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Expression quantitative trait loci

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https://www.readbyqxmd.com/read/28814792/genetic-regulatory-effects-modified-by-immune-activation-contribute-to-autoimmune-disease-associations
#1
Sarah Kim-Hellmuth, Matthias Bechheim, Benno Pütz, Pejman Mohammadi, Yohann Nédélec, Nicholas Giangreco, Jessica Becker, Vera Kaiser, Nadine Fricker, Esther Beier, Peter Boor, Stephane E Castel, Markus M Nöthen, Luis B Barreiro, Joseph K Pickrell, Bertram Müller-Myhsok, Tuuli Lappalainen, Johannes Schumacher, Veit Hornung
The immune system plays a major role in human health and disease, and understanding genetic causes of interindividual variability of immune responses is vital. Here, we isolate monocytes from 134 genotyped individuals, stimulate these cells with three defined microbe-associated molecular patterns (LPS, MDP, and 5'-ppp-dsRNA), and profile the transcriptomes at three time points. Mapping expression quantitative trait loci (eQTL), we identify 417 response eQTLs (reQTLs) with varying effects between conditions...
August 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28811335/the-conserved-and-unique-genetic-architecture-of-kernel-size-and-weight-in-maize-and-rice
#2
Jie Liu, Juan Huang, Huan Guo, Liu Lan, Hongze Wang, Yuancheng Xu, Xiaohong Yang, Wenqiang Li, Hao Tong, Yingjie Xiao, Qingchun Pan, Feng Qiao, Mohammad Sharif Raihan, Haijun Liu, Xuehai Zhang, Ning Yang, Xiaqing Wang, Min Deng, Minliang Jin, Lijun Zhao, Xin Luo, Yang Zhou, Xiang Li, Wei Zhan, Nannan Liu, Hong Wang, Gengshen Chen, Qing Li, Jianbing Yan
Maize is a major staple crop. Maize kernel size and weight are important contributors to its yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight and kernel test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three statistical models. In total, 729 quantitative trait loci (QTLs) were identified, many of which were identified in all three models, including 22 major QTLs that each can explain more than 10% of phenotypic variation...
August 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28807804/joint-parameter-estimation-in-the-qtl-mapping-of-ordinal-traits
#3
Xiaona Sheng, Yihong Qiu, Ying Zhou, Wensheng Zhu
With the rapid development of statistical genetics, the deep researches of ordinal traits have been gradually emphasized. The data of these traits bear relatively less information than those of continuous phenotypes, therefore it is more complex to map the quantitative trait loci (QTL) of ordinal traits. In this paper, the multiple-interval mapping method is considered in the genetic mapping of ordinal traits. By combining threshold model and statistical model, we build a cumulative logistic regression model to express the relationship between the ordinal data and the QTL genotypes...
August 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28805909/genomewide-association-study-for-production-and-meat-quality-traits-in-canchim-beef-cattle
#4
G G Santiago, F Siqueira, F F Cardoso, L C A Regitano, R Ventura, B P Sollero, M D Souza, F B Mokry, A B R Ferreira, R A A Torres
The commercial value of the bovine carcass is determined by a set of traits, such as weight, yield, back fat thickness, and marbling; therefore, the genetic improvement of growth, meat, and carcass quality traits is an important tool to add value to the supply chain. Genomewide association studies (GWAS) enable the identification of loci that control phenotypic expression of quantitative traits (QTL). Therefore, the objective of this work was to perform a GWAS to identify genomic regions and genes associated with growth, carcass traits, and meat quality in Canchim beef cattle...
August 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28805827/transcriptional-risk-scores-link-gwas-to-eqtls-and-predict-complications-in-crohn-s-disease
#5
Urko M Marigorta, Lee A Denson, Jeffrey S Hyams, Kajari Mondal, Jarod Prince, Thomas D Walters, Anne Griffiths, Joshua D Noe, Wallace V Crandall, Joel R Rosh, David R Mack, Richard Kellermayer, Melvin B Heyman, Susan S Baker, Michael C Stephens, Robert N Baldassano, James F Markowitz, Mi-Ok Kim, Marla C Dubinsky, Judy Cho, Bruce J Aronow, Subra Kugathasan, Greg Gibson
Gene expression profiling can be used to uncover the mechanisms by which loci identified through genome-wide association studies (GWAS) contribute to pathology. Given that most GWAS hits are in putative regulatory regions and transcript abundance is physiologically closer to the phenotype of interest, we hypothesized that summation of risk-allele-associated gene expression, namely a transcriptional risk score (TRS), should provide accurate estimates of disease risk. We integrate summary-level GWAS and expression quantitative trait locus (eQTL) data with RNA-seq data from the RISK study, an inception cohort of pediatric Crohn's disease...
