Abstract
Comparative population genomics analysis is an effective approach to identify selection signatures in farm animals. In this study, we systematically investigated the selection signatures in six phenotypically diverse goat breeds using SNPs obtained from pooled whole-genome resequencing data. More than 95.5% of 446–642 million clean reads were mapped to the latest reference goat genome, which generated a sequencing depth ranging from 22.30 to 31.75-fold for each breed. A total of 5,802,307, 6,794,020, 7,562,312, 5,325,119, 8,764,136, and 9,488,057 putative SNPs were detected in Boer, Meigu, Jintang Black, Nanjiang Yellow, Tibetan, and Tibetan cashmere goats, respectively. Based on the genome-wide FST and expected heterozygosity scores along 100-kb sliding windows, 68, 89, 44, 44, 19, and 35 outlier windows were deemed as the selection signatures in the six goat breeds. After genome annotation, several genes within the selection signals were found to be possibly associated with important traits in goats, such as coat color (IRF4, EXOC2, RALY, EIF2S2, and KITLG), high-altitude adaptation (EPAS1), growth (LDB2), and reproduction traits (KHDRBS2). In summary, we provide an improved understanding of the genetic diversity and the genomic footprints under positive selection or the adaptations to the local environments in the domestic goat genome.
Highlights
Comparative population genomics analysis is an effective approach to identify selection signatures in farm animals
Abundant genetic variation detected in the six goat breeds
Genome sequencing yielded a total of 478 Gb of paired-end raw reads with a length of 150-bp from six goat breeds, and approximately 446–642 million clean reads were obtained per breed after quality control (Supplementary Table S1)
Summary
Comparative population genomics analysis is an effective approach to identify selection signatures in farm animals. During the past several years, many studies on the genome-wide identification of selection signals have emerged in pigs[6], cattle[7,8,9], sheep[10,11,12], and goats[11,13], based on SNP chips. These results have demonstrated how positive selection acting on complex and Mendelian traits has changed the genetic composition of domestic animals. The density of this chip was too limited to obtain more precise selection mapping
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