Genetic Diversity and Selection Signatures in Jianchang Black Goats Revealed by Whole-Genome Sequencing Data

SIMPLE SUMMARY: Jianchang Black goats are one of the indigenous black goat breeds in China. They are known for their crude feed tolerance but have a low growth rate and small body size. However, little is known about the genetic composition of Jianchang Black goats. The purpose of this study was to systematically examine the genetic composition of this breed by conducting multiple population genetic analyses. Our results revealed that Jintang Black and Yunshang Black goats showed a close genetic relationship with a non-negligible amount of gene flows but were genetically distant from Jianchang Black goats. Jianchang Black goats generally showed moderate inbreeding levels. Importantly, we identified several putatively selected genes that may be potentially related to immunity, behavior, and reproduction in this breed. The current study provides valuable references and genomic resources for the future breeding of Jianchang Black goats. ABSTRACT: Understanding the genetic composition of indigenous goats is essential to promote the scientific conservation and sustainable utilization of these breeds. The Jianchang Black (JC) goat, a Chinese native breed, is solid black and exhibits crude feed tolerance, but is characterized by a low growth rate and small body size. Based on the whole-genome sequencing data for 30 JC, 41 Jintang Black (JT), and 40 Yunshang Black (YS) goats, and 21 Bezoar ibexes, here, we investigated the genetic composition of JC goats by conducting analyses of the population structure, runs of homozygosity (ROH), genomic inbreeding, and selection signature. Our results revealed that JT and YS showed a close genetic relationship with a non-negligible amount of gene flows but were genetically distant from JC, apart from Bezoars. An average of 2039 ROHs were present in the autosomal genome per individual. The ROH-based inbreeding estimates in JC goats generally showed moderate values ranging from 0.134 to 0.264, mainly due to rapid declines in the effective population size during recent generations. The annotated genes (e.g., IL2, IL7, and KIT) overlapping with ROH islands were significantly enriched in immune-related biological processes. Further, we found 61 genes (e.g., STIM1, MYO9A, and KHDRBS2) under positive selection in JC goats via three complementary approaches, which may underly genetic adaptations to local environmental conditions. Our findings provided references for the conservation and sustainable utilization of JC goats.