Experts and Doctors on quantitative trait loci in Davis, California, United States


Locale: Davis, California, United States
Topic: quantitative trait loci

Top Publications

  1. Joseph B, Corwin J, Züst T, Li B, Iravani M, Schaepman Strub G, et al. Hierarchical nuclear and cytoplasmic genetic architectures for plant growth and defense within Arabidopsis. Plant Cell. 2013;25:1929-45 pubmed publisher
    ..Therefore, other growth QTLs can mask the effects of defense upon growth. Investigating direct links across phenotypic hierarchies is fraught with difficulty; we identify issues complicating this analysis. ..
  2. Ersoz E, Wright M, González Martínez S, Langley C, Neale D. Evolution of disease response genes in loblolly pine: insights from candidate genes. PLoS ONE. 2010;5:e14234 pubmed publisher
  3. Neale D, Savolainen O. Association genetics of complex traits in conifers. Trends Plant Sci. 2004;9:325-30 pubmed
    ..Allele discovery using association approaches should lead to more-efficient methods of marker-assisted breeding and a deeper understanding of genetic adaptation in forest trees. ..
  4. Dvorak J, Deal K, Luo M. Discovery and mapping of wheat Ph1 suppressors. Genetics. 2006;174:17-27 pubmed
    ..ucd-5S may primarily regulate recombination between homologous chromosomes. ..
  5. Smit McBride Z, Oltjen S, Lavail M, Hjelmeland L. A strong genetic determinant of hyperoxia-related retinal degeneration on mouse chromosome 6. Invest Ophthalmol Vis Sci. 2007;48:405-11 pubmed
    ..A significant genetic effect of susceptibility to HRRD is located on chromosome 6. In silico analysis of transcribed sequences results in a fairly small number of candidate genes. ..
  6. Farber C, Medrano J. Fine mapping reveals sex bias in quantitative trait loci affecting growth, skeletal size and obesity-related traits on mouse chromosomes 2 and 11. Genetics. 2007;175:349-60 pubmed
    ..These results highlight the importance of assessing the contribution of sex in complex trait analyses. ..
  7. Krutovsky K, Neale D. Nucleotide diversity and linkage disequilibrium in cold-hardiness- and wood quality-related candidate genes in Douglas fir. Genetics. 2005;171:2029-41 pubmed
    ..LD decayed relatively slowly but steadily within genes. Haploblock analysis was used to define haplotype tag SNPs (htSNPs). These data will help to select SNPs for association mapping, which is already in progress. ..
  8. Yang J, Mezmouk S, Baumgarten A, Buckler E, Guill K, McMullen M, et al. Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize. PLoS Genet. 2017;13:e1007019 pubmed publisher
  9. Schwember A, Bradford K. A genetic locus and gene expression patterns associated with the priming effect on lettuce seed germination at elevated temperatures. Plant Mol Biol. 2010;73:105-18 pubmed publisher
    ..Developmental and temperature regulation of hormonal biosynthetic pathways is associated with seed priming effects on germination temperature sensitivity. ..

More Information


  1. Johnson E, Haggard J, St Clair D. Fractionation, stability, and isolate-specificity of QTL for resistance to Phytophthora infestans in cultivated tomato (Solanum lycopersicum). G3 (Bethesda). 2012;2:1145-59 pubmed publisher
    ..Map-based comparisons between QTL mapped in this study and Solanaceae resistance genes/QTL detected in other published studies revealed multiple cases of co-location, suggesting conservation of gene function. ..
  2. Yang L, Zhang X, Zhang X, Wang J, Luo M, Yang M, et al. Identification and evaluation of resistance to powdery mildew and yellow rust in a wheat mapping population. PLoS ONE. 2017;12:e0177905 pubmed publisher
    ..Interactions between the YR QTLs gave insights into the pathogen populations in the different locations as well as showing genetic interactions between these loci. ..
  3. Martínez García P, Fresnedo Ramírez J, Parfitt D, Gradziel T, Crisosto C. Effect prediction of identified SNPs linked to fruit quality and chilling injury in peach [Prunus persica (L.) Batsch]. Plant Mol Biol. 2013;81:161-74 pubmed publisher
    ..The interaction and expression of affected proteins could explain the variation observed in each individual and facilitate understanding of gene regulatory networks for fruit quality traits in peach...
  4. Yarnes S, Ashrafi H, Reyes Chin Wo S, Hill T, Stoffel K, Van Deynze A. Identification of QTLs for capsaicinoids, fruit quality, and plant architecture-related traits in an interspecific Capsicum RIL population. Genome. 2013;56:61-74 pubmed publisher
    ..Twenty-one loci showed correlation among seemingly unrelated phenotypic categories, highlighting tight linkage or shared genetics between previously unassociated traits in pepper...
