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Expression quantitative trait loci

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https://www.readbyqxmd.com/read/28727040/genome-wide-association-studies-and-meta-analysis-reveal-novel-quantitative-trait-loci-and-pleiotropic-loci-for-swine-head-related-traits
#1
H Chen, T Huang, Z Zhang, B Yang, C Jiang, J Wu, Z Zhou, H Zheng, W Xin, M Huang, M Zhang, C Chen, J Ren, H Ai, L Huang
The pig is an important domestic animal that provides a larger amount of meat and serves as a biomedical animal model for human. Head and facial features are closely linked to identity recognition in mammal communication. To uncover the genetic architecture of swine head and facial features, we constructed 5 experimental pig populations and accurately measured 10 traits related to head and facial features, for which genome-wide association studies and meta-analysis were later carried out. As a result, we identified a total of 24 loci harboring 437 SNP on 8 swine chromosomes (SSC) that surpassed suggestively significant levels, of which 17 loci on 6 chromosomes exceeded the 5% genome-wide significance thresholds...
June 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28719732/genome-wide-association-meta-analysis-reveals-novel-juvenile-idiopathic-arthritis-susceptibility-loci
#2
Laura A McIntosh, Miranda C Marion, Marc Sudman, Mary E Comeau, Mara L Becker, John F Bohnsack, Tasha E Fingerlin, Thomas A Griffin, J Peter Haas, Daniel J Lovell, Lisa A Maier, Peter A Nigrovic, Sampath Prahalad, Marilynn Punaro, Carlos D Rosé, Carol A Wallace, Carol A Wise, Halima Moncrieffe, Timothy D Howard, Carl D Langefeld, Susan D Thompson
OBJECTIVE: Juvenile idiopathic arthritis (JIA) is the most common childhood rheumatic disease and has a strong genomic component. To date, JIA genetic association studies have had limited sample sizes, used heterogeneous patient populations, or included only candidate regions. This study focuses on identifying new associations among oligoarticular and polyarticular rheumatoid factor negative (RF(-) ) JIA, which are clinically similar and the most prevalent JIA disease subtypes. METHODS: Three cohorts totaling 2,751 oligoarticular and polyarticular RF(-) JIA cases were genotyped on the Affymetrix Genome-Wide SNP Array 6...
July 18, 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/28716969/genetic-determinants-of-susceptibility-to-silver-nanoparticle-induced-acute-lung-inflammation-in-mice
#3
David K Scoville, Dianne Botta, Karen Galdanes, Stefanie C Schmuck, Collin C White, Patricia L Stapleton, Theo K Bammler, James W MacDonald, William A Altemeier, Michelle Hernandez, Steven R Kleeberger, Lung-Chi Chen, Terry Gordon, Terrance J Kavanagh
Silver nanoparticles (AgNPs) are employed in a variety of consumer products; however, in vivo rodent studies indicate that AgNPs can cause lung inflammation and toxicity in a strain- and particle type-dependent manner, but mechanisms of susceptibility remain unclear. The aim of this study was to assess the variation in AgNP-induced lung inflammation and toxicity across multiple inbred mouse strains and to use genome-wide association (GWA) mapping to identify potential candidate susceptibility genes. Mice received doses of 0...
July 17, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28706526/molecular-breeding-for-ascochyta-blight-resistance-in-lentil-current-progress-and-future-directions
#4
REVIEW
Matthew S Rodda, Jennifer Davidson, Muhammad Javid, Shimna Sudheesh, Sara Blake, John W Forster, Sukhjiwan Kaur
Lentil (Lens culinaris Medik.) is a diploid (2n = 2x = 14), self-pollinating, cool-season, grain legume that is cultivated worldwide and is highly valuable due to its high protein content. However, lentil production is constrained by many factors including biotic stresses, majority of which are fungal diseases such as ascochyta blight (AB), fusarium wilt, rust, stemphylium blight, anthracnose, and botrytis gray mold. Among various diseases, AB is a major -problem in many lentil-producing countries and can significantly reduce crop production...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28703219/genome-wide-association-and-expression-quantitative-trait-loci-studies-identify-multiple-susceptibility-loci-for-thyroid-cancer
#5
Ho-Young Son, Yul Hwangbo, Seong-Keun Yoo, Sun-Wha Im, San Duk Yang, Soo-Jung Kwak, Min Seon Park, Soo Heon Kwak, Sun Wook Cho, Jun Sun Ryu, Jeongseon Kim, Yuh-Seog Jung, Tae Hyun Kim, Su-Jin Kim, Kyu Eun Lee, Do Joon Park, Nam Han Cho, Joohon Sung, Jeong-Sun Seo, Eun Kyung Lee, Young Joo Park, Jong-Il Kim
Thyroid cancer is the most common cancer in Korea. Several susceptibility loci of differentiated thyroid cancer (DTC) were identified by previous genome-wide association studies (GWASs) in Europeans only. Here we conducted a GWAS and a replication study in Koreans using a total of 1,085 DTC cases and 8,884 controls, and validated these results using expression quantitative trait loci (eQTL) analysis and clinical phenotypes. The most robust associations were observed in the NRG1 gene (rs6996585, P=1.08 × 10(-10)) and this SNP was also associated with NRG1 expression in thyroid tissues...