August 14, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28803857/mapping-of-quantitative-trait-loci-for-temporal-growth-and-age-at-maturity-in-coho-salmon-evidence-for-genotype-by-sex-interactions
#6
Miyako Kodama, Jeffrey J Hard, Kerry A Naish
Phenotypic differences between males and females are ubiquitous throughout the animal kingdom. Therefore, investigating the extent to which sex-dependent genetic effects contribute to phenotypic variation is important in understanding the evolutionary response of each sex to natural and artificial selection. Sex-specific differences in growth patterns and age at sexual maturity have been observed in a number of anadromous salmonid fishes. In these species, faster growing individuals in a given cohort often mature earlier than conspecifics, and earlier maturing individuals are often males...
August 10, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28794258/genetic-architecture-and-molecular-networks-underlying-leaf-thickness-in-desert-adapted-tomato
#7
Viktoriya Coneva, Margaret Frank, Maria A de Luis Balaguer, Mao Li, Rosangela Sozzani, Daniel H Chitwood
Thicker leaves allow plants to grow in water-limited conditions. However, our understanding of the genetic underpinnings of this highly functional leaf shape trait is poor. We used a custom-built confocal profilometer to directly measure leaf thickness in a set of introgression lines (ILs) derived from the desert tomato species Solanum pennellii, and identified quantitative trait loci (QTL). We report evidence of a complex genetic architecture of this trait and roles for both genetic and environmental factors...
August 9, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28793908/transcriptomic-analysis-comparing-mouse-strains-with-extreme-total-lung-capacities-identifies-novel-candidate-genes-for-pulmonary-function
#8
Leema George, Ankita Mitra, Tania A Thimraj, Martin Irmler, Sangeetha Vishweswaraiah, Lars Lunding, Dorothea Hühn, Alicia Madurga, Johannes Beckers, Heinz Fehrenbach, Swapna Upadhyay, Holger Schulz, George D Leikauf, Koustav Ganguly
BACKGROUND: Failure to attain peak lung function by early adulthood is a risk factor for chronic lung diseases. Previously, we reported that C3H/HeJ mice have about twice total lung capacity (TLC) compared to JF1/MsJ mice. We identified seven lung function quantitative trait loci (QTL: Lfnq1-Lfnq7) in backcross/intercross mice derived from these inbred strains. We further demonstrated, superoxide dismutase 3, extracellular (Sod3), Kit oncogene (Kit) and secreted phosphoprotein 1 (Spp1) located on these Lfnqs as lung function determinants...
August 9, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28793313/deciphering-the-genetic-control-of-gene-expression-following-mycobacterium-leprae-antigen-stimulation
#9
Jérémy Manry, Yohann Nédélec, Vinicius M Fava, Aurélie Cobat, Marianna Orlova, Nguyen Van Thuc, Vu Hong Thai, Guillaume Laval, Luis B Barreiro, Erwin Schurr
Leprosy is a human infectious disease caused by Mycobacterium leprae. A strong host genetic contribution to leprosy susceptibility is well established. However, the modulation of the transcriptional response to infection and the mechanism(s) of disease control are poorly understood. To address this gap in knowledge of leprosy pathogenicity, we conducted a genome-wide search for expression quantitative trait loci (eQTL) that are associated with transcript variation before and after stimulation with M. leprae sonicate in whole blood cells...
August 9, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28792098/identification-of-expression-quantitative-trait-loci-eqtls-in-human-peripheral-blood-mononuclear-cells-pbmcs-and-shared-with-liver-and-brain
#10
Pei He, Wei Xia, Lan Wang, Jian Wu, Yu-Fan Guo, Ke-Qin Zeng, Ming-Jun Wang, Peng-Fei Bing, Fang-Fei Xie, Xin Lu, Yong-Hong Zhang, Shu-Feng Lei, Fei-Yan Deng
PBMCs are essential for immunity and involved in various diseases. To identify genetic variations contributing to PBMCs transcriptome-wide gene expression, we performed a genome-wide eQTL analysis by using genome-wide SNPs data and transcriptome-wide mRNA expression data. To assess whether there are common regulation patterns shared among different tissues/organs, public datasets were utilized to identify common eQTLs shared with PBMCs in lymphoblastoid, monocytes, liver, and brain. Allelic expression imbalance (AEI) assay was employed to validate representative eQTLs identified...
