globalchange  > 气候变化与战略
DOI: 10.1073/pnas.1904159116
论文题名:
Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits
作者: 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.
刊名: Proceedings of the National Academy of Sciences of the United States of America
ISSN: 0027-8424
出版年: 2019
卷: 116, 期:39
起始页码: 19398
结束页码: 19408
语种: 英语
英文关键词: Animal breeding ; Cattle ; Evolution ; Gene regulation ; Quantitative traits
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
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.
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资源类型: 期刊论文
标识符: http://119.78.100.158/handle/2HF3EXSE/163533
Appears in Collections:气候变化与战略

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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 3083, Australia, Centre for Animal Science, University of Queensland, St. Lucia, QLD 4067, Australia; Bolormaa, S., Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia; Liu, Z., Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia; Rochfort, S.J., Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia, School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia; Reich, C.M., Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia; Mason, B.A., Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia; Vander Jagt, C.J., Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia; Daetwyler, H.D., Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia, School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia; Lund, M.S., Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, DK-8830, Denmark; Chamberlain, A.J., Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia; Goddard, M.E., Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville, VIC 3052, Australia, Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia

Recommended Citation:
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]. Proceedings of the National Academy of Sciences of the United States of America,2019-01-01,116(39)
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