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Quantitative trait loci

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https://www.readbyqxmd.com/read/28088792/impact-of-nudt15-polymorphisms-on-thiopurines-induced-myelotoxicity-and-thiopurines-tolerance-dose
#1
Dandan Yin, Xuyang Xia, Junlong Zhang, Shouyue Zhang, Fei Liao, Ge Zhang, Yan Zhang, Qianqian Hou, Xue Yang, Hong Wang, Zhigui Ma, Heyao Wang, Yiping Zhu, Wei Zhang, Yuelan Wang, Bo Liu, Lanlan Wang, Heng Xu, Yang Shu
Thiopurines are widely used as anticancer and immunosuppressive agents. However, life-threatening myelotoxicity has been noticed and largely explained by genetic variations, including NUDT15 polymorphisms (e.g., rs116855232). In this study, we conduct a meta-analysis to investigate the impact of rs116855232 on thiopurines-induced myelotoxicity susceptibility (1752 patients from 7 independent cohorts), as well as on thiopurines intolerance dose (2745 patients from 13 cohorts). Variant allele of rs116855232 contributes 7...
January 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28088409/genome-wide-association-analysis-and-pathways-enrichment-for-lactation-persistency-in-canadian-holstein-cattle
#2
D N Do, N Bissonnette, P Lacasse, F Miglior, M Sargolzaei, X Zhao, E M Ibeagha-Awemu
Lactation persistency (LP), defined as the rate of declining milk yield after milk peak, is an economically important trait for dairy cattle. Improving LP is considered a good alternative method for increasing overall milk production because it does not cause the negative energy balance and other health issues that cows experience during peak milk production. However, little is known about the biology of LP. A genome-wide association study (GWAS) and pathway enrichment were used to explore the genetic mechanisms underlying LP...
January 11, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28087756/fine-mapping-of-genes-determining-extrafusal-fiber-properties-in-murine-soleus-muscle
#3
Andrew Carroll, Riyan Cheng, Elaina Collie-Duguid, Caroline Meharg, Michael E Scholz, Steven N Fiering, Jennifer L Fields, Abraham A Palmer, Arimantas Lionikas
INTRODUCTION: Muscle fiber cross-sectional area (CSA) and proportion of different fiber types are important determinants of muscle function and overall metabolism. Genetic variation plays a substantial role in phenotypic variation of these traits, however, the underlying genes remain poorly understood. AIMS: This study aimed to map quantitative trait loci (QTL) affecting differences in soleus muscle fiber traits between the LG/J and SM/J mouse strains. METHODS: Fiber number, CSA, and proportion of oxidative type I fibers were assessed in the soleus of 334 genotyped male and female mice of the F34 generation of advanced intercross lines (AIL) derived from the LG/J and SM/J strains...
January 13, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28079935/regional-heritability-mapping-and-genome-wide-association-identify-loci-for-complex-growth-wood-and-disease-resistance-traits-in-eucalyptus
#4
Rafael Tassinari Resende, Marcos Deon Vilela Resende, Fabyano Fonseca Silva, Camila Ferreira Azevedo, Elizabete Keiko Takahashi, Orzenil Bonfim Silva-Junior, Dario Grattapaglia
Although genome-wide association studies (GWAS) have provided valuable insights into the decoding of the relationships between sequence variation and complex phenotypes, they have explained little heritability. Regional heritability mapping (RHM) provides heritability estimates for genomic segments containing both common and rare allelic effects that individually contribute too little variance to be detected by GWAS. We carried out GWAS and RHM for seven growth, wood and disease resistance traits in a breeding population of 768 Eucalyptus hybrid trees using EuCHIP60K...
February 2017: New Phytologist
https://www.readbyqxmd.com/read/28079294/a-locus-on-chromosome-16-is-significantly-associated-with-increased-tendency-to-lose-pups-in-females-of-the-rr-sgn-inbred-mouse-strain
#5
Jun-Ichi Suto
Females of the inbred mouse strain RR/Sgn have an apparent tendency to lose pups during rearing. To identify genes underlying this abnormal maternal phenotype, we performed quantitative trait loci (QTL) mapping in 349 (C57BL/6 J × RR/Sgn) F1  × RR/Sgn backcross mice and identified one significant and one suggestive QTL on chromosomes 16 and 4, respectively. We assigned the gene symbol nurturing ability QTL 3 (Naq3) to the QTL on chromosome 16. Twenty of the 21 mothers who lost entire litters were homozygous for RR/Sgn allele at Naq3; i...
