Population structure and genome-wide association study of body conformation traits of two native goat breeds in China

Body conformation traits have a direct impact on carcass performance in the meat goat industry. This study explored the population genetics of two Chinese goat breeds and identified the genomic variates contributing to their body conformation traits. The Guizhou black goat (GBG, n=104) and Hezhang black goat (HBG, n=100) were genotyped by whole-genome sequencing and phenotyped by measuring their body height (BH), body length (BL), chest depth (CD), chest width (CW), chest girth (CG), rump width (RW), rump height (RH), and cannon circumference (CC). The relatedness analysis showed that these goats were low genetically kinship-related, with the GBG and HBG being relatively independent but with some genetic introgression. The lambda values showed that the GWAS model was reliable, and a total of 33, 1, 6, 2, 5, 10, 21, and 13 SNPs were identified as significantly correlated (P<8.33e-8) with BH, BL, CD, CW, CG, RW, RH, and CC, respectively. Interestingly, the GWAS for BH and RH identified the greatest number of significant SNPs, with a large proportion of these SNPs overlapping and being mainly located in four regions: chr13_63286230-69784740 (10 SNPs), chr14_60354209-60376549 (six SNPs), and chr15_65605417-73873841 (five SNPs), and chr23_42819635-43332716 (nine SNPs). Individuals carrying more of these SNPs had higher BH and RH values. After annotation for all the significant SNPs, 103 genes located in a ±100 Kb region were identified, where the most significantly enriched KEGG pathway was "Olfactory transduction", and the most significantly enriched GO terms were "cellular process" and "molecular transducer activity". This study investigated the population genetics of two prominent Chinese goat breeds and identified several SNPs that are significantly associated with body conformation traits. These findings provide biological insights on enhancing growth performance and have great potential for practical application in the genomic selection of meat goats.