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Expression quantitative trait loci

Zi-Ru Chen, Lu Kuang, Yi-Qun Gao, Ya-Ling Wang, David E Salt, Dai-Yin Chao
Zinc (Zn) is an essential element for plant growth and development, and Zn derived from crop plants in the diet is also important for human health. Here, we report that genetic variation in Heavy Metal-ATPase 4 ( HMA4 ) controls natural variation in leaf Zn content. Investigation of the natural variation in leaf Zn content in a world-wide collection of 349 Arabidopsis thaliana wild collected accessions identified two accessions, Van-0 and Fab-2, which accumulate significantly lower Zn when compared with Col-0...
2018: Frontiers in Plant Science
Jeffrey Hsu, Shamone Gore-Panter, Gregory Tchou, Laurie Castel, Beth Lovano, Christine S Moravec, Gosta B Pettersson, Eric E Roselli, A Marc Gillinov, Kenneth R McCurry, Nicholas G Smedira, John Barnard, David R Van Wagoner, Mina K Chung, Jonathan D Smith
BACKGROUND: Genome-wide association studies have identified 23 loci for atrial fibrillation (AF), but the mechanisms responsible for these associations, as well as the causal genes and genetic variants, remain undefined. METHODS: To identify the effect of common genetic variants on gene expression that might explain the mechanisms linking genome-wide association loci with AF risk, we performed RNA sequencing of left atrial appendages from a biracial cohort of 265 subjects...
March 2018: Circ Genom Precis Med
Qian-Wen Deng, Xiang-Dong Luo, Ya-Ling Chen, Yi Zhou, Fan-Tao Zhang, Biao-Lin Hu, Jian-Kun Xie
BACKGROUND: Low phosphorus availability is a major factor restricting rice growth. Dongxiang wild rice (Oryza rufipogon Griff.) has many useful genes lacking in cultivated rice, including stress resistance to phosphorus deficiency, cold, salt and drought, which is considered to be a precious germplasm resource for rice breeding. However, the molecular mechanism of regulation of phosphorus deficiency tolerance is not clear. RESULTS: In this study, cDNA libraries were constructed from the leaf and root tissues of phosphorus stressed and untreated Dongxiang wild rice seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in phosphorus stress response...
March 15, 2018: Biological Research
Karl A G Kremling, Shu-Yun Chen, Mei-Hsiu Su, Nicholas K Lepak, M Cinta Romay, Kelly L Swarts, Fei Lu, Anne Lorant, Peter J Bradbury, Edward S Buckler
Here we report a multi-tissue gene expression resource that represents the genotypic and phenotypic diversity of modern inbred maize, and includes transcriptomes in an average of 255 lines in seven tissues. We mapped expression quantitative trait loci and characterized the contribution of rare genetic variants to extremes in gene expression. Some of the new mutations that arise in the maize genome can be deleterious; although selection acts to keep deleterious variants rare, their complete removal is impeded by genetic linkage to favourable loci and by finite population size...
March 14, 2018: Nature
Xiaochen Lin, Katie Kei-Hang Chan, Yen-Tsung Huang, Xi Luo, Liming Liang, James Wilson, Adolfo Correa, Daniel Levy, Simin Liu
PURPOSE: Leisure-time physical activity (LTPA) is a well-established modifiable lifestyle determinant for multiple cardio-metabolic outcomes. However, current understanding of the genetic architecture that may determine LTPA remains very limited. Therefore, we aimed to examine the role of genetic factors in affecting LTPA, which has yet to be investigated comprehensively and in-depth. METHODS: We conducted a genome-wide analysis using 1000 Genomes Project imputed data from the Women's Health Initiative (n=11,865), the Jackson Heart Study (n=3,015) and the Framingham Heart Study (n=7,339)...
March 13, 2018: Medicine and Science in Sports and Exercise
Jeanie K Meckes, Patrick H Lim, Stephanie L Wert, Wendy Luo, Stephanie A Gacek, Dana Platt, Ryan Jankord, Kathrin Saar, Eva E Redei
Acute stress responsiveness is a quantitative trait that varies in severity from one individual to another; however, the genetic component underlying the individual variation is largely unknown. Fischer 344 (F344) and Wistar Kyoto (WKY) rat strains show large differences in behavioral responsiveness to acute stress, such as freezing behavior in response to footshock during the conditioning phase of contextual fear conditioning (CFC). Quantitative trait loci (QTL) have been identified for behavioral responsiveness to acute stress in the defensive burying (DB) and open field test (OFT) from a reciprocal F2 cross of F344 and WKY rat strains...
