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Expression quantitative trait loci

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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
#1
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
https://www.readbyqxmd.com/read/28635624/effects-of-type-1-diabetes-risk-alleles-on-immune-cell-gene-expression
#2
REVIEW
Ramesh Ram, Grant Morahan
Genetic studies have identified 61 variants associated with the risk of developing Type 1 Diabetes (T1D). The functions of most of the non-HLA (Human Leukocyte Antigen) genetic variants remain unknown. We found that only 16 of these risk variants could potentially be linked to a protein-coding change. Therefore, we investigated whether these variants affected susceptibility by regulating changes in gene expression. To do so, we examined whole transcriptome profiles of 600 samples from the Type 1 Diabetes Genetics Consortium (T1DGC)...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28634304/redox-dependent-interaction-between-thaumatin-like-protein-and-%C3%AE-glucan-influences-malting-quality-of-barley
#3
Surinder Singh, Rajiv K Tripathi, Peggy G Lemaux, Bob B Buchanan, Jaswinder Singh
Barley is the cornerstone of the malting and brewing industry. It is known that 250 quantitative trait loci (QTLs) of the grain are associated with 19 malting-quality phenotypes. However, only a few of the contributing genetic components have been identified. One of these, on chromosome 4H, contains a major malting QTL, QTL2, located near the telomeric region that accounts, respectively, for 28.9% and 37.6% of the variation in the β-glucan and extract fractions of malt. In the current study, we dissected the QTL2 region using an expression- and microsynteny-based approach...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28633642/prediction-and-analysis-of-three-gene-families-related-to-leaf-rust-puccinia-triticina-resistance-in-wheat-triticum-aestivum-l
#4
Fred Y Peng, Rong-Cai Yang
BACKGROUND: The resistance to leaf rust (Lr) caused by Puccinia triticina in wheat (Triticum aestivum L.) has been well studied over the past decades with over 70 Lr genes being mapped on different chromosomes and numerous QTLs (quantitative trait loci) being detected or mapped using DNA markers. Such resistance is often divided into race-specific and race-nonspecific resistance. The race-nonspecific resistance can be further divided into resistance to most or all races of the same pathogen and resistance to multiple pathogens...
June 20, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28626070/potential-susceptibility-loci-identified-for-renal-cell-carcinoma-by-targeting-obesity-related-genes
#5
Xiang Shu, Mark P Purdue, Yuanqing Ye, Huakang Tu, Christopher G Wood, Nizar M Tannir, Zhaoming Wang, Demetrius Albanes, Susan M Gapstur, Victoria L Stevens, Nathaniel Rothman, Stephen J Chanock, Xifeng Wu
BACKGROUND: Obesity is an established risk factor for renal cell carcinoma (RCC). Although genome-wide association studies (GWAS) of RCC have identified several susceptibility loci, additional variants might be missed due to the highly conservative selection. METHODS: We conducted a multiphase study utilizing three independent genome-wide scans at MD Anderson Cancer Center (MDA RCC GWAS and MDA RCC OncoArray) and National Cancer Institute (NCI RCC GWAS), which consisted of a total of 3,530 cases and 5,714 controls, to investigate genetic variations in obesity-related genes and RCC risk...
June 16, 2017: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/28623561/variation-in-cucumber-cucumis-sativus-l-fruit-size-and-shape-results-from-multiple-components-acting-pre-anthesis-and-post-pollination
#6
Marivi Colle, Yiqun Weng, Yunyan Kang, Ron Ophir, Amir Sherman, Rebecca Grumet
Morphological, QTL, and gene expression analyses indicate variation in cucumber fruit size and shape results from orientation, timing, and extent of cell division and expansion, and suggest candidate gene factors. Variation in cucumber (Cucumis sativus L.) fruit size and shape is highly quantitative, implicating interplay of multiple components. Recent studies have identified numerous fruit size and shape quantitative trait loci (QTL); however, underlying factors remain to be determined. We examined ovary and fruit development of two sequenced cucumber genotypes with extreme differences in fruit size and shape, Chinese Long '9930' (CL9930), and pickling type 'Gy14'...
