Population structure and genome-wide association study of body conformation traits of two native goat breeds in China
Population structure and genome-wide association study of body conformation traits of two native goat breeds in China
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Objective: Body conformation traits directly impact carcass performance in the meat goat industry. This study explored the population genetics of two Chinese goat breeds and identified the genomic variants associated with their body conformation traits.Methods: The Guizhou black goat (GBG, n = 104) and Hezhang black goat (HBG, n = 100) underwent genotyping through whole-genome sequencing and phenotyping 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).Results: The relatedness analysis showed that these goats exhibited low genetic kinship-related, with the GBG and HBG being relatively independent, albeit with some genetic introgression present. The lambda values showed that the reliability of the genome-wide association studies (GWAS) model, identifying a total of 33, 1, 6, 2, 5, 10, 21, and 13 single nucleotide polymorphisms (SNPs) as significantly correlated (p<8.33e-8) with BH, BL, CD, CW, CG, RW, RH, and CC, respectively. The GWAS for BH and RH identified the greatest number of significant SNPs, with a substantial overlap among them, 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 with a greater number of these SNPs displayed elevated BH and RH values. Following the annotation of all significant SNPs, 102 genes within a ±100 Kb region were identified. The most significantly enriched KEGG pathway was “Olfactory transduction”, while the most significantly enriched GO terms included “cellular process” and “molecular transducer activity”.Conclusion: 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 offer biological insights into enhancing growth performance and hold significant potential for practical application in the genomic selection of meat goats.
Abstract
Objective: Body conformation traits directly impact carcass performance in the meat goat industry. This study explored the population genetics of two Chinese goat breeds and iden tified the genomic variants associated with their body conformation traits. Methods: The Guizhou black goat (GBG, n = 104) and Hezhang black goat (HBG, n = 100) underwent genotyping through whole-genome sequencing and phenotyping by mea suring 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). Results: The relatedness analysis showed that these goats exhibited low genetic kinship-re lated, with the GBG and HBG being relatively independent, albeit with some genetic intro gression present. The lambda values showed that the reliability of the genome-wide associ ation studies (GWAS) model, identifying a total of 33, 1, 6, 2, 5, 10, 21, and 13 single nucleotide polymorphisms (SNPs) as significantly correlated (p<8.33e-8) with BH, BL, CD, CW, CG, RW, RH, and CC, respectively. The GWAS for BH and RH identified the greatest number of significant SNPs, with a substantial overlap among them, mainly locat ed 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 with a greater number of these SNPs displayed elevated BH and RH values. Following the annotation of all significant SNPs, 102 genes within a ±100 Kb region were identified. The most significantly enriched KEGG pathway was “Olfactory transduc tion”, while the most significantly enriched GO terms included “cellular process” and “mo lecular transducer activity”. Conclusion: This study investigated the population genetics of two prominent Chinese goat breeds and identified several SNPs that are significantly associated with body confor mation traits. These findings offer biological insights into enhancing growth performance and hold significant potential for practical application in the genomic selection of meat goats.