July 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/28702049/endurance-exercise-ability-in-the-horse-a-trait-with-complex-polygenic-determinism
#6
Anne Ricard, Céline Robert, Christine Blouin, Fanny Baste, Gwendoline Torquet, Caroline Morgenthaler, Julie Rivière, Nuria Mach, Xavier Mata, Laurent Schibler, Eric Barrey
Endurance horses are able to run at more than 20 km/h for 160 km (in bouts of 30-40 km). This level of performance is based on intense aerobic metabolism, effective body heat dissipation and the ability to endure painful exercise. The known heritabilities of endurance performance and exercise-related physiological traits in Arabian horses suggest that adaptation to extreme endurance exercise is influenced by genetic factors. The objective of the present genome-wide association study (GWAS) was to identify single nucleotide polymorphisms (SNPs) related to endurance racing performance in 597 Arabian horses...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28700989/doritool-a-bioinformatics-integrative-tool-for-post-association-functional-annotation
#7
Isabel Martín-Antoniano, Lola Alonso, Miguel Madrid, Evangelina López de Maturana, Núria Malats
The emergence of high-throughput data in biology has increased the need for functional in silico analysis and prompted the development of integrative bioinformatics tools to facilitate the obtainment of biologically meaningful data. In this paper, we present DoriTool, a comprehensive, easy, and friendly pipeline integrating biological data from different functional tools. The tool was designed with the aim to maximize reproducibility and reduce the working time of the researchers, especially of those with limited bioinformatics skills, and to help them with the interpretation of the results...
July 13, 2017: Public Health Genomics
https://www.readbyqxmd.com/read/28698960/genome-wide-qtl-analysis-identified-significant-associations-between-hypoxia-tolerance-and-mutations-in-the-gpr132-and-abcg4-genes-in-nile-tilapia
#8
Hong Lian Li, Xiao Hui Gu, Bi Jun Li, Chao Hao Chen, Hao Ran Lin, Jun Hong Xia
Exposure to hypoxia induces both acute and chronic stress responses, which plays an important role in health of cultured organisms including growth, reproduction, immunity, and other energy demanding activities. Application of advanced genomic technologies allows rapid identification of hypoxia trait-associated genes and precise selection of superior brood stocks with high tolerance in tilapia. By applying QTL-seq and double-digest restriction-site associated DNA sequencing (ddRAD-seq) techniques, we identified four genome-wide significant quantitative trait loci (QTLs) for hypoxia tolerance and many suggestive QTLs in Nile tilapia...
July 11, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28697783/validation-of-qtl-mapping-and-transcriptome-profiling-for-identification-of-candidate-genes-associated-with-nitrogen-stress-tolerance-in-sorghum
#9
Malleswari Gelli, Anji Reddy Konda, Kan Liu, Chi Zhang, Thomas E Clemente, David R Holding, Ismail M Dweikat
BACKGROUND: Quantitative trait loci (QTLs) detected in one mapping population may not be detected in other mapping populations at all the time. Therefore, before being used for marker assisted breeding, QTLs need to be validated in different environments and/or genetic backgrounds to rule out statistical anomalies. In this regard, we mapped the QTLs controlling various agronomic traits in a recombinant inbred line (RIL) population in response to Nitrogen (N) stress and validated these with the reported QTLs in our earlier study to find the stable and consistent QTLs across populations...
July 11, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28696249/haploinsufficiency-of-the-transcription-factor-ets-1-is-renoprotective-in-dahl-salt-sensitive-rats
#10
Wenguang Feng, Bo Chen, Dongqi Xing, Xingsheng Li, Huma Fatima, Edgar A Jaimes, Paul W Sanders
Studies using Dahl salt-sensitive (SS) rats identified specific quantitative trait loci that predispose animals to hypertension-associated albuminuria and kidney injury. We explored the hypothesis that kidney-specific expression of the transcription factor Ets-1, located within one of these loci on chromosome 8, mediates glomerular injury in SS hypertension. During the first week on a high-salt diet, SS rats and SS rats with only one functioning Ets-1 gene (ES rats) demonstrated similar increases in BP. However, serum creatinine concentration, albuminuria, and glomerular expression of ETS-1 and two ETS-1 targets, MCP-1 and MMP2, did not increase as substantially in ES rats as in SS rats...