June 16, 2017: Planta
https://www.readbyqxmd.com/read/28613276/genetic-loci-associated-with-heart-rate-variability-and-their-effects-on-cardiac-disease-risk
#7
Ilja M Nolte, M Loretto Munoz, Vinicius Tragante, Azmeraw T Amare, Rick Jansen, Ahmad Vaez, Benedikt von der Heyde, Christy L Avery, Joshua C Bis, Bram Dierckx, Jenny van Dongen, Stephanie M Gogarten, Philippe Goyette, Jussi Hernesniemi, Ville Huikari, Shih-Jen Hwang, Deepali Jaju, Kathleen F Kerr, Alexander Kluttig, Bouwe P Krijthe, Jitender Kumar, Sander W van der Laan, Leo-Pekka Lyytikäinen, Adam X Maihofer, Arpi Minassian, Peter J van der Most, Martina Müller-Nurasyid, Michel Nivard, Erika Salvi, James D Stewart, Julian F Thayer, Niek Verweij, Andrew Wong, Delilah Zabaneh, Mohammad H Zafarmand, Abdel Abdellaoui, Sulayma Albarwani, Christine Albert, Alvaro Alonso, Foram Ashar, Juha Auvinen, Tomas Axelsson, Dewleen G Baker, Paul I W de Bakker, Matteo Barcella, Riad Bayoumi, Rob J Bieringa, Dorret Boomsma, Gabrielle Boucher, Annie R Britton, Ingrid Christophersen, Andrea Dietrich, George B Ehret, Patrick T Ellinor, Markku Eskola, Janine F Felix, John S Floras, Oscar H Franco, Peter Friberg, Maaike G J Gademan, Mark A Geyer, Vilmantas Giedraitis, Catharina A Hartman, Daiane Hemerich, Albert Hofman, Jouke-Jan Hottenga, Heikki Huikuri, Nina Hutri-Kähönen, Xavier Jouven, Juhani Junttila, Markus Juonala, Antti M Kiviniemi, Jan A Kors, Meena Kumari, Tatiana Kuznetsova, Cathy C Laurie, Joop D Lefrandt, Yong Li, Yun Li, Duanping Liao, Marian C Limacher, Henry J Lin, Cecilia M Lindgren, Steven A Lubitz, Anubha Mahajan, Barbara McKnight, Henriette Meyer Zu Schwabedissen, Yuri Milaneschi, Nina Mononen, Andrew P Morris, Mike A Nalls, Gerjan Navis, Melanie Neijts, Kjell Nikus, Kari E North, Daniel T O'Connor, Johan Ormel, Siegfried Perz, Annette Peters, Bruce M Psaty, Olli T Raitakari, Victoria B Risbrough, Moritz F Sinner, David Siscovick, Johannes H Smit, Nicholas L Smith, Elsayed Z Soliman, Nona Sotoodehnia, Jan A Staessen, Phyllis K Stein, Adrienne M Stilp, Katarzyna Stolarz-Skrzypek, Konstantin Strauch, Johan Sundström, Cees A Swenne, Ann-Christine Syvänen, Jean-Claude Tardif, Kent D Taylor, Alexander Teumer, Timothy A Thornton, Lesley E Tinker, André G Uitterlinden, Jessica van Setten, Andreas Voss, Melanie Waldenberger, Kirk C Wilhelmsen, Gonneke Willemsen, Quenna Wong, Zhu-Ming Zhang, Alan B Zonderman, Daniele Cusi, Michele K Evans, Halina K Greiser, Pim van der Harst, Mohammad Hassan, Erik Ingelsson, Marjo-Riitta Järvelin, Stefan Kääb, Mika Kähönen, Mika Kivimaki, Charles Kooperberg, Diana Kuh, Terho Lehtimäki, Lars Lind, Caroline M Nievergelt, Chris J O'Donnell, Albertine J Oldehinkel, Brenda Penninx, Alexander P Reiner, Harriëtte Riese, Arie M van Roon, John D Rioux, Jerome I Rotter, Tamar Sofer, Bruno H Stricker, Henning Tiemeier, Tanja G M Vrijkotte, Folkert W Asselbergs, Bianca J J M Brundel, Susan R Heckbert, Eric A Whitsel, Marcel den Hoed, Harold Snieder, Eco J C de Geus
Reduced cardiac vagal control reflected in low heart rate variability (HRV) is associated with greater risks for cardiac morbidity and mortality. In two-stage meta-analyses of genome-wide association studies for three HRV traits in up to 53,174 individuals of European ancestry, we detect 17 genome-wide significant SNPs in eight loci. HRV SNPs tag non-synonymous SNPs (in NDUFA11 and KIAA1755), expression quantitative trait loci (eQTLs) (influencing GNG11, RGS6 and NEO1), or are located in genes preferentially expressed in the sinoatrial node (GNG11, RGS6 and HCN4)...
