A multi-tissue atlas of regulatory variants in cattle
2022
Liu, Shuli | Gao, Yahui | Canela-Xandri, Oriol | Wang, Sheng | Yu, Ying | Cai, Wentao | Li, Bingjie | Xiang, Ruidong | Chamberlain, Amanda | Pairo-Castineira, Erola | D’mellow, Kenton | Rawlik, Konrad | Xia, Charley | Yao, Yuelin | Navarro, Pau | Rocha, Dominique | Li, Xiujin | Yan, Ze | Li, Congjun | Rosen, Benjamin | van Tassell, Curtis | Vanraden, Paul | Zhang, Shengli | Ma, Li | Cole, John | Liu, George | Tenesa, Albert | Fang, Lingzhao | Génétique Animale et Biologie Intégrative (GABI) ; AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | Agriculture and Food Research Initiative (AFRI) grant from United States Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) Animal Genome and Reproduction Programs2016-67015-248862019-67015-293212021-67015-33409US-Israel Binational Agricultural Research and Development (BARD) grant from the BARD FundUS-4997-17Health Data Research UK (HDRUK)HDR-9004European Union (EU)801215UK Research & Innovation (UKRI)Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/D/10002070BBS/E/D/30002275UK Research & Innovation (UKRI)Medical Research Council UK (MRC)MR/P015514/1HDRUK awardHDR-9004Australian Research CouncilDP200100499National Science Foundation of China-Pakistan Science Foundation Joint Project31961143009National Key R&D Program of China2021YFD12009002021YFD1200903AFRI grant from NIFA2021-67015-334092020-67015-31398'Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection' of the Agricultural Research Service (ARS) of the USDA8042-31000-001-00-D'Improving Feed Efficiency and Environmental Sustainability of Dairy Cattle through Genomics and Novel Technologies' of ARS-USDA8042-31310-078-00-D'Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals' of ARS-USDA8042-31000-002-00-DSCINet project of the ARS-USDA0500-00093-001-00-DCouncil on Dairy Cattle Breeding under ARS-USDA Material Transfer Research Agreement58-8042-8-007ARS-USDA Data Transfer Agreement15443MR/R025851/1Australian Research CouncilDP200100499
International audience
Show more [+] Less [-]English. Characterization of genetic regulatory variants acting on livestock gene expression is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here we build a Cattle Genotype-Tissue Expression atlas (CattleGTEx) as part of the pilot phase of the Farm animal GTEx (FarmGTEx) project for the research community based on 7,180 publicly available RNA-sequencing (RNA-seq) samples. We describe the transcriptomic landscape of more than 100 tissues/cell types and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 23 distinct tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multiomics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle.
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