Carcass Quality Profiles and Associated Genomic Regions of South African Goat Populations Investigated Using Goat SNP50K Genotypes.

Carcass quality includes a battery of essential economic meat traits that play a significant role in influencing farmer breed preferences. A preliminary study was undertaken to investigate the carcass quality and the associated genomic regions in a small nucleus of animals that are representative of South African goat genetic resources. Samples of the South African Boer ( n = 14), Northern Cape Speckled ( n = 14), Eastern Cape Xhosa Lob ear ( n = 12), Nguni/Mbuzi ( n = 13), and Village ( n = 20) were genotyped using the Illumina goat SNP50K and were phenotyped for carcass quality traits. SA Boer goats had heavier warm and cold carcass weights (17.2 ± 2.3 kg and 16.3 ± 2.3 kg). Pella village goats raised under an intensive system had significantly ( p < 0.05) heavier warm and cold carcass weights (9.9 ± 1.1 kg and 9.2 ± 1.2 kg) compared to the village goats that are raised extensively (9.1 ± 2.0 kg and 8.4 ± 1.9). A total of 40 SNPs located on chromosomes 6, 10, 12, 13, 19, and 21 were significantly associated with carcass traits at (-log10 [ p < 0.05]). Candidate genes that were associated with carcass characteristics ( GADD45G , IGF2R , GAS1 , VAV3 , CAPN8 , CAPN7 , CAPN2 , GHSR , COLQ , MRAS , and POU1F1 ) were also observed. Results from this study will inform larger future studies that will ultimately find use in breed improvement programs.