June 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28611791/regional-association-analysis-of-metaqtls-delineates-candidate-grain-size-genes-in-rice
#8
Anurag V Daware, Rishi Srivastava, Ashok K Singh, Swarup K Parida, Akhilesh K Tyagi
Molecular mapping studies which aim to identify genetic basis of diverse agronomic traits are vital for marker-assisted crop improvement. Numerous Quantitative Trait Loci (QTLs) mapped in rice span long genomic intervals with hundreds to thousands of genes, which limits their utilization for marker-assisted genetic enhancement of rice. Although potent, fine mapping of QTLs is challenging task as it requires screening of large number of segregants to identify suitable recombination events. Association mapping offers much higher resolution as compared to QTL mapping, but detects considerable number of spurious QTLs...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28607429/genetic-mapping-with-testcrossing-associations-and-f2-3-populations-reveals-the-importance-of-heterosis-in-chilling-tolerance-at-maize-seedling-stage
#9
Jinbo Yan, Yu Wu, Wenming Li, Xiner Qin, Yi Wang, Bing Yue
Maize seedlings are sensitive to low temperatures, and genetic mapping for chilling tolerance at the seedling stage with genetically diverse populations would facilitate the genetic improvement of this important trait. In this study, quantitative trait loci (QTL) mapping for four chilling tolerance-related traits at the seedling stage was conducted via a genome-wide association study (GWAS) with 338 testcrosses. A total of 32 significant loci and 36 stress tolerance-related candidate genes were identified, though none of them have been revealed by QTL mapping using maize inbred lines in previous reports...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28604730/large-scale-association-analysis-identifies-new-lung-cancer-susceptibility-loci-and-heterogeneity-in-genetic-susceptibility-across-histological-subtypes
#10
James D McKay, Rayjean J Hung, Younghun Han, Xuchen Zong, Robert Carreras-Torres, David C Christiani, Neil E Caporaso, Mattias Johansson, Xiangjun Xiao, Yafang Li, Jinyoung Byun, Alison Dunning, Karen A Pooley, David C Qian, Xuemei Ji, Geoffrey Liu, Maria N Timofeeva, Stig E Bojesen, Xifeng Wu, Loic Le Marchand, Demetrios Albanes, Heike Bickeböller, Melinda C Aldrich, William S Bush, Adonina Tardon, Gad Rennert, M Dawn Teare, John K Field, Lambertus A Kiemeney, Philip Lazarus, Aage Haugen, Stephen Lam, Matthew B Schabath, Angeline S Andrew, Hongbing Shen, Yun-Chul Hong, Jian-Min Yuan, Pier Alberto Bertazzi, Angela C Pesatori, Yuanqing Ye, Nancy Diao, Li Su, Ruyang Zhang, Yonathan Brhane, Natasha Leighl, Jakob S Johansen, Anders Mellemgaard, Walid Saliba, Christopher A Haiman, Lynne R Wilkens, Ana Fernandez-Somoano, Guillermo Fernandez-Tardon, Henricus F M van der Heijden, Jin Hee Kim, Juncheng Dai, Zhibin Hu, Michael P A Davies, Michael W Marcus, Hans Brunnström, Jonas Manjer, Olle Melander, David C Muller, Kim Overvad, Antonia Trichopoulou, Rosario Tumino, Jennifer A Doherty, Matt P Barnett, Chu Chen, Gary E Goodman, Angela Cox, Fiona Taylor, Penella Woll, Irene Brüske, H-Erich Wichmann, Judith Manz, Thomas R Muley, Angela Risch, Albert Rosenberger, Kjell Grankvist, Mikael Johansson, Frances A Shepherd, Ming-Sound Tsao, Susanne M Arnold, Eric B Haura, Ciprian Bolca, Ivana Holcatova, Vladimir Janout, Milica Kontic, Jolanta Lissowska, Anush Mukeria, Simona Ognjanovic, Tadeusz M Orlowski, Ghislaine Scelo, Beata Swiatkowska, David Zaridze, Per Bakke, Vidar Skaug, Shanbeh Zienolddiny, Eric J Duell, Lesley M Butler, Woon-Puay Koh, Yu-Tang Gao, Richard S Houlston, John McLaughlin, Victoria L Stevens, Philippe Joubert, Maxime Lamontagne, David C Nickle, Ma'en Obeidat, Wim Timens, Bin Zhu, Lei Song, Linda Kachuri, María Soler Artigas, Martin D Tobin, Louise V Wain, Thorunn Rafnar, Thorgeir E Thorgeirsson, Gunnar W Reginsson, Kari Stefansson, Dana B Hancock, Laura J Bierut, Margaret R Spitz, Nathan C Gaddis, Sharon M Lutz, Fangyi Gu, Eric O Johnson, Ahsan Kamal, Claudio Pikielny, Dakai Zhu, Sara Lindströem, Xia Jiang, Rachel F Tyndale, Georgia Chenevix-Trench, Jonathan Beesley, Yohan Bossé, Stephen Chanock, Paul Brennan, Maria Teresa Landi, Christopher I Amos
