Whole-genome sequencing reveals selection signatures shaping the Dazu Black goat

Researchers have mapped the genomic landscape of the Dazu Black goat, an indigenous breed from Southwest China prized for its high prolificacy and exceptional environmental adaptability, using whole-genome resequencing of 151 individuals drawn from six goat breeds. The analysis, published in BMC Genomics, generated a catalogue of 13.09 million high-quality single nucleotide polymorphisms (SNPs) that the team used to dissect the breed’s population structure, diversity and evolutionary history.

The study set out with two main goals: to characterize the genetic diversity and population structure of the Dazu Black goat, whose specific genetic architecture had remained largely unexplored, and to build a robust SNP-based fingerprinting system that could support the identification and conservation of this valuable genetic resource.

Population structure analysis revealed distinct breed differentiation across the six breeds, with the Dazu Black goat placed in close phylogenetic proximity to the Chuannan Black goat and the Yudong Black goat populations.

To pinpoint regions shaped by selection, the researchers integrated two complementary genomic metrics, the fixation index (FST) and nucleotide diversity (θπ). Cross-referencing these signals identified 468 consensus candidate genes under positive selection in the Dazu Black goat.

Functional analysis showed that these candidate genes are significantly enriched in biological pathways governing prolificacy, immunity and energy metabolism. The authors suggest this enrichment aligns with the traits for which the breed is known, including its reproductive performance and adaptability, although the study identifies candidate genes rather than experimentally validating their effects.

The ROH analysis revealed a predominance of short homozygous segments and a relatively low ROH-based inbreeding coefficient, consistent with the observed moderate-to-high diversity and low differentiation across the evaluated populations.

As a practical outcome, the researchers developed a highly informative 344-SNP panel designed as a DNA fingerprinting tool with potential applications in authenticating Dazu Black goat animals.

The authors conclude that the study identifies key candidate genes associated with the superior reproductive and adaptive traits of the Dazu Black goat and establishes a 344-SNP fingerprinting system with potential applications in breed authentication and genetic conservation.

Subject of Research: Genomic signatures of selection and genetic diversity in the indigenous Dazu Black goat

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

Article References: Qin, G., Deng, Q., Xia, Z., Zhang, M., Zhang, T., Lu, C., Guo, J., Zhao, Z., Huang, Y., E, G., Zhao, Y., & Han, Y. (2026). Genomic signatures of selection in Dazu Black goat (Capra hircus) revealed by whole-genome resequencing. BMC Genomics. https://doi.org/10.1186/s12864-026-13501-4

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13501-4

Keywords: Dazu Black goat, whole-genome resequencing, selective sweeps, SNPs, genetic diversity, runs of homozygosity, FST, nucleotide diversity, DNA fingerprinting, goat conservation, prolificacy, BMC Genomics