of nodes and edges and same degree distribution. We also found significant within-module functional coherence. The analysis of genetic overlaps and the evidences from biomedical literature have linked some eQTL modules to physiological phenotypes. Functional coherence within the eQTL modules and genetic overlaps between the modules and physiological phenotypes suggests that eQTL modules may act as functional units underlying the higher-order phenotypes.

  12. QTL mapping for yield components and agronomic traits in a Brazilian soybean population

    Directory of Open Access Journals (Sweden)

    Josiane Isabela da Silva Rodrigues

    2016-11-01

    Full Text Available The objective of this work was to map QTL for agronomic traits in a Brazilian soybean population. For this, 207 F2:3 progenies from the cross CS3035PTA276-1-5-2x UFVS2012 were genotyped and cultivated in Viçosa-MG, using randomized block design with three replications. QTL detection was carried out by linear regression and composite interval mapping. Thirty molecular markers linked to QTL were detected by linear regression for the total of nine agronomic traits. QTL for SWP (seed weight per plant, W100S (weight of 100 seeds, NPP (number of pods per plant, and NSP (number of seeds per plant were detected by composite interval mapping. Four QTL with additive effect are promising for marker-assisted selection (MAS. Particularly, the markers Satt155 and Satt300 could be useful in simultaneous selection for greater SWP, NPP, and NSP.

  13. 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.

  14. The flowering repressor SVP underlies a novel Arabidopsis thaliana QTL interacting with the genetic background.

    Directory of Open Access Journals (Sweden)

    Belén Méndez-Vigo

    Full Text Available The timing of flowering initiation is a fundamental trait for the adaptation of annual plants to different environments. Large amounts of intraspecific quantitative variation have been described for it among natural accessions of many species, but the molecular and evolutionary mechanisms underlying this genetic variation are mainly being determined in the model plant Arabidopsis thaliana. To find novel A. thaliana flowering QTL, we developed introgression lines from the Japanese accession Fuk, which was selected based on the substantial transgression observed in an F(2 population with the reference strain Ler. Analysis of an early flowering line carrying a single Fuk introgression identified Flowering Arabidopsis QTL1 (FAQ1. We fine-mapped FAQ1 in an 11 kb genomic region containing the MADS transcription factor gene SHORT VEGETATIVE PHASE (SVP. Complementation of the early flowering phenotype of FAQ1-Fuk with a SVP-Ler transgen demonstrated that FAQ1 is SVP. We further proved by directed mutagenesis and transgenesis that a single amino acid substitution in SVP causes the loss-of-function and early flowering of Fuk allele. Analysis of a worldwide collection of accessions detected FAQ1/SVP-Fuk allele only in Asia, with the highest frequency appearing in Japan, where we could also detect a potential ancestral genotype of FAQ1/SVP-Fuk. In addition, we evaluated allelic and epistatic interactions of SVP natural alleles by analysing more than one hundred transgenic lines carrying Ler or Fuk SVP alleles in five genetic backgrounds. Quantitative analyses of these lines showed that FAQ1/SVP effects vary from large to small depending on the genetic background. These results support that the flowering repressor SVP has been recently selected in A. thaliana as a target for early flowering, and evidence the relevance of genetic interactions for the intraspecific evolution of FAQ1/SVP and flowering time.

  15. Characterization of blowholes as radon and thoron sources in the volcanic region of La Garrotxa, Spain

    Energy Technology Data Exchange (ETDEWEB)

    Moreno, V., E-mail: victoria.moreno@uab.ca [Grup de Fisica de les Radiacions, Departament de Fisica, Edifici Cc, Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona (Spain); Bach, J. [Unitat de Geodinamica Externa i d' Hidrogeologia, Departament de Geologia, Edifici Cs, Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona (Spain); Baixeras, C.; Font, Ll. [Grup de Fisica de les Radiacions, Departament de Fisica, Edifici Cc, Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona (Spain)

    2009-10-15

    In the volcanic region of La Garrotxa there are natural holes in the soil from which a flow of air can reach the outdoor/indoor environment. In a previous study, these holes (called blowholes) have been found to have a big influence on indoor radon levels in a couple of houses. This finding triggered the interest to characterize these blowholes as radon/thoron sources. In this work, a total of 26 holes have been identified and characterized by geological field observations and by measuring their dimensions, air speed, temperature, humidity, and radon and thoron concentrations. Radon has been measured with passive (Makrofol) and active detectors (monitors PRASSI and RAD 7, being the latter used also to measure thoron). One of the indoor blowholes has been studied in detail and important temporal variations have been found, showing that radon levels are clearly correlated with the soil-outdoor temperature difference. There is not a significant radiological risk for the inhabitants and workers of the studied homes and workplaces with indoor blowholes. However, taking into account that in warm seasons buildings with blowholes in pyroclastic materials from volcanoes or in volcanic scoria under a compact lava flow may have high indoor radon levels (up to 1.5 kBq m{sup -3}) we conclude that volcanic regions with similar geological features and with presence of blowholes should be considered as areas with a potential radon/thoron radiological risk.

  16. Meta-QTL for resistance to white mold in common bean

    Science.gov (United States)

    Vasconcellos, Renato C. C.; Oraguzie, O. Blessing; Soler, Alvaro; Arkwazee, Haidar; Myers, James R.; Ferreira, Juan J.; Song, Qijian; McClean, Phil; Miklas, Phillip N.

    2017-01-01

    White mold, caused by the fungus Sclerotinia sclerotiorum (Lib.) de Bary, is a major disease that limits common bean production and quality worldwide. The host-pathogen interaction is complex, with partial resistance in the host inherited as a quantitative trait with low to moderate heritability. Our objective was to identify meta-QTL conditioning partial resistance to white mold from individual QTL identified across multiple populations and environments. The physical positions for 37 individual QTL were identified across 14 recombinant inbred bi-parental populations (six new, three re-genotyped, and five from the literature). A meta-QTL analysis of the 37 QTL was conducted using the genetic linkage map of Stampede x Red Hawk population as the reference. The 37 QTL condensed into 17 named loci (12 previously named and five new) of which nine were defined as meta-QTL WM1.1, WM2.2, WM3.1, WM5.4, WM6.2, WM7.1, WM7.4, WM7.5, and WM8.3. The nine meta-QTL had confidence intervals ranging from 0.65 to 9.41 Mb. Candidate genes shown to express under S. sclerotiorum infection in other studies, including cell wall receptor kinase, COI1, ethylene responsive transcription factor, peroxidase, and MYB transcription factor, were found within the confidence interval for five of the meta-QTL. The nine meta-QTL are recommended as potential targets for MAS for partial resistance to white mold in common bean. PMID:28199342

  17. 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.

  18. 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.

  19. 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

    2011-01-01

    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...... 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...

  20. Mapping eQTL networks with mixed graphical models

    OpenAIRE

    Tur Mongé, Inma 1985-

    2014-01-01

    La cartogra a gen etica dels trets quantitatius d'expressi o (eQTL) esdev e un gran repte degut a la naturalesa multivariant d'alta dimensionalitat dels trets continus d'expressi o g enica i els genotips discrets dels experiments de gen omica gen etica. A m es de l'heterogene tat de l'expressi o produ da pels factors de confusi o i altres fonts de variabilitat no desitjada, els efectes indirectes s'estenen per tots els gens com a resultat de perturbacions gen etiques, molecul...

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Characterization of tabique walls nails of the Alto Douro Wine Region

    Science.gov (United States)

    Cardoso, Rui; Pinto, Jorge; Paiva, Anabela; Lanzinha, João Carlos

    2016-11-01

    Tabique is one of the main Portuguese traditional building techniques which use raw materials as stone, earth andwood. In general, a tabique building component as a wall consist of a wooden structure made up of vertical boards connected to laths by metal nails and covered on both sides by an earth based material. This traditional building technology as an expressive incidence in the Alto Douro Wine Region located in the interior of Northern Portugal, added to the UNESCO's Word Heritage Sites List in December 2001 as an `evolved continuing cultural landscape'. Furthermore, previous research works have shown that the existing tabique construction, in this region, reveals a certain lack of maintenance partially justified by the knowledge loosed on that technique, consequently this construction technique present an advanced stage of deterioration. This aspect associated to the fact that there is still a lack of scientific studies in this field motivated the writing of this paper, the main objectives are to identify and characterize the nails used in the timber connections. The nails samples were collected from tabique walls included in tabique buildings located in LamegoMunicipality, near Douro River, in the Alto Douro Wine Region. This work also intends to give guidelines to the rehabilitation and preservation of this important legacy.

  7. 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.

  8. Demonstration of a Relocatable Regional Ocean Atmosphere Modeling System with Coastal Autonomous Sampling Networks: Turbulence Characterization from an AUV

    Science.gov (United States)

    2016-06-07

    Demonstration Of A Relocatable Regional Ocean Atmosphere Modeling System with Coastal Autonomous Sampling Networks : Turbulence Characterization from...characterization tool in combined coastal ocean observation/prediction networks . OBJECTIVES I wish to use AUV-based turbulence measurements to quantify mixing... Services , Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington VA 22202-4302. Respondents should be

  9. 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.

  10. Mapping QTL affecting resistance to Marek's disease in an F6 advanced intercross population of commercial layer chickens

    Directory of Open Access Journals (Sweden)

    Wang Jing

    2009-01-01

    Full Text Available Abstract Background Marek's disease (MD is a T-cell lymphoma of chickens caused by the Marek's disease virus (MDV, an oncogenic avian herpesvirus. MD is a major cause of economic loss to the poultry industry and the most serious and persistent infectious disease concern. A full-sib intercross population, consisting of five independent families was generated by crossing and repeated intercrossing of two partially inbred commercial White Leghorn layer lines known to differ in genetic resistance to MD. At the F6 generation, a total of 1615 chicks were produced (98 to 248 per family and phenotyped for MD resistance measured as survival time in days after challenge with a very virulent plus (vv+ strain of MDV. Results QTL affecting MD resistance were identified by selective DNA pooling using a panel of 15 SNPs and 217 microsatellite markers. Since MHC blood type (BT is known to affect MD resistance, a total of 18 independent pool pairs were constructed according to family × BT combination, with some combinations represented twice for technical reasons. Twenty-one QTL regions (QTLR affecting post-challenge survival time were identified, distributed among 11 chromosomes (GGA1, 2, 3, 4, 5, 8, 9, 15, 18, 26 and Z, with about two-thirds of the MD resistance alleles derived from the more MD resistant parental line. Eight of the QTLR associated with MD resistance, were previously identified in a backcross (BC mapping study with the same parental lines. Of these, 7 originated from the more resistant line, and one from the less resistant line. Conclusion There was considerable evidence suggesting that MD resistance alleles tend to be recessive. The width of the QTLR for these QTL appeared to be reduced about two-fold in the F6 as compared to that found in the previous BC study. These results provide a firm basis for high-resolution linkage disequilibrium mapping and positional cloning of the resistance genes.

  11. 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

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

    Directory of Open Access Journals (Sweden)

    Yu Zhang

    2016-09-01

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

  13. Identification and Characterization of Quantitative Trait Loci for Shattering in Rice Landrace Jiucaiqing from Taihu Lake Valley, China.

    Science.gov (United States)

    Cheng, Jinping; He, Yongqi; Zhan, Chengfang; Yang, Bin; Xu, Enshun; Zhang, Hongsheng; Wang, Zhoufei

    2016-11-01

    Easy shattering reduces yield from grain loss during rice ( L.) harvest. We characterized a nonshattering rice landrace Jiucaiqing from Taihu Lake valley in China. The breaking tensile strength (BTS; grams force, gf) of the grain pedicel was measured using a digital force gauge to evaluate the degree of shattering at 0, 7, 14, 21, 28, and 35 d after heading (DAH). The BTS of Jiucaiqing did not significantly decrease with increasing DAH, maintaining a level of 152.2 to 195.9 gf, while that of IR26 decreased greatly during 0 to 14 DAH and finally stabilized at ∼100 gf. Then the chromosome segment substitution lines (CSSLs) and near isogenic lines (NILs) of Jiucaiqing in IR26 background were developed for quantitative trait loci (QTL) mapping. Four putative QTL (, , , and ) for shattering were detected, and the was confirmed on chromosome 1. We further mapped to a 98.4-kb region, which contains 14 genes. Os01g62920 was considered to be a strong candidate for , which colocated with . Further quantitative real-time polymerase chain reaction (PCR) analyses confirmed that the QTL can significantly decrease the expression of shattering related genes (, , , , and ) especially at the middle development stage at 10 and 15 cm panicle length, which causes rice shattering decrease. The elite allele and the NIL with desirable agronomic traits identified in this study could be useful for rice breeding.

  14. Integrating Small RNA Sequencing with QTL Mapping for Identification of miRNAs and Their Target Genes Associated with Heat Tolerance at the Flowering Stage in Rice

    Science.gov (United States)

    Liu, Qing; Yang, Tifeng; Yu, Ting; Zhang, Shaohong; Mao, Xingxue; Zhao, Junliang; Wang, Xiaofei; Dong, Jingfang; Liu, Bin

    2017-01-01

    Although, microRNAs (miRNAs) have been reported to be associated with heat tolerance at the seedling stage in rice, their involvement in heat tolerance at the flowering stage is still unknown. In this study, small RNA profiling was conducted in a heat-tolerant variety Gan-Xiang-Nuo (GXN) and a heat-sensitive variety Hua-Jing-Xian-74 (HJX), respectively. Totally, 102 miRNAs were differentially expressed (DE) under heat stress. Compared to HJX, GXN had more DE miRNAs and its DE miRNAs changed earlier under heat stress. Plant Ontology (PO) analysis of the target genes revealed that many DE miRNAs were involved in flower development. As a parallel experiment, QTL mapping was also conducted and four QTLs for heat tolerance at the flowering stage were identified using chromosome single-segment substitution lines derived from GXN and HJX. Further, through integrating analysis of DE miRNAs with QTLs, we identified 8 target genes corresponding to 26 miRNAs within the four QTL regions. Some meaningful target genes such as LOC_Os12g42400, SGT1, and pectinesterase were within the QTL regions. The negative correlation between miR169r-5p and its target gene LOC_Os12g42400 was confirmed under heat stress, and overexpression of miR169r-5p enhanced heat tolerance at flowering stage in rice. Our results demonstrate that the integrated analysis of genome-wide miRNA profiling with QTL mapping can facilitate identification of miRNAs and their target genes associated with the target traits and the limited candidates identified in this study offer an important source for further functional analysis and molecular breeding for heat tolerance in rice. PMID:28174587

  15. Statistical Properties of Solar Active Regions Based on Objective Detection and Characterization

    Science.gov (United States)

    Zhang, Jie

    2010-05-01

    We present a study of the statistical properties of solar magnetic regions based on objective detection and characterization. The uniformity and consistency of the magnetogram images provided by SOHO/MDI make it an ideal database for automated detection of solar magnetic features. The results of detection are mainly controlled by the following four parameters or thresholds: (1) magnetic intensity threshold of kernel pixels (to find strong field regions), (2) erosion size threshold for morphological opening operation (to remove small patches), (3) magnetic intensity threshold of AR pixels (to recover the whole size of an AR), (4) dilation size threshold for morphological closing operation (to merge neighboring patches to form a whole AR). We find that the best combination of the above four parameters is (1) 250 Gauss, (2) 10 Mm, (3) 50 Gauss, and (4) 10 Mm, which yields a detection of 1772 ARs that is most similar to the NOAA catalog based on human operators; as a comparison, NOAA/SWPC reports 2281 ARs during the same period. By varying the values of the control parameters, the number of ARs detected can range from as small as 1000 to as large as 10000. With these data, we are now able to make detailed statistical study of solar active regions, including (1) how AR number and emerged magnetic flux vary with solar cycle? (2) how AR number and emerged magnetic flux vary with latitude during different phases of solar cycle? (3) the distribution of AR number with respect to the size; Is the distribution power-law, Gaussian or log-normal, and the implication on the mechanisms of generating ARs? Is there a north-south asymmetry of ARs? How the strong magnetic patches distribute within an AR? This study provides us new insights on the properties and generations of solar active regions.

  16. Land surface thermal characterization of Asian-pacific region with Japanese geostationary satellite

    Science.gov (United States)

    Oyoshi, K.; Tamura, M.

    2010-12-01

    Land Surface Temperature (LST) is a significant indicator of energy balance at the Earth's surface. It is required for a wide variety of climate, hydrological, ecological, and biogeochemical studies. Although LST is highly variable both temporally and spatially, it is impossible for polar-orbiting satellite to detect hourly changes in LST, because the satellite is able to only collect data of the same area at most twice a day. On the other hand, geostationary satellite is able to collect hourly data and has a possibility to monitor hourly changes in LST, therefore hourly measurements of geostationary satellite enables us to characterize detailed thermal conditions of the Earth's surface and improve our understanding of the surface energy balance. Multi-functional Transport Satellite (MTSAT) is a Japanese geostationary satellite launched in 2005 and covers Asia-Pacific region. MTSAT provides hourly data with 5 bands including two thermal infrared (TIR) bands in the 10.5-12.5 micron region. In this research, we have developed a methodology to retrieve hourly LST from thermal infrared data of MTSAT. We applied Generalized Split-window (GSW) equation to estimate LST from TIR data. First, the brightness temperatures measured at sensor on MTSAT was simulated by radiative transfer code (MODTRAN), and the numerical coefficients of GSW equation were optimized based on the simulation results with non-linear minimization algorithm. The standard deviation of derived GSW equation was less than or equal to 1.09K in the case of viewing zenith angle lower than 40 degree and 1.73K in 60 degree. Then, spatial distributions of LST have been mapped optimized GSW equation with brightness temperatures of MTSAT IR1 and IR2 and emissivity map from MODIS product. Finally, these maps were validated with MODIS LST product (MOD11A1) over four Asian-pacific regions such as Bangkok, Tokyo, UlanBator and Jakarta , It is found that RMSE of these regions were 4.57K, 2.22K, 2.71K and 3.92K

  17. 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.

  18. [Dynamic QTL and correlated characters of tomato soluble solid content.].

    Science.gov (United States)

    Jia, Jun-Zhong; Tian, Li-Ping; Xue, Lin; Wei, Yi-Nong

    2010-10-01

    Two hundred and six F2:3 families from the cross between TD22 and HT-1-1-1-1 were used for dynamic QTL research of tomato soluble solid content and correlative traits, and correlation analysis of soluble solid content (SSC) with fruit weight (FW), fruit shape index (FSI), soluble sugar, vitamin C (VC), and organic acid at three different development stages. The results showed that there were differences in QTL loci for soluble solid content during the three stages of tomato fruit development. Four and eight QTLs were detected in green ripe stage and red ripe stage, respectively. These QTLs showed dynamic changes, and two markers LEaat006 and Tomato|TC162363 were detected in two stages, which might be useful in molecular-marker assisted selection (MAS). The result also showed that there was extremely significant difference in SSC at the three different stages, and its main correlative traits were different at different stages. Soluble solid content was positively correlated with soluble sugar, but negatively correlated with FW at green ripe stage; SSC was positively correlated with soluble sugar and organic acid at yellow ripe stage; SSC was positively correlated with soluble sugar and organic acid, but negatively correlated with fruit weight at red ripe stage. Based on correlation analysis of these traits, linear regression model was constructed. Non-tested varieties were used to test the fitness, and the result showed that it is well fitted, and the fitness is above 95%.

  19. Improvement of Rice Biomass Yield through QTL-Based Selection.

    Directory of Open Access Journals (Sweden)

    Kazuki Matsubara

    Full Text Available Biomass yield of rice (Oryza sativa L. is an important breeding target, yet it is not easy to improve because the trait is complex and phenotyping is laborious. Using progeny derived from a cross between two high-yielding Japanese cultivars, we evaluated whether quantitative trait locus (QTL-based selection can improve biomass yield. As a measure of biomass yield, we used plant weight (aboveground parts only, which included grain weight and stem and leaf weight. We measured these and related traits in recombinant inbred lines. Phenotypic values for these traits showed a continuous distribution with transgressive segregation, suggesting that selection can affect plant weight in the progeny. Four significant QTLs were mapped for plant weight, three for grain weight, and five for stem and leaf weight (at α = 0.05; some of them overlapped. Multiple regression analysis showed that about 43% of the phenotypic variance of plant weight was significantly explained (P < 0.0001 by six of the QTLs. From F2 plants derived from the same parental cross as the recombinant inbred lines, we divergently selected lines that carried alleles with positive or negative additive effects at these QTLs, and performed successive selfing. In the resulting F6 lines and parents, plant weight significantly differed among the genotypes (at α = 0.05. These results demonstrate that QTL-based selection is effective in improving rice biomass yield.

  20. 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)

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. A geometrical characterization of regions of uniqueness and applications to discrete tomography

    Science.gov (United States)

    Dulio, Paolo; Frosini, Andrea; Pagani, Silvia M. C.