Although several lung cancer susceptibility loci have been identified, much of the heritability for lung cancer remains unexplained. Here 14,803 cases and 12,262 controls of European descent were genotyped on the OncoArray and combined with existing data for an aggregated genome-wide association study (GWAS) analysis of lung cancer in 29,266 cases and 56,450 controls. We identified 18 susceptibility loci achieving genome-wide significance, including 10 new loci. The new loci highlight the striking heterogeneity in genetic susceptibility across the histological subtypes of lung cancer, with four loci associated with lung cancer overall and six loci associated with lung adenocarcinoma...
June 12, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28603537/flowering-locus-c-flc-is-a-potential-major-regulator-of-glucosinolate-content-across-developmental-stages-of-aethionema-arabicum-brassicaceae
#11
Setareh Mohammadin, Thu-Phuong Nguyen, Marco S van Weij, Michael Reichelt, Michael E Schranz
The biochemical defense of plants can change during their life-cycle and impact herbivore feeding and plant fitness. The annual species Aethionema arabicum is part of the sister clade to all other Brassicaceae. Hence, it holds a phylogenetically important position for studying crucifer trait evolution. Glucosinolates (GS) are essentially Brassicales-specific metabolites involved in plant defense. Using two Ae. arabicum accessions (TUR and CYP) we identify substantial differences in glucosinolate profiles and quantities between lines, tissues and developmental stages...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28600722/genetic-dissection-of-plant-growth-habit-in-chickpea
#12
Hari D Upadhyaya, Deepak Bajaj, Rishi Srivastava, Anurag Daware, Udita Basu, Shailesh Tripathi, Chellapilla Bharadwaj, Akhilesh K Tyagi, Swarup K Parida
A combinatorial genomics-assisted breeding strategy encompassing association analysis, genetic mapping and expression profiling is found most promising for quantitative dissection of complex traits in crop plants. The present study employed GWAS (genome-wide association study) using 24,405 SNPs (single nucleotide polymorphisms) obtained with genotyping-by-sequencing (GBS) of 92 sequenced desi and kabuli accessions of chickpea. This identified eight significant genomic loci associated with erect (E)/semi-erect (SE) vs...
June 9, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28600539/genetic-determinants-of-crop-timing-and-quality-traits-in-two-interspecific-petunia-recombinant-inbred-line-populations
#13
Yufang Guo, Wei-Kuang Lin, QiuXia Chen, Veronica A Vallejo, Ryan M Warner
The rate at which plants develop new nodes (development rate) is a major determinant of crop production time, yet the genetic control of this process, including genetic interactions with crop quality parameters, is poorly understood. We employed a modified genotyping-by-sequencing approach and generated genetic linkage maps with 6,291 and 3,297 single nucleotide polymorphisms (SNPs) for the interspecific Petunia recombinant inbred line (RIL) population - P. axillaris × P. exserta (AE) and P. integrifolia × P...
