title: Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits.
abstract: The goat (Capra hircus) is one of the first farm animals that have undergone domestication and extensive natural and artificial selection by adapting to various environments, which in turn has resulted in its high level of phenotypic diversity. Here, we generated medium-coverage (9-13×) sequences from eight domesticated goat breeds, representing morphologically or geographically specific populations, to identify genomic regions representing selection signatures. We discovered ~10 million single nucleotide polymorphisms (SNPs) for each breed. By combining two approaches, ZHpand di values, we identified 22 genomic regions that may have contributed to the phenotypes in coat color patterns, body size, cashmere traits, as well as high altitude adaptation in goat populations. Candidate genes underlying strong selection signatures including coloration (ASIP, KITLG, HTT, GNA11, and OSTM1), body size (TBX15, DGCR8, CDC25A, and RDH16), cashmere traits (LHX2, FGF9, and WNT2), and hypoxia adaptation (CDK2, SOCS2, NOXA1, and ENPEP) were identified. We also identified candidate functional SNPs within selected genes that may be important for each trait. Our results demonstrated the potential of using sequence data in identifying genomic regions that are responsible for agriculturally significant phenotypes in goats, which in turn can be used in the selection of goat breeds for environmental adaptation and domestication.
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
authors.forename: Xiaolong
authors.initials: X
authors.lastname: Wang
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Liu
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
authors.forename: Guangxian
authors.initials: G
authors.lastname: Zhou
authors.affiliation: College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, 625000, China.
authors.forename: Jiazhong
authors.initials: J
authors.lastname: Guo
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.|College of Life Science, Yulin University, Yulin, 719000, China.
authors.forename: Hailong
authors.initials: H
authors.lastname: Yan
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
authors.forename: Yiyuan
authors.initials: Y
authors.lastname: Niu
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.affiliation: Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou 730050, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Yuan
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.|College of Pharmacy, Yancheng Teachers University, Yancheng, 224051, China.
authors.forename: Rongqing
authors.initials: R
authors.lastname: Geng
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
authors.forename: Xianyong
authors.initials: X
authors.lastname: Lan
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: An
authors.affiliation: Guizhou University, Guiyang, 550000, China.
authors.forename: Xingui
authors.initials: X
authors.lastname: Tian
authors.affiliation: Guangzhou Gene de-novo Biotechnology Co. Ltd. Guangzhou, 510000, China.
authors.forename: Huangkai
authors.initials: H
authors.lastname: Zhou
authors.affiliation: Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742,USA.
authors.forename: Jiuzhou
authors.initials: J
authors.lastname: Song
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
authors.forename: Yulin
authors.initials: Y
authors.lastname: Chen
mesh_terms: D000818:Animals; D016678:Genome; D023281:Genomics; D006041:Goats / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA