Genome-wide association studies reveal novel loci associated with carcass and body measures in goats ( Capra hircus )

Elucidating the genetic architecture of local goat populations is crucial for improving breeding strategies and conservation efforts. In southwestern China, there are numerous local goat resources, featuring rich phenotypic and genetic variations. Nevertheless, in-depth research on their production performance is scarce. Therefore, in this study, whole-genome 7× resequencing was performed on 776 individuals of six goat breeds (Dazu Black Goat, Yudong Black Goat, Banjiao Goat, Hechuan White Goat, Chuandong White Goat, and Youzhou Black Goat) in Chongqing to deeply investigate their population structure, genetic relationships, and heritability, and to identify significant genes related to growth traits and carcass traits. The mapping of significant genes for growth and carcass traits identified novel genetic loci, including a significant association at position 63,248,396 within ASIP on chromosome 13, which was linked to both traits, indicating a potential pleiotropic effect. Additional candidate genes for growth traits included CXCL14, PTGFR , and DPYD (body weight); CCSER1, HMCN1 , and MYOM1 (body length); MALRD1 and ASIP (withers height); and MEIS2 and NLRC5 (chest circumference). For carcass traits, key candidate genes included ASIP, ATP5G1, COX3 and BCAR3 . Functional enrichment analysis highlighted the calcium signaling pathway, glycan biosynthesis, and cytokine receptor interactions as key biological pathways influencing these traits. These findings provide novel insights into the genetic mechanisms underlying economically important traits in Chongqing local goats. The identification of ASIP as a pleiotropic gene, along with other newly discovered loci, offers valuable targets for genetic improvement and selective breeding programs, enhancing the productivity and sustainability of local goat populations.