2018: PloS One
Zixiang Wen, Ruijuan Tan, Shichen Zhang, Paul J Collins, Jiazheng Yuan, Wenyan Du, Cuihua Gu, Shujun Ou, Qijian Song, Yong-Qiang Charles An, John F Boyse, Martin I Chilvers, Dechun Wang
White mold of soybean, caused by Sclerotinia sclerotiorum (Lib.) de Bary, is a necrotrophic fungus capable of infecting a wide range of plants. To dissect the genetic architecture of resistance to white mold, a high-density customized single nucleotide polymorphism (SNP) array (52,041 SNPs) was used to genotype two soybean diversity panels. Combined with resistance variation data observed in the field and greenhouse environments, genome-wide association studies (GWAS) were conducted to identify quantitative trait loci (QTL) controlling resistance against white mold...
March 12, 2018: Plant Biotechnology Journal
S-S Dong, Y-J Zhang, Y-X Chen, S Yao, R-H Hao, Y Rong, H-M Niu, J-B Chen, Y Guo, T-L Yang
We aimed to summarize the results of genetic association studies for obesity and provide a comprehensive annotation of all susceptibility single nucleotide polymorphisms (SNPs). A total of 72 studies were summarized, resulting in 90,361 susceptibility SNPs (738 index SNPs and 89,623 linkage disequilibrium SNPs). Over 90% of the susceptibility SNPs are located in non-coding regions, and it is challenging to understand their functional significance. Therefore, we annotated these SNPs by using various functional databases...
March 12, 2018: Obesity Reviews: An Official Journal of the International Association for the Study of Obesity
Sonal Singh, Caitrin W McDonough, Yan Gong, Wael A Alghamdi, Meghan J Arwood, Salma A Bargal, Leanne Dumeny, Wen-Yi Li, Mai Mehanna, Bradley Stockard, Guang Yang, Felipe A de Oliveira, Natalie C Fredette, Mohamed H Shahin, Kent R Bailey, Amber L Beitelshees, Eric Boerwinkle, Arlene B Chapman, John G Gums, Stephen T Turner, Rhonda M Cooper-DeHoff, Julie A Johnson
BACKGROUND: Thiazide and thiazide-like diuretics are first-line medications for treating uncomplicated hypertension. However, their use has been associated with adverse metabolic events, including hyperglycemia and incident diabetes mellitus, with incompletely understood mechanisms. Our goal was to identify genomic variants associated with thiazide-like diuretic/chlorthalidone-induced glucose change. METHODS AND RESULTS: Genome-wide analysis of glucose change after treatment with chlorthalidone was performed by race among the white (n=175) and black (n=135) participants from the PEAR-2 (Pharmacogenomic Evaluation of Antihypertensive Responses-2)...
March 9, 2018: Journal of the American Heart Association
Gen Li, Dereje Jima, Fred A Wright, Andrew B Nobel
BACKGROUND: Expression quantitative trait loci (eQTL) analysis identifies genetic markers associated with the expression of a gene. Most existing eQTL analyses and methods investigate association in a single, readily available tissue, such as blood. Joint analysis of eQTL in multiple tissues has the potential to improve, and expand the scope of, single-tissue analyses. Large-scale collaborative efforts such as the Genotype-Tissue Expression (GTEx) program are currently generating high quality data in a large number of tissues...
March 9, 2018: BMC Bioinformatics
Timothy J Stodola, Pengyuan Liu, Yong Liu, Andrew Vallejos, Aron M Geurts, Andrew S Greene, Mingyu Liang
A challenge to understanding enhancer-gene relationships is that enhancers are not always sequentially close to the gene they regulate. Physical proximity mapping through sequencing can provide an unbiased view of the chromatin close to the proximal promoter of the renin gene (Ren). Our objective was to determine genomic regions that physically interact with the renin proximal promoter, using two different genetic backgrounds, the Dahl salt sensitive and normotensive SS-13BN, which have been shown to have different regulation of plasma renin in vivo...