November 2, 2016: Congenital Anomalies
https://www.readbyqxmd.com/read/28079285/a-pathway-based-association-study-reveals-variants-from-wnt-signaling-genes-contributing-to-asthma-susceptibility
#6
A Barreto-Luis, A Corrales, M Acosta-Herrera, C Gonzalez-Colino, J Cumplido, J Martinez-Tadeo, A Carracedo, J Villar, T Carrillo, M Pino-Yanes, C Flores
BACKGROUND: Genetic susceptibility to asthma is currently linked to a handful of genes which have a limited ability to predict the overall disease risk, suggesting the existence of many other genes involved in disease development. Accumulated evidence from association studies in genes related by biological pathways could reveal novel asthma genes. OBJECTIVE: To reveal novel asthma susceptibility genes by means of a pathway-based association study. METHODS: Based on summary data from a previous a genome-wide association study (GWAS) of asthma, we first identified significant biological pathways using a gene-set enrichment analysis...
January 12, 2017: Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28079101/comparing-gwas-results-of-complex-traits-using-full-genetic-model-and-additive-models-for-revealing-genetic-architecture
#7
Md Mamun Monir, Jun Zhu
Most of the genome-wide association studies (GWASs) for human complex diseases have ignored dominance, epistasis and ethnic interactions. We conducted comparative GWASs for total cholesterol using full model and additive models, which illustrate the impacts of the ignoring genetic variants on analysis results and demonstrate how genetic effects of multiple loci could differ across different ethnic groups. There were 15 quantitative trait loci with 13 individual loci and 3 pairs of epistasis loci identified by full model, whereas only 14 loci (9 common loci and 5 different loci) identified by multi-loci additive model...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28077070/scopa-and-meta-scopa-software-for-the-analysis-and-aggregation-of-genome-wide-association-studies-of-multiple-correlated-phenotypes
#8
Reedik Mägi, Yury V Suleimanov, Geraldine M Clarke, Marika Kaakinen, Krista Fischer, Inga Prokopenko, Andrew P Morris
BACKGROUND: Genome-wide association studies (GWAS) of single nucleotide polymorphisms (SNPs) have been successful in identifying loci contributing genetic effects to a wide range of complex human diseases and quantitative traits. The traditional approach to GWAS analysis is to consider each phenotype separately, despite the fact that many diseases and quantitative traits are correlated with each other, and often measured in the same sample of individuals. Multivariate analyses of correlated phenotypes have been demonstrated, by simulation, to increase power to detect association with SNPs, and thus may enable improved detection of novel loci contributing to diseases and quantitative traits...
January 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28075479/different-contributions-of-local-and-distant-regulatory-changes-to-transcriptome-divergence-between-stickleback-ecotypes
#9
Asano Ishikawa, Makoto Kusakabe, Kohta Yoshida, Mark Ravinet, Takashi Makino, Atsushi Toyoda, Asao Fujiyama, Jun Kitano
Differential gene expression can play an important role in phenotypic evolution and divergent adaptation. Although differential gene expression can be caused by both local- and distant-regulatory changes, we know little about their relative contribution to transcriptome evolution in natural populations. Here, we conducted expression quantitative trait loci (eQTL) analysis to investigate the genetic architecture underlying transcriptome divergence between marine and stream ecotypes of threespine sticklebacks (Gasterosteus aculeatus)...