August 9, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28790316/a-plasmodium-yoelii-hect-like-e3-ubiquitin-ligase-regulates-parasite-growth-and-virulence
#11
Sethu C Nair, Ruixue Xu, Sittiporn Pattaradilokrat, Jian Wu, Yanwei Qi, Martine Zilversmit, Sundar Ganesan, Vijayaraj Nagarajan, Richard T Eastman, Marlene S Orandle, John C Tan, Timothy G Myers, Shengfa Liu, Carole A Long, Jian Li, Xin-Zhuan Su
Infection of mice with strains of Plasmodium yoelii parasites can result in different pathology, but molecular mechanisms to explain this variation are unclear. Here we show that a P. yoelii gene encoding a HECT-like E3 ubiquitin ligase (Pyheul) influences parasitemia and host mortality. We genetically cross two lethal parasites with distinct disease phenotypes, and identify 43 genetically diverse progeny by typing with microsatellites and 9230 single-nucleotide polymorphisms. A genome-wide quantitative trait loci scan links parasite growth and host mortality to two major loci on chromosomes 1 and 7 with LOD (logarithm of the odds) scores = 6...
August 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28790145/inter-chromosomal-transfer-of-immune-regulation-during-infection-of-barley-with-the-powdery-mildew-pathogen
#12
Priyanka Surana, Ruo Xu, Gregory Fuerst, Antony Ve Chapman, Dan Nettleton, Roger P Wise
Powdery mildew pathogens colonize over 9,500 plant species, causing critical yield loss. The Ascomycete fungus, Blumeria graminis f. sp. hordei (Bgh), causes powdery mildew disease in barley (Hordeum vulgare L.). Successful infection begins with penetration of host epidermal cells, culminating in haustorial feeding structures, facilitating delivery of fungal effectors to the plant and exchange of nutrients from host to pathogen. We used expression Quantitative Trait Locus (eQTL) analysis to dissect the temporal control of immunity-associated gene expression in a doubled haploid barley population challenged with Bgh Two highly significant regions possessing trans eQTL were identified near the telomeric ends of chromosomes 2HL and 1HS...
August 8, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28767102/allocation-to-male-vs-female-floral-function-varies-by-currency-and-responds-differentially-to-density-and-moisture-stress
#13
M T Brock, R L Winkelman, M J Rubin, C E Edwards, B E Ewers, C Weinig
Allocation of finite resources to separate reproductive functions is predicted to vary across environments and affect fitness. Biomass is the most commonly measured allocation currency; however, in comparison with nutrients it may be less limited and express different environmental and evolutionary responses. Here, we measured carbon, nitrogen, phosphorus, and biomass allocation among floral whorls in recombinant inbred lines of Brassica rapa in multiple environments to characterize the genetic architecture of floral allocation, including its sensitivity to environmental heterogeneity and to choice of currency...
August 2, 2017: Heredity
https://www.readbyqxmd.com/read/28764798/an-interaction-map-of-circulating-metabolites-immune-gene-networks-and-their-genetic-regulation
#14
Artika P Nath, Scott C Ritchie, Sean G Byars, Liam G Fearnley, Aki S Havulinna, Anni Joensuu, Antti J Kangas, Pasi Soininen, Annika Wennerström, Lili Milani, Andres Metspalu, Satu Männistö, Peter Würtz, Johannes Kettunen, Emma Raitoharju, Mika Kähönen, Markus Juonala, Aarno Palotie, Mika Ala-Korpela, Samuli Ripatti, Terho Lehtimäki, Gad Abraham, Olli Raitakari, Veikko Salomaa, Markus Perola, Michael Inouye
BACKGROUND: Immunometabolism plays a central role in many cardiometabolic diseases. However, a robust map of immune-related gene networks in circulating human cells, their interactions with metabolites, and their genetic control is still lacking. Here, we integrate blood transcriptomic, metabolomic, and genomic profiles from two population-based cohorts (total N = 2168), including a subset of individuals with matched multi-omic data at 7-year follow-up. RESULTS: We identify topologically replicable gene networks enriched for diverse immune functions including cytotoxicity, viral response, B cell, platelet, neutrophil, and mast cell/basophil activity...
