identified positive selection sweeps of three indigenous goat populations in Morocco 14, whereas Dong et al. By using whole-genome resequencing (WGS) data, Benjelloun et al. Array- or sequencing-based detection of signatures during the selection process has been described in cattle 4, 5, 6, chicken 7, pigs 8, 9, 10, sheep 11, 12, and recently in goats 13, 14, 15. The genome of goats, which have diverse production potentials and extensive adaptation to diverse environments, provides a unique opportunity for identifying signatures associated with selection. Since the Neolithic age, goats have played economically important roles by providing various products (e.g., fiber, milk, meat, and hide) to the human population.Īrtificial selection during domestication and production-oriented breeding has greatly shaped the level of genomic variability in goats. A variety of natural or artificial factors (e.g., environmental changes, human migration, and socioeconomic influences) have shaped the phenotypic diversity of goats, leading to 557 registered goat breeds worldwide (FAO) 3. The goat ( Capra hircus) is believed to be one of the first livestock species that underwent domestication approximately 10,000 years ago 1, 2, and therefore has been a witness to the historical progress of human civilization. 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. We also identified candidate functional SNPs within selected genes that may be important for each trait. 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. By combining two approaches, ZH p and 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. We discovered ~10 million single nucleotide polymorphisms (SNPs) for each breed. 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. 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.
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