January 11, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28072738/expression-quantitative-trait-loci-for-pi3k-akt-pathway
#10
Dongchan Ryu, Chaeyoung Lee
A genome-wide association study (GWAS) was conducted to identify expression quantitative trait loci (eQTLs) for the genes involved in phosphatidylinositol-3-kinase/v-akt murine thymoma viral oncogene homolog (PI3K/AKT) pathway.Data on mRNA expression of 341 genes in lymphoblastoid cell lines of 373 Europeans recruited by the 1000 Genomes Project using Illumina HiSeq2000 were utilized. We used their genotypes at 5,941,815 nucleotide variants obtained by Genome Analyzer II and SOLiD.The association analysis revealed 4166 nucleotide variants associated with expression of 85 genes (P < 5 × 10)...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28070759/qtls-for-heading-date-and-plant-height-under-multiple-environments-in-rice
#11
Zhongmin Han, Wei Hu, Cong Tan, Yongzhong Xing
Both heading date and plant height are important traits related to grain yield in rice. In this study, a recombinant inbred lines (RILs) population was used to map quantitative trait loci (QTLs) for both traits under 3 long-day (LD) environments and 1 short-day (SD) environment. A total of eight QTLs for heading date and three QTLs for plant height were detected by composite interval mapping under LD conditions. Additional one QTL for heading date and three QTLs for plant height were identified by Two-QTL model under LD conditions...
January 9, 2017: Genetica
https://www.readbyqxmd.com/read/28070295/quantitative-evaluation-of-hybridization-and-the-impact-on-biodiversity-conservation
#12
Anna M van Wyk, Desiré L Dalton, Sean Hoban, Michael W Bruford, Isa-Rita M Russo, Coral Birss, Paul Grobler, Bettine Janse van Vuuren, Antoinette Kotzé
Anthropogenic hybridization is an increasing conservation threat worldwide. In South Africa, recent hybridization is threatening numerous ungulate taxa. For example, the genetic integrity of the near-threatened bontebok (Damaliscus pygargus pygargus) is threatened by hybridization with the more common blesbok (D. p. phillipsi). Identifying nonadmixed parental and admixed individuals is challenging based on the morphological traits alone; however, molecular analyses may allow for accurate detection. Once hybrids are identified, population simulation software may assist in determining the optimal conservation management strategy, although quantitative evaluation of hybrid management is rarely performed...
January 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28068921/co-localization-of-major-quantitative-trait-loci-for-pod-size-and-weight-to-a-3-7%C3%A2-cm-interval-on-chromosome-a05-in-cultivated-peanut-arachis-hypogaea-l
#13
Huaiyong Luo, Xiaoping Ren, Zhendong Li, Zhijun Xu, Xinping Li, Li Huang, Xiaojing Zhou, Yuning Chen, Weigang Chen, Yong Lei, Boshou Liao, Manish K Pandey, Rajeev K Varshney, Baozhu Guo, Xiangguo Jiang, Fei Liu, Huifang Jiang
BACKGROUND: Cultivated peanut (Arachis hypogaea L.), an important source of edible oil and protein, is widely grown in tropical and subtropical areas of the world. Genetic improvement of yield-related traits is essential for improving yield potential of new peanut varieties. Genomics-assisted breeding (GAB) can accelerate the process of genetic improvement but requires linked markers for the traits of interest. In this context, we developed a recombinant inbred line (RIL) mapping population (Yuanza 9102 × Xuzhou 68-4) with 195 individuals and used to map quantitative trait loci (QTLs) associated with three important pod features, namely pod length, pod width and hundred-pod weight...
January 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28068351/phenotype-and-tissue-expression-as-a-function-of-genetic-risk-in-polycystic-ovary-syndrome
#14
Cindy T Pau, Tim Mosbruger, Richa Saxena, Corrine K Welt
Genome-wide association studies and replication analyses have identified (n = 5) or replicated (n = 10) DNA variants associated with risk for polycystic ovary syndrome (PCOS) in European women. However, the causal gene and underlying mechanism for PCOS risk at these loci have not been determined. We hypothesized that analysis of phenotype, gene expression and metformin response as a function of genotype would identify candidate genes and pathways that could provide insight into the underlying mechanism for risk at these loci...