  5. Tang R, Wei Y, Li Z, Chen H, Miao Q, Bian Z, et al. A Common Variant in CLDN14 is Associated with Primary Biliary Cirrhosis and Bone Mineral Density. Sci Rep. 2016;6:19877 pubmed publisher
    ..003 and 0.016, respectively). In conclusion, our study identified a novel PBC susceptibility variant that has been shown to be strongly associated with BMD, highlighting the potential of pleiotropy to improve gene discovery. ..
  6. Warden C, Gularte Merida R, Fisler J, Hansen S, Shibata N, Le A, et al. Leptin receptor interacts with rat chromosome 1 to regulate renal disease traits. Physiol Genomics. 2012;44:1052-62 pubmed publisher
    ..Hydronephrosis exhibited one or two QTLs contingent on adjustment for body weight. The results now demonstrate at least two sets of coincident traits with different correlations to kidney function. ..
  7. Lowe I, Jankuloski L, Chao S, Chen X, See D, Dubcovsky J. Mapping and validation of QTL which confer partial resistance to broadly virulent post-2000 North American races of stripe rust in hexaploid wheat. Theor Appl Genet. 2011;123:143-57 pubmed publisher
    ..This paper discusses the individual contributions to resistance of these four QTL, their epistatic interactions, and their potential in durable resistance breeding strategies based on combinations of partial resistance genes. ..
  8. Duncan R, Singh S, Gilbertson R. Interaction of common bacterial blight bacteria with disease resistance quantitative trait loci in common bean. Phytopathology. 2011;101:425-35 pubmed publisher
  9. Xu K, Riaz S, Roncoroni N, Jin Y, Hu R, Zhou R, et al. Genetic and QTL analysis of resistance to Xiphinema index in a grapevine cross. Theor Appl Genet. 2008;116:305-11 pubmed
    ..The XiR1 QTL was supported by a LOD score of 36.9 and explained 59.9% of the resistance variance in the mapping population...
  10. Verdugo R, Farber C, Warden C, Medrano J. Serious limitations of the QTL/microarray approach for QTL gene discovery. BMC Biol. 2010;8:96 pubmed publisher
    ..Alternatives are proposed that make use of microarray data from multiple experiments to overcome the outlined limitations. ..
  11. Oberbauer A, Belanger J, Grossman D, Regan K, Famula T. Genome-wide linkage scan for loci associated with epilepsy in Belgian shepherd dogs. BMC Genet. 2010;11:35 pubmed publisher
    ..The study also underscores the complexity of genomic linkage studies for polygenic disorders. ..
  12. Chan E, Rowe H, Kliebenstein D. Understanding the evolution of defense metabolites in Arabidopsis thaliana using genome-wide association mapping. Genetics. 2010;185:991-1007 pubmed publisher
  13. Giri A, Hartmann K, Aldrich M, Ward R, Wu J, Park A, et al. Admixture mapping of pelvic organ prolapse in African Americans from the Women's Health Initiative Hormone Therapy trial. PLoS ONE. 2017;12:e0178839 pubmed publisher
    ..Unique non-overlapping European and African ancestry-specific susceptibility loci may be associated with increased POP risk. ..
  14. Schwember A, Bradford K. Quantitative trait loci associated with longevity of lettuce seeds under conventional and controlled deterioration storage conditions. J Exp Bot. 2010;61:4423-36 pubmed publisher
    ..QTL analyses may enable identification of mechanisms responsible for the sensitivity of primed seeds to CD conditions and breeding for improved seed longevity. ..
  15. Diament A, Warden C. Multiple linked mouse chromosome 7 loci influence body fat mass. Int J Obes Relat Metab Disord. 2004;28:199-210 pubmed
    ..Congenic mouse strains contain donor mouse strain DNA in genomes otherwise identical to a background strain. They can be used to identify defined chromosomal regions containing obesity genes with small effects...
  16. Farber C, Medrano J. Dissection of a genetically complex cluster of growth and obesity QTLs on mouse chromosome 2 using subcongenic intercrosses. Mamm Genome. 2007;18:635-45 pubmed
    ..These data represent a significant advancement toward the identification of mouse chromosome 2 growth and obesity quantitative trait genes...
  17. Brown G, Bassoni D, Gill G, Fontana J, Wheeler N, Megraw R, et al. Identification of quantitative trait loci influencing wood property traits in loblolly pine (Pinus taeda L.). III. QTL Verification and candidate gene mapping. Genetics. 2003;164:1537-46 pubmed
    ..Several candidate genes colocated with wood property QTL; however, these relationships must be verified in future experiments...
