Work

Genomic signatures of selection in Dazu Black goat (Capra hircus) revealed by whole-genome resequencing

Year: 2026

Type: article

Abstract: The Dazu Black goat ( DZ ), an indigenous breed in Southwest China, is renowned for its high prolificacy and exceptional environmental adaptability. However, its specific genetic architecture and the genomic basis of its unique traits remain largely unexplored. This study aimed to characterize the genetic diversity and population structure of DZ and develop a robust single nucleotide polymorphism (SNP)-based fingerprinting system to support the identification and conservation of this valuable genetic resource. We conducted whole-genome resequencing of 151 individuals from 6 goat breeds. Utilizing 13.09 million high-quality SNPs, we systematically characterized the population structure, revealing distinct breed differentiation and placing DZ in close phylogenetic proximity to Chuannan Black goat ( CN ) and Yudong Black goat ( YD ) populations. The evaluated populations exhibited moderate-to-high genetic diversity with low overall differentiation. By integrating fixation index ( F ST ) and nucleotide diversity ( θπ ) metrics, we identified 468 consensus candidate genes under positive selection in DZ. These genes are significantly enriched in biological pathways governing prolificacy, immunity, and energy metabolism. Furthermore, runs of homozygosity ( ROH ) profiling revealed a predominance of short homozygous segments and a relatively low ROH-based inbreeding coefficient. To facilitate genetic resource management, we developed a highly informative, 344-SNP panel as a DNA fingerprinting panel with potential applications in DZ authentication. Our study identifies key candidate genes associated with superior reproductive and adaptive traits of the Dazu Black goat . Furthermore, we established a 344-SNP fingerprinting system with potential applications in breed authentication and genetic conservation. These findings contribute valuable insights into the sustainable utilization of indigenous goat genetic resources.

Source: BMC Genomics

DOI: 10.1186/s12864-026-13501-4