    2015-12-01

    In the reconstruction problem of discrete tomography, projections are considered from a finite set {S} of lattice directions. Employing a limited number of projections implies that the injectivity of the Radon transform is lost, and, in general, images consistent with a given set of projections form a huge class. In order to lower the number of allowed solutions, one usually tries to include in the problem some a priori information. This suggests that modelling the tomographic reconstruction problem as a linear system of equations is preferable. In this paper we propose to restrict the usual notion of uniqueness, related to the solutions of the linear system, and to provide, for each set {S}, a geometrical characterization of the shape of a lattice subset, say region of uniqueness (ROU), forming a partial, fast reconstructible, solution. Any selected set {S} intrinsically determines its ROU inside an arbitrary lattice grid. For instance, trivially, if | {S}| =1, the ROU is represented by two rectangles having sizes equal to the absolute values of the entries of the unique direction in {S}, and placed at two opposite corners of the chosen grid. Surprisingly, if | {S}| =2, the problem becomes much more complicated. Our purpose is to provide a geometrical characterization of the ROU. This is based on a double Euclidean division algorithm (DEDA), which runs in polynomial time. It turns out that the ROU is delimited by a zigzag profile obtained by means of numerical relations among the entries of the employed directions. According to different inputs in DEDA, the shape of the ROU can change consistently, as it can be easily observed from the provided examples. Moreover, after selecting a region of interest (ROI) from a given phantom, we exploit DEDA to reconstruct the part of the ROI which falls in the ROU and, with a few further a priori knowledge, even parts of the ROI which are outside the ROU.

  6. Characterization of the promoter region of biosynthetic enzyme genes involved in berberine biosynthesis in Coptis japonica

    Directory of Open Access Journals (Sweden)

    Yasuyuki Yamada

    2016-09-01

    Full Text Available The presence of alkaloids is rather specific to certain plant species. However, berberine, an isoquinoline alkaloid, is relatively broadly distributed in the plant kingdom. Thus, berberine biosynthesis has been intensively investigated, especially using Coptis japonica cell cultures. Almost all biosynthetic enzyme genes have already been characterized at the molecular level. Particularly, two transcription factors (TFs, a plant-specific WRKY-type transcription factor, CjWRKY1, and a basic helix-loop-helix (bHLH transcription factor, CjbHLH1, were shown to comprehensively regulate berberine biosynthesis in C. japonica cells. In this study, we characterized the promoter region of some biosynthetic enzyme genes and associated cis-acting elements involved in the transcriptional regulation via two TFs. The promoter regions of three berberine biosynthetic enzyme genes (CYP80B2, 4’OMT and CYP719A1 were isolated, and their promoter activities were dissected by a transient assay involving the sequentially truncated promoter::luciferase (LUC reporter constructs. Furthermore, transactivation activities of CjWRKY1 were determined using the truncated promoter::LUC reporter constructs or constructs with mutated cis-elements. These results suggest the involvement of a putative W-box in the regulation of biosynthetic enzyme genes. Direct binding of CjWRKY1 to the W-box DNA sequence was also confirmed by an electrophoresis mobility shift assay (EMSA and by a chromatin immunoprecipitation (ChIP assay. In addition, CjbHLH1 also activated transcription from truncated 4’OMT and CYP719A1 promoters independently of CjWRKY1, suggesting the involvement of a putative E-box. Unexpected transcriptional activation of biosynthetic enzyme genes via a non-W-box sequence and by CjWRKY1 as well as the possible involvement of a GCC-box in berberine biosynthesis in C. japonica are discussed.

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

    Directory of Open Access Journals (Sweden)

    Daniel Fulop

    2016-10-01

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

  8. Mapping of quantitative trait loci (QTL) for production, resistance and tolerance traits in Salix. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Roennberg-Waestljung, Ann Christin; Bertholdsson, Nils-Ove; Glynn, Carolyn; Weih, Martin; Aahman, Inger [SLU, Uppsala (Sweden). Dept. of Plant Biology and Forest Genetics

    2004-05-01

    Quantitative trait loci (QTL) for growth traits, water use efficiency and tolerance/resistance against metals and herbivores have been identified. A hybrid F2 population originating from a cross between a Salix dasyclados-clone (SW901290) and a S. viminalis-clone ('Jorunn') was used for the different studies in this project. The growth response was analyzed in a greenhouse experiment with two water treatments, normal and drought. In addition, three field experiments with contrasting soils and climates were established. QTL specific for each treatment or field environment but also QTL stable over the treatments or field environments were detected. Each QTL explained from 8 to 29 % of the phenotypic variation depending on trait, treatment or field environment. Clusters of QTL for different traits were mapped indicating a common genetic base or tightly-linked QTL. Stable QTL identified for dryweight can be useful tools for early selection in Salix. In a separate greenhouse experiment, with a subset of ten genotypes from the F2 population, we show that genotype is more important than irrigation treatment for production of phenolic substances as well as for resistance to herbivory by P vulgatissima.

  9. Relative efficiency of markerassisted selection whenmarker and QTL are incom-pletely linked

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The relative superiority in selection response of two basic marker-assisted selection strategies, marker-as- sisted BLUP (MBLUP) and two-stage selection, in comparison to standard BLUP was investigated using stochastic simulation of a closed nucleus herd. In marker-assisted BLUP the marker information and the phenotypic information were utilized simultaneously for selecting parental animals, whereas in two-stage selection they were utilized separately in two stages. Different heritabilities and QTL sizes were considered in the simulation. The QTL was assumed to be referred only via flanking markers, which were incompletely linked to the QTL. It was shown that both MBLUP and two-stage selection increased the QTL response but decreased the polygenic response. When the heritability was low or the QTL effect was large MBLUP was superior to standard BLUP by up to 5% with respect to total genetic response. While the two-stage selection did not show any superiority although it gave extremely large increase in QTL response due to a rapid increase in favorable QTL allele frequency. The relative responses of MAS were stark associated with the generations of selection. The superiority or inferiority of MAS was large in the early generations and became small or vanished in the later generations.

  10. Global identification and characterization of transcriptionally active regions in the rice genome.

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    Lei Li

    Full Text Available Genome tiling microarray studies have consistently documented rich transcriptional activity beyond the annotated genes. However, systematic characterization and transcriptional profiling of the putative novel transcripts on the genome scale are still lacking. We report here the identification of 25,352 and 27,744 transcriptionally active regions (TARs not encoded by annotated exons in the rice (Oryza. sativa subspecies japonica and indica, respectively. The non-exonic TARs account for approximately two thirds of the total TARs detected by tiling arrays and represent transcripts likely conserved between japonica and indica. Transcription of 21,018 (83% japonica non-exonic TARs was verified through expression profiling in 10 tissue types using a re-array in which annotated genes and TARs were each represented by five independent probes. Subsequent analyses indicate that about 80% of the japonica TARs that were not assigned to annotated exons can be assigned to various putatively functional or structural elements of the rice genome, including splice variants, uncharacterized portions of incompletely annotated genes, antisense transcripts, duplicated gene fragments, and potential non-coding RNAs. These results provide a systematic characterization of non-exonic transcripts in rice and thus expand the current view of the complexity and dynamics of the rice transcriptome.

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

    Energy Technology Data Exchange (ETDEWEB)

    Wladis, D.; Joensson, P.; Wallroth, T. [Chalmers Univ. of Technology., Goeteborg (Sweden). Dept. of Geology

    1997-11-01

    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 33 refs, 21 figs, 6 tabs

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

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    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.

  13. Detection and mapping of QTL for earliness components in a bread wheat recombinant inbred lines population.

    Science.gov (United States)

    Hanocq, E; Niarquin, M; Heumez, E; Rousset, M; Le Gouis, J

    2004-12-01

    Earliness, an adaptative trait and factor of variation for agronomic characters, is a major trait in plant breeding. Its constituent traits, photoperiod sensitivity (PS), vernalization requirement (VR) and intrinsic earliness (IE), are largely under independent genetic controls. Mapping of major genes and quantitative trait loci (QTL) controlling these components is in progress. Most of the studies focusing on earliness considered it as a whole or through one (or two) of its components. The purpose of this study was to detect and map QTL for the three traits together through an experimental design combining field trials and controlled growth conditions. QTL were mapped in a population of F(7) recombinant inbred lines derived by single-seed descent from a cross between two French varieties, 'Renan' and 'Recital'. A map was previously constructed, based on 194 lines and 254 markers, covering about 77% of the genome. Globally, 13 QTL with a LOD>2.5 were detected, of which four control PS, five control VR and four control IE. Two major photoperiod sensitive QTL, together explaining more than 31% of the phenotypic variation, were mapped on chromosomes 2B and 2D, at the same position as the two major genes Ppd-B1 and Ppd-D1. One major VR QTL explaining (depending on the year) 21.8-39.6% of the phenotypic variation was mapped on 5A. Among the other QTL, two QTL of PS and VR not referenced so far were detected on 5A and 6D, respectively. A VR QTL already detected on 2B in a connected population was confirmed.

  14. Modelling QTL effect on BTA06 using random regression test day models.

    Science.gov (United States)

    Suchocki, T; Szyda, J; Zhang, Q

    2013-02-01

    In statistical models, a quantitative trait locus (QTL) effect has been incorporated either as a fixed or as a random term, but, up to now, it has been mainly considered as a time-independent variable. However, for traits recorded repeatedly, it is very interesting to investigate the variation of QTL over time. The major goal of this study was to estimate the position and effect of QTL for milk, fat, protein yields and for somatic cell score based on test day records, while testing whether the effects are constant or variable throughout lactation. The analysed data consisted of 23 paternal half-sib families (716 daughters of 23 sires) of Chinese Holstein-Friesian cattle genotyped at 14 microsatellites located in the area of the casein loci on BTA6. A sequence of three models was used: (i) a lactation model, (ii) a random regression model with a QTL constant in time and (iii) a random regression model with a QTL variable in time. The results showed that, for each production trait, at least one significant QTL exists. For milk and protein yields, the QTL effect was variable in time, while for fat yield, each of the three models resulted in a significant QTL effect. When a QTL is incorporated into a model as a constant over time, its effect is averaged over lactation stages and may, thereby, be difficult or even impossible to be detected. Our results showed that, in such a situation, only a longitudinal model is able to identify loci significantly influencing trait variation.

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

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    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.

  16. Joint QTL analysis of three connected F2-crosses in pigs

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    Bennewitz Jörn

    2010-11-01

    Full Text Available Abstract Background Numerous QTL mapping resource populations are available in livestock species. Usually they are analysed separately, although the same founder breeds are often used. The aim of the present study was to show the strength of analysing F2-crosses jointly in pig breeding when the founder breeds of several F2-crosses are the same. Methods Three porcine F2-crosses were generated from three founder breeds (i.e. Meishan, Pietrain and wild boar. The crosses were analysed jointly, using a flexible genetic model that estimated an additive QTL effect for each founder breed allele and a dominant QTL effect for each combination of alleles derived from different founder breeds. The following traits were analysed: daily gain, back fat and carcass weight. Substantial phenotypic variation was observed within and between crosses. Multiple QTL, multiple QTL alleles and imprinting effects were considered. The results were compared to those obtained when each cross was analysed separately. Results For daily gain, back fat and carcass weight, 13, 15 and 16 QTL were found, respectively. For back fat, daily gain and carcass weight, respectively three, four, and five loci showed significant imprinting effects. The number of QTL mapped was much higher than when each design was analysed individually. Additionally, the test statistic plot along the chromosomes was much sharper leading to smaller QTL confidence intervals. In many cases, three QTL alleles were observed. Conclusions The present study showed the strength of analysing three connected F2-crosses jointly. In this experiment, statistical power was high because of the reduced number of estimated parameters and the large number of individuals. The applied model was flexible and was computationally fast.

  17. Mapping QTL for Resistance Against Viral Nervous Necrosis Disease in Asian Seabass.

    Science.gov (United States)

    Liu, Peng; Wang, Le; Wan, Zi Yi; Ye, Bao Qing; Huang, Shuqing; Wong, Sek-Man; Yue, Gen Hua

    2016-02-01

    Viral nervous necrosis disease (VNN), caused by nervous necrosis virus (NNV), leads to mass mortality in mariculture. However, phenotypic selection for resistance against VNN is very difficult. To facilitate marker-assisted selection (MAS) for resistance against VNN and understanding of the genetic architecture underlying the resistance against this disease, we mapped quantitative trait loci (QTL) for resistance against VNN in Asian seabass. We challenged fingerlings at 37 days post-hatching (dph), from a single back-cross family, with NNV at a concentration of 9 × 10(6) TCID50/ml for 2 h. Daily mortalities were recorded and collected. A panel of 330 mortalities and 190 surviving fingerlings was genotyped using 149 microsatellites with 145 successfully mapped markers covering 24 linkage groups (LGs). Analysis of QTL for both resistance against VNN and survival time was conducted using interval mapping. Five significant QTL located in four LGs and eight suggestive QTL in seven LGs were identified for resistance. Another five significant QTL in three LGs and five suggestive QTL in three LGs were detected for survival time. One significant QTL, spanning 3 cM in LG20, was identified for both resistance and survival time. These QTL explained 2.2-4.1% of the phenotypic variance for resistance and 2.2-3.3% of the phenotypic variance for survival time, respectively. Our results suggest that VNN resistance in Asian seabass is controlled by many loci with small effects. Our data provide information for fine mapping of QTL and identification of candidate genes for a better understanding of the mechanism of disease resistance.

  18. Tabique walls composite earth-based material characterization in the Alto Douro wine region, Portugal

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    Rui CARDOSO

    2015-12-01

    Full Text Available The Alto Douro Wine Region, located in the northeast of Portugal, a UNESCO World Heritage Site, presents a relevant tabique building stock, a traditional vernacular building technology. A technology based on a timber framed structure filled with a composite earth-based material. Meanwhile, previous research works have revealed that, principally in rural areas, this Portuguese heritage is highly deteriorated and damaged because of the rareness of conservation and strengthening works, which is partly related to the non-engineered character of this technology and to the growing phenomenon of rural to urban migration. Those aspects associated with the lack of scientific studies related to this technology motivated the writing of this paper, whose main purpose is the physical and chemical characterization of the earth-based material applied in the tabique buildings of that region. Consequently, an experimental work was conducted and the results obtained allowed, among others, the proposal of a particle size distribution envelope in respect to this material. This information will provide the means to assess the suitability of a given earth-based material in regard to this technology. The knowledge from this study could be very useful for the development of future normative documents and as a reference for architects and engineers that work with earth to guide and regulate future conservation, rehabilitation or construction processes helping to preserve this fabulous legacy.

  19. Characterization of the OmyY1 Region on the Rainbow Trout Y Chromosome

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    Ruth B. Phillips

    2013-01-01

    Full Text Available We characterized the male-specific region on the Y chromosome of rainbow trout, which contains both sdY (the sex-determining gene and the male-specific genetic marker, OmyY1. Several clones containing the OmyY1 marker were screened from a BAC library from a YY clonal line and found to be part of an 800 kb BAC contig. Using fluorescence in situ hybridization (FISH, these clones were localized to the end of the short arm of the Y chromosome in rainbow trout, with an additional signal on the end of the X chromosome in many cells. We sequenced a minimum tiling path of these clones using Illumina and 454 pyrosequencing. The region is rich in transposons and rDNA, but also appears to contain several single-copy protein-coding genes. Most of these genes are also found on the X chromosome; and in several cases sex-specific SNPs in these genes were identified between the male (YY and female (XX homozygous clonal lines. Additional genes were identified by hybridization of the BACs to the cGRASP salmonid 4x44K oligo microarray. By BLASTn evaluations using hypothetical transcripts of OmyY1-linked candidate genes as query against several EST databases, we conclude at least 12 of these candidate genes are likely functional, and expressed.

  20. Characterization of the OmyY1 region on the rainbow trout Y chromosome

    Science.gov (United States)

    Phillips, Ruth B.; DeKoning, Jenefer J.; Brunelli, Joseph P.; Faber-Hammond, Joshua J.; Hansen, John D.; Christensen, Kris A.; Renn, Suzy C.P.; Thorgaard, Gary H.

    2013-01-01

    We characterized the male-specific region on the Y chromosome of rainbow trout, which contains both sdY (the sex-determining gene) and the male-specific genetic marker, OmyY1. Several clones containing the OmyY1 marker were screened from a BAC library from a YY clonal line and found to be part of an 800 kb BAC contig. Using fluorescence in situ hybridization (FISH), these clones were localized to the end of the short arm of the Y chromosome in rainbow trout, with an additional signal on the end of the X chromosome in many cells. We sequenced a minimum tiling path of these clones using Illumina and 454 pyrosequencing. The region is rich in transposons and rDNA, but also appears to contain several single-copy protein-coding genes. Most of these genes are also found on the X chromosome; and in several cases sex-specific SNPs in these genes were identified between the male (YY) and female (XX) homozygous clonal lines. Additional genes were identified by hybridization of the BACs to the cGRASP salmonid 4x44K oligo microarray. By BLASTn evaluations using hypothetical transcripts of OmyY1-linked candidate genes as query against several EST databases, we conclude at least 12 of these candidate genes are likely functional, and expressed.

  1. Characterizing and Assessing the Agricultural Land Use Intensity of the Beijing Mountainous Region

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    Weiwei Zhang

    2016-11-01

    Full Text Available Recently, land use and land cover change have received increased attention, and an approach is required that can assess agricultural land use intensity on a general basis. This study demonstrated the usefulness of a tool for characterizing and assessing agricultural land use intensity in Beijing mountainous region. An emergy analysis and principal component analysis (PCA were adopted to obtain agricultural input and output intensity data. Correlation and regression analyses were used to study the relationship among land capability, agricultural input, output intensity, and agricultural system sustainability. Ultimately, the agricultural land use intensity types in the Beijing mountainous region were identified through a cluster analysis. The results produced five indices of agricultural input intensity and five indices of output intensity. Non-renewable energy was the overwhelming input, and grain, meat, eggs, and vegetables were the major outputs of the agricultural system. The results also showed that there was better natural land quality, higher input intensity, greater output intensity, and lower agricultural system sustainability. Eight types of agricultural intensity were classified and assessed, and they may be used to evaluate and monitor sustainable land use and provide baseline measurements of land use intensity for land use analyses and change detection.

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

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    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.

  3. 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.

  4. Genomic characterization of Sinorhizobium meliloti AK21, a wild isolate from the Aral Sea Region.

    Science.gov (United States)

    Molina-Sánchez, María Dolores; López-Contreras, José Antonio; Toro, Nicolás; Fernández-López, Manuel

    2015-01-01

    The symbiotic, nitrogen-fixing bacterium Sinorhizobium meliloti has been widely studied due to its ability to improve crop yields through direct interactions with leguminous plants. S. meliloti AK21 is a wild type strain that forms nodules on Medicago plants in saline and drought conditions in the Aral Sea Region. The aim of this work was to establish the genetic similarities and differences between S. meliloti AK21 and the reference strain S. meliloti 1021. Comparative genome hybridization with the model reference strain S. meliloti 1021 yielded 365 variable genes, grouped into 11 regions in the three main replicons in S. meliloti AK21. The most extensive regions of variability were found in the symbiotic plasmid pSymA, which also contained the largest number of orthologous and polymorphic sequences identified by suppression subtractive hybridization. This procedure identified a large number of divergent sequences and others without homology in the databases, the further investigation of which could provide new insight into the alternative metabolic pathways present in S. meliloti AK21. We identified a plasmid replication module from the repABC replicon family, together with plasmid mobilization-related genes (traG and a VirB9-like protein), which suggest that this indigenous isolate harbors an accessory plasmid. Furthermore, the transcriptomic profiles reflected differences in gene content and regulation between S. meliloti AK21 and S. meliloti 1021 (ExpR and PhoB regulons), but provided evidence for an as yet unknown, alternative mechanism involving activation of the cbb3 terminal oxidase. Finally, phenotypic microarrays characterization revealed a greater versatility of substrate use and chemical degradation than for S. meliloti 1021.

  5. 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.

  6. Identification and characterization of a liver stage-specific promoter region of the malaria parasite Plasmodium.

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    Susanne Helm

    Full Text Available During the blood meal of a Plasmodium-infected mosquito, 10 to 100 parasites are inoculated into the skin and a proportion of these migrate via the bloodstream to the liver where they infect hepatocytes. The Plasmodium liver stage, despite its clinical silence, represents a highly promising target for antimalarial drug and vaccine approaches. Successfully invaded parasites undergo a massive proliferation in hepatocytes, producing thousands of merozoites that are transported into a blood vessel to infect red blood cells. To successfully develop from the liver stage into infective merozoites, a tight regulation of gene expression is needed. Although this is a very interesting aspect in the biology of Plasmodium, little is known about gene regulation in Plasmodium parasites in general and in the liver stage in particular. We have functionally analyzed a novel promoter region of the rodent parasite Plasmodium berghei that is exclusively active during the liver stage of the parasite. To prove stage-specific activity of the promoter, GFP and luciferase reporter assays have been successfully established, allowing both qualitative and accurate quantitative analysis. To further characterize the promoter region, the transcription start site was mapped by rapid amplification of cDNA ends (5'-RACE. Using promoter truncation experiments and site-directed mutagenesis within potential transcription factor binding sites, we suggest that the minimal promoter contains more than one binding site for the recently identified parasite-specific ApiAP2 transcription factors. The identification of a liver stage-specific promoter in P. berghei confirms that the parasite is able to tightly regulate gene expression during its life cycle. The identified promoter region might now be used to study the biology of the Plasmodium liver stage, which has thus far proven problematic on a molecular level. Stage-specific expression of dominant-negative mutant proteins and

  7. Molecular characterization of monoclonal antibodies that inhibit acetylcholinesterase by targeting the peripheral site and backdoor region.

