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Abstract
Yak has been subject to natural selection, human domestication and interspecific introgression during its evolution. However, genetic variants favored by each of these processes have not been distinguished previously. We constructed a graph-genome for 47 genomes of 7 cross-fertile bovine species. This allowed detection of 57,432 high-resolution structural variants (SVs) within and across the species, which were genotyped in 386 individuals. We distinguished the evolutionary origins of diverse SVs in domestic yaks by phylogenetic analyses. We further identified 334 genes overlapping with SVs in domestic yaks that bore potential signals of selection from wild yaks, plus an additional 686 genes introgressed from cattle. Nearly 90% of the domestic yaks were introgressed by cattle. Introgression of an SV spanning the KIT gene triggered the breeding of white domestic yaks. We validated a significant association of the selected stratified SVs with gene expression, which contributes to phenotypic variations. Our results highlight that SVs of different origins contribute to the phenotypic diversity of domestic yaks.
Yaks have been subject to natural selection, human domestication and interspecific introgression during their evolution. Here, the authors have identified genomic structural variations and the linked genes involved in these processes in domestic yaks, to reveal new insight into genetic basis of phenotypic diversity.
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1 Lanzhou University, State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou, China (GRID:grid.32566.34) (ISNI:0000 0000 8571 0482); Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Lanzhou, China (GRID:grid.410727.7) (ISNI:0000 0001 0526 1937); Qinghai Normal University, Academy of Plateau Science and Sustainability, Xining, China (GRID:grid.462704.3) (ISNI:0000 0001 0694 7527)
2 Lanzhou University, State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou, China (GRID:grid.32566.34) (ISNI:0000 0000 8571 0482)
3 Utrecht University, Faculty of Veterinary Medicine, Utrecht, The Netherlands (GRID:grid.5477.1) (ISNI:0000 0001 2034 6234)
4 Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Lanzhou, China (GRID:grid.410727.7) (ISNI:0000 0001 0526 1937)
5 Anhui Agricultural University, Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Hefei, China (GRID:grid.411389.6) (ISNI:0000 0004 1760 4804)
6 University of St Andrews, School of Biology, St Andrews, UK (GRID:grid.11914.3c) (ISNI:0000 0001 0721 1626)
7 Lanzhou University, State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou, China (GRID:grid.32566.34) (ISNI:0000 0000 8571 0482); Qinghai Normal University, Academy of Plateau Science and Sustainability, Xining, China (GRID:grid.462704.3) (ISNI:0000 0001 0694 7527)