August 1, 2017: Genome Biology
https://www.readbyqxmd.com/read/28758171/qtl-mapping-for-resistance-to-iridovirus-in-asian-seabass-using-genotyping-by-sequencing
#15
Le Wang, Bin Bai, Shuqing Huang, Peng Liu, Zi Yi Wan, Baoqing Ye, Jinlu Wu, Gen Hua Yue
Identifying quantitative trait loci (QTL) for viral disease resistance is of particular importance in selective breeding programs of fish species. Genetic markers linked to QTL can be useful in marker-assisted selection (MAS) for elites resistant to specific pathogens. Here, we conducted a genome scan for QTL associated with Singapore grouper iridovirus (SGIV) resistance in an Asian seabass (Lates calcarifer) family, using a high-density linkage map generated with genotyping-by-sequencing. One genome-wide significant and three suggestive QTL were detected at LG21, LG6, LG13, and LG15, respectively...
July 31, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28754724/trans-ancestry-fine-mapping-and-molecular-assays-identify-regulatory-variants-at-the-angptl8-hdl-c-gwas-locus
#16
Maren E Cannon, Qing Duan, Ying Wu, Monica Zeynalzadeh, Zheng Xu, Antti J Kangas, Pasi Soininen, Mika Ala-Korpela, Mete Civelek, Aldons J Lusis, Johanna Kuusisto, Francis S Collins, Michael Boehnke, Hua Tang, Markku Laakso, Yun Li, Karen Mohlke
Recent genome-wide association studies (GWAS) have identified variants associated with high-density lipoprotein cholesterol (HDL-C) located in or near the ANGPTL8 gene. Given the extensive sharing of GWAS loci across populations, we hypothesized that at least one shared variant at this locus affects HDL-C. The HDL-C-associated variants are coincident with expression quantitative trait loci for ANGPTL8 and DOCK6 in subcutaneous adipose tissue; however, only ANGPTL8 expression levels are associated with HDL-C levels...
July 28, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28747083/a-novel-variant-with-positive-natural-selection-influenced-hb-a2-levels-in-chinese-individuals-with-%C3%AE-thalassemia
#17
Shanjuan Yu, Yang Chen, Ketong Lai, Roma Kajal Dewan, Yunyan He
β-Thalassemia (β-thal) is the most common inherited hemolytic anemia worldwide. Elevated Hb A2 is a mark of β-thal carriers. The aim of this study was to identify the pathogenic variants associated with the Hb A2 levels. One thousand and thirty β-thal carriers were recruited for this study. Using positive natural expression quantitative trait loci (eQTL) analysis, a significant variant was selected. Genotyping for the rs231841 polymorphism was performed by the Sequenom MassARRAY IPLEX platform. All genetic association analyses were performed with the PLINK program...
July 26, 2017: Hemoglobin
https://www.readbyqxmd.com/read/28746715/identification-of-genetic-loci-jointly-influencing-schizophrenia-risk-and-the-cognitive-traits-of-verbal-numerical-reasoning-reaction-time-and-general-cognitive-function
#18
Olav B Smeland, Oleksandr Frei, Karolina Kauppi, W David Hill, Wen Li, Yunpeng Wang, Florian Krull, Francesco Bettella, Jon A Eriksen, Aree Witoelar, Gail Davies, Chun C Fan, Wesley K Thompson, Max Lam, Todd Lencz, Chi-Hua Chen, Torill Ueland, Erik G Jönsson, Srdjan Djurovic, Ian J Deary, Anders M Dale, Ole A Andreassen
Importance: Schizophrenia is associated with widespread cognitive impairments. Although cognitive deficits are one of the factors most strongly associated with functional outcome in schizophrenia, current treatment strategies largely fail to ameliorate these impairments. To develop more efficient treatment strategies in patients with schizophrenia, a better understanding of the pathogenesis of these cognitive deficits is needed. Accumulating evidence indicates that genetic risk of schizophrenia may contribute to cognitive dysfunction...
July 26, 2017: JAMA Psychiatry
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
#19
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
#20
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
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