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    Yves Bourne

    Full Text Available The inhibition properties and target sites of monoclonal antibodies (mAbs Elec403, Elec408 and Elec410, generated against Electrophorus electricus acetylcholinesterase (AChE, have been defined previously using biochemical and mutagenesis approaches. Elec403 and Elec410, which bind competitively with each other and with the peptidic toxin inhibitor fasciculin, are directed toward distinctive albeit overlapping epitopes located at the AChE peripheral anionic site, which surrounds the entrance of the active site gorge. Elec408, which is not competitive with the other two mAbs nor fasciculin, targets a second epitope located in the backdoor region, distant from the gorge entrance. To characterize the molecular determinants dictating their binding site specificity, we cloned and sequenced the mAbs; generated antigen-binding fragments (Fab retaining the parental inhibition properties; and explored their structure-function relationships using complementary x-ray crystallography, homology modeling and flexible docking approaches. Hypermutation of one Elec403 complementarity-determining region suggests occurrence of antigen-driven selection towards recognition of the AChE peripheral site. Comparative analysis of the 1.9Å-resolution structure of Fab408 and of theoretical models of its Fab403 and Fab410 congeners evidences distinctive surface topographies and anisotropic repartitions of charges, consistent with their respective target sites and inhibition properties. Finally, a validated, data-driven docking model of the Fab403-AChE complex suggests a mode of binding at the PAS that fully correlates with the functional data. This comprehensive study documents the molecular peculiarities of Fab403 and Fab410, as the largest peptidic inhibitors directed towards the peripheral site, and those of Fab408, as the first inhibitor directed toward the backdoor region of an AChE and a unique template for the design of new, specific modulators of AChE catalysis.

  8. [Sequence characterization of the 5'-Flanking region of the GHR gene in Tibetan sheep].

    Science.gov (United States)

    Ma, Zhi-Jie; Wei, Ya-Ping; Zhong, Jin-Cheng; Chen, Zhi-Hua; Lu, Hong; Tong, Zi-Bao

    2007-08-01

    The 5'-Flanking sequence (including the P1 promotor and exon 1A) of the GHR gene in Oura-type Tibetan sheep (O. aries) was cloned by T-A method and sequenced (GenBank accession No. EF116490). Characterization and comparison of this sequence with mouflons (O. musimon), goat (C. hircus), cattle (B. taurus) and European bison (B. bonasus) orthologues were also conducted. Results showed that: 1) The 5'-flanking region contained many potential transcriptional factor binding sites such as those for C/EBPb, C/EBP, SP1, Cap, USF, HFH-2, HNF-3b, and Oct-1, which might have an important effect on transcription activation and regulation as well as tissue-specific expression. The rate of repetitive sequences was 2.55% and no SINEs, LINEs, LTR anti-transcription elements or DNA transposon elements were found, although one (TG)11 microsatellite was found. 2) In the P1 promotor region, sequence homology between the Tibetan sheep and mouflon, goat, cattle and European bison was 99.7%, 94.2%, 85.9% and 86.5%, respectively, while that for exon 1A was 99.0%, 97.0%, 92.7% and 94.6%, respectively. 3) The molecular phylogenetic tree among these species, constructed by the neighborhood joining method based on the sequences of no-coding region of the GHR genes, placed the two Bovinae species on one branch and the three Caprinae species on the other. Tibetan sheep and mouflons were joined first, followed by the goat, and then the Bovinae species, including the cattle and European bison. This result of phylogenetic clustering was not only identical to the taxonomy, but also to the phylogenetic clustering using the mitochondrial DNA of these species.

  9. 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.

  10. 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.

  11. 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.

  12. Detection of QTL for exudation rate at ripening stage in rice and its contribution to hydraulic conductance.

    Science.gov (United States)

    Yamamoto, Toshio; Suzuki, Tadafumi; Suzuki, Kenji; Adachi, Shunsuke; Sun, Jian; Yano, Masahiro; Ookawa, Taiichiro; Hirasawa, Tadashi

    2016-01-01

    Dry matter production of crops is determined by how much light they intercept and how efficiently they use it for carbon fixation; i.e., photosynthesis. The high-yielding rice cultivar, Akenohoshi, maintains a high photosynthetic rate in the middle of the day owing to its high hydraulic conductance in comparison with the elite commercial rice cultivar, Koshihikari. We developed 94 recombinant inbred lines derived from Akenohoshi and Koshihikari and measured their exudation rate to calculate hydraulic conductance to osmotic water transport in a paddy field. A quantitative trait locus (QTL) for exudation rate was detected on the long arm of chromosome 2 at the heading and ripening stages. We developed chromosome segment substitution lines which carried Akenohoshi segments in the Koshihikari genetic background, and measured hydraulic conductance to both osmotic and passive water transport. The QTL was confirmed to be located within a region of about 4.2Mbp on the distal end of long arm of chromosome 2. The Akenohoshi allele increased root surface area and hydraulic conductance, but didn't increase hydraulic conductivity of a plant.

  13. Cloning and functional characterization of the 5' regulatory region of ovine Hormone Sensitive Lipase (HSL) gene.

    Science.gov (United States)

    Lampidonis, Antonis D; Stravopodis, Dimitrios J; Voutsinas, Gerassimos E; Messini-Nikolaki, Niki; Stefos, George C; Margaritis, Lukas H; Argyrokastritis, Alexandros; Bizelis, Iosif; Rogdakis, Emmanuel

    2008-12-31

    Hormone Sensitive Lipase (HSL) catalyzes the rate-limiting step in the mobilization of fatty acids from adipose tissue, thus determining the supply of energy substrates in the body. HSL enzymatic activity is increased by adrenergic agonists, such as catecholamines and glucagons, which induce cyclic AMP (cAMP) intracellular production, subsequently followed by the activation of Protein Kinase A (PKA) and its downstream signaling cascade reactions. HSL constitutes the critical enzyme in the modulation of lipid stores and the only component being subjected to hormonal control in terms of the recently identified Adipose Triglyceride Lipase (ATGL). In order to acquire detailed knowledge with regard to the mechanisms regulating ovine HSL (ovHSL) gene transcription activity, we initially isolated and cloned the 5' proximal and distal promoter regions through a genome walking approach, with the utilization of the already characterized ovHSL cDNAs. As evinced by BLAST analysis and a multiple alignment procedure, the isolated genomic fragment of 2.744 kb appeared to contain the already specified 5'-untranslated region (5'-UTR), which was interrupted by a relatively large intron of 1.448 kb. Regarding the upstream remaining part of 1.224 kb, it was demonstrated to represent a TATA-less promoter area, harboring several cis-regulatory elements that could be putatively recognized by relatively more general transcription factors, mainly including Stimulating protein 1 (Sp1), CCAAT-box Binding Factors (CBFs), Activator Protein 2 (AP2) and Glucocorticoid Receptor (GR), as well as other cis-acting regions denominated as Insulin Response Element (IRE), Glucose Response Element (GRE), Fat Specific Element (FSE) and cAMP Response Element (CRE), which could likely function in a nourishment (i.e. glucose)-/hormone-dependent fashion. When different genomic fragments were directionally (5' to 3') cloned into a suitable reporter vector upstream of a promoter-less luciferase gene and

  14. 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;

    2009-01-01

    , it is of 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...

  15. 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.

  16. 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.

  17. Expression QTL analysis of top loci from GWAS meta-analysis highlights additional schizophrenia candidate genes.

    Science.gov (United States)

    de Jong, Simone; van Eijk, Kristel R; Zeegers, Dave W L H; Strengman, Eric; Janson, Esther; Veldink, Jan H; van den Berg, Leonard H; Cahn, Wiepke; Kahn, René S; Boks, Marco P M; Ophoff, Roel A

    2012-09-01

    There is genetic evidence that schizophrenia is a polygenic disorder with a large number of loci of small effect on disease susceptibility. Genome-wide association studies (GWASs) of schizophrenia have had limited success, with the best finding at the MHC locus at chromosome 6p. A recent effort of the Psychiatric GWAS consortium (PGC) yielded five novel loci for schizophrenia. In this study, we aim to highlight additional schizophrenia susceptibility loci from the PGC study by combining the top association findings from the discovery stage (9394 schizophrenia cases and 12 462 controls) with expression QTLs (eQTLs) and differential gene expression in whole blood of schizophrenia patients and controls. We examined the 6192 single-nucleotide polymorphisms (SNPs) with significance threshold at Pschizophrenia cases and controls (n=202). After correction for multiple testing, the eQTL analysis yielded 40 significant cis-acting effects of the SNPs. Seven of these transcripts show differential expression between cases and controls. Of these, the effect of three genes (RNF5, TRIM26 and HLA-DRB3) coincided with the direction expected from meta-analysis findings and were all located within the MHC region. Our results identify new genes of interest and highlight again the involvement of the MHC region in schizophrenia susceptibility.

  18. QTL mapping of protein content and seed characteristics under water-stress conditions in sunflower.

    Science.gov (United States)

    Ebrahimi, A; Maury, P; Berger, M; Calmon, A; Grieu, P; Sarrafi, A

    2009-05-01

    The purpose of this study was to identify genomic regions controlling seed protein content, kernel and hull weights, and seed density in water-stress conditions in sunflower (Helianthus annuus L.). The experiments consisted of a split-plot design (water treatment and recombinant inbred lines) with three blocks in two environments (greenhouse and field). High significant variation was observed between genotypes for all traits as well as for water treatment x genotype interaction. Several specific and nonspecific QTLs were detected for all traits under well-watered and water-stress conditions. Two SSR markers, ORS671_2 and HA2714, linked to protein content were identified that have no interaction with water treatments in greenhouse conditions. We also detected the E35M60_4 marker associated with kernel weight that had no interaction with water treatments. A specific QTL for protein content was detected with important phenotypic variance (17%) under water-stress conditions. Overlapping QTLs for protein content and seed density were identified in linkage group 15. This region probably has a peliotropic effect on protein content and seed density. QTLs for protein content colocated with grain weight traits were also identified.

  19. MOLECULAR CHARACTERIZATION OF MYCOBACTERIUM TUBERCULOSIS STRAINS CIRCULATING IN THE URAL REGION, RUSSIA

    Directory of Open Access Journals (Sweden)

    T. V. Umpeleva

    2013-01-01

    Full Text Available Abstract. Overall 178 Mycobacterium tuberculosis isolates recovered in 2009–2011 from newly diagnosed epidemiologically unlinked to TB patients in the Ural region of Russia have been studied. The absolute concentration method was used for drug susceptibility testing. Mutations katG, inhA and rpoB associated with resistance to isoniazid and rifampicin were detected by microchip technology («TB-Biochip». The isolates were genotyped by real-time PCR for the detection of Beijing/non-Beijing genotypes and 15-locus MIRU-VNTR typing according to «MIRU-VNTRplus» (http://www.miru-vntrplus.org. More than half (55.1% of 178 isolates belonged to the Beijing family, 58.7% of them were multiple drug resistant (MDR mostly due to rpoBSer531→Leu and katGSer315→Thr1 substitutions. Fifty VNTR profiles were found in 98 Beijing isolates; 57 of them grouped into 9 clusters. The largest VNTR cluster included 23 (23.5% Beijing isolates and 21 of them were MDR. The 80 non-Beijing isolates showed 64 distinct VNTR patterns which belonged to 6 genetic families: LAM, Ural, Haarlem, etc. Among LAM and Ural isolates 30.4% and 28.6% were MDR, respectively. The 5 of 7 MDR LAM isolates had specific mutation profile:  rpoBAsp516→Val substitution and mutations katGSer315→Thr1 and inhA_T15. The MDR Ural isolates showed the heterogeneity of mutations in rpoB gene compared to other genotypes. Taken together, these findings suggest the emergence and spread of MDR-TB in the Ural region which is characterized by circulation of MDR strains of different genotypes with the Beijing family genotype to be predominant.

  20. 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.

  1. QTL mapping of sake brewing characteristics of yeast.

    Science.gov (United States)

    Katou, Taku; Namise, Masahiro; Kitagaki, Hiroshi; Akao, Takeshi; Shimoi, Hitoshi

    2009-04-01

    A haploid sake yeast strain derived from the commercial diploid sake yeast strain Kyokai no. 7 showed better characteristics for sake brewing compared to the haploid laboratory yeast strain X2180-1B, including higher production of ethanol and aromatic components. A hybrid of these two strains showed intermediate characteristics in most cases. After sporulation of the hybrid strain, we obtained 100 haploid segregants of the hybrid. Small-scale sake brewing tests of these segregants showed a smooth continuous distribution of the sake brewing characteristics, suggesting that these traits are determined by multiple quantitative trait loci (QTLs). To examine these sake brewing characteristics at the genomic level, we performed QTL analysis of sake brewing characteristics using 142 DNA markers that showed heterogeneity between the two parental strains. As a result, we identified 25 significant QTLs involved in the specification of sake brewing characteristics such as ethanol fermentation and the production of aromatic components.

  2. QTL mapping of flowering and fruiting traits in olive.

    Directory of Open Access Journals (Sweden)

    Inès Ben Sadok

    Full Text Available One of the challenge fruit growers are facing is to balance between tree production and vegetative growth from year to year. To investigate the existence of genetic determinism for reproductive behaviour in olive tree, we studied an olive segregating population derived from a cross between 'Olivière' and 'Arbequina' cultivars. Our strategy was based on (i an annual assessment of individual trees yield, and (ii a decomposition of adult growth units at the crown periphery into quantitative variables related to both flowering and fruiting process in relation to their growth and branching. Genetic models, including the year, genotype effects and their interactions, were built with variance function and correlation structure of residuals when necessary. Among the progeny, trees were either 'ON' or 'OFF' for a given year and patterns of regular vs. irregular bearing were revealed. Genotype effect was significant on yield but not for flowering traits at growth unit (GU scale, whereas the interaction between genotype and year was significant for both traits. A strong genetic effect was found for all fruiting traits without interaction with the year. Based on the new constructed genetic map, QTLs with small effects were detected, revealing multigenic control of the studied traits. Many were associated to alleles from 'Arbequina'. Genetic correlations were found between Yield and Fruit set at GU scale suggesting a common genetic control, even though QTL co-localisations were in spe`cific years only. Most QTL were associated to flowering traits in specific years, even though reproductive traits at GU scale did not capture the bearing status of the trees in a given year. Results were also interpreted with respect to ontogenetic changes of growth and branching, and an alternative sampling strategy was proposed for capturing tree fruiting behaviour. Regular bearing progenies were identified and could constitute innovative material for selection programs.

  3. An information-theoretic machine learning approach to expression QTL analysis.

    Directory of Open Access Journals (Sweden)

    Tao Huang

    Full Text Available Expression Quantitative Trait Locus (eQTL analysis is a powerful tool to study the biological mechanisms linking the genotype with gene expression. Such analyses can identify genomic locations where genotypic variants influence the expression of genes, both in close proximity to the variant (cis-eQTL, and on other chromosomes (trans-eQTL. Many traditional eQTL methods are based on a linear regression model. In this study, we propose a novel method by which to identify eQTL associations with information theory and machine learning approaches. Mutual Information (MI is used to describe the association between genetic marker and gene expression. MI can detect both linear and non-linear associations. What's more, it can capture the heterogeneity of the population. Advanced feature selection methods, Maximum Relevance Minimum Redundancy (mRMR and Incremental Feature Selection (IFS, were applied to optimize the selection of the affected genes by the genetic marker. When we applied our method to a study of apoE-deficient mice, it was found that the cis-acting eQTLs are stronger than trans-acting eQTLs but there are more trans-acting eQTLs than cis-acting eQTLs. We compared our results (mRMR.eQTL with R/qtl, and MatrixEQTL (modelLINEAR and modelANOVA. In female mice, 67.9% of mRMR.eQTL results can be confirmed by at least two other methods while only 14.4% of R/qtl result can be confirmed by at least two other methods. In male mice, 74.1% of mRMR.eQTL results can be confirmed by at least two other methods while only 18.2% of R/qtl result can be confirmed by at least two other methods. Our methods provide a new way to identify the association between genetic markers and gene expression. Our software is available from supporting information.

  4. Avoidance of Linkage Drag Between Blast Resistance Gene and the QTL Conditioning Spikelet Fertility Based on Genotype Selection Against Heading Date in Rice

    Institute of Scientific and Technical Information of China (English)

    LIU Wen-qiang; FAN Ye-yang; CHEN Jie; SHI Yong-feng; WU Jian-li

    2009-01-01

    Previous study showed that a linkage drag between a blast resistance gene Pi25(t) and QTLs conditioning spikelet fertility (qSF-6) and number of filled grains per panicle (qNFGP-6) was detected on the short arm of chromosome 6. A larger population was used for further verification, and the results confirmed the linkage drag between the blast resistance gene and QTL conditioning spikelet fertility, other than QTL conditioning number of filled grains per panicle. Breakdown or avoidance of the linkage drag could be achieved by selection against the genotype background of a heading-date gene (qHD-7) that resided in the region between RM2 and RM214 on chromosome 7. For further validation, two lines with almost identical genotypes on all chromosomal regions except the Pi25(t) region on chromosome 6 were chosen to develop a new population. The results showed that qSF-6 could be further subdivided into qSF-6-1 and qSF-6-2. When the genotype of the region between RM2 and RM214 was from rice variety Zhong 156, the linkage drag between Pi25(t) and qSF-6-2 was detected and the allele of qSF-6-2 from rice variety Gumei 2 reduced the spikelet fertility. When the genotype of the region between RM2 and RM214 was from Gumei 2, no linkage drag was detected. This indicates that the linkage drag between the blast resistance gene and the QTL conditioning spikelet fertility could be broken down or avoided under a certain background genotype selection against heading-date and provides a marker aided solution for high level of blast resistance and yield breeding in rice and other crops as well.

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

    OpenAIRE

    Shuaidong Hu; Thomas Lübberstedt; Guangwu Zhao; Michael Lee

    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...

  6. 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.

  7. Regional characterization of freshwater Use in LCA: modeling direct impacts on human health.

    Science.gov (United States)

    Boulay, Anne-Marie; Bulle, Cécile; Bayart, Jean-Baptiste; Deschênes, Louise; Margni, Manuele

    2011-10-15

    Life cycle assessment (LCA) is a methodology that quantifies potential environmental impacts for comparative purposes in a decision-making context. While potential environmental impacts from pollutant emissions into water are characterized in LCA, impacts from water unavailability are not yet fully quantified. Water use can make the resource unavailable to other users by displacement or quality degradation. A reduction in water availability to human users can potentially affect human health. If financial resources are available, there can be adaptations that may, in turn, shift the environmental burdens to other life cycle stages and impact categories. This paper proposes a model to evaluate these potential impacts in an LCA context. It considers the water that is withdrawn and released, its quality and scarcity in order to evaluate the loss of functionality associated with water uses. Regionalized results are presented for impacts on human health for two modeling approaches regarding affected users, including or not domestic uses, and expressed in disability-adjusted life years (DALY). A consumption and quality based scarcity indicator is also proposed as a midpoint. An illustrative example is presented for the production of corrugated board with different effluents, demonstrating the importance of considering quality, process effluents and the difference between the modeling approaches.

  8. Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions.

    Science.gov (United States)

    He, Tianliang; Zhang, Xiaobo

    2016-04-01

    Deep-sea hydrothermal vents are considered to be one of the most spectacular ecosystems on Earth. Microorganisms form the basis of the food chain in vents controlling the vent communities. However, the diversity of bacterial communities in deep-sea hydrothermal vents from different oceans remains largely unknown. In this study, the pyrosequencing of 16S rRNA gene was used to characterize the bacterial communities of the venting sulfide, seawater, and tubeworm trophosome from East Pacific Rise, South Atlantic Ridge, and Southwest Indian Ridge, respectively. A total of 23,767 operational taxonomic units (OTUs) were assigned into 42 different phyla. Although Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant phyla in all vents, differences of bacterial diversity were observed among different vents from three oceanic regions. The sulfides of East Pacific Rise possessed the most diverse bacterial communities. The bacterial diversities of venting seawater were much lower than those of vent sulfides. The symbiotic bacteria of tubeworm Ridgeia piscesae were included in the bacterial community of vent sulfides, suggesting their significant ecological functions as the primary producers in the deep-sea hydrothermal vent ecosystems. Therefore, our study presented a comprehensive view of bacterial communities in deep-sea hydrothermal vents from different oceans.

  9. Spectrophotometric characterization of red wine color from the vineyard region of Metohia

    Directory of Open Access Journals (Sweden)

    Babincev Ljiljana M.

