Identification of Genomic Characteristics and Selective Signals in a Du’an Goat Flock

SIMPLE SUMMARY: Goat plays an irreplaceable role as domestic animals by providing milk, meat, and fiber. With the advancement in human civilization, over 500 goat breeds with various adaptive traits have been established. Whole-genome sequencing and subsequent analyses (including selective sweep analysis) are important tools to reveal the genetic basis underlying these adaptive traits. In this study, we investigated the sequenced genomes of 15 Du’an goats from one flock to identify the genomic characteristics and candidate genomic regions which might be involved in the adaptive traits. Selective sweep analysis revealed selected genes and/or pathways related to immune resistance, small body size, and heat tolerance. The identification of genomic characteristics and selective signals will not only help understand the demographic history and the genetic mechanism underlying adaptive traits but can provide novel insights into genetic diversity and development of breeding strategies in Du’an goats. ABSTRACT: The Du’an goat is one of the most important farm animals in the Guangxi Autonomous Region of China, but the genetic basis underlying its adaptive traits has still not been investigated. Firstly, in this study, the genomes of 15 Du’an goats from a breeding farm were sequenced (mean depth: 9.50X) to analyze the patterns of genetic variation. A comparable diversity (17.3 million single nucleotide polymorphisms and 2.1 million indels) was observed to be associated with a lower runs of homozygosity-based inbreeding coefficient and smaller effective population size in comparison with other breeds. From selective sweep and gene set enrichment analyses, we revealed selective signals related to adaptive traits, including immune resistance (serpin cluster, INFGR1, TLR2, and immune-related pathways), body size (HMGA2, LCOR, ESR1, and cancer-related pathways) and heat tolerance (MTOR, ABCG2, PDE10A, and purine metabolism pathway). Our findings uncovered the unique diversity at the genomic level and will provide the opportunities for improvement of productivity in the Du’an goat.