  18. Diament A, Farahani P, Chiu S, Fisler J, Warden C. A novel mouse Chromosome 2 congenic strain with obesity phenotypes. Mamm Genome. 2004;15:452-9 pubmed
    ..The obesity phenotype of the QTL is retained in the congenic. The congenic can now be used to model the genetic and physiological basis for a relatively simple, perhaps monogenic, obesity...
  19. Argyris J, Truco M, Ochoa O, Knapp S, Still D, Lenssen G, et al. Quantitative trait loci associated with seed and seedling traits in Lactuca. Theor Appl Genet. 2005;111:1365-76 pubmed
    ..serriola alleles increased germination at these QTL. The estimate of narrow-sense heritability (h2) of Htg6.1 was 0.84, indicating potential for L. serriola as a source of germination thermotolerance for lettuce introgression programs. ..
  20. Kliebenstein D, West M, van Leeuwen H, Loudet O, Doerge R, St Clair D. Identification of QTLs controlling gene expression networks defined a priori. BMC Bioinformatics. 2006;7:308 pubmed
    ..The use of a priori definitions for network eQTL identification has enormous potential for providing direction toward future eQTL analyses. ..
  21. González Martínez S, Wheeler N, Ersoz E, Nelson C, Neale D. Association genetics in Pinus taeda L. I. Wood property traits. Genetics. 2007;175:399-409 pubmed
    ..This approach is of particular utility in species such as conifers, where genomewide strategies are limited by their large genomes...
  22. Farber C, Chitwood J, Lee S, Verdugo R, Islas Trejo A, Rincon G, et al. Overexpression of Scg5 increases enzymatic activity of PCSK2 and is inversely correlated with body weight in congenic mice. BMC Genet. 2008;9:34 pubmed publisher
    ..The identification of novel genes is critical to understanding the molecular basis of body weight. Towards this goal, we have identified secretogranin V (Scg5; also referred to as Sgne1), as a candidate gene for growth traits...
  23. Lemay D, Lynn D, Martin W, Neville M, Casey T, Rincon G, et al. The bovine lactation genome: insights into the evolution of mammalian milk. Genome Biol. 2009;10:R43 pubmed publisher
    ..The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes...
  24. John Goodstal F, Kohler G, Randall L, Bloom A, St Clair D. A major QTL introgressed from wild Lycopersicon hirsutum confers chilling tolerance to cultivated tomato (Lycopersicon esculentum). Theor Appl Genet. 2005;111:898-905 pubmed
    ..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. ..
  25. Kliebenstein D. Quantitative genomics: analyzing intraspecific variation using global gene expression polymorphisms or eQTLs. Annu Rev Plant Biol. 2009;60:93-114 pubmed publisher
    ..This review introduces eQTL analysis and begins to illustrate how these data can be applied to multiple research fields. ..
  26. Rowe H, Hansen B, Halkier B, Kliebenstein D. Biochemical networks and epistasis shape the Arabidopsis thaliana metabolome. Plant Cell. 2008;20:1199-216 pubmed publisher
    ..We also generated two de novo biochemical network models from the available data, one of unknown function and the other associated with central plant metabolism. ..
  27. Haggard J, Johnson E, St Clair D. Linkage relationships among multiple QTL for horticultural traits and late blight (P. infestans) resistance on chromosome 5 introgressed from wild tomato Solanum habrochaites. G3 (Bethesda). 2013;3:2131-46 pubmed publisher
    ..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. ..
  28. Kliebenstein D. Advancing genetic theory and application by metabolic quantitative trait loci analysis. Plant Cell. 2009;21:1637-46 pubmed publisher
    ..Additionally, the review describes how new observations from metabolic QTL mapping analyses are helping to shape and expand the concepts of genetic epistasis. ..
  29. Chiu S, Kim K, Haus K, Espinal G, Millon L, Warden C. Identification of positional candidate genes for body weight and adiposity in subcongenic mice. Physiol Genomics. 2007;31:75-85 pubmed
    ..Using subcongenic mapping, we successfully narrowed a body weight and obesity QTL interval and identified PC2 as a positional candidate gene...
  30. Graze R, Barmina O, Tufts D, Naderi E, Harmon K, Persianinova M, et al. New candidate genes for sex-comb divergence between Drosophila mauritiana and Drosophila simulans. Genetics. 2007;176:2561-76 pubmed
    ..Further supporting the potential involvement of these genes in sex-comb divergence, we found a significant difference in sex-comb tooth number between co-isogenic D. melanogaster lines with and without P-element insertions at CG2791. ..