    2016-01-01

    Full Text Available Five types of red wine produced from the grape varieties from the Metohia region (vintage 2014 were characterized on the basis of their chromatic properties. The properties of bottled wines: Merlot, Vranac, Prokupac, Cabernet and Game were analyzed. Chromatic characteristics of these wines were observed four times during the year - spectrophotometer measurements were performed on wines aged 0, 4, 8 and 12 months. Intensity, hue and brilliance of color of these wines were determined (by the usual method of Glories. The amount of coloring matter was determined by the usual method of Durmishidze and the percentage of polymeric anthocyanins was calculated as well. Wine ageing decreased the color intensity while the color hue value increased. It was also found that contribution of wine color red pigment decreased with wine ageing, while the percentage of yellow pigment in wine increased. The total amount of colored substances in wines studied decreased with wine ageing, while the percentage of polymeric pigments in wine increased. This study presents the methodology for analyses of the chromatic characteristics, and explains the origin influence of wine on these properties. On the basis of these correlations the quality of red wine can be established.

  10. 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.

  11. 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.

  12. Expression QTL mapping in grapevine--revisiting the genetic determinism of grape skin colour.

    Science.gov (United States)

    Huang, Yung-Fen; Bertrand, Yves; Guiraud, Jean-Luc; Vialet, Sandrine; Launay, Amandine; Cheynier, Véronique; Terrier, Nancy; This, Patrice

    2013-06-01

    Expression quantitative locus (eQTL) mapping was proposed as a valuable approach to dissect the genetic basis of transcript variation, one of the prime causes of natural phenotypic variation. Few eQTL studies have been performed on woody species due to the difficulty in sample homogenisation. Based on previous knowledge on berry colour formation, we performed eQTL mapping in field experimentation of grapevine with appropriate sampling criteria. The transcript level of VvUFGT, a key enzyme for anthocyanin synthesis was measured by real-time qRT-PCR in grape berry on a 191-individual pseudo-F1 progeny, derived from a cross between Syrah and Grenache cultivars. Two eQTLs were identified: one, explaining 20%, of genotypic variance and co-locating with VvUFGT itself (cis-eQTL), was principally due to the contrast between Grenache alleles; the other, explaining 35% of genotypic variance, was a trans-eQTL due to Syrah allelic contrast and co-located with VvMYBAs, transcription factors known to activate the expression of VvUFGT. This study assessed and validated the feasibility of eQTL mapping approach in grapevine and offered insights and new hypotheses on grape skin colour formation.

  13. Power analysis of QTL detection in half-sib families using selective DNA pooling

    Directory of Open Access Journals (Sweden)

    López Teresa

    2001-05-01

    Full Text Available Abstract Individual loci of economic importance (QTL can be detected by comparing the inheritance of a trait and the inheritance of loci with alleles readily identifiable by laboratory methods (genetic markers. Data on allele segregation at the individual level are costly and alternatives have been proposed that make use of allele frequencies among progeny, rather than individual genotypes. Among the factors that may affect the power of the set up, the most important are those intrinsic to the QTL: the additive effect of the QTL, and its dominance, and distance between markers and QTL. Other factors are relative to the choice of animals and markers, such as the frequency of the QTL and marker alleles among dams and sires. Data collection may affect the detection power through the size of half-sib families, selection rate within families, and the technical error incurred when estimating genetic frequencies. We present results for a sensitivity analysis for QTL detection using pools of DNA from selected half-sibs. Simulations showed that conclusive detection may be achieved with families of at least 500 half-sibs if sires are chosen on the criteria that most of their marker alleles are either both missing, or one is fixed, among dams.

  14. 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.

  15. 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.

  16. Analysis of morphine responses in mice reveals a QTL on Chromosome 7 [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Wim E. Crusio

    2016-09-01

    Full Text Available In this study we identified a quantitative trait locus (QTL on mouse Chromosome 7 associated with locomotor activity and rearing post morphine treatment. This QTL was revealed after correcting for the effects of another QTL peak on Chromosome 10 using composite interval mapping. The positional candidate genes are Syt9 and Ppfibp2. Several other genes within the interval are linked to neural processes, locomotor activity, and the defensive response to harmful stimuli.

  17. Analysis of morphine responses in mice reveals a QTL on Chromosome 7 [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Wim E. Crusio

    2016-10-01

    Full Text Available In this study we identified a quantitative trait locus (QTL on mouse Chromosome 7 associated with locomotor activity and rearing post morphine treatment. This QTL was revealed after correcting for the effects of another QTL peak on Chromosome 10 using composite interval mapping. The positional candidate genes are Syt9 and Ppfibp2. Several other genes within the interval are linked to neural processes, locomotor activity, and the defensive response to harmful stimuli.

  18. 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.

  19. 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.

  20. Interaction-Point Phase-Space Characterization using Single-Beam and Luminous-Region Measurements at PEP-II

    Energy Technology Data Exchange (ETDEWEB)

    Kozanecki, W; /Saclay; Bevan, A.J.; /Queen Mary, U. of London; Viaud, B.F.; /Montreal U.; Cai, Y.; Fisher, A.S.; O' Grady, C.; Lindquist, B.; Roodman, A.; J.M.Thompson, M.Weaver; /SLAC

    2008-09-09

    We present an extensive experimental characterization of the e{sup {+-}} phase space at the interaction point of the SLAC PEP-II B-Factory, that combines a detailed mapping of luminous-region observables using the BABAR detector, with stored-beam measurements by accelerator techniques.

  1. Characterization of fungal spores in ambient particulate matter: A study from the Himalayan region

    Science.gov (United States)

    Kumar, Ajay; Attri, Arun K.

    2016-10-01

    Fungal spores as a constituent of ambient particulate matter (PM) is of concern; they not only display the physical traits of a particle, but are also potential allergens and health risk. An investigation over fourteen month was undertaken at a rural site located in the Western Himalayan region, to evaluate the PM associated fungal spores' concentration and diversity. The season-wise change in the fungal spores concentration in the Coarse Particulate Matter (CPM) fraction (aerodynamic diameter > 10 μm) varied from 500 to 3899 spores m-3. Their average concentration over 14 months was 1517 spores m-3. Significant diversity of fungal spores in the CPM samples was observed; 27 individual genera of fungal spores were identified, of which many were known allergens. Presence of Ascomycota and Basidiomycota fungal spores was dominant in the samples; ∼20% of the spores were un-characterized. The season-wise variability in fungal spores showed a statistically significant high correlation with CPM load. Maximum number concentration of the spores in CPM was recorded in the summer, while minimum in the winter. The high diversity of spores occurred during monsoon and post monsoon months. The meteorological factors played an important role in the fungal spores' distribution profile. The temporal profile of the spores showed significant correlation with the ambient temperature (T), relative humidity (RH), wind speed (WS) and planetary boundary layer (PBL) height. Strong correlation of WS with fungal spores and CPM, and wind back trajectories suggest that re-suspension and wind assisted transport of PM contributes to ambient CPM associated fungal spores.

  2. 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.

  3. Domestic water uses: characterization of daily cycles in the north region of Portugal.

    Science.gov (United States)

    Matos, Cristina; Teixeira, Carlos A; Duarte, A A L S; Bentes, I

    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.

  4. A consensus microsatellite-based linkage map for the hermaphroditic bay scallop (Argopecten irradians and its application in size-related QTL analysis.

    Directory of Open Access Journals (Sweden)

    Hongjun Li

    Full Text Available Bay scallop (Argopecten irradians is one of the most economically important aquaculture species in China. In this study, we constructed a consensus microsatellite-based genetic linkage map with a mapping panel containing two hybrid backcross-like families involving two subspecies of bay scallop, A. i. irradians and A. i. concentricus. One hundred sixty-one microsatellite and one phenotypic (shell color markers were mapped to 16 linkage groups (LGs, which corresponds to the haploid chromosome number of bay scallop. The sex-specific map was 779.2 cM and 781.6 cM long in female and male, respectively, whereas the sex-averaged map spanned 849.3 cM. The average resolution of integrated map was 5.9 cM/locus and the estimated coverage was 81.3%. The proportion of distorted markers occurred more in the hybrid parents, suggesting that the segregation distortion was possibly resulted from heterospecific interaction between genomes of two subspecies of bay scallop. The overall female-to-male recombination rate was 1.13:1 across all linked markers in common to both parents, and considerable differences in recombination also existed among different parents in both families. Four size-related traits, including shell length (SL, shell height (SH, shell width (SW and total weight (TW were measured for quantitative trait loci (QTL analysis. Three significant and six suggestive QTL were detected on five LGs. Among the three significant QTL, two (qSW-10 and qTW-10, controlling SW and TW, respectively were mapped on the same region near marker AiAD121 on LG10 and explained 20.5% and 27.7% of the phenotypic variance, while the third (qSH-7, controlling SH was located on LG7 and accounted for 15.8% of the phenotypic variance. Six suggestive QTL were detected on four different LGs. The linkage map and size-related QTL obtained in this study may facilitate marker-assisted selection (MAS in bay scallop.

  5. Genetic mapping of sulfur assimilation genes reveals a QTL for onion bulb pungency.

    Science.gov (United States)

    McCallum, John; Pither-Joyce, Meeghan; Shaw, Martin; Kenel, Fernand; Davis, Sheree; Butler, Ruth; Scheffer, John; Jakse, Jernej; Havey, Michael J

    2007-03-01

    Onion exhibits wide genetic and environmental variation in bioactive organosulfur compounds that impart pungency and health benefits. A PCR-based molecular marker map that included candidate genes for sulfur assimilation was used to identify genomic regions affecting pungency in the cross 'W202A' x 'Texas Grano 438'. Linkage mapping revealed that genes encoding plastidic ferredoxin-sulfite reductase (SiR) and plastidic ATP sulfurylase (ATPS) are closely linked (1-2 cM) on chromosome 3. Inbred F(3) families derived from the F(2 )population used to construct the genetic map were grown in replicated trials in two environments and bulb pungency was evaluated as pyruvic acid or lachrymatory factor. Broad-sense heritability of pungency was estimated to be 0.78-0.80. QTL analysis revealed significant associations of both pungency and bulb soluble solids content with marker intervals on chromosomes 3 and 5, which have previously been reported to condition pleiotropic effects on bulb carbohydrate composition. Highly significant associations (LOD 3.7-8.7) were observed between ATPS and SiR Loci and bulb pungency but not with bulb solids content. This association was confirmed in two larger, independently derived F(2) families from the same cross. Single-locus models suggested that the partially dominant locus associated with these candidate genes controls 30-50% of genetic variation in pungency in these pedigrees. These markers may provide a practical means to select for lower pungency without correlated selection for lowered solids.

  6. 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.

  7. 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 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 surface

  8. 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

  9. Characterization of HIV type 1 envelope sequence among viral isolates circulating in the northern region of Colombia, South America.

    Science.gov (United States)

    Villarreal, José-Luis; Gutiérrez, Jaime; Palacio, Lucy; Peñuela, Martha; Hernández, Robin; Lemay, Guy; Cervantes-Acosta, Guillermo

    2012-12-01

    To characterize human immunodeficiency virus (HIV-1) strains circulating in the Northern region of Colombia in South America, sequences of the viral envelope C2V3C3 region were obtained from patients with different high-risk practices. Close to 60% of the sequences were predicted to belong to macrophage-tropic viruses, according to the positions of acidic amino acids and putative N-linked glycosylation sites. This is in agreement with the fact that most of the patients were recently diagnosed individuals. Phylogenic analysis then allowed assignment of all 35 samples to subtype B viruses. This same subtype was found in previous studies carried out in other Colombian regions. This study thus expands previous analyses with previously missing data from the Northern region of the country. The number and the length of the sequences examined also help to provide a clearer picture of the prevailing situation of the present HIV epidemics in this country.

  10. Inheritance and QTL Mapping of Salt Tolerance in Rice

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    An F2 population derived from the cross between Jiucaiqing (japonica) and IR36 (indica) was used to analyze the inheritance of salt tolerance in rice by genetic model of major-genes plus polygenes, and to map the corresponding QTLs by SSR molecular markers. Rice plants of P1, P2, F1 and F2 at 5- to 6- leaf stage were treated under 140 mmol/L NaCl for 10 days. Three indices representing the ability of salt tolerance of rice seedlings were measured, including salt tolerance rating (STR), Na+/K+ ratio in roots and dry matter weight of shoots (DWS). STR, Na+/K+ and DWS were all controlled by two major genes with modification by polygenes. Heritability of these traits from major genes was 17.8, 53.3 and 52.3%, respectively. The linkage map constructed by 62 SSR molecular markers covered a total length of about 1 142 cM. There were three QTLs detected for STR located on chromosome 1, 5 and 9, two QTLs for DWS on chromosomes 8 and 9, and two QTLs for Na+/K+ on chromosomes 2 and 6, one on each chromosome respectively. Single QTL accounted for 6.7 to 19.3% of phenotypic variation. Identification method of salt tolerance in rice and breeding of rice varieties with salt tolerance based on molecular markers assisted selection had been discussed.

  11. QTL Analysis of Major Agronomic Traits in Soybean

    Institute of Scientific and Technical Information of China (English)

    CHEN Qing-shan; ZHANG Zhong-chen; LIU Chun-yan; XIN Da-wei; QIU Hong-mei; SHAN Da-peng; SHAN Cai-yun; HU Guo-hua

    2007-01-01

    Soybean is a main crop, and most agronomic traits of soybean are quantitative; therefore, there is very important studying and applying value to locating these traits. A F2:10 RIL population containing 154 lines, derived from the cross between Charleston as female and Dongnong 594 as male parent, were used in this experiment. A genetic linkage map was constructed with 164 SSR primers, which were screened with the two parents and amplified on the 154 lines. 12 agronomic traits different between the two parents were investigated, and QTLs of all the traits were analyzed using the software Windows QTL Cartographer V2.0. The agronomic traits included quality traits: protein content, oil content, and content of protein and oil; yield traits: pods per plant, seed weight per plant, arnd 100 seeds weight; and other agronomic traits: plant height, days to maturity, branches, nod number in main stem, average leaf length, and average leaf width. The results showed that 68 QTLs in total were found for the 12 agronomic traits. The number of QTLs per trait varied from 3 for the average leaf width to 11 for 100 seeds weight and plant height, and was 5.8 on average. Good accordance was seen in many QTLs between the results of this study and the results obtained by other similar studies; therefore, these QTLs may be valuable for molecular marker assistant selection in soybean. In this study, 68 major QTLs of 12 important traits of soybean were analyzed.

  12. 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/16 h, 18°C/8 h and optimum temperature (28°C/24 h 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.

  13. 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/16 h, 18°C/8 h) and optimum temperature (28°C/24 h) 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.

  14. Characterization of FRA7B, a human common fragile site mapped at the 7p chromosome terminal region.

    Science.gov (United States)

    Bosco, Nazario; Pelliccia, Franca; Rocchi, Angela

    2010-10-01

    Common fragile sites (CFS) are specific regions of the mammalian chromosomes that are particularly prone to gaps and breaks. They are a cause of genome instability, and the location of many CFS correlates with breakpoints of aberrations recurrent in some cancers. The molecular characterization of some CFS has not clarified the causes of their fragility. In this work, by using fluorescence in situ hybridization analysis with BAC and PAC clones, we determined the DNA sequence of the CFS FRA7B. The FRA7B sequence was then analyzed to identify coding sequences and some structural features possibly involved in fragility. FRA7B spans about 12.2 megabases, and is therefore one of the largest CFS analyzed. It maps at the 7p21.3-22.3 chromosome bands, therefore at the interface of G- and R-band regions that are probably difficult to replicate. A 90-kilobase long sequence that presents very high flexibility values was identified at the very beginning of the more fragile CFS region. Three large genes (THSD7A, SDK1, and MAD1L1) and two miRNA genes (MIRN589 and MIRN339) map in the fragile region. The chromosome band 7p22 is a recurrent breakpoint in chromosome abnormalities in different types of neoplasm. FRA7B is the first characterized CFS located in a chromosome terminal region.

  15. Identification of QTL for dorso-caudal chronic pleuritis in 12 crossbred porcine families.

    Science.gov (United States)

    Gregersen, V R; Sørensen, K K; Christensen, O F; Busch, M E; Vingborg, R K K; Velander, I H; Lund, M S; Bendixen, C

    2010-10-01

    Pleuropneumonia is a major problem in pig production. At the time of slaughter, chronic pleuritis (CP) developed from pleuropneumonia is a common finding, and breeding for a reduced incidence of CP using marker-assisted selection (MAS) would be advantageous. Before applying MAS, quantitative trait 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 identified within boar families using both a Binomial logistic regression method and a chi-square test of association. Significant QTL for CP were detected on Sus scrofa chromosomes (SSC) 2, 8, 12, 13, 14 and 18 using both methods. One QTL on SSC 8 was also detected across families. For the QTL identified 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 part of the lungs.

  16. QTL linkage analysis of connected populations using ancestral marker and pedigree information.

    Science.gov (United States)

    Bink, Marco C A M; Totir, L Radu; ter Braak, Cajo J F; Winkler, Christopher R; Boer, Martin P; Smith, Oscar S

    2012-04-01

    The common assumption in quantitative trait locus (QTL) linkage mapping studies that parents of multiple connected populations are unrelated is unrealistic for many plant breeding programs. We remove this assumption and propose a Bayesian approach that clusters the alleles of the parents of the current mapping populations from locus-specific identity by descent (IBD) matrices that capture ancestral marker and pedigree information. Moreover, we demonstrate how the parental IBD data can be incorporated into a QTL linkage analysis framework by using two approaches: a Threshold IBD model (TIBD) and a Latent Ancestral Allele Model (LAAM). The TIBD and LAAM models are empirically tested via numerical simulation based on the structure of a commercial maize breeding program. The simulations included a pilot dataset with closely linked QTL on a single linkage group and 100 replicated datasets with five linkage groups harboring four unlinked QTL. The simulation results show that including parental IBD data (similarly for TIBD and LAAM) significantly improves the power and particularly accuracy of QTL mapping, e.g., position, effect size and individuals' genotype probability without significantly increasing computational demand.

  17. WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp.

    Science.gov (United States)

    Snoek, L Basten; Van der Velde, K Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O; Poulin, Gino B; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C; Kammenga, Jan E; Swertz, Morris A

    2013-01-01

    Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype-phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers.

  18. Identification of QTL Affecting Protein and Amino Acid Contents in Rice

    Institute of Scientific and Technical Information of China (English)

    ZHONG Ming; WANG Ling-qiang; YuAN De-jun; LUO Li-jun; Xu Cai-guo; HE Yu-qing

    2011-01-01

    The phenotypes of protein and amino acid contents were measured in an F9 recombinant inbred line population derived from a cross between Zhenshan 97B and Delong 208.A total of 48 and 64 QTLs were identified in 2004 and 2005,respectively.The contribution of each QTL to the phenotypic variation ranged from 4.0% to 43.7%.Most QTLs co-localized,forming 29 QTL clusters on the chromosomes with three major ones detected in both years,which were mapped on chromosomes 1,7 and 9,respectively.The two QTL clusters for amino acid content,qAa1 and qAa7,influenced almost all the traits with the allele from Zhenshan 97B,and the third QTL cluster for amino acid content,qAa9,increased the lysine content with the allele from Delong 208.A wide coincidence was found between the QTL detected under this study and the loci involved in amino acid metabolism pathways in nitrogen assimilation and transport,or protein biosynthesis.The results would facilitate the identification of candidate genes and could be used in marker-assisted selection for the favorable allele in rice quality improvement.

  19. Identification and QTL mapping of whitefly resistance components in Solanum galapagense.

    Science.gov (United States)

    Firdaus, Syarifin; van Heusden, Adriaan W; Hidayati, Nurul; Supena, Ence Darmo Jaya; Mumm, Roland; de Vos, Ric C H; Visser, Richard G F; Vosman, Ben

    2013-06-01

    Solanum galapagense is closely related to the cultivated tomato and can show a very good resistance towards whitefly. A segregating population resulting from a cross between the cultivated tomato and a whitefly resistant S. galapagense was created and used for mapping whitefly resistance and related traits, which made it possible to study the genetic basis of the resistance. Quantitative trait loci (QTL) for adult survival co-localized with type IV trichome characteristics (presence, density, gland longevity and gland size). A major QTL (Wf-1) was found for adult survival and trichome characters on Chromosome 2. This QTL explained 54.1 % of the variation in adult survival and 81.5 % of the occurrence of type IV trichomes. A minor QTL (Wf-2) for adult survival and trichome characters was identified on Chromosome 9. The major QTL was confirmed in F3 populations. Comprehensive metabolomics, based on GCMS profiling, revealed that 16 metabolites segregating in the F2 mapping population were associated with Wf-1 and/or Wf-2. Analysis of the 10 most resistant and susceptible F2 genotypes by LCMS showed that several acyl sugars were present in significantly higher concentration in the whitefly resistant genotypes, suggesting a role for these components in the resistance as well. Our results show that whitefly resistance in S. galapagense seems to inherit relatively simple compared to whitefly resistance from other sources and this offers great prospects for resistance breeding as well as elucidating the underlying molecular mechanism(s) of the resistance.