June 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28598434/genome-wide-association-study-identifies-multiple-risk-loci-for-renal-cell-carcinoma
#14
Ghislaine Scelo, Mark P Purdue, Kevin M Brown, Mattias Johansson, Zhaoming Wang, Jeanette E Eckel-Passow, Yuanqing Ye, Jonathan N Hofmann, Jiyeon Choi, Matthieu Foll, Valerie Gaborieau, Mitchell J Machiela, Leandro M Colli, Peng Li, Joshua N Sampson, Behnoush Abedi-Ardekani, Celine Besse, Helene Blanche, Anne Boland, Laurie Burdette, Amelie Chabrier, Geoffroy Durand, Florence Le Calvez-Kelm, Egor Prokhortchouk, Nivonirina Robinot, Konstantin G Skryabin, Magdalena B Wozniak, Meredith Yeager, Gordana Basta-Jovanovic, Zoran Dzamic, Lenka Foretova, Ivana Holcatova, Vladimir Janout, Dana Mates, Anush Mukeriya, Stefan Rascu, David Zaridze, Vladimir Bencko, Cezary Cybulski, Eleonora Fabianova, Viorel Jinga, Jolanta Lissowska, Jan Lubinski, Marie Navratilova, Peter Rudnai, Neonila Szeszenia-Dabrowska, Simone Benhamou, Geraldine Cancel-Tassin, Olivier Cussenot, Laura Baglietto, Heiner Boeing, Kay-Tee Khaw, Elisabete Weiderpass, Borje Ljungberg, Raviprakash T Sitaram, Fiona Bruinsma, Susan J Jordan, Gianluca Severi, Ingrid Winship, Kristian Hveem, Lars J Vatten, Tony Fletcher, Kvetoslava Koppova, Susanna C Larsson, Alicja Wolk, Rosamonde E Banks, Peter J Selby, Douglas F Easton, Paul Pharoah, Gabriella Andreotti, Laura E Beane Freeman, Stella Koutros, Demetrius Albanes, Satu Männistö, Stephanie Weinstein, Peter E Clark, Todd L Edwards, Loren Lipworth, Susan M Gapstur, Victoria L Stevens, Hallie Carol, Matthew L Freedman, Mark M Pomerantz, Eunyoung Cho, Peter Kraft, Mark A Preston, Kathryn M Wilson, J Michael Gaziano, Howard D Sesso, Amanda Black, Neal D Freedman, Wen-Yi Huang, John G Anema, Richard J Kahnoski, Brian R Lane, Sabrina L Noyes, David Petillo, Bin Tean Teh, Ulrike Peters, Emily White, Garnet L Anderson, Lisa Johnson, Juhua Luo, Julie Buring, I-Min Lee, Wong-Ho Chow, Lee E Moore, Christopher Wood, Timothy Eisen, Marc Henrion, James Larkin, Poulami Barman, Bradley C Leibovich, Toni K Choueiri, G Mark Lathrop, Nathaniel Rothman, Jean-Francois Deleuze, James D McKay, Alexander S Parker, Xifeng Wu, Richard S Houlston, Paul Brennan, Stephen J Chanock
Previous genome-wide association studies (GWAS) have identified six risk loci for renal cell carcinoma (RCC). We conducted a meta-analysis of two new scans of 5,198 cases and 7,331 controls together with four existing scans, totalling 10,784 cases and 20,406 controls of European ancestry. Twenty-four loci were tested in an additional 3,182 cases and 6,301 controls. We confirm the six known RCC risk loci and identify seven new loci at 1p32.3 (rs4381241, P=3.1 × 10(-10)), 3p22.1 (rs67311347, P=2.5 × 10(-8)), 3q26...
June 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28594911/candidate-genes-on-murine-chromosome-8-are-associated-with-susceptibility-to-staphylococcus-aureus-infection-in-mice-and-are-involved-with-staphylococcus-aureus-septicemia-in-humans
#15
Qin Yan, Sun Hee Ahn, Felix Mba Medie, Batu K Sharma-Kuinkel, Lawrence P Park, William K Scott, Hitesh Deshmukh, Ephraim L Tsalik, Derek D Cyr, Christopher W Woods, Chen-Hsin Albert Yu, Carlton Adams, Robert Qi, Brenda Hansen, Vance G Fowler
We previously showed that chromosome 8 of A/J mice was associated with susceptibility to S. aureus infection. However, the specific genes responsible for this susceptibility are unknown. Chromosome substitution strain 8 (CSS8) mice, which have chromosome 8 from A/J but an otherwise C57BL/6J genome, were used to identify the genetic determinants of susceptibility to S. aureus on chromosome 8. Quantitative trait loci (QTL) mapping of S. aureus-infected N2 backcross mice (F1 [C8A] × C57BL/6J) identified a locus 83180780-88103009 (GRCm38/mm10) on A/J chromosome 8 that was linked to S...
