Genomic Analysis Reveals Candidate Genes Underlying Sex-Linked Eyelid Coloboma, Feather Color Traits, and Climatic Adaptation in Huoyan Geese
Junhui Wen,
Jincheng Yu,
Li Zhang,
Haiying Li,
Huie Wang,
Hongchang Gu,
Xiurong Zhao,
Xinye Zhang,
Xufang Ren,
Gang Wang,
Anqi Chen,
Lujiang Qu
Affiliations
Junhui Wen
Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
Jincheng Yu
Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
Li Zhang
Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
Haiying Li
College of Animal Science, Xinjiang Agricultural University, Urumqi 830000, China
Huie Wang
Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar 843300, China
Hongchang Gu
Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
Xiurong Zhao
Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Xinye Zhang
Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Xufang Ren
Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Gang Wang
Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Anqi Chen
Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Lujiang Qu
Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Driven by natural and artificial selection, the domestic Huoyan geese from Northern China have gradually generated specific phenotypes and climatic adaptations. To understand the genetic basis of the two specific phenotypes that are sex linked, including upper eyelid coloboma and gosling feather color, as well as the climatic adaptations of the Huoyan goose, which can contribute to the artificial selection and breeding of geese. We selected Huoyan geese and nine Southern Chinese goose breeds and identified their divergence on the genomic level. Using selective sweep analysis, we found that PTPRM on chromosome Z influences the upper eyelid coloboma phenotype of the Huoyan goose, and TYRP1 is a plausible candidate gene for the Huoyan gosling feather color. We obtained a number of genes related to cold adaptation in Huoyan geese, mainly involved in physiological functions such as metabolism, angiogenesis contraction and circulatory system, apoptosis, immunity, stress, and neural system. The most interesting candidates for cold adaptation are PIP5K1B and NMNAT3 that are associated with energy metabolism and stress. We also obtained some genes related to heat adaptation, including AGTPBP1, associated with neurology; GDA, associated with skin pigmentation; and NAA35, associated with apoptosis. These findings deepen our understanding of the genetics of specific phenotypes and climate adaptation in local geese and provide insights for the selection of goose breeds.