  20. Identification of a QTL in Mus musculus for alcohol preference, withdrawal, and Ap3m2 expression using integrative functional genomics and precision genetics.

    Science.gov (United States)

    Bubier, Jason A; Jay, Jeremy J; Baker, Christopher L; Bergeson, Susan E; Ohno, Hiroshi; Metten, Pamela; Crabbe, John C; Chesler, Elissa J

    2014-08-01

    Extensive genetic and genomic studies of the relationship between alcohol drinking preference and withdrawal severity have been performed using animal models. Data from multiple such publications and public data resources have been incorporated in the GeneWeaver database with >60,000 gene sets including 285 alcohol withdrawal and preference-related gene sets. Among these are evidence for positional candidates regulating these behaviors in overlapping quantitative trait loci (QTL) mapped in distinct mouse populations. Combinatorial integration of functional genomics experimental results revealed a single QTL positional candidate gene in one of the loci common to both preference and withdrawal. Functional validation studies in Ap3m2 knockout mice confirmed these relationships. Genetic validation involves confirming the existence of segregating polymorphisms that could account for the phenotypic effect. By exploiting recent advances in mouse genotyping, sequence, epigenetics, and phylogeny resources, we confirmed that Ap3m2 resides in an appropriately segregating genomic region. We have demonstrated genetic and alcohol-induced regulation of Ap3m2 expression. Although sequence analysis revealed no polymorphisms in the Ap3m2-coding region that could account for all phenotypic differences, there are several upstream SNPs that could. We have identified one of these to be an H3K4me3 site that exhibits strain differences in methylation. Thus, by making cross-species functional genomics readily computable we identified a common QTL candidate for two related bio-behavioral processes via functional evidence and demonstrate sufficiency of the genetic locus as a source of variation underlying two traits.

  1. Toward closing rice telomere gaps: mapping and sequence characterization of rice subtelomere regions.

    NARCIS (Netherlands)

    Yang, T.J.; Yu, Y.; Chang, S.B.; Jong, de J.H.S.G.M.; Oh, C.S.; Ahn, S.N.; Fang, E.; Wing, R.A.

    2005-01-01

    Despite the collective efforts of the international community to sequence the complete rice genome, telomeric regions of most chromosome arms remain uncharacterized. In this report we present sequence data from subtelomere regions obtained by analyzing telomeric clones from two 8.8 × genome equivale

  2. 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.

  3. QTL analysis for early-maturing traits in cotton using two upland cotton (Gossypium hirsutum L.) crosses.

    Science.gov (United States)

    Li, Chengqi; Wang, Xiaoyun; Dong, Na; Zhao, Haihong; Xia, Zhe; Wang, Rui; Converse, Richard L; Wang, Qinglian

    2013-06-01

    Making use of the markers linked closely to QTL for early-maturing traits for MAS (Marker-assisted selection) is an effective method for the simultaneous improvement of early maturity and other properties in cotton. In this study, two F2 populations and their F2:3 families were generated from the two upland cotton (Gossypium hirsutum L.) crosses, Baimian2 × TM-1 and Baimian2 × CIR12. QTL for early-maturing traits were analyzed using F2:3 families. A total of 54 QTL (31 suggestive and 23 significant) were detected. Fourteen significant QTL had the LOD scores not only > 3 but also exceeding permutation threshold. At least four common QTL, qBP-17 for bud period (BP), qGP-17a/qGP-17b (qGP-17) for growth period (GP), qYPBF-17a/qYPBF-17b (qYPBF-17) for yield percentage before frost (YPBF) and qHFFBN-17 for height of first fruiting branch node (HFFBN), were found in both populations. These common QTL should be reliable and could be used for MAS to facilitate early maturity. The common QTL, qBP-17, had a LOD score not only > 3 but also exceeding permutation threshold, explaining 12.6% of the phenotypic variation. This QTL should be considered preferentially in MAS. Early-maturing traits of cotton are primarily controlled by dominant and over-dominant effects.

  4. Regional land cover characterization using Landsat thematic mapper data and ancillary data sources

    Science.gov (United States)

    Vogelmann, J.E.; Sohl, T.L.; Campbell, P.V.; Shaw, D.M.; ,

    1998-01-01

    As part of the activities of the Multi-Resolution Land Characteristics (MRLC) Interagency Consortium, an intermediate-scale land cover data set is being generated for the conterminous United States. This effort is being conducted on a region-by-region basis using U.S. Standard Federal Regions. To date, land cover data sets have been generated for Federal Regions 3 (Pennsylvania, West Virginia, Virginia, Maryland, and Delaware) and 2 (New York and New Jersey). Classification work is currently under way in Federal Region 4 (the southeastern United States), and land cover mapping activities have been started in Federal Regions 5 (the Great Lakes region) and 1 (New England). it is anticipated that a land cover data set for the conterminous United States will be completed by the end of 1999. A standard land cover classification legend is used, which is analogous to and compatible with other classification schemes. The primary MRLC regional classification scheme contains 23 land cover classes. The primary source of data for the project is the Landsat thematic mapper (TM) sensor. For each region, TM scenes representing both leaf-on and leaf-off conditions are acquired, preprocessed, and georeferenced to MRLC specifications. Mosaicked data are clustered using unsupervised classification, and individual clusters are labeled using aerial photographs. Individual clusters that represent more than one land cover unit are split using spatial modeling with multiple ancillary spatial data layers (most notably, digital elevation model, population, land use and land cover, and wetlands information). This approach yields regional land cover information suitable for a wide array of applications, including landscape metric analyses, land management, land cover change studies, and nutrient and pesticide runoff modeling.

  5. Southern California Earthquake Center - SCEC1: Final Report Summary Alternative Earthquake Source Characterization for the Los Angeles Region

    Energy Technology Data Exchange (ETDEWEB)

    Foxall, B

    2003-02-26

    The objective my research has been to synthesize current understanding of the tectonics and faults of the Los Angeles Basin and surrounding region to quantify uncertainty in the characterization of earthquake sources used for geologically- and geodetically-based regional earthquake likelihood models. This work has focused on capturing epistemic uncertainty; i.e. uncertainty stemming from ignorance of the true characteristics of the active faults in the region and of the tectonic forces that drive them. In the present context, epistemic uncertainty has two components: First, the uncertainty in source geometrical and occurrence rate parameters deduced from the limited geological, geophysical and geodetic observations available; and second. uncertainties that result from fundamentally different interpretations of regional tectonic deformation and faulting. Characterization of the large number of active and potentially active faults that need to be included in estimating earthquake occurrence likelihoods for the Los Angeles region requires synthesis and evaluation of large amounts of data and numerous interpretations. This was accomplished primarily through a series of carefully facilitated workshops, smaller meetings involving key researchers, and email groups. The workshops and meetings were made possible by the unique logistical and financial resources available through SCEC, and proved to be extremely effective forums for the exchange and critical debate of data and interpretations that are essential in constructing fully representative source models. The main products from this work are a complete source model that characterizes all know or potentially active faults in the greater Los Angeles region. which includes the continental borderland as far south as San Diego, the Ventura Basin, and the Santa Barbara Channel. The model constitutes a series of maps and representative cross-sections that define alternative fault geometries, a table containing rault

  6. Structural and functional characterization of the 5' upstream region of a glutamine synthetase gene from Scots pine

    OpenAIRE

    Avila, Concepción; Cantón, Francisco; Barnestein, Pilar; Suárez, María-Fernanda; Marraccini, Pierre; Rey, Manuel; Humara, Jaime; Ordás, Ricardo; Cánovas, Francisco

    2002-01-01

    International audience; We report here the isolation and characterization of a genomic clone encoding Scots pine (P. sylvestris) cytosolic glutamine synthetase GS1a. The clone contains the 5' half of the gene including part of the coding region organized in seven exons, interrupted by 6 introns and 980 bp upstream of the translation initiation codon. Earlier experiments carried out in our lab have shown that the GS1a gene is expressed in a light dependent fashion during the initial stages of ...

  7. Fuzzy statistic and comprehensive evaluating study for activity characterization of the active region

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    In this paper, the theory and method of the fuzzy mathematics areused to probe the connection between the activity of the active region and characterizat ion of the sunspot groups, to build the subordinating function according to the rela tionship between them and to evaluate comprehensively the activity of the active region on t he solar disk. The precise prediction of activity of the active regions has been obta ined by data reduction and analysis. The predicting accuracy is higher th an 95% . Forecast results indicate that the method of the fuzzy comprehensive evaluatio n is a good one for the solar activity prediction.

  8. 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.

  9. 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.

  10. A cis-eQTL in AHI1 confers risk to schizophrenia in European populations.

    Science.gov (United States)

    Ren, Zhimin; Qiu, Anli; Zhang, Aiqi; Huang, Lijun; Rao, Shuquan

    2016-10-06

    Schizophrenia is a devastating mental disorder, with heritability as high as 80%. Although genome-wide association studies have identified multiple promising risk variants of schizophrenia, they could only explain a small portion of the disease heritability, and other variants with low to moderate effect remain to be identified. Abelson helper integration site 1 (AHI1) is highly expressed in mammals throughout the developing brain, with lower expression continuing into adulthood. Besides, previous evidence suggested that AHI1 expression was changed in schizophrenia patients. Furthermore, association signal between AHI1 variants and schizophrenia has been reported in several European samples. In the present study, we first analyzed two expression quantitative trait loci (eQTL) datasets in healthy individuals and investigated the associations of eQTL of AHI1 with schizophrenia in independent European samples. We observed that a cis-eQTL of AHI1, rs11154801, showed significant association with AHI1 expression in both datasets (PEuropean populations.

  11. Short communication: QTL mapping for ear tip-barrenness in maize

    Energy Technology Data Exchange (ETDEWEB)

    Ding, J.; Ma, J.; Chen, J.; Ai, T.; Li, Z.; Tian, Z.; Wu, S.; Chen, W.; Wu, J.

    2016-11-01

    Barren tip on corn ear is an important agronomic trait in maize, which is highly associated with grain yield. Understanding the genetic basis of tip-barrenness may help to reduce the ear tip-barrenness in breeding programs. In this study, ear tip-barrenness was evaluated in two environments in a F2:3 population, and it showed significant genotypic variation for ear tip-barrenness in both environments. Using mixed-model composite interval mapping method, three additive effects quantitative trait loci (QTL) for ear tip-barrenness were mapped on chromosomes 2, 3 and 6, respectively. They explained 16.6% of the phenotypic variation, and no significant QTL × Environment interactions and digenic interactions were detected. The results indicated that additive effect was the main genetic basis for ear tip-barrenness in maize. This is the first report of QTL mapped for ear tip-barrenness in maize. (Author)

  12. cis-Expression QTL analysis of established colorectal cancer risk variants in colon tumors and adjacent normal tissue.

    Directory of Open Access Journals (Sweden)

    Lenora W M Loo

    Full Text Available Genome-wide association studies (GWAS have identified 19 risk variants associated with colorectal cancer. As most of these risk variants reside outside the coding regions of genes, we conducted cis-expression quantitative trait loci (cis-eQTL analyses to investigate possible regulatory functions on the expression of neighboring genes. Forty microsatellite stable and CpG island methylator phenotype-negative colorectal tumors and paired adjacent normal colon tissues were used for genome-wide SNP and gene expression profiling. We found that three risk variants (rs10795668, rs4444235 and rs9929218, using near perfect proxies rs706771, rs11623717 and rs2059252, respectively were significantly associated (FDR q-value ≤0.05 with expression levels of nearby genes (<2 Mb up- or down-stream. We observed an association between the low colorectal cancer risk allele (A for rs10795668 at 10p14 and increased expression of ATP5C1 (q = 0.024 and between the colorectal cancer high risk allele (C for rs4444235 at 14q22.2 and increased expression of DLGAP5 (q = 0.041, both in tumor samples. The colorectal cancer low risk allele (A for rs9929218 at 16q22.1 was associated with a significant decrease in expression of both NOL3 (q = 0.017 and DDX28 (q = 0.046 in the adjacent normal colon tissue samples. Of the four genes, DLGAP5 and NOL3 have been previously reported to play a role in colon carcinogenesis and ATP5C1 and DDX28 are mitochondrial proteins involved in cellular metabolism and division, respectively. The combination of GWAS findings, prior functional studies, and the cis-eQTL analyses described here suggest putative functional activities for three of the colorectal cancer GWAS identified risk loci as regulating the expression of neighboring genes.

  13. 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.

  14. 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 \

  15. Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens.

    Science.gov (United States)

    Joung, Je-Gun; Bae, Joon Seol; Kim, Sang Cheol; Jung, HyunChul; Park, Woong-Yang; Song, Sang-Yong

    2016-01-01

    A single tumor biopsy specimen is typically used in cancer genome studies. However, it may represent incompletely the underlying mutational and transcriptional profiles of tumor biology. Multi-regional biopsies have the advantage of increased sensitivity for genomic profiling, but they are not cost-effective. The concept of an alternative method such as the pooling of multiple biopsies is a challenge. In order to determine if the pooling of distinct regions is representative at the genomic and transcriptome level, we performed sequencing of four regional samples and pooled samples for four cancer types including colon, stomach, kidney and liver cancer. Subsequently, a comparative analysis was conducted to explore differences in mutations and gene expression profiles between multiple regional biopsies and pooled biopsy for each tumor. Our analysis revealed a marginal level of regional difference in detected variants, but in those with low allele frequency, considerable discrepancies were observed. In conclusion, sequencing pooled samples has the benefit of detecting many variants with moderate allele frequency that occur in partial regions, but it is not applicable for detecting low-frequency mutations that require deep sequencing.

  16. 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.

  17. Genetic determinism of bone and mineral metabolism in meat-type chickens: A QTL mapping study.

    Science.gov (United States)

    Mignon-Grasteau, Sandrine; Chantry-Darmon, Céline; Boscher, Marie-Yvonne; Sellier, Nadine; Chabault-Dhuit, Marie; Le Bihan-Duval, Elisabeth; Narcy, Agnès

    2016-12-01

    Skeletal integrity in meat-type chickens is affected by many factors including rapid growth rate, nutrition and genetics. To investigate the genetic basis of bone and mineral metabolism, a QTL detection study was conducted in an intercross between two lines of meat-type chickens divergently selected for their high (D +) or low (D -) digestive efficiency. Tibia size (length, diameter, volume) and ash content were determined at 3 weeks of age as well as phosphorus (P) retention and plasma concentration. Heritability of these traits and their genetic correlations with digestive efficiency were estimated. A QTL mapping study was performed using 3379 SNP markers. Tibia size, weight, ash content and breaking strength were highly heritable (0.42 to 0.61). Relative tibia diameter and volume as well as P retention were strongly and positively genetically correlated with digestive efficiency (0.57 to 0.80). A total of 35 QTL were identified (9 for tibia weight, 13 for tibia size, 5 for bone strength, 5 for bone mineralization, 2 for plasma P concentration and 1 for P retention). Six QTL were genome-wide significant, and 3 QTL for tibia relative volume, weight and ash weight on chromosome 6 were fixed, the positive allele coming from the D-line. For two QTL for ash content on chromosome 18 and relative tibia length on chromosome 26, the confidence intervals were small enough to identify potential candidate genes. These findings support the evidence of multiple genetic loci controlling bone and mineral metabolism. The identification of candidate genes may provide new perspectives in the understanding of bone regulation, even beyond avian species.

  18. Quantitative genomics of voluntary exercise in mice: transcriptional analysis and mapping of expression QTL in muscle.

    Science.gov (United States)

    Kelly, Scott A; Nehrenberg, Derrick L; Hua, Kunjie; Garland, Theodore; Pomp, Daniel

    2014-08-15

    Motivation and ability both underlie voluntary exercise, each with a potentially unique genetic architecture. Muscle structure and function are one of many morphological and physiological systems acting to simultaneously determine exercise ability. We generated a large (n = 815) advanced intercross line of mice (G4) derived from a line selectively bred for increased wheel running (high runner) and the C57BL/6J inbred strain. We previously mapped quantitative trait loci (QTL) contributing to voluntary exercise, body composition, and changes in body composition as a result of exercise. Using brain tissue in a subset of the G4 (n = 244), we have also previously reported expression QTL (eQTL) colocalizing with the QTL for the higher-level phenotypes. Here, we examined the transcriptional landscape of hind limb muscle tissue via global mRNA expression profiles. Correlations revealed an ∼1,168% increase in significant relationships between muscle transcript expression levels and the same exercise and body composition phenotypes examined previously in the brain. The exercise trait most often significantly correlated with gene expression in the brain was running duration while in the muscle it was maximum running speed. This difference may indicate that time spent engaging in exercise behavior may be more influenced by central (neurobiological) mechanisms, while intensity of exercise may be largely controlled by peripheral mechanisms. Additionally, we used subsets of cis-acting eQTL, colocalizing with QTL, to identify candidate genes based on both positional and functional evidence. We discuss three plausible candidate genes (Insig2, Prcp, Sparc) and their potential regulatory role.

  19. 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.

  20. Application of alternative models to identify QTL for growth traits in an F2 Duroc x Pietrain pig resource population

    Directory of Open Access Journals (Sweden)

    Rumph Janice M

    2010-11-01

    Full Text Available Abstract Background A variety of analysis approaches have been applied to detect quantitative trait loci (QTL in experimental populations. The initial genome scan of our Duroc x Pietrain F2 resource population included 510 F2 animals genotyped with 124 microsatellite markers and analyzed using a line-cross model. For the second scan, 20 additional markers on 9 chromosomes were genotyped for 954 F2 animals and 20 markers used in the first scan were genotyped for 444 additional F2 animals. Three least-squares Mendelian models 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. Results In total, 26 QTL using the line-cross model, 12 QTL using the half-sib model and 3 additional QTL using the combined line-cross and half-sib model were detected for growth traits with a 5% false discovery rate (FDR significance level. In the line-cross analysis, highly significant QTL for fat deposition at 10-, 13-, 16-, 19-, and 22-wk of age were detected on SSC6. In the half-sib analysis, a QTL for loin muscle area at 19-wk of age was detected on SSC7 and QTL for 10th-rib backfat at 19- and 22-wk of age were detected on SSC15. Conclusions Additional markers and animals contributed to reduce the confidence intervals and increase the test statistics for QTL detection. Different models allowed detection of new QTL which indicated differing frequencies for alternative alleles in parental breeds.

  1. The phenotypic difference discards sib-pair QTL linkage information

    Energy Technology Data Exchange (ETDEWEB)

    Wright, F.A. [Univ. of California, San Diego, CA (United States)]|[Univ. of Texas, El Paso, TX (United States)

    1997-03-01

    Kruglyak and Lander provide an important synthesis of methods for (IBD) sib-pair linkage mapping, with an emphasis on the use of complete multipoint inheritance information for each sib pair. These procedures are implemented in the computer program MAPMAKER/SIBS, which performs interval mapping for dichotomous and quantitative traits. The authors present three methods for mapping quantitative trait loci (QTLs): a variant of the commonly used Haseman-Elston regression approach, a maximum-likelihood procedure involving variance components, and a rank-based nonparametric procedure. These approaches and related work use the magnitude of the difference in the sibling phenotype values for each sib pair as the observation for analysis. Linkage is detected if siblings sharing more alleles IBD have similar phenotypes (i.e., a small difference in the phenotype values), while siblings sharing fewer alleles IBD have less similar phenotypes. Such techniques have been used to detect linkage for a number of quantitative traits. However, the exclusive reliance on the phenotypic differences may be due in large part to historical inertia. A likelihood argument is presented here to show that, under certain classical assumptions, the phenotypic differences do not contain the full likelihood information for QTL mapping. Furthermore, considerable gains in power to detect linkage can be achieved with an expanded likelihood model. The development here is related to previous work, which incorporates the full set of phenotypic data using likelihood and robust quasi-likelihood methods. The purpose of this letter is not to endorse a particular approach but to spur research in alternative and perhaps more powerful linkage tests. 17 refs.

  2. Identification and characterization of two distinct ligand binding regions of cubilin.

    Science.gov (United States)

    Yammani, R R; Seetharam, S; Seetharam, B

    2001-11-30

    Using polymerase chain reaction-amplified fragments of cubilin, an endocytic receptor of molecular mass 460 kDa, we have identified two distinct ligand binding regions. Region 1 of molecular mass 71 kDa, which included the 113-residue N terminus along with the eight epidermal growth factor (EGF)-like repeats and CUB domains 1 and 2, and region 2 of molecular mass 37 kDa consisting of CUB domains 6-8 bound both intrinsic factor-cobalamin (vitamin B(12); Cbl) (IF-Cbl) and albumin. Within these two regions, the binding of both ligands was confined to a 110-115-residue stretch that encompassed either the 113-residue N terminus or CUB domain 7 and 8. Ca(2+) dependence of ligand binding or the ability of cubilin antiserum to inhibit ligand binding to the 113-residue N terminus was 60-65%. However, a combination of CUB domains 7 and 8 or 6-8 was needed to demonstrate significant Ca(2+) dependence or inhibition of ligand binding by cubilin antiserum. Antiserum to EGF inhibited albumin but not IF-Cbl binding to the N-terminal cubilin fragment that included the eight EGF-like repeats. While the presence of excess albumin had no effect on binding to IF-Cbl, IF-Cbl in excess was able to inhibit albumin binding to both regions of cubilin. Reductive alkylation of the 113-residue N terminus or CUB 6-8, CUB 7, or CUB 8 domain resulted in the abolishment of ligand binding. These results indicate that (a) cubilin contains two distinct regions that bind both IF-Cbl and albumin and that (b) binding of both IF-Cbl and albumin to each of these regions can be distinguished and is regulated by the nonassisted formation of local disulfide bonds.