March 9, 2018: Physiological Genomics
Palle Duun Rohde, Solveig Østergaard, Torsten Nygaard Kristensen, Peter Sørensen, Volker Loeschcke, Trudy F C Mackay, Pernille Sarup
Understanding the genetic underpinnings of complex traits requires knowledge of the genetic variants that contribute to phenotypic variability. Reliable statistical approaches are needed to obtain such knowledge. In genome-wide association studies, variants are tested for association with trait variability to pinpoint loci that contribute to the quantitative trait. Because stringent genome-wide significance thresholds are applied to control the false positive rate, many true causal variants can remain undetected...
March 8, 2018: G3: Genes—Genomes—Genetics
Dag Leonard, Elisabet Svenungsson, Johanna Dahlqvist, Andrei Alexsson, Lisbeth Ärlestig, Kimberly E Taylor, Johanna K Sandling, Christine Bengtsson, Martina Frodlund, Andreas Jönsen, Susanna Eketjäll, Kerstin Jensen-Urstad, Iva Gunnarsson, Christopher Sjöwall, Anders A Bengtsson, Maija-Leena Eloranta, Ann-Christine Syvänen, Solbritt Rantapää-Dahlqvist, Lindsey A Criswell, Lars Rönnblom
OBJECTIVES: Patients with systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) have increased risk of cardiovascular disease (CVD). We investigated whether single nucleotide polymorphisms (SNPs) at autoimmunity risk loci were associated with CVD in SLE and RA. METHODS: Patients with SLE (n=1045) were genotyped using the 200K Immunochip SNP array (Illumina). The allele frequency was compared between patients with and without different manifestations of CVD...
March 7, 2018: Annals of the Rheumatic Diseases
Marie-Julie Favé, Fabien C Lamaze, David Soave, Alan Hodgkinson, Héloïse Gauvin, Vanessa Bruat, Jean-Christophe Grenier, Elias Gbeha, Kimberly Skead, Audrey Smargiassi, Markey Johnson, Youssef Idaghdour, Philip Awadalla
Uncovering the interaction between genomes and the environment is a principal challenge of modern genomics and preventive medicine. While theoretical models are well defined, little is known of the G × E interactions in humans. We used an integrative approach to comprehensively assess the interactions between 1.6 million data points, encompassing a range of environmental exposures, health, and gene expression levels, coupled with whole-genome genetic variation. From ∼1000 individuals of a founder population in Quebec, we reveal a substantial impact of the environment on the transcriptome and clinical endophenotypes, overpowering that of genetic ancestry...
March 6, 2018: Nature Communications
Shijia Zhu, Gang Fang
Motivation: For many traits, causal loci uncovered by genetic-mapping studies explain only a minority of the heritable contribution to trait variation. Multiple explanations for this 'missing heritability' have been proposed. SNP-SNP interaction (epistasis), as one of the compelling models, has been widely studied. However, the genome-wide scan of epistasis, especially for quantitative traits, poses huge computational challenges. Moreover, covariate adjustment is largely ignored in epistasis analysis due to the massive extra computational undertaking...