  31. Dilkes B, Spielman M, Weizbauer R, Watson B, Burkart Waco D, Scott R, et al. The maternally expressed WRKY transcription factor TTG2 controls lethality in interploidy crosses of Arabidopsis. PLoS Biol. 2008;6:2707-20 pubmed publisher
    ..Furthermore, the role of the sporophytically active TTG2 gene in interploidy crosses indicates that the developmental programming of the mother regulates the viability of interploidy hybrid offspring. ..
  32. Zhang Z, Ober J, Kliebenstein D. The gene controlling the quantitative trait locus EPITHIOSPECIFIER MODIFIER1 alters glucosinolate hydrolysis and insect resistance in Arabidopsis. Plant Cell. 2006;18:1524-36 pubmed
    ..The glucosinolate hydrolysis profile change influenced by ESM1 is associated with the ability to deter herbivory by Trichoplusia ni. This gene could provide unique approaches toward improving human nutrition. ..
  33. Argyris J, Truco M, Ochoa O, McHale L, Dahal P, Van Deynze A, et al. A gene encoding an abscisic acid biosynthetic enzyme (LsNCED4) collocates with the high temperature germination locus Htg6.1 in lettuce (Lactuca sp.). Theor Appl Genet. 2011;122:95-108 pubmed publisher
    ..1 phenotype and indicate that decreased ABA biosynthesis at high imbibition temperatures is a major factor responsible for the increased germination thermotolerance of UC96US23 seeds. ..
  34. Ogundiwin E, Peace C, Gradziel T, Parfitt D, Bliss F, Crisosto C. A fruit quality gene map of Prunus. BMC Genomics. 2009;10:587 pubmed publisher
    ..Here we present an integrated fruit quality gene map of Prunus containing 133 genes putatively involved in the determination of fruit texture, pigmentation, flavor, and chilling injury resistance...
  35. Baerwald M, Petersen J, Hedrick R, Schisler G, May B. A major effect quantitative trait locus for whirling disease resistance identified in rainbow trout (Oncorhynchus mykiss). Heredity (Edinb). 2011;106:920-6 pubmed publisher
    ..This is the first genetic region discovered that contributes directly to the whirling disease phenotype and the finding moves the field closer to a mechanistic understanding of resistance to this important disease of salmonid fish. ..
  36. Jimenez Gomez J, Wallace A, Maloof J. Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis. PLoS Genet. 2010;6:e1001100 pubmed publisher
    ..In summary, we show that development of networks to inform candidate gene identification for QTLs is a promising technique that can significantly accelerate the process of QTL cloning. ..
  37. Filiault D, Wessinger C, DINNENY J, Lutes J, Borevitz J, Weigel D, et al. Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light. Proc Natl Acad Sci U S A. 2008;105:3157-62 pubmed publisher
    ..Together with earlier studies linking variation in light sensitivity to photoreceptor genes, our work suggests that photoreceptors may be a common target of natural selection. ..
  38. Brouwer D, Jones E, St Clair D. QTL analysis of quantitative resistance to Phytophthora infestans (late blight) in tomato and comparisons with potato. Genome. 2004;47:475-92 pubmed
    ..infestans resistance QTLs detected in tomato coincided with chromosomal locations of previously mapped R genes and QTLs for resistance to P. infestans in potato, suggesting functional conservation of resistance within the Solanaceae. ..
  39. St Clair D. Quantitative disease resistance and quantitative resistance Loci in breeding. Annu Rev Phytopathol. 2010;48:247-68 pubmed publisher
    ..Strategies for optimum deployment of QRLs require research to understand effects of QDR on pathogen populations over time. ..
  40. Chan E, Rowe H, Corwin J, Joseph B, Kliebenstein D. Combining genome-wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in Arabidopsis thaliana. PLoS Biol. 2011;9:e1001125 pubmed publisher
    ..Additionally, while GWA is highly conditional upon genetics, the use of additional genomic information can rapidly identify causal loci en masse. ..
  41. Van Eenennaam A, Weaber R, Drake D, Penedo M, Quaas R, Garrick D, et al. DNA-based paternity analysis and genetic evaluation in a large, commercial cattle ranch setting. J Anim Sci. 2007;85:3159-69 pubmed
  42. Farber C, Corva P, Medrano J. Genome-wide isolation of growth and obesity QTL using mouse speed congenic strains. BMC Genomics. 2006;7:102 pubmed
    ..To confirm and further characterize each QTL, two panels of speed congenic strains were developed by introgressing CAST/EiJ (CAST) QTL alleles onto either mutant C57Bl/6J-hg/hg (HG) or wild type C57Bl/6J (B6) genetic backgrounds...