  3. [download] (969dlmap: An R Package for Mixed Model QTL and Association Analysis

    Directory of Open Access Journals (Sweden)

    B. Emma Huang

    2012-08-01

    Full Text Available dlmap is a software package capable of mapping quantitative trait loci (QTL in a variety of genetic studies. Unlike most other QTL mapping packages, dlmap is built on a linear mixed model platform, and thus can simultaneously handle multiple sources of genetic and environmental variation. Furthermore, it can accommodate both experimental crosses and association mapping populations within a versatile modeling framework. The software implements a mapping algorithm with separate detection and localization stages in a user-friendly manner. It accepts data in various common formats, has a flexible modeling environment, and summarizes results both graphically and numerically.

  4. STATISTICAL GROWTH MODELING OF LONGITUDINAL DT-MRI FOR REGIONAL CHARACTERIZATION OF EARLY BRAIN DEVELOPMENT.

    Science.gov (United States)

    Sadeghi, Neda; Prastawa, Marcel; Fletcher, P Thomas; Gilmore, John H; Lin, Weili; Gerig, Guido

    2012-01-01

    A population growth model that represents the growth trajectories of individual subjects is critical to study and understand neurodevelopment. This paper presents a framework for jointly estimating and modeling individual and population growth trajectories, and determining significant regional differences in growth pattern characteristics applied to longitudinal neuroimaging data. We use non-linear mixed effect modeling where temporal change is modeled by the Gompertz function. The Gompertz function uses intuitive parameters related to delay, rate of change, and expected asymptotic value; all descriptive measures which can answer clinical questions related to growth. Our proposed framework combines nonlinear modeling of individual trajectories, population analysis, and testing for regional differences. We apply this framework to the study of early maturation in white matter regions as measured with diffusion tensor imaging (DTI). Regional differences between anatomical regions of interest that are known to mature differently are analyzed and quantified. Experiments with image data from a large ongoing clinical study show that our framework provides descriptive, quantitative information on growth trajectories that can be directly interpreted by clinicians. To our knowledge, this is the first longitudinal analysis of growth functions to explain the trajectory of early brain maturation as it is represented in DTI.

  5. Experimental characterization of transition region in rotating-disk boundary layer

    Science.gov (United States)

    Siddiqui, M. E.; Mukund, V.; Scott, J.; Pier, B.

    2013-03-01

    The three-dimensional boundary layer due to a disk rotating in otherwise still fluid is well known for its sudden transition from a laminar to a turbulent regime, the location of which closely coincides with the onset of local absolute instability. The present experimental investigation focuses on the region around transition and analyses in detail the features that lead from the unperturbed boundary layer to a fully turbulent flow. Mean velocity profiles and high-resolution spectra are obtained by constant-temperature hot-wire anemometry. By carefully analysing these measurements, regions in the flow are identified that correspond to linear, weakly nonlinear, or turbulent dynamics. The frequency that dominates the flow prior to transition is explained in terms of spatial growth rates, derived from the exact linear dispersion relation. In the weakly nonlinear region, up to six clearly identifiable harmonic peaks are found. High-resolution spectra reveal the existence of discrete frequency components that are deemed to correspond to fluctuations stationary with respect to the disk surface. These discrete components are only found in the weakly nonlinear region. By systematically acquiring low- and high-resolution spectra over a range of narrowly spaced radial and axial positions, it is shown that while the transition from laminar to turbulent regimes occurs sharply at some distance from the disk surface, a complex weakly nonlinear region of considerable radial extent continues to prevail close to the disk surface.

  6. 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.

  7. 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

  8. Expression in Pichia pastoris and characterization of Rhizomucor miehei lipases containing a new propeptide region.

    Science.gov (United States)

    Wang, Zhiyuan; Lv, Pengmei; Luo, Wen; Yuan, Zhenhong; He, Dong

    2016-01-01

    A large number of propeptide regions from various proteins have been identified which function as intramolecular chaperones and assist the folding of the respective functional domains. The same polypeptide can fold into an altered conformation because of a mutated intramolecular chaperone and can maintain the "memory" of the folding process (new physicochemical properties). Two new kinds of Rhizomucor miehei lipase (RML) were constructed by replacing its propeptide region with that from either Rhizopus chinensis lipase (RCL) or Rhizopus oryzae lipase (ROL). The enzymatic properties were also analyzed and compared between wild-type RML and the mutants. The results indicated that the same polypeptide can fold into different conformations because of changes in the propeptide region.

  9. 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.

  10. 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.

  11. 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.

    2016-09-01

    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.

  12. HIV and HCV coinfection: prevalence, associated factors and genotype characterization in the Midwest Region of Brazil.

    Science.gov (United States)

    Freitas, Solange Zacalusni; Teles, Sheila Araújo; Lorenzo, Paulo Cesar; Puga, Marco Antonio Moreira; Tanaka, Tayana Serpa Ortiz; Thomaz, Danilo Yamamoto; Martins, Regina Maria Bringel; Druzian, Angelita Fernandes; Lindenberg, Andréa Siqueira Campos; Torres, Marina Sawada; Pereira, Sérgio A; Villar, Livia Melo; Lampe, Elisabete; Motta-Castro, Ana Rita Coimbra

    2014-01-01

    A cross-sectional study on prevalence, associated factors and genotype distribution of HCV infection was conducted among 848 HIV-infected patients recruited at reference centers in the Midwest Region of Brazil. The prevalence rate of HIV-HCV coinfection was 6.9% (95% CI: 5.2 to 8.6). In multivariable analysis, increasing age, use of illicit drugs (injection and non-injection), a history of blood transfusion before 1994, and the absence of a steady partnership were significant independent associated factors for HIV-HCV coinfection. The phylogenetic analysis based on the NS5B region revealed the presence of two major circulating genotypes of HCV: genotypes 1 (58.3%) and 3 (41.7%). The prevalence of HIV-HCV coinfection was lower than those reported in studies conducted with HIV-infected patients in different regions of Brazil, due to the fact that illicit drug use is not a frequent mode of HIV transmission in this region of Brazil. Serologic screening of HIV-patients for HCV before initiating antiretroviral treatment, a comprehensive identification of associated factors, and the implementation of effective harm reduction programs are highly recommended to provide useful information for treatment and to prevent HCV coinfection in these patients.

  13. The bovine Mx1 gene: characterization of the gene structure, alternative splicing, and promoter region.

    Science.gov (United States)

    Kojima, Takatoshi; Oshima, Kazunaga; Watanabe, Hiroko; Komatsu, Masanori

    2003-12-01

    The Mx gene encodes an antiviral protein and is induced by type 1 interferons (IFNs). In this study, a new bovine Mx gene (designated Mx1B) was isolated from the endometrial cDNA library of the early pregnant cow. Although the Mx1B cDNA contained a single open reading frame (ORF) the same as the known Mx1, the 5' untranslated region (UTR) and 5' coding region of Mx1B were rather different from the corresponding regions of Mx1. Genomic structure analysis revealed that bovine Mx1B was an alternative splicing variant of Mx1 and had transcription regulatory sequences in the upstream region. RT-PCR and its sequencing identified another Mx1 splicing variant and demonstrated that these bovine Mx1 splicing variants were ubiquitously expressed in various tissues. Furthermore, it was found that all the bovine breeds investigated had identical splice sites of Mx1 and Mx1B. It is speculated that cattle have at least two functional Mx isoforms that might provide strong natural resistance to specific viruses.

  14. Mapping and characterization of non-HLA multigene assemblages in the human MHC class I region

    Energy Technology Data Exchange (ETDEWEB)

    Venditti, C.P.; Harris, J.M.; Geraghty, D.E. [Pennsylvania State Univ. College of Medicine, Hershey, PA (United States)] [and others

    1994-07-15

    The major histocompatibility complex (MHC) class I region has been shown to be associated with a variety of immune and nonimmune disorders. In an effort to initiate steps designed to identify the idiopathic hemochromatosis disease gene (HFE), the authors have cloned and mapped two expressed messages using probes from the HLA-H subregion that lie immediately distal to the HLA-A9 breakpoint. Although the cDNA clones identify distinct multifragment families that are dispersed throughout the MHC, the gene sequences from which the two cDNA clones derive map centromeric to the HLA-B locus and are absent from the genomes of higher nonhuman primates. This suggests that a syntenic coding segment arose within a highly polymorphic region (TNF to HLA-B interval) as the result of an insertion event following the emergence of Homo sapiens. An additional syntenic cluster exists within a peak of linkage disequilibrium with the HFE gene and may define coding sequences that underlie the defect in genetic iron overload. These data generally support the concept that the class I region is potentially gene-rich and further highlight the possibility that these new coding sequences may play a role in the development of a variety of HLA-linked diseases. The observations presented suggest that interlocus exchanges have played a structural role in the genesis of the human class I region. 46 refs., 6 refs.

  15. Interstitial duplications of chromosome region 15q11q13 : Clinical and molecular characterization

    NARCIS (Netherlands)

    Repetto, GR; White, LM; Bader, PJ; Johnson, D; Knoll, JHM

    1998-01-01

    Duplications of chromosome region 15q11q13 often occur as a supernumerary chromosome 15. Less frequently they occur as interstitial duplications [dup(15)]. We describe the clinical and molecular characteristics of three patients with de novo dup(15). The patients, two males and one female (ages 3-21

  16. HIV AND HCV COINFECTION: PREVALENCE, ASSOCIATED FACTORS AND GENOTYPE CHARACTERIZATION IN THE MIDWEST REGION OF BRAZIL

    Directory of Open Access Journals (Sweden)

    Solange Zacalusni Freitas

    2014-12-01

    Full Text Available A cross-sectional study on prevalence, associated factors and genotype distribution of HCV infection was conducted among 848 HIV-infected patients recruited at reference centers in the Midwest Region of Brazil. The prevalence rate of HIV-HCV coinfection was 6.9% (95% CI: 5.2 to 8.6. In multivariable analysis, increasing age, use of illicit drugs (injection and non-injection, a history of blood transfusion before 1994, and the absence of a steady partnership were significant independent associated factors for HIV-HCV coinfection. The phylogenetic analysis based on the NS5B region revealed the presence of two major circulating genotypes of HCV: genotypes 1 (58.3% and 3 (41.7%. The prevalence of HIV-HCV coinfection was lower than those reported in studies conducted with HIV-infected patients in different regions of Brazil, due to the fact that illicit drug use is not a frequent mode of HIV transmission in this region of Brazil. Serologic screening of HIV-patients for HCV before initiating antiretroviral treatment, a comprehensive identification of associated factors, and the implementation of effective harm reduction programs are highly recommended to provide useful information for treatment and to prevent HCV coinfection in these patients.

  17. Detection and Molecular Characterization of Zoonotic Poxviruses Circulating in the Amazon Region of Colombia, 2014

    Science.gov (United States)

    Usme-Ciro, Jose A.; Paredes, Andrea; Walteros, Diana M.; Tolosa-Pérez, Erica Natalia; Laiton-Donato, Katherine; Pinzón, Maria del Carmen; Petersen, Brett W.; Gallardo-Romero, Nadia F.; Li, Yu; Wilkins, Kimberly; Davidson, Whitni; Gao, Jinxin; Patel, Nishi; Nakazawa, Yoshinori; Reynolds, Mary G.; Satheshkumar, P. S.; Emerson, Ginny L.

    2017-01-01

    During 2014, cutaneous lesions were reported in dairy cattle and farmworkers in the Amazon Region of western Colombia. Samples from 6 patients were analyzed by serologic and PCR testing, and results demonstrated the presence of vaccinia virus and pseudocowpox virus. These findings highlight the need for increased poxvirus surveillance in Colombia. PMID:28322708

  18. Characterization of monoaminergic systems in brain regions of prematurely ageing mice.

    Science.gov (United States)

    De la Fuente, Monica; Hernanz, Angel; Medina, Sonia; Guayerbas, Noelia; Fernández, Beatriz; Viveros, Maria Paz

    2003-07-01

    We have previously shown that differences in life span among members of Swiss mouse populations appear to be related to their exploration of a T-maze, with a slow exploration ("slow mice") being linked to increased levels of emotionality/anxiety, an impaired immune function and a shorter life span. Thus, we proposed the slow mice as prematurely ageing mice (PAM). We have now compared the monoaminergic systems of the PAM and of the non-prematurely ageing mice (NPAM), in discrete brain regions. PAM had decreased noradrenaline (NA) levels in all the brain regions analysed, whereas the 3-methoxy-4-hydroxyphenyl glycol (MHPG)/NA ratios were not significantly modified. PAM also showed decreased serotonine (5-HT) levels in hypothalamus, striatum and midbrain, as well as increased 5-hydroxyindol-3-acetic acid (5-HIAA)/5-HT ratios in hypothalamus and hippocampus. The dopamine (DA) content was lower in PAM in most regions, whereas the 3,4-dihydroxyphenylacetic acid (DOPAC)/DA and homovanillic acid (HVA)/DA ratios were either increased or unchanged depending on the region analysed. In most cases, the differences between PAM and NPAM involved both sexes. One exception was the hypothalamus where the differences only affected the male mice. The neurochemical alterations found in PAM resemble some changes reported for aged animals and are related with their behavioural features.

  19. Molecular characterization of HIV-1 subtype C gp-120 regions potentially involved in virus adaptive mechanisms.

    Directory of Open Access Journals (Sweden)

    Alessandra Cenci

    Full Text Available The role of variable regions of HIV-1 gp120 in immune escape of HIV has been investigated. However, there is scant information on how conserved gp120 regions contribute to virus escaping. Here we have studied how molecular sequence characteristics of conserved C3, C4 and V3 regions of clade C HIV-1 gp120 that are involved in HIV entry and are target of the immune response, are modulated during the disease course. We found an increase of "shifting" putative N-glycosylation sites (PNGSs in the α2 helix (in C3 and in C4 and an increase of sites under positive selection pressure in the α2 helix during the chronic stage of disease. These sites are close to CD4 and to co-receptor binding sites. We also found a negative correlation between electric charges of C3 and V4 during the late stage of disease counteracted by a positive correlation of electric charges of α2 helix and V5 during the same stage. These data allow us to hypothesize possible mechanisms of virus escape involving constant and variable regions of gp120. In particular, new mutations, including new PNGSs occurring near the CD4 and CCR5 binding sites could potentially affect receptor binding affinity and shield the virus from the immune response.

  20. 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.

  1. 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.

  2. QTL Mapping for Adult Plant Resistance to Powdery Mildew in Italian Wheat cv. Strampelli

    Institute of Scientific and Technical Information of China (English)

    Asad Muhammad Azeem; BAI Bin; LAN Cai-xia; YAN Jun; XIA Xian-chun; ZHANG Yong; HE Zhong-hu

    2013-01-01

    The Italian wheat cv. Strampelli displays high resistance to powdery mildew caused by Blumeria graminis f. sp. tritici. The objective of this study was to map quantitative trait loci (QTLs) for resistance to powdery mildew in a population of 249 F2:3 lines from Strampelli/Huixianhong. Adult plant powdery mildew tests were conducted over 2 yr in Beijing and 1 yr in Anyang and simple sequence repeat (SSR) markers were used for genotyping. QTLs Qpm.caas-3BS, Qpm.caas-5BL.1, and Qpm.caas-7DS were consistent across environments whereas, Qpm.caas-2BS.1 found in two environments, explained 0.4-1.6, 5.5-6.9, 27.1-34.5, and 1.0-3.5%of the phenotypic variation respectively. Qpm.caas-7DS corresponded to the genomic location of Pm38/Lr34/Yr18. Qpm.caas-4BL was identified in Anyang 2010 and Beijing 2011, accounting for 1.9-3.5%of phenotypic variation. Qpm.caas-2BS.1 and Qpm.caas-5BL.1 contributed by Strampelli and Qpm.caas-3BS by Huixianhong, seem to be new QTL for powdery mildew resistance. Qpm.caas-4BL, Qpm.caas-5BL.3, and Qpm.caas-7DS contributed by Strampelli appeared to be in the same genomic regions as those mapped previously for stripe rust resistance in the same population, indicating that these loci conferred resistance to both stripe rust and powdery mildew. Strampelli could be a valuable genetic resource for improving durable resistance to both powdery mildew and stripe rust in wheat.

  3. Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue

    Science.gov (United States)

    Quiroz-Zárate, Alejandro; Harshfield, Benjamin J.; Hu, Rong; Knoblauch, Nick; Beck, Andrew H.; Hankinson, Susan E.; Carey, Vincent; Tamimi, Rulla M.; Hunter, David J.; Quackenbush, John; Hazra, Aditi

    2017-01-01

    We investigate 71 single nucleotide polymorphisms (SNPs) identified in meta-analytic studies of genome-wide association studies (GWAS) of breast cancer, the majority of which are located in intergenic or intronic regions. To explore regulatory impacts of these variants we conducted expression quantitative loci (eQTL) analyses on tissue samples from 376 invasive postmenopausal breast cancer cases in the Nurses’ Health Study (NHS) diagnosed from 1990–2004. Expression analysis was conducted on all formalin-fixed paraffin-embedded (FFPE) tissue samples (and on 264 adjacent normal samples) using the Affymetrix Human Transcriptome Array. Significance and ranking of associations between tumor receptor status and expression variation was preserved between NHS FFPE and TCGA fresh-frozen sample sets (Spearman r = 0.85, p<10^-10 for 17 of the 21 Oncotype DX recurrence signature genes). At an FDR threshold of 10%, we identified 27 trans-eQTLs associated with expression variation in 217 distinct genes. SNP-gene associations can be explored using an open-source interactive browser distributed in a Bioconductor package. Using a new a procedure for testing hypotheses relating SNP content to expression patterns in gene sets, defined as molecular function pathways, we find that loci on 6q14 and 6q25 affect various gene sets and molecular pathways (FDR < 10%). Although the ultimate biological interpretation of the GWAS-identified variants remains to be uncovered, this study validates the utility of expression analysis of this FFPE expression set for more detailed integrative analyses. PMID:28152060

  4. 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...

  5. 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.

  6. Characterization of severe fever with thrombocytopenia syndrome in rural regions of Zhejiang, China.

    Science.gov (United States)

    Zhang, Lei; Ye, Ling; Ojcius, David M; Lou, Xiuyu; Wang, Chengwei; feng, Cen; Sun, Yi; Wang, Zhongfa; Li, Shibo; Zhang, Yanjun

    2014-01-01

    Severe fever with thrombocytopenia syndrome virus (SFTSV) infections have recently been found in rural regions of Zhejiang. A severe fever with thrombocytopenia syndrome (SFTS) surveillance and sero-epidemiological investigation was conducted in the districts with outbreaks. During the study period of 2011-2014, a total of 51 SFTSV infection cases were identified and the case fatality rate was 12% (6/51). Ninety two percent of the patients (47/51) were over 50 years of age, and 63% (32/51) of laboratory confirmed cases occurred from May to July. Nine percent (11/120) of the serum samples from local healthy people without symptoms were found to be positive for antibodies to the SFTS virus. SFTSV strains were isolated by culture using Vero, and the whole genomic sequences of two SFTSV strains (01 and Zhao) were sequenced and submitted to the GenBank. Homology analysis showed that the similarity of the target nucleocapsid gene from the SFTSV strains from different geographic areas was 94.2-100%. From the constructed phylogenetic tree, it was found that all the SFTSV strains diverged into two main clusters. Only the SFTSV strains from the Zhejiang (Daishan) region of China and the Yamaguchi, Miyazakj regions of Japan, were clustered into lineage II, consistent with both of these regions being isolated areas with similar geographic features. Two out of eight predicted linear B cell epitopes from the nucleocapsid protein showed mutations between the SFTSV strains of different clusters, but did not contribute to the binding ability of the specific SFTSV antibodies. This study confirmed that SFTSV has been circulating naturally and can cause a seasonal prevalence in Daishan, China. The results also suggest that the molecular characteristics of SFTSV are associated with the geographic region and all SFTSV strains can be divided into two genotypes.

  7. Characterization of promoter region and genomic structure of the murine and human genes encoding Src like adapter protein.

