Journal article
A multi-tissue atlas of regulatory variants in cattle
S Liu, Y Gao, O Canela-Xandri, S Wang, Y Yu, W Cai, B Li, R Xiang, AJ Chamberlain, E Pairo-Castineira, K D’Mellow, K Rawlik, C Xia, Y Yao, P Navarro, D Rocha, X Li, Z Yan, C Li, BD Rosen Show all
Nature Genetics | Published : 2022
Abstract
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 ..
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Awarded by National Institute of Food and Agriculture
Funding Acknowledgements
This work was supported in part by Agriculture and Food Research Initiative (AFRI) grant numbers 2016-67015-24886, 2019-67015-29321 and 2021-67015-33409 from the United States Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) Animal Genome and Reproduction Programs, and US-Israel Binational Agricultural Research and Development (BARD) grant number US-4997-17 from the BARD Fund. L.F. was partially funded through Health Data Research UK (HDRUK) award HDR-9004 and the European Union's Horizon 2020 research and innovation programme under the Marie Skodowska-Curie grant agreement No. 801215. A.T. acknowledged funding from the Biotechnology and Biological Sciences Research Council through program grants BBS/E/D/10002070 and BBS/E/D/30002275, Medical Research Council research grant MR/P015514/1 and HDRUK award HDR-9004. O.C.-X. was supported by MR/R025851/1. R.X. was supported by Australian Research Council's Discovery Projects (DP200100499). Y. Yu. was supported by the National Science Foundation of China-Pakistan Science Foundation Joint Project (31961143009) and National Key R&D Program of China (2021YFD1200900 and 2021YFD1200903). L.M. was supported in part by AFRI grant numbers 2020-67015-31398 and 2021-67015-33409 from the NIFA. G.E.L., B.D.R. and C.P.V.T. were supported by appropriated project 8042-31000-001-00-D, 'Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection' of the Agricultural Research Service (ARS) of the USDA. C.-J.L. was supported by appropriated project 8042-31310-078-00-D, 'Improving Feed Efficiency and Environmental Sustainability of Dairy Cattle through Genomics and Novel Technologies' of ARS-USDA. J.B.C. was supported by appropriated project 8042-31000-002-00-D, 'Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals' of ARS-USDA. This research used resources provided by the SCINet project of the ARS-USDA project number 0500-00093-001-00-D. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. The USDA is an equal opportunity provider and employer. All the funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. We thank US dairy producers for providing phenotypic, genomic and pedigree data through the Council on Dairy Cattle Breeding under ARS-USDA Material Transfer Research Agreement 58-8042-8-007. Access to 1000 Bull Genomes Project data was provided under ARS-USDA Data Transfer Agreement 15443. International genetic evaluations were calculated by the International Bull Evaluation Service (Interbull; Uppsala, Sweden).