July 10, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28691663/quantitative-trait-loci-in-pepper-control-the-effective-population-size-of-two-rna-viruses-at-inoculation
#11
Lucie Tamisier, Elsa Rousseau, Sebastien Barraillé, Ghislaine Nemouchi, Marion Szadkowski, Ludovic Mailleret, Frederic Grognard, Frederic Fabre, Benoit Moury, Alain Palloix
Infection of plants by viruses is a complex process involving several steps: inoculation into plant cells, replication in inoculated cells and plant colonization. The success of the different steps depends, in part, on the viral effective population size (Ne), defined as the number of individuals passing their genes to the next generation. During infection, the virus population will undergo bottlenecks, leading to drastic reductions in Ne and, potentially, to the loss of the fittest variants. Therefore, it is crucial to better understand how plants affect Ne...
July 8, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28686183/development-and-evaluation-of-a-novel-set-of-est-ssr-markers-based-on-transcriptome-sequences-of-black-locust-robinia-pseudoacacia-l
#12
Qi Guo, Jin-Xing Wang, Li-Zhuo Su, Wei Lv, Yu-Han Sun, Yun Li
Black locust (Robinia pseudoacacia L. of the family Fabaceae) is an ecologically and economically important deciduous tree. However, few genomic resources are available for this forest species, and few effective expressed sequence tag-derived simple sequence repeat (EST-SSR) markers have been developed to date. In this study, paired-end sequencing was used to sequence transcriptomes of R. pseudoacacia by the Illumina HiSeq TM2000 platform, and EST-SSR loci were identified by de novo assembly. Furthermore, a total of 1697 primer pairs were successfully designed, from which 286 primers met the selection screening criteria; 94 pairs were randomly selected and tested for validation using polymerase chain reaction amplification...
July 7, 2017: Genes
https://www.readbyqxmd.com/read/28683716/putative-enhancer-sites-in-the-bovine-genome-are-enriched-with-variants-affecting-complex-traits
#13
Min Wang, Timothy P Hancock, Iona M MacLeod, Jennie E Pryce, Benjamin G Cocks, Benjamin J Hayes
BACKGROUND: Enhancers are non-coding DNA sequences, which when they are bound by specific proteins increase the level of gene transcription. Enhancers activate unique gene expression patterns within cells of different types or under different conditions. Enhancers are key contributors to gene regulation, and causative variants that affect quantitative traits in humans and mice have been located in enhancer regions. However, in the bovine genome, enhancers as well as other regulatory elements are not yet well defined...
July 6, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28667827/the-identification-of-new-candidate-genes-triticum-aestivum-flowering-locus-t3-b1-taft3-b1-and-target-of-eat1-tatoe1-b1-controlling-the-short-day-photoperiod-response-in-bread-wheat
#14
Meluleki Zikhali, Luzie U Wingen, Michelle Leverington-Waite, Sebastien Specel, Simon Griffiths
Perception of photoperiod changes enables plants to flower under optimum conditions for survival. We used doubled haploid populations of crosses between Avalon × Cadenza, Charger × Badger and Spark × Rialto and identified short day flowering time response quantitative trait loci (QTL) on wheat chromosomes 1BS and 1BL. We used synteny between Brachypodium distachyon and wheat to identify potential candidates for both QTL. The 1BL QTL peak coincided with TaFT3-B1, a homologue of the barley gene HvFT3, the most likely candidate gene...
July 1, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28664150/coexpression-and-expression-quantitative-trait-loci-analyses-of-the-angiogenesis-gene-gene-interaction-network-in-prostate-cancer
#15
Hui-Yi Lin, Chia-Ho Cheng, Dung-Tsa Chen, Y Ann Chen, Jong Y Park
BACKGROUND: Prostate cancer (PCa) shows a substantial clinical heterogeneity. The existing risk classification for PCa prognosis based on clinical factors is not sufficient. Although some biomarkers for PCa aggressiveness have been identified, their underlying functional mechanisms are still unclear. We previously reported a gene-gene interaction network associated with PCa aggressiveness based on single nucleotide polymorphism (SNP)-SNP interactions in the angiogenesis pathway. The goal of this study is to investigate potential functional evidence of the involvement of the genes in this gene-gene interaction network...