    Science.gov (United States)

    Kratchmarova, I; Sosinowski, T; Weiss, A; Witter, K; Vincenz, C; Pandey, A

    2001-01-10

    Src-like adapter protein (SLAP) was identified as a signaling molecule in a yeast two-hybrid system using the cytoplasmic domain of EphA2, a receptor protein tyrosine kinase (Pandey et al., 1995. Characterization of a novel Src-like adapter protein that associates with the Eck receptor tyrosine kinase. J. Biol. Chem. 270, 19201-19204). It is very similar to members of the Src family of cytoplasmic tyrosine kinases in that it contains very homologous SH3 and SH2 domains (Abram and Courtneidge, 2000. Src family tyrosine kinases and growth factor signaling. Exp. Cell. Res. 254, 1-13.). However, instead of a kinase domain at the C-terminus, it contains a unique C-terminal region. In order to exclude the possibility that an alternative form exists, we have isolated genomic clones containing the murine Slap gene as well as the human SLA gene. The coding regions of murine Slap and human SLA genes contain seven exons and six introns. Absence of any kinase domain in the genomic region confirm its designation as an adapter protein. Additionally, we have cloned and sequenced approximately 2.6 kb of the region 5' to the initiator methionine of the murine Slap gene. When subcloned upstream of a luciferase gene, this fragment increased the transcriptional activity about 6-fold in a human Jurkat T cell line and approximately 52-fold in a murine T cell line indicating that this region contains promoter elements that dictate SLAP expression. We have also cloned the promoter region of the human SLA gene. Since SLAP is transcriptionally regulated by retinoic acid and by activation of B cells, the cloning of its promoter region will permit a detailed analysis of the elements required for its transcriptional regulation.

  8. Utilizing ribosomal DNA gene marker regions to characterize the metacercariae (Trematoda: Digenea) parasitizing piscine intermediate hosts in Manipur, Northeast India.

    Science.gov (United States)

    Athokpam, Voleentina D; Jyrwa, Donald B; Tandon, Veena

    2016-06-01

    Freshwater fishes in Manipur, Northeast India frequently harbour several types of metacercariae, which based on morphological criteria were identified as Clinostomoides brieni, Euclinostomum heterostomum (Clinostomidae) and Polylekithum sp. (Allocreadiidae). Molecular techniques utilizing PCR amplification of rDNA regions of larger subunit (LSU or 28S), smaller subunit (SSU or 18S) and inter transcribed spacers (ITS1, 2) were used for molecular characterization of these types. Sequences generated from the metacercariae were compared with their related sequences available in public databases; an analysis of the identity matrices and phylogenetic trees constructed was also carried out, which confirmed their identification. Similarly, the sequences generated from Polylekithum sp. were found to be highly similar to the species of the same genus. The rDNA ITS2 secondary structure provided additional confirmation of the robustness of the molecular marker as a tool for taxon-specific characterization.

  9. Cloning and characterizing of the ovine MX1 gene promoter/enhancer region.

    Science.gov (United States)

    Assiri, A M; Ott, T L

    2007-01-01

    Ovine MX1 (MX1) is expressed in the uterus during the estrous cycle and is strongly up-regulated during early pregnancy in the uterus and peripheral blood leukocytes. In this study we cloned the MX1 gene promoter/enhancer, and tested its response to interferon tau (IFN-tau). To address the role of IFN tau in regulating MX1 expression, serial deletion mutants were prepared along with a clone that contained a full-length promoter including the two proximal ISREs but lacking an intronic ISRE site. Promoter deletions showed the two proximal ISRE sites, but not the intronic ISRE site, were required for maximal response to IFN tau. Interestingly, MX1 promoter deletion mutants revealed the presence of distal positive (-920 to -715) and negative (-715 to -437) regulatory regions. Identifying positive and negative regulatory regions in MX1 promoter will help define the complex regulation of MX1 during early pregnancy in ruminants.

  10. Characterization of the hemA-prs region of the Escherichia coli and Salmonella typhimurium chromosomes

    DEFF Research Database (Denmark)

    Post, David A.; Hove-Jensen, Bjarne; Switzer, Robert L.

    1993-01-01

    The prs gene, encoding phosphoribosylpyrophosphate synthetase, is preceded by a leader, which is 302 bp long in Escherichia coli and 417 bp in Salmonella typhimurium. A potential open reading frame (ORF) extends across the prs promoter and into the leader. The region between the prs coding region...... direction as the prs gene with ORF 2 extending into the prs leader. Northern blot analysis showed that the prs message in E. coli was on 1.3 and 2.7 kb transcripts. The shorter transcript encoded the prs gene only, while the longer transcript also encoded the two ORFs. Thus, the prs gene is transcribed from...... two promoters, the first promoter (P1) originating upstream of ORF 1, and expressing the prs gene in a tricistronic operon and a second promoter (P2), located within the ORF 2 coding frame, which transcribes the prs gene only. The transcripts encoding prs only were 20 times as abundant...

  11. Characterization of the agricultural sector and conditions of corporatization in the region of Yopal, Casanare

    Directory of Open Access Journals (Sweden)

    Diana Milena Carmona Muñoz

    2012-01-01

    Full Text Available This paper seeks to present the partial results of a research process that aimed to identify the determinants of corporate development in the region of Yopal, Casanare, where La Salle University’s Utopia Project is contextualized. This paper presents the first progress based on a national and regional diagnostic component of the agricultural sector and the corporatization conditions surrounding it. The significance of the progress and results of this research process lies in the contribution that the different faculties can make to the growth and consolidation of the Utopia Project, the foundation of which is: “To transform young high school graduates in rural areas affected by violence into agricultural engineers [...] and to make them leaders for the socio-political transformation and the corporatization of the countryside at their places of origin” (Utopia Project.

  12. 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.

  13. Mechanical characterization of adobe bricks in existing constructions in Aveiro Region, Portugal

    OpenAIRE

    H. Varum; Martins, T.

    2005-01-01

    In Portugal it is common to find earth constructions all over the country, being predominant in the centre and south. In the past, earth was massified as a construction material, used with different typologies and applications. Adobe construction is confined mainly to the central part of the country and more viewed in the west coast (gandaresa region). Aveiro, an Atlantic sea line city is an excellent example of a place with several ancient adobe constructions, some with architectural and ...

  14. 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.

  15. 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.

  16. Hydrological extremes in hyperarid regions: A diagnostic characterization of intense precipitation over the Central Arabian Peninsula

    Science.gov (United States)

    Kumar, Kondapalli Niranjan; Entekhabi, Dara; Molini, Annalisa

    2015-03-01

    Aridity is typically associated with deep and dry daytime boundary layers, stable nighttime stratification, divergent flows, and limited large-scale moisture advection. All these factors are paramount in regulating the hydroclimatology of hyperarid regions, resulting in extremely intermittent—and often intense—local precipitation patterns. However, the link between synoptic-scale forcing and intense precipitation over arid regions has been scarcely investigated in the literature and still remains exceedingly unexplored. We present here a diagnostic study of intense precipitation in the Central Arabian Peninsula, based on the analysis of local extreme signatures embedded in synoptic patterns. Special emphasis is given to the genesis of winter extremes over the Peninsula, and to possible effects of synchronization between the atmospheric circulation over the Mediterranean and the Indian Ocean. Based on composites of the tropospheric circulation for a large ensemble of intense events, we show that moisture necessary to trigger winter extremes over the Peninsula starts to build up in average 8 days before heavy rainfall occurrence, mainly as a consequence of the interplay between the Mediterranean and the Monsoonal circulation. Moisture advection is in turn associated with an upper troposphere cyclonic circulation and pronounced potential vorticity intrusions. Overall, our results demonstrate how large-scale precursors can be effectively used to improve the predictability of rainfall extremes in hyperarid regions.

  17. 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.

  18. 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...

  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. Bismaleimide/Preceramic Polymer Blends for Hybrid Material Transition Regions. Part 1. Processing and Characterization (Postprint)

    Science.gov (United States)

    2014-01-01

    polymer matrix composite to a ceramic matrix composite. Thermal and elemental analysis, and morphology characterization of RD-730 preceramic polymer blends, which convert to silicon carbide upon pyrolysis, and Matrimid A/B polymer (a bismaleimide), were carried out as a function of cure cycle. Cure cycles were chosen to vary the resin viscosity during processing in order to affect the amount of phase separation observed. The results were then used to associate processing parameters with the miscibility of the two resins and the likelihood of producing a hybrid

  1. Molecular and biological characterization of Potato mop-top virus (PMTV, Pomovirus) isolates from potato-growing regions in Colombia

    DEFF Research Database (Denmark)

    Gil, José; Adams, Ian; Boonham, Neil

    2016-01-01

    samples were taken from the main potato-producing regions in Colombia and virus was recovered by planting Nicotiana benthamiana as bait plants. The complete genomes of five isolates were sequenced and three of the isolates were inoculated to four different indicator plants. Based on sequence comparisons......Potato mop-top virus (PMTV) causes necrotic flecks inside and on tubers in temperate countries. In South America, these symptoms have not been observed, although the presence of the virus has been confirmed in the Andes and in Central America. To characterize PMTV isolates from the Andes, soil...

  2. 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

    , 3, 4, 6, 11, and 13, for guard hair length on chromosomes 2, 3, and 6 and for wool density on chromosome 6, 7, and 13. Similar locations of QTL for guard hair length and guard hair thickness on chromosomes 2, 3, and 6 suggest that these traits are in part under the influence of the same genes...

  3. Probability genotype imputation method and integrated weighted lasso for QTL identification

    NARCIS (Netherlands)

    Demetrashvili, Nino; Van den Heuvel, Edwin R; Wit, Ernst C

    2013-01-01

    Background: Many QTL studies have two common features: (1) often there is missing marker information, (2) among many markers involved in the biological process only a few are causal. In statistics, the second issue falls under the headings "sparsity" and "causal inference". The goal of this work is

  4. Identification of nutrient and physical seed trait QTL in the model legume Lotus japonicus.

    Science.gov (United States)

    Klein, Melinda A; Grusak, Michael A

    2009-08-01

    Legume seeds have the potential to provide a significant portion of essential micronutrients to the human diet. To identify the genetic basis for seed nutrient density, quantitative trait locus (QTL) analysis was conducted with the Miyakojima MG-20 x Gifu B-129 recombinant inbred population from the model legume Lotus japonicus. This population was grown to seed under greenhouse conditions in 2006 and 2007. Phenotypic data were collected for seed calcium (Ca), copper (Cu), iron (Fe), potassium (K), magnesium (Mg), manganese (Mn), phosphorus (P), sulfur (S), and zinc (Zn) concentrations and content. Data for physical seed traits (average seed mass and seed-pod allocation values) were also collected. Based on these phenotypic data, QTL analyses identified 103 QTL linked to 55 different molecular markers. Transgressive segregation, identified within this recombinant inbred population for both seed nutrient and physical traits, suggests new allelic combinations are available for agronomic trait improvement. QTL co-localization was also seen, suggesting that common transport processes might contribute to seed nutrient loading. Identification of loci involved in seed mineral density can be an important first step in identifying the genetic factors and, consequently, the physiological processes involved in mineral distribution to developing seeds. Longer term research efforts will focus on facilitating agronomic breeding efforts through ortholog identification in related crop legumes.

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

    NARCIS (Netherlands)

    Heuven, H.C.M.; van Wijk, R.H.J.; Dibbits, B.; van Kampen, T.A.; Knol, E.F.

    2009-01-01

    Genet Sel Evol. 2009 Jan 5;41:4. Mapping carcass and meat quality QTL on Sus Scrofa chromosome 2 in commercial finishing pigs. Heuven HC, van Wijk RH, Dibbits B, van Kampen TA, Knol EF, Bovenhuis H. Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands. h.c.m.heuven

  6. QTL linkage analysis of connected populations using ancestral marker and pedigree information

    NARCIS (Netherlands)

    Bink, M.C.A.M.; Radu Totir, L.; Braak, ter C.J.F.; Winkler, C.R.; Boer, M.P.; Smith, O.S.

    2012-01-01

    The common assumption in quantitative trait locus (QTL) linkage mapping studies that parents of multiple connected populations are unrelated is unrealistic for many plant breeding programs. We remove this assumption and propose a Bayesian approach that clusters the alleles of the parents of the curr

  7. QTL detection power of multi-parental RIL populations in Arabidopsis thaliana

    Science.gov (United States)

    Klasen, J R; Piepho, H-P; Stich, B

    2012-01-01

    A major goal of today's biology is to understand the genetic basis of quantitative traits. This can be achieved by statistical methods that evaluate the association between molecular marker variation and phenotypic variation in different types of mapping populations. The objective of this work was to evaluate the statistical power of quantitative trait loci (QTL) detection of various multi-parental mating designs, as well as to assess the reasons for the observed differences. Our study was based on an empirical data of 20 Arabidopsis thaliana accessions, which have been selected to capture the maximum genetic diversity. The examined mating designs differed strongly with respect to the statistical power to detect QTL. We observed the highest power to detect QTL for the diallel cross with random mating design. The results of our study suggested that performing sibling mating within subpopulations of joint-linkage mapping populations has the potential to considerably increase the power for QTL detection. Our results, however, revealed that using designs in which more than two parental alleles segregate in each subpopulation increases the power even more. PMID:22334115

  8. Detection of QTL for immune response to Sheep Red Blood Cells in laying hens

    NARCIS (Netherlands)

    Siwek-Gapinska, M.Z.; Cornelissen, S.J.B.; Nieuwland, M.G.B.; Buitenhuis, A.J.; Bovenhuis, H.; Crooijmans, R.P.M.A.; Groenen, M.A.M.; Vries Reilingh, de G.; Parmentier, H.K.; Poel, van der J.J.

    2003-01-01

    The aim of this study is to detect quantitative trait loci (QTL) involved in the regulation of the primary and the secondary immune response to sheep red blood cells (SRBC) in a resource population using microsatellite DNA markers. The F2 resource population originates from a cross of two divergentl

  9. Conditional QTL mapping of three yield components in common wheat(Triticum aestivum L.)

    Institute of Scientific and Technical Information of China (English)

    Han Zhang; Jiansheng Chen; Ruyu Li; Zhiying Deng; Kunpu Zhang; Bin Liu; Jichun Tian

    2016-01-01

    Spike number per m~2(SN),kernel number per spike(KNPS) and thousand-kernel weight(TKW)are the three main components determining wheat(Triticum aestivum L.) yield.To evaluate the relationships among them a doubled haploid(DH) population consisting of 168 lines grown at three locations for three years was analyzed by unconditional and conditional QTL mapping.Thirty-three unconditional QTL and fifty-nine conditional QTL were detected.Among them,two QTL(QSN-DH-2B and QSN-DH-3A-1.1) improved SN,with no effect on KNPS.QKNPS-DH-2B-2.1 improved KNPS,with no effect on SN.QKNPS-DH-1A-1.1,QKNPS-DH-2D-1.1and QKNPS-DH-6A improved KNPS,with no effect on SN or TKW.QKNPS-DH-6B was associated with increased SN and TKW.In addition,QTKW-DH-4B,QTKW-DH-5B and QTKW-DH-7B increased TKW without decreasing KNPS.These results provide useful information for marker assisted selection(MAS) and improvement in wheat yield.

  10. 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;

    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...

  11. QTL analysis of the genetic architecture determining resistance to fire blight in an apple progeny

    NARCIS (Netherlands)

    Calenge, F.; Drouet, D.; Weg, van de W.E.; Brisset, M.N.; Paulin, J.P.; Durel, C.E.

    2004-01-01

    Fire blight, caused by the bacterial pathogen Erwinia amylovora, is one of the most destructive diseases of apple (Malus x domestica). In order to analyse the genetic determinism of resistance to fire blight in apple, a quantitative trait analysis (QTL) approach was used. A F1 progeny of 164 individ

  12. Identification of QTL associated with flower and runner production in octoploid strawberry (Fragaria × ananassa)

    Science.gov (United States)

    Seasonal flowering of strawberry is described as remontant and non-remontant. The genetic basis of this trait is important for breeding. This study was conducted to validate the existence of a major QTL for remontancy and weeks of flowering in F. × ananassa on LG IV, to determine if the level of flo...

  13. QTL for body weight, morphometric traits and stress response in European sea bass Dicentrarchus labrax.

    NARCIS (Netherlands)

    Massault, C.; Hellemans, J.; Louro, B.; Batargias, C.; Houdt, van I.S.; Canario, A.; Volckaert, F.A.M.; Bovenhuis, H.; Haley, C.S.; Koning, de D.J.

    2010-01-01

    Natural mating and mass spawning in the European sea bass (Dicentrarchus labrax L., Moronidae, Teleostei) complicate genetic studies and the implementation of selective breeding schemes. We utilized a two-step experimental design for detecting QTL in mass-spawning species: 2122 offspring from natura

  14. Transcriptomic and QTL analysis suggest candidate fruit shape factors in cucumber (Cucumis sativus)

    Science.gov (United States)

    Fruit size and shape are important determinants of market class and value in cucumber; however, underlying mechanisms regulating size and shape have not been identified. To gain insight into possible factors regulating cucumber fruit growth, we used a combined QTL and transcriptome approach to exami...

  15. WormQTL-public archive and analysis web portal for natural variation data in Caenorhabditis spp

    NARCIS (Netherlands)

    Snoek, L. Basten; Van der Velde, K. Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O.; Poulin, Gino B.; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C.; Kammenga, Jan E.; Swertz, Morris A.

    2013-01-01

    Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the sy

  16. A new method to infer causal phenotype networks using QTL and phenotypic information.

    Directory of Open Access Journals (Sweden)

    Huange Wang

    Full Text Available In the context of genetics and breeding research on multiple phenotypic traits, reconstructing the directional or causal structure between phenotypic traits is a prerequisite for quantifying the effects of genetic interventions on the traits. Current approaches mainly exploit the genetic effects at quantitative trait loci (QTLs to learn about causal relationships among phenotypic traits. A requirement for using these approaches is that at least one unique QTL has been identified for each trait studied. However, in practice, especially for molecular phenotypes such as metabolites, this prerequisite is often not met due to limited sample sizes, high noise levels and small QTL effects. Here, we present a novel heuristic search algorithm called the QTL+phenotype supervised orientation (QPSO algorithm to infer causal directions for edges in undirected phenotype networks. The two main advantages of this algorithm are: first, it does not require QTLs for each and every trait; second, it takes into account associated phenotypic interactions in addition to detected QTLs when orienting undirected edges between traits. We evaluate and compare the performance of QPSO with another state-of-the-art approach, the QTL-directed dependency graph (QDG algorithm. Simulation results show that our method has broader applicability and leads to more accurate overall orientations. We also illustrate our method with a real-life example involving 24 metabolites and a few major QTLs measured on an association panel of 93 tomato cultivars. Matlab source code implementing the proposed algorithm is freely available upon request.

  17. Factors influencing QTL mapping accuracy under complicated genetic models by computer simulation.

    Science.gov (United States)

    Su, C F; Wang, W; Gong, S L; Zuo, J H; Li, S J

    2016-12-19

    The accuracy of quantitative trait loci (QTLs) identified using different sample sizes and marker densities was evaluated in different genetic models. Model I assumed one additive QTL; Model II assumed three additive QTLs plus one pair of epistatic QTLs; and Model III assumed two additive QTLs with opposite genetic effects plus two pairs of epistatic QTLs. Recombinant inbred lines (RILs) (50-1500 samples) were simulated according to the Models to study the influence of different sample sizes under different genetic models on QTL mapping accuracy. RILs with 10-100 target chromosome markers were simulated according to Models I and II to evaluate the influence of marker density on QTL mapping accuracy. Different marker densities did not significantly influence accurate estimation of genetic effects with simple additive models, but influenced QTL mapping accuracy in the additive and epistatic models. The optimum marker density was approximately 20 markers when the recombination fraction between two adjacent markers was 0.056 in the additive and epistatic models. A sample size of 150 was sufficient for detecting simple additive QTLs. Thus, a sample size of approximately 450 is needed to detect QTLs with additive and epistatic models. Sample size must be approximately 750 to detect QTLs with additive, epistatic, and combined effects between QTLs. The sample size should be increased to >750 if the genetic models of the data set become more complicated than Model III. Our results provide a theoretical basis for marker-assisted selection breeding and molecular design breeding.

  18. 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

  19. Regional characterization of longitudinal DT-MRI to study white matter maturation of the early developing brain.

    Science.gov (United States)

    Sadeghi, Neda; Prastawa, Marcel; Fletcher, P Thomas; Wolff, Jason; Gilmore, John H; Gerig, Guido

    2013-03-01

    The human brain undergoes rapid and dynamic development early in life. Assessment of brain growth patterns relevant to neurological disorders and disease requires a normative population model of growth and variability in order to evaluate deviation from typical development. In this paper, we focus on maturation of brain white matter as shown in diffusion tensor MRI (DT-MRI), measured by fractional anisotropy (FA), mean diffusivity (MD), as well as axial and radial diffusivities (AD, RD). We present a novel methodology to model temporal changes of white matter diffusion from longitudinal DT-MRI data taken at discrete time points. Our proposed framework combines nonlinear modeling of trajectories of individual subjects, population analysis, and testing for regional differences in growth pattern. We first perform deformable mapping of longitudinal DT-MRI of healthy infants imaged at birth, 1 year, and 2 years of age, into a common unbiased atlas. An existing template of labeled white matter regions is registered to this atlas to define anatomical regions of interest. Diffusivity properties of these regions, presented over time, serve as input to the longitudinal characterization of changes. We use non-linear mixed effect (NLME) modeling where temporal change is described by the Gompertz function. The Gompertz growth function uses intuitive parameters related to delay, rate of change, and expected asymptotic value; all descriptive measures which can answer clinical questions related to quantitative analysis of growth patterns. Results suggest that our proposed framework provides descriptive and quantitative information on growth trajectories that can be interpreted by clinicians using natural language terms that describe growth. Statistical analysis of regional differences between anatomical regions which are known to mature differently demonstrates the potential of the proposed method for quantitative assessment of brain growth and differences thereof. This will

  20. Characterizing Land-cover Changes Since 1650 in the Southeastern United States for Application to Regional Climate Modeling

    Science.gov (United States)

    Reker, R. R.; Loveland, T. R.; Bernhardt, C. E.; Hostetler, S. W.; Sundquist, E. T.; Thompson, R. S.; Willard, D. A.

