Genome characteristics and identification of reproduction-related genes in Southwest meat goats

Researching the genetic structure, genetic diversity, and the identification of reproduction-related genes in local goat populations is essential for developing effective conservation strategies and enhancing breeding efficiency. This study detected a total of 22,117,964 single nucleotide polymorphism sites and 5,563,682 insertion/deletion polymorphism sites across 136 samples from seven varieties. Population structure analysis divided the seven goat breeds into three primary genetic clades: Bor constituted an independent cluster; DZ and JC shared a common clade; while QB, MG, CZ, and YS formed a third distinct genetic group. Phylogenetic analysis indicated that indigenous meat goat breeds in Southwest China shared close genetic relationships and exhibited inbreeding. Gene flow results further confirmed the existence of genetic exchange among these southwestern meat goat populations. Genetic diversity analysis indicated that these local southwestern meat goat breeds possessed higher genetic diversity compared to Bor, suggesting potential heterozygote selection advantages. Genomics selection scans detected signatures of positive selection in genes regulating ovarian steroid biosynthesis (3BHSD, LOC102181972, PPP3CA), ovum development (EREG, MLH1), and meiotic division in oocytes (CDK2). These discoveries have significant implications for enhancing thegenetic diversity of these local breeds, facilitating conservation efforts, and improving the adaptability of goats in Southwest China. Additionally, this research provides a foundation for investigating genomic characteristics in other important local goat breeds.