March 2, 2018: Bioinformatics
Angel Cy Mak, Marquitta J White, Walter L Eckalbar, Zachary A Szpiech, Sam S Oh, Maria Pino-Yanes, Donglei Hu, Pagé Goddard, Scott Huntsman, Joshua Galanter, Ann Chen Wu, Blanca E Himes, Soren Germer, Julia M Vogel, Karen L Bunting, Celeste Eng, Sandra Salazar, Kevin L Keys, Jennifer Liberto, Thomas J Nuckton, Thomas A Nguyen, Dara G Torgerson, Pui-Yan Kwok, Albert M Levin, Juan C Celedón, Erick Forno, Hakon Hakonarson, Patrick M Sleiman, Amber Dahlin, Kelan G Tantisira, Scott T Weiss, Denise Serebrisky, Emerita Brigino-Buenaventura, Harold J Farber, Kelley Meade, Michael A Lenoir, Pedro C Avila, Saunak Sen, Shannon M Thyne, William Rodriguez-Cintron, Cheryl A Winkler, Andrés Moreno-Estrada, Karla Sandoval, Jose R Rodriguez-Santana, Rajesh Kumar, L Keoki Williams, Nadav Ahituv, Elad Ziv, Max A Seibold, Robert B Darnell, Noah Zaitlen, Ryan D Hernandez, Esteban G Burchard
Rationale Albuterol, a bronchodilator medication, is the first-line therapy for asthma worldwide. There are significant racial/ethnic differences in albuterol drug response. Objective To identify genetic variants important for bronchodilator drug response (BDR) in racially diverse children. Methods We performed the first whole genome sequencing (WGS) pharmacogenetics study from 1,441 children with asthma from the tails of the BDR distribution to identify genetic association with BDR. Measurements and Main Results We identified population-specific and shared genetic variants associated with BDR, including genome-wide significant (p < 3...
March 6, 2018: American Journal of Respiratory and Critical Care Medicine
Raffaella Nativio, Greg Donahue, Amit Berson, Yemin Lan, Alexander Amlie-Wolf, Ferit Tuzer, Jon B Toledo, Sager J Gosai, Brian D Gregory, Claudio Torres, John Q Trojanowski, Li-San Wang, F Brad Johnson, Nancy M Bonini, Shelley L Berger
Aging is the strongest risk factor for Alzheimer's disease (AD), although the underlying mechanisms remain unclear. The chromatin state, in particular through the mark H4K16ac, has been implicated in aging and thus may play a pivotal role in age-associated neurodegeneration. Here we compare the genome-wide enrichment of H4K16ac in the lateral temporal lobe of AD individuals against both younger and elderly cognitively normal controls. We found that while normal aging leads to H4K16ac enrichment, AD entails dramatic losses of H4K16ac in the proximity of genes linked to aging and AD...
March 5, 2018: Nature Neuroscience
Lu Wang, I King Jordan
A convergence of novel genome analysis technologies is enabling population genomic studies of human transposable elements (TEs). Population surveys of human genome sequences have uncovered thousands of individual TE insertions that segregate as common genetic variants, i.e. TE polymorphisms. These recent TE insertions provide an important source of naturally occurring human genetic variation. Investigators are beginning to leverage population genomic data sets to execute genome-scale association studies for assessing the phenotypic impact of human TE polymorphisms...
March 2, 2018: Current Opinion in Genetics & Development
Helen H Tai, David De Koeyer, Mads Sønderkær, Sanne Hedegaard, Martin Lagüe, Claudia Goyer, Lana Nolan, Charlotte Davidson, Kyle Gardner, Jonathan Neilson, Jamuna Risal Paudel, Agnes Murphy, Benoit Bizimungu, Hui Ying Wang, Xingyao Xiong, Dennis Halterman, Kåre Lehmann Nielsen
Kleb. is a pathogenic fungus causing wilting, chlorosis, and early dying in potato ( L.). Genetic mapping of resistance to was done using a diploid population of potato. The major quantitative trait locus (QTL) for resistance was found on chromosome 5. The gene, controlling earliness of maturity and tuberization, was mapped within the interval. Another QTL on chromosome 9 co-localized with the wilt resistance gene marker. Epistasis analysis indicated that the loci on chromosomes 5 and 9 had a highly significant interaction, and that functioned downstream of The alleles were sequenced and found to encode StCDF1...
March 2018: Plant Genome
Rhonda Flores, Peng Zhang, Wei Wu, Xu Wang, Peiying Ye, Pan Zheng, Yang Liu
A recent meta-analysis revealed the contribution of the SIGLEC6 locus to the risk of developing systemic lupus erythematosus (SLE). However, no specific Siglec (sialic acid-binding immunoglobulin-like lectin) genes (Siglecs) have been implicated in the pathogenesis of SLE. Here, we performed in silico analysis of the function of three major protective alleles in the locus and found that these alleles were expression quantitative trait loci that enhanced expression of the adjacent SIGLEC12 gene. These data suggest that SIGLEC12 may protect against the development of SLE in Asian populations...
March 5, 2018: Cellular & Molecular Immunology
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