    2015-12-01

    Land-cover change is a fundamental contributor to changes in climate, hydrology, and carbon cycling. European settlers introduced a series of widespread land-cover changes in eastern North America beginning in the early 17th century. These changes varied both temporally and spatially, and were related to population growth, emerging technology, and land-use. To examine the potential influence of historical land-cover changes on local to regional climate, we adapted reconstructed fractional land cover from 1650, 1850, and 1920 as well as land cover interpreted from Landsat imagery circa 1992 (Steyaert and Knox, 2008) as input for regional climate model experiments. Observed changes included: deforestation and conversion to agriculture in the mid-Atlantic region from 1650 to 1850, region-wide expansion of agriculture from 1850 to 1920, and wetland drainage, reforestation, and increased urbanization from 1920 to 1992. We translated the land cover datasets to the BATS (Biosphere-Atmosphere Transfer Scheme) thematic classification on a 20 km2 grid for ingestion into the RegCM4 regional climate model. In BATS, land-cover classifications determine biophysical parameters such as the seasonal albedo cycle, fractional vegetation condition, stomatal resistance, leaf area index (LAI), and rooting depth. By defining and characterizing land cover in a consistent manner across the four time slices, we are able to explore interactions and feedbacks between land cover and regional climate in late prehistoric and historic times. Steyaert, L. T., & Knox, R. G. (2008). Reconstructed historical land cover and biophysical parameters for studies of land-atmosphere interactions within the eastern United States. Journal of Geophysical Research: Atmospheres, 113(D2).

  1. Microphthalmia with linear skin defects syndrome (MLS): Characterization of the critical region and isolation of candidate genes

    Energy Technology Data Exchange (ETDEWEB)

    Schaefer, L.; Wapenaar, M.C.; Grillo, A. [Baylor College of Medicine, Houston, TX (United States)] [and others

    1994-09-01

    Microphthalmia with linear skin defects syndrome (MLS) is an X-linked male-lethal disorder characterized by abnormalities in the development of the eye, skin, and brain. We defined the MLS critical region through analysis of hybrid cell lines retaining various deletion breakpoints in Xp22, including cell lines from 17 female patients showing features of MLS. Using a combination of YAC cloning and long-range restriction analysis, the MLS candidate region was estimated to be 450-550 kb. A minimally overlapping cosmid contig comprised of 20 cosmid clones was subsequently developed in this region. These cosmids are currently being used to isolate expressed sequences using cross-species conservation studies and exon-trapping. An evolutionarily conserved sequence isolated from a cosmid within the critical region has been used to isolate several overlapping cDNAs from a human embryonic library. Northern analysis using these cDNA clones identified a 5.2 kb transcript in all tissues examined. Sequence analysis revealed a 777 base pair open reading frame encoding a putative 258 amino acid protein. Using the exon-trapping method, fifty-four putative exons have been isolated from fourteen cosmids within the critical region. The expression patterns of the genes containing these exons are being analyzed by polymerase chain reaction (PCR) using reverse-transcribed mRNA from several human tissues and primers corresponding to the exon sequences. Using this approach in combination with exon connection, we determined the four of the trapped exons belong to the same cDNA transcript, which is expressed in adult retina, lymphoblast, skeletal muscle, and fetal brain. To date, we have isolated and sequenced 1 kilobase of this gene, all of which appears to be open reading frame. Both of the genes isolated from the critical region are being analyzed as possible candidates for MLS.

  2. Characterization of Vibrio cholerae bacteriophages isolated from the environmental waters of the Lake Victoria region of Kenya.

    Science.gov (United States)

    Maina, Alice Nyambura; Mwaura, Francis B; Oyugi, Julius; Goulding, David; Toribio, Ana L; Kariuki, Samuel

    2014-01-01

    Over the last decade, cholera outbreaks have become common in some parts of Kenya. The most recent cholera outbreak occurred in Coastal and Lake Victoria region during January 2009 and May 2010, where a total of 11,769 cases and 274 deaths were reported by the Ministry of Public Health and Sanitation. The objective of this study is to isolate Vibrio cholerae bacteriophages from the environmental waters of the Lake Victoria region of Kenya with potential for use as a biocontrol for cholera outbreaks. Water samples from wells, ponds, sewage effluent, boreholes, rivers, and lakes of the Lake Victoria region of Kenya were enriched for 48 h at 37 °C in broth containing a an environmental strain of V. cholerae. Bacteriophages were isolated from 5 out of the 42 environmental water samples taken. Isolated phages produced tiny, round, and clear plaques suggesting that these phages were lytic to V. cholerae. Transmission electron microscope examination revealed that all the nine phages belonged to the family Myoviridae, with typical icosahedral heads, long contractile tails, and fibers. Head had an average diameter of 88.3 nm and tail of length and width 84.9 and 16.1 nm, respectively. Vibriophages isolated from the Lake Victoria region of Kenya have been characterized and the isolated phages may have a potential to be used as antibacterial agents to control pathogenic V. cholerae bacteria in water reservoirs.

  3. 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.

  4. QTL analysis of Kernel-related traits in maize using an immortalized F2 population.

    Science.gov (United States)

    Zhang, Zhanhui; Liu, Zonghua; Hu, Yanmin; Li, Weihua; Fu, Zhiyuan; Ding, Dong; Li, Haochuan; Qiao, Mengmeng; Tang, Jihua

    2014-01-01

    Kernel size and weight are important determinants of grain yield in maize. In this study, multivariate conditional and unconditional quantitative trait loci (QTL), and digenic epistatic analyses were utilized in order to elucidate the genetic basis for these kernel-related traits. Five kernel-related traits, including kernel weight (KW), volume (KV), length (KL), thickness (KT), and width (KWI), were collected from an immortalized F2 (IF2) maize population comprising of 243 crosses performed at two separate locations over a span of two years. A total of 54 unconditional main QTL for these five kernel-related traits were identified, many of which were clustered in chromosomal bins 6.04-6.06, 7.02-7.03, and 10.06-10.07. In addition, qKL3, qKWI6, qKV10a, qKV10b, qKW10a, and qKW7a were detected across multiple environments. Sixteen main QTL were identified for KW conditioned on the other four kernel traits (KL, KWI, KT, and KV). Thirteen main QTL were identified for KV conditioned on three kernel-shape traits. Conditional mapping analysis revealed that KWI and KV had the strongest influence on KW at the individual QTL level, followed by KT, and then KL; KV was mostly strongly influenced by KT, followed by KWI, and was least impacted by KL. Digenic epistatic analysis identified 18 digenic interactions involving 34 loci over the entire genome. However, only a small proportion of them were identical to the main QTL we detected. Additionally, conditional digenic epistatic analysis revealed that the digenic epistasis for KW and KV were entirely determined by their constituent traits. The main QTL identified in this study for determining kernel-related traits with high broad-sense heritability may play important roles during kernel development. Furthermore, digenic interactions were shown to exert relatively large effects on KL (the highest AA and DD effects were 4.6% and 6.7%, respectively) and KT (the highest AA effects were 4.3%).

  5. Mapping of angular leaf spot resistance QTL in common bean (Phaseolus vulgaris L. under different environments

    Directory of Open Access Journals (Sweden)

    Oblessuc Paula

    2012-06-01

    Full Text Available Abstract Background Common bean (Phaseolus vulgaris L. is the most important grain legume for human diet worldwide and the angular leaf spot (ALS is one of the most devastating diseases of this crop, leading to yield losses as high as 80%. In an attempt to breed resistant cultivars, it is important to first understand the inheritance mode of resistance and to develop tools that could be used in assisted breeding. Therefore, the aim of this study was to identify quantitative trait loci (QTL controlling resistance to ALS under natural infection conditions in the field and under inoculated conditions in the greenhouse. Results QTL analyses were made using phenotypic data from 346 recombinant inbreed lines from the IAC-UNA x CAL 143 cross, gathered in three experiments, two of which were conducted in the field in different seasons and one in the greenhouse. Joint composite interval mapping analysis of QTL x environment interaction was performed. In all, seven QTLs were mapped on five linkage groups. Most of them, with the exception of two, were significant in all experiments. Among these, ALS10.1DG,UC presented major effects (R2 between 16% - 22%. This QTL was found linked to the GATS11b marker of linkage group B10, which was consistently amplified across a set of common bean lines and was associated with the resistance. Four new QTLs were identified. Between them the ALS5.2 showed an important effect (9.4% under inoculated conditions in the greenhouse. ALS4.2 was another major QTL, under natural infection in the field, explaining 10.8% of the variability for resistance reaction. The other QTLs showed minor effects on resistance. Conclusions The results indicated a quantitative inheritance pattern of ALS resistance in the common bean line CAL 143. QTL x environment interactions were observed. Moreover, the major QTL identified on linkage group B10 could be important for bean breeding, as it was stable in all the environments. Thereby, the GATS11b

  6. 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.

  7. 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.

  8. 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

  9. 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...

  10. Characterization and genesis of waterfalls of the Presidente Figueiredo region, Northeast State of Amazonas, Brazil

    Directory of Open Access Journals (Sweden)

    NOGUEIRA AFONSO C. R.

    2001-01-01

    Full Text Available The waterfalls of the Presidente Figueiredo municipality represent a fascinating natural scenery of northeast state of Amazonas, northern Brazil. The falls, generally less than 10m high, are developed on siliciclastic rocks of the Nhamundá (Lower Silurian, and Manacapuru (Upper Silurian - Lower Devonian formations. Morphological and structural analyses of these features indicate that most of them originated through Quaternary neotectonics and are installed in NE-trending normal fault escarpments. Waterfalls also developed within pseudokarstic features, but are less frequent. The origin of the Presidente Figueiredo waterfalls probably goes back to the Neogene, when the region was submitted to laterization processes associated with a humid climate and a dense rainforest. These conditions favored the development of caves in quartzarenites of the Nhamundá Formation. During the Quaternary, the region was subjected to NE-trending normal faulting which displaced laterite layers, rivers and streams giving rise to waterfalls. These climatic and tectonic phenomena promoted intense relief dissection, as indicated by fault escarpment retreat and cave dismantlement, responsible for the present-day morphologic configuration.

  11. Characterization of integrons among Escherichia coli in a region at high incidence of ESBL-EC.

    Science.gov (United States)

    Li, Lu-Ming; Wang, Ming-Yi; Yuan, Xiao-Yan; Wang, Hong-Jun; Li, Qin; Zhu, Ya-Mei

    2014-01-01

    Objective : The aim of study was to investigate the distribution of the integrons in Escherichia coli (E. coli) isolates, and analyze the possible relationship between the antimicrobial resistance profiles and the integrons. Methods : The antimicrobial profiles of 376 E. coli strains were analysed by disk diffusion test. The integron genes and variable regions were detected by PCR. Some amplicons were sequenced to determine the gene cassettes style. Results : Of 376 isolates, 223 isolates (59.3%) were confirmed as ESBL-EC. Comparison to ESBL-negative E. coli, the high rates of resistance to the third and fourth generation of cephalosporins, penicillins and amikacin were found in ESBL-EC. Only class 1 was integron detected in the isolates, and the prevalence of it was 66.5%. It was commonly found in ESBL-EC (77.6%, 173/223), which was higher than that of ESBL-negative E. coli (50.3%, 77/153) (pESBL-EC, while in 9.1% isolates of ESBL-negative E.coli. Conclusion : The high incidence of ESBL-EC with resistance to multiple antibiotics were detected in the isolates from Blood stream infection (BSI). More resistant gene cassettes in ESBL-EC may partially underlie the high resistance to amikacin, while no relation exists between the high incidence of ESBL-EC and classes 1~ 3 integrons in this region.

  12. Molecular characterization of genes encoding the quinolone resistance determining regions of Malaysian Streptococcus pneumoniae strains

    Directory of Open Access Journals (Sweden)

    Kumari N

    2008-01-01

    Full Text Available Genes encoding the quinolones resistance determining regions (QRDRs in Streptococcus pneumoniae were detected by PCR and the sequence analysis was carried out to identify point mutations within these regions. The study was carried out to observe mutation patterns among S. pneumoniae strains in Malaysia. Antimicrobial susceptibility testing of 100 isolates was determined against various antibiotics, out of which 56 strains were categorised to have reduced susceptibility to ciprofloxacin (≥2 μg/mL. These strains were subjected to PCR amplification for presence of the gyrA, parC , gyrB and parE genes. Eight representative strains with various susceptibilities to fluoroquinolones were sequenced. Two out of the eight isolates that were sequenced were shown to have a point mutation in the gyrA gene at position Ser81. The detection of mutation at codon Ser81 of the gyrA gene suggested the potential of developing fluoroquinolone resistance among S. pneumoniae isolates in Malaysia. However, further experimental work is required to confirm the involvement of this mutation in the development of fluoroquinolone resistance in Malaysia.

  13. 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.

  14. Functional characterization of the cardiac ryanodine receptor pore-forming region.

    Directory of Open Access Journals (Sweden)

    Joanne Euden

    Full Text Available Ryanodine receptors are homotetrameric intracellular calcium release channels. The efficiency of these channels is underpinned by exceptional rates of cation translocation through the open channel and this is achieved at the expense of the high degree of selectivity characteristic of many other types of channel. Crystallization of prokaryotic potassium channels has provided insights into the structures and mechanisms responsible for ion selection and movement in these channels, however no equivalent structural detail is currently available for ryanodine receptors. Nevertheless both molecular modeling and cryo-electron microscopy have identified the probable pore-forming region (PFR of the ryanodine receptor (RyR and suggest that this region contains structural elements equivalent to those of the PFRs of potassium-selective channels. The aim of the current study was to establish if the isolated putative cardiac RyR (RyR2 PFR could form a functional ion channel. We have expressed and purified the RyR2 PFR and shown that function is retained following reconstitution into planar phospholipid bilayers. Our data provide the first direct experimental evidence to support the proposal that the conduction pathway of RyR2 is formed by structural elements equivalent to those of the potassium channel PFR.

  15. Characterization of Dielectric Responses of Human Cancer Cells in the Terahertz Region

    Science.gov (United States)

    Shiraga, Keiichiro; Ogawa, Yuichi; Suzuki, Tetsuhito; Kondo, Naoshi; Irisawa, Akiyoshi; Imamura, Motoki

    2014-05-01

    Terahertz time-domain attenuated total reflection spectroscopy, in combination with a two-interface model, is used to determine the complex dielectric constants of cultured human cancer cells (DLD-1, HEK293 and HeLa). Picosecond and sub-picosecond water dynamics are dominant in the measured complex dielectric constants of these cells. We demonstrate that dielectric responses below 1.0 THz best characterize the particular water dynamics of cancer cells when compared with extracellular water. Debye-Lorentz fitting revealed that this is due to a significantly attenuated slow relaxation mode and enhanced fast relaxation mode of the water in these cancer cells. These findings could lead to a new procedure to digitally evaluate cellular activities or functions, in terms of intracellular water dynamics, and remove the veil from the mysterious intracellular milieu.

  16. 茶树炭疽病抗性的 QTL 分析%QTL Analysis for Anthracnose Resistance in Tea Plant (Camellia sinensis)

    Institute of Scientific and Technical Information of China (English)

    徐礼羿; 谭礼强; 王丽鸳; 齐桂年; 成浩; 韦康

    2016-01-01

    In order to provide a basis for breeding tea plants with anthracnose resistance, 170 F1 plants, derived from LJ43♀×BHZ♂, were used to constructed a linkage map by SSR markers. Field observation and indoor test were carried out in 2014. The data of phenotypic characters were used for QTL mapping and analysis by the method of MQM mapping. A pathogen was isolated from a diseased leaf of the F1 plants, and its gene sequence of ITS had 99%similarity with Colletotrichum sp. based on NCBI BLAST. The plants grown in open field were more easy to be infected by the pathogen than those grown in rooms. Eight QTLs were detected in six different linkage groups by QTL analysis. The LOD and PVE of individual QTLs ranged from 2.53 to 6.80 and 5.6% to 13.8%, respectively. A main QTL with LOD 6.80 and PVE 13.8% was detected in LG10.%以茶树 SSR 遗传连锁图谱为基础,选取龙井43为母本,白毫早为父本的170株 F1遗传群体为试验材料,于2014年对该群体分别进行了茶树炭疽病抗性性状的田间观测和室内侵染试验,并采用复合区间作图法对该性状进行 QTL 定位与分析。结果显示:从 F1群体病叶上分离纯化出一种茶树炭疽病病菌 HZ-1,经NCBI BLAST 比对,其 ITS 基因序列与炭疽菌(Colletotrichum sp.)的亲缘关系最近,序列相似度为99%。对F1群体的炭疽病抗性表型分析发现,田间环境下的感病单株的占比(41%)高于室内环境(24%)。QTL 分析显示,在6个不同的遗传连锁群(Linkage group,LG)上共检测到8个 QTLs,单个 QTL 的 LOD 阈值变幅为2.53~6.80,单个 QTL 的表型变异贡献率的变幅为5.6%~13.8%。LG10存在1个控制茶树炭疽病抗性性状的主效 QTL,LOD 值6.80,表型变异贡献率13.8%。

  17. Fine-mapping of qRL6.1, a major QTL for root length of rice seedlings grown under a wide range of NH4+ concentrations in hydroponic conditions

    Science.gov (United States)

    Tamura, Wataru; Ebitani, Takeshi; Yano, Masahiro; Sato, Tadashi; Yamaya, Tomoyuki

    2010-01-01

    Root system development is an important target for improving yield in cereal crops. Active root systems that can take up nutrients more efficiently are essential for enhancing grain yield. In this study, we attempted to identify quantitative trait loci (QTL) involved in root system development by measuring root length of rice seedlings grown in hydroponic culture. Reliable growth conditions for estimating the root length were first established to renew nutrient solutions daily and supply NH4+ as a single nitrogen source. Thirty-eight chromosome segment substitution lines derived from a cross between ‘Koshihikari’, a japonica variety, and ‘Kasalath’, an indica variety, were used to detect QTL for seminal root length of seedlings grown in 5 or 500 μM NH4+. Eight chromosomal regions were found to be involved in root elongation. Among them, the most effective QTL was detected on a ‘Kasalath’ segment of SL-218, which was localized to the long-arm of chromosome 6. The ‘Kasalath’ allele at this QTL, qRL6.1, greatly promoted root elongation under all NH4+ concentrations tested. The genetic effect of this QTL was confirmed by analysis of the near-isogenic line (NIL) qRL6.1. The seminal root length of the NIL was 13.5–21.1% longer than that of ‘Koshihikari’ under different NH4+ concentrations. Toward our goal of applying qRL6.1 in a molecular breeding program to enhance rice yield, a candidate genomic region of qRL6.1 was delimited within a 337 kb region in the ‘Nipponbare’ genome by means of progeny testing of F2 plants/F3 lines derived from a cross between SL-218 and ‘Koshihikari’. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1328-3) contains supplementary material, which is available to authorized users. PMID:20390245

  18. 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.

  19. Genetic Characterization of Indigenous Rice Varieties in Eastern Himalayan Region of Northeast India

    Institute of Scientific and Technical Information of China (English)

    Baharul Islam CHOUDHURY; Mohammed Latif KHAN; Selvadurai DAYANANDAN

    2014-01-01

    The eastern Himalayan region of Northeast (NE) India is home to a large number of indigenous rice varieties, which are traditionally classified as Oryza sativa subspecies indica, japonica or intermediate types. The classification based on traditional Cheng’s index is often inconclusive due to phenotypic plasticity of morphological characters, which are influenced by environmental conditions. We used molecular markers specific for indica and japonica subspecies to assess the degree of genetic relatedness of indigenous rice varieties in NE India. The results revealed that majority of upland (jum) and glutinous rice varieties, traditionally considered as japonica, were genetically close to the subspecies indica. All varieties of boro ecotype were found to be indica type, and only a few varieties cultivated in lowland and upland areas were japonica type. Some of the lowland varieties of the sali ecotype were intermediate between indica and japonica, and they showed a closer genetic affinity to O. rufipogon.

  20. Fuzzy statistic and comprehensive evaluating study for activity characterization of the active region

    Institute of Scientific and Technical Information of China (English)

    HAN; Zhengzhong

    2001-01-01

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