气候变化领域集成服务门户(CCPortal): Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits

CCPortal

DOI	10.1073/pnas.1904159116
	Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits
	Xiang R.; Van Den Berg I.; MacLeod I.M.; Hayes B.J.; Prowse-Wilkins C.P.; Wang M.; Bolormaa S.; Liu Z.; Rochfort S.J.; Reich C.M.; Mason B.A.; Vander Jagt C.J.; Daetwyler H.D.; Lund M.S.; Chamberlain A.J.; Goddard M.E.
发表日期	2019
ISSN	0027-8424
起始页码	19398
结束页码	19408
卷号	116 期号:39
英文摘要	Many genome variants shaping mammalian phenotype are hypothesized to regulate gene transcription and/or to be under selection. However, most of the evidence to support this hypothesis comes from human studies. Systematic evidence for regulatory and evolutionary signals contributing to complex traits in a different mammalian model is needed. Sequence variants associated with gene expression (expression quantitative trait loci [eQTLs]) and concentration of metabolites (metabolic quantitative trait loci [mQTLs]) and under histone-modification marks in several tissues were discovered from multiomics data of over 400 cattle. Variants under selection and evolutionary constraint were identified using genome databases of multiple species. These analyses defined 30 sets of variants, and for each set, we estimated the genetic variance the set explained across 34 complex traits in 11,923 bulls and 32,347 cows with 17,669,372 imputed variants. The per-variant trait heritability of these sets across traits was highly consistent (r > 0.94) between bulls and cows. Based on the per-variant heritability, conserved sites across 100 vertebrate species and mQTLs ranked the highest, followed by eQTLs, young variants, those under histone-modification marks, and selection signatures. From these results,we defined a Functional-And-Evolutionary Trait Heritability (FAETH) score indicating the functionality and predicted heritability of each variant. In additional 7,551 cattle, the high FAETH-ranking variants had significantly increased genetic variances and genomic prediction accuracies in 3 production traits compared to the low FAETH-ranking variants. The FAETH framework combines the information of gene regulation, evolution, and trait heritability to rank variants, and the publicly available FAETH data provide a set of biological priors for cattle genomic selection worldwide. © 2019 National Academy of Sciences. All rights reserved.
英文关键词	Animal breeding; Cattle; Evolution; Gene regulation; Quantitative traits
语种	英语
scopus关键词	animal experiment; animal tissue; article; breeding; cow; expression quantitative trait locus; female; gene control; gene expression; genetic variability; heritability; histone modification; nonhuman; prediction
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/160349
作者单位	Xiang, R., Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville, VIC 3052, Australia, Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia; Van Den Berg, I., Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville, VIC 3052, Australia, Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia; MacLeod, I.M., Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia; Hayes, B.J., Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia, Centre for Animal Science, University of Queensland, St. Lucia, QLD 4067, Australia; Prowse-Wilkins, C.P., Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville, VIC 3052, Australia, Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia; Wang, M., Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC...
推荐引用方式 GB/T 7714	Xiang R.,Van Den Berg I.,MacLeod I.M.,et al. Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits[J],2019,116(39).
APA	Xiang R..,Van Den Berg I..,MacLeod I.M..,Hayes B.J..,Prowse-Wilkins C.P..,...&Goddard M.E..(2019).Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits.Proceedings of the National Academy of Sciences of the United States of America,116(39).
MLA	Xiang R.,et al."Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits".Proceedings of the National Academy of Sciences of the United States of America 116.39(2019).