October 2016: Translational Cancer Research
https://www.readbyqxmd.com/read/28659949/quantitative-trait-locus-mapping-of-salt-tolerance-and-identification-of-salt-tolerant-genes-in-brassica-napus-l
#16
Lina Lang, Aixia Xu, Juan Ding, Yan Zhang, Na Zhao, Zhengshu Tian, Yaping Liu, Yang Wang, Xia Liu, Fenghao Liang, Bingbing Zhang, Mengfan Qin, Jazira Dalelhan, Zhen Huang
Salinity stress is one of typical abiotic stresses that seriously limit crop production. In this study, a genetic linkage map based on 532 molecular markers covering 1341.1 cM was constructed to identify the loci associated with salt tolerance in Brassica napus. Up to 45 quantitative trait loci (QTLs) for 10 indicators were identified in the F2:3 populations. These QTLs can account for 4.80-51.14% of the phenotypic variation. A major QTL, qSPAD5 on LG5 associated with chlorophyll can be detected in three replicates...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28656603/a-genetic-variant-near-gata3-implicated-in-inherited-susceptibility-and-etiology-of-benign-prostatic-hyperplasia-bph-and-lower-urinary-tract-symptoms-luts
#17
Rong Na, Brian T Helfand, Haitao Chen, Carly A Conran, Susan E Crawford, Simon W Hayward, Teuvo L J Tammela, Judy Hoffman-Bolton, Siqun L Zheng, Patrick C Walsh, Johanna Schleutker, Elizabeth A Platz, William B Isaacs, Jianfeng Xu
BACKGROUND: Benign prostatic hyperplasia (BPH) and associated lower urinary tract symptoms (LUTS) are common conditions. Little is known about their etiologies except that studies have suggested a substantial heritable component. Our objective is to provide a comprehensive, genome-wide evaluation of inherited risks and possible mechanisms of etiology in BPH. METHODS: We performed a three-stage, genome-wide association study (GWAS) of men from three independent populations, the REduction by DUtasteride of prostate Cancer Events (REDUCE) trial, the CLUE II cohort, and a Finnish hospital-based population...
June 28, 2017: Prostate
https://www.readbyqxmd.com/read/28643332/integrative-eqtl-analysis-of-tumor-and-host-omics-data-in-individuals-with-bladder-cancer
#18
Silvia Pineda, Kristel Van Steen, Núria Malats
Integrative analyses of several omics data are emerging. The data are usually generated from the same source material (i.e., tumor sample) representing one level of regulation. However, integrating different regulatory levels (i.e., blood) with those from tumor may also reveal important knowledge about the human genetic architecture. To model this multilevel structure, an integrative-expression quantitative trait loci (eQTL) analysis applying two-stage regression (2SR) was proposed. This approach first regressed tumor gene expression levels with tumor markers and the adjusted residuals from the previous model were then regressed with the germline genotypes measured in blood...
June 23, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28642272/networks-underpinning-symbiosis-revealed-through-cross-species-eqtl-mapping
#19
Yuelong Guo, Sylwia Fudali, Jacinta Gimeno, Peter DiGennaro, Stella Chang, Valerie M Williamson, David McK Bird, Dahlia M Nielsen
Organisms engage in extensive cross-species molecular dialogue, yet the underlying molecular actors are known for only a few interactions. Many techniques have been designed to uncover genes involved in signaling between organisms. Typically, these focus on only one of the partners. We developed an expression quantitative trait locus (eQTL) mapping-based approach to identify cause-and-effect relationships between genes from two partners engaged in an interspecific interaction. We demonstrated the approach by assaying expression of ninety-eight isogenic plants (Medicago truncatula), each inoculated with a genetically distinct line of the diploid parasitic nematode Meloidogyne hapla With this design, systematic differences in gene expression across host plants could be mapped to genetic polymorphisms of their infecting parasites...
June 22, 2017: Genetics
https://www.readbyqxmd.com/read/28640939/global-transcriptome-and-co-expression-network-analyses-reveal-cultivar-specific-molecular-signatures-associated-with-seed-development-and-seed-size-weight-determination-in-chickpea
#20
Rohini Garg, Vikash K Singh, Mohan Singh Rajkumar, Vinay Kumar, Mukesh Jain
Seed development is an intricate process regulated via a complex transcriptional regulatory network. To understand the molecular mechanisms governing seed development and seed size/weight in chickpea, we performed a comprehensive analysis of transcriptome dynamics during seed development in two cultivars with contrasting seed size/weight (small seeded, Himchana 1 and large-seeded, JGK 3). Our analysis identified stage-specific expression for a significant proportion (>13%) of the genes. About one-fourth of total genes exhibited significant differential expression in JGK 3 as compared to Himchana 1...
June 22, 2017: Plant Journal: for Cell and Molecular Biology
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