2017: PloS One
https://www.readbyqxmd.com/read/28592500/epistatic-networks-jointly-influence-phenotypes-related-to-metabolic-disease-and-gene-expression-in-diversity-outbred-mice
#16
Anna L Tyler, Bo Ji, Daniel M Gatti, Steven C Munger, Gary A Churchill, Karen L Svenson, Gregory W Carter
Genetic studies of multidimensional phenotypes can potentially link genetic variation, gene expression, and physiological data to create multi-scale models of complex traits. The challenge of reducing these data to specific hypotheses has become increasingly acute with the advent of genome-scale data resources. Multi-parent populations derived from model organisms provide a resource for developing methods to understand this complexity. In this study, we simultaneously modeled body composition, serum biomarkers, and liver transcript abundances from 474 Diversity Outbred mice...
June 2017: Genetics
https://www.readbyqxmd.com/read/28589911/comparative-analyses-of-long-non-coding-rna-in-lean-and-obese-pig
#17
Lin Yu, Lina Tai, Lifang Zhang, Yi Chu, Yixing Li, Lei Zhou
OBJECTIVES: Current studies have revealed that long non-coding RNA plays a crucial role in fat metabolism. However, the difference of lncRNA between lean (Duroc) and obese (Luchuan) pig remain undefined. Here, we investigated the expressional profile of lncRNA in these two pigs and discussed the relationship between lncRNA and fat deposition. MATERIALS AND METHODS: The Chinese Luchuan pig has a dramatic differences in backfat thickness as compared with Duroc pig...
May 26, 2017: Oncotarget
https://www.readbyqxmd.com/read/28575649/genetic-variation-driven-gene-expression-changes-highlight-genes-with-important-functions-for-kidney-disease
#18
Yi-An Ko, Huiguang Yi, Chengxiang Qiu, Shizheng Huang, Jihwan Park, Nora Ledo, Anna Köttgen, Hongzhe Li, Daniel J Rader, Michael A Pack, Christopher D Brown, Katalin Susztak
Chronic kidney disease (CKD) is a complex gene-environmental disease affecting close to 10% of the US population. Genome-wide association studies (GWASs) have identified sequence variants, localized to non-coding genomic regions, associated with kidney function. Despite these robust observations, the mechanism by which variants lead to CKD remains a critical unanswered question. Expression quantitative trait loci (eQTL) analysis is a method to identify genetic variation associated with gene expression changes in specific tissue types...
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28575251/hierarchical-probabilistic-models-for-multiple-gene-variant-associations-based-on-next-generation-sequencing-data
#19
Dimitrios V Vavoulis, Jenny C Taylor, Anna Schuh
Motivation: The identification of genetic variants influencing gene expression (known as expression quantitative trait loci or eQTLs ) is important in unravelling the genetic basis of complex traits. Detecting multiple eQTLs simultaneously in a population based on paired DNA-seq and RNA-seq assays employs two competing types of models: models which rely on appropriate transformations of RNA-seq data (and are powered by a mature mathematical theory), or count-based models , which represent digital gene expression explicitly, thus rendering such transformations unnecessary...
May 31, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28569138/identification-of-candidate-genes-for-fiber-length-quantitative-trait-loci-through-rna-seq-and-linkage-and-physical-mapping-in-cotton
#20
Xihua Li, Man Wu, Guoyuan Liu, Wenfeng Pei, Honghong Zhai, Jiwen Yu, Jinfa Zhang, Shuxun Yu
BACKGROUND: Cotton (Gossypium spp.) fibers are single-celled elongated trichomes, the molecular aspects of genetic variation in fiber length (FL) among genotypes are currently unknown. In this study, two backcross inbred lines (BILs), i.e., NMGA-062 ("Long") and NMGA-105 ("Short") with 32.1 vs. 27.2 mm in FL, respectively, were chosen to perform RNA-Seq on developing fibers at 10 days post anthesis (DPA). The two BILs differed in 4 quantitative trait loci (QTL) for FL and were developed from backcrosses between G...
May 31, 2017: BMC Genomics
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