Genome-wide association study identifies candidate genes affecting major traits of Ziwuling black goat

Ziwuling black goat (ZBG) is the main breed of indigenous goat for meat, wool, and skin in northwest china. However, the population has faced a sharp decline in the past few decades, mainly due to the declining efficiency of goat farming, which has led to the reluctance of farmers to raise goats. Litter size (LS), horn or no horn (HN), wool color (WC), and body conformation (BC) traits are the four main economic indicators of goat culture, which have the potential to increase population growth rate. The aim of the study was to identify potential genomic regions associated with body conformation traits of ZBG using genome-wide association studies (GWAS), and to identify molecular markers that influence LS, HN, WC, and BC traits of goats for the improvement of genetic resources of goats. In the study, we used the Illumina sequencing platform to re-sequence the genomes of 318 ZBG (12 males and 306 females) belonging to natural populations in 4 different regions, including LS, HN, WC, body height (BH), body weight (BW), body diagonal length (BL), and chest circumference (CC). The GWAS were conducted to identify candidate genes with different phenotypes which laid a foundation for further studies on the biological functions of these genes. A total of 41 single nucleotide polymorphisms (SNPs) and 89 candidate genes were obtained in 7 phenotypes of goats. Among them, 5 SNPs and 18 genes were significantly associated with the LS traits in goats, and these loci were located on 2 chromosomes. There are 5 SNPs and 10 genes significantly associated with the HN traits, and these loci are located on 5 chromosomes. There were 18 SNPs and 31 genes significantly associated with the WC traits, and these loci were located on 16 chromosomes. There are 6 SNPs and 13 genes significantly associated with the BH traits, and these loci are located on 6 chromosomes. There are 2 SNPs and 7 genes were significantly associated with the BL traits, and these loci were located on 2 chromosomes. There are 2 SNPs and 2 genes significantly associated with the BW traits, and these loci are located on 2 chromosomes. There are 3 SNPs and 8 genes were significantly associated with the CC traits, and these loci were located on 3 chromosomes. We investigated the molecular genetic mechanism of LS, HN, WC, and BC traits of ZBG by analyzing its genome data. The study identified a series of SNPs and candidate genes associated with growth and reproductive traits, which helped accelerate the breeding process of goat breeds.