2017: PloS One
https://www.readbyqxmd.com/read/28065468/the-genetic-architecture-of-gene-expression-in-peripheral-blood
#15
Luke R Lloyd-Jones, Alexander Holloway, Allan McRae, Jian Yang, Kerrin Small, Biao Zeng, Andrew Bakshi, Andres Metspalu, Manolis Dermitzakis, Greg Gibson, Tim Spector, Grant Montgomery, Tonu Esko, Peter M Visscher, Joseph E Powell
We analyzed the mRNA levels for 36,778 transcript expression traits (probes) from 2,765 individuals to comprehensively investigate the genetic architecture and degree of missing heritability for gene expression in peripheral blood. We identified 11,204 cis and 3,791 trans independent expression quantitative trait loci (eQTL) by using linear mixed models to perform genome-wide association analyses. Furthermore, using information on both closely and distantly related individuals, heritability was estimated for all expression traits...
December 24, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28062411/mapping-morphological-shape-as-a-high-dimensional-functional-curve
#16
Guifang Fu, Mian Huang, Wenhao Bo, Han Hao, Rongling Wu
Detecting how genes regulate biological shape has become a multidisciplinary research interest because of its wide application in many disciplines. Despite its fundamental importance, the challenges of accurately extracting information from an image, statistically modeling the high-dimensional shape and meticulously locating shape quantitative trait loci (QTL) affect the progress of this research. In this article, we propose a novel integrated framework that incorporates shape analysis, statistical curve modeling and genetic mapping to detect significant QTLs regulating variation of biological shape traits...
January 6, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28060815/consequences-of-epistasis-on-growth-in-an-erhualian-%C3%A3-white-duroc-pig-cross
#17
Lucy Crooks, Yuanmei Guo
Epistasis describes an interaction between the effects of loci. We included epistasis in quantitative trait locus (QTL) mapping of growth at a series of ages in a cross of a Chinese pig breed, Erhualian, with a commercial line, White Duroc. Erhualian pigs have much lower growth rates than White Duroc. We improved a method for genomewide testing of epistasis and present a clear analysis workflow. We also suggest a new approach for interpreting epistasis results where significant additive and dominance effects of a locus in specific backgrounds are determined...
2017: PloS One
https://www.readbyqxmd.com/read/28056770/genetic-architecture-of-kernel-composition-in-global-sorghum-germplasm
#18
Davina H Rhodes, Leo Hoffmann, William L Rooney, Thomas J Herald, Scott Bean, Richard Boyles, Zachary W Brenton, Stephen Kresovich
BACKGROUND: Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop for dryland areas in the United States and for small-holder farmers in Africa. Natural variation of sorghum grain composition (protein, fat, and starch) between accessions can be used for crop improvement, but the genetic controls are still unresolved. The goals of this study were to quantify natural variation of sorghum grain composition and to identify single-nucleotide polymorphisms (SNPs) associated with variation in grain composition concentrations...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28056769/a-genome-wide-association-study-of-seed-composition-traits-in-wild-soybean-glycine-soja
#19
Larry J Leamy, Hengyou Zhang, Changbao Li, Charles Y Chen, Bao-Hua Song
BACKGROUND: Cultivated soybean (Glycine max) is a major agricultural crop that provides a crucial source of edible protein and oil. Decreased amounts of saturated palmitic acid and increased amounts of unsaturated oleic acid in soybean oil are considered optimal for human cardiovascular health and therefore there has considerable interest by breeders in discovering genes affecting the relative concentrations of these fatty acids. Using a genome-wide association (GWA) approach with nearly 30,000 single nucleotide polymorphisms (SNPs), we investigated the genetic basis of protein, oil and all five fatty acid levels in seeds from a sample of 570 wild soybeans (Glycine soja), the progenitor of domesticated soybean, to identify quantitative trait loci (QTLs) affecting these seed composition traits...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28055133/drought-coping-strategies-in-cotton-increased-crop-per-drop
#20
REVIEW
Abid Ullah, Heng Sun, Xiyan Yang, Xianlong Zhang
The growth and yield of many crops, including cotton, are affected by water deficit. Cotton has evolved drought-specific as well as general morpho-physiological, biochemical and molecular responses to drought stress, which are discussed in this review. The key physiological responses against drought stress in cotton, including stomata closing, root development, cellular adaptations, photosynthesis, abscisic acid (ABA) and jasmonic acid (JA) production, and reactive oxygen species (ROS) scavenging, have been identified by researchers...
January 5, 2017: Plant Biotechnology Journal
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