A genome wide association study of body weight and reproduction traits in two South African sheep breeds

This study aimed to identify genomic regions of significance that are associated with body weight traits and reproduction traits in sheep by using estimated breeding values in a genome wide association study (GWAS). The following traits were investigated: body weight recorded at selection age of 14 months (BW), number of lambs born (NLB), number of lambs weaned (NLW) and total weight of lamb weaned (TWW). A total of 411 animal were genotyped using the Illumina® Ovine SNP50 BeadChip, and consisted of 152 Afrino, 129 Cradock Merino and 130 Grootfontein Merino sheep. Quality control (QC) were implemented using PLINK v1.07 where the parameters were set as 90% for individual call rate, 95% for SNP call rate, minor allele frequency of less than 2% and P <0.001 for Hardy-Weinberg equilibrium. Population parameters were calculated per dataset. The average MAF values estimated for the populations were 0.252, 0.372 and 0.372 for the Afrino, Cradock Merino and Grootfontein Merino, respectively. Inbreeding coefficients were estimated at - 0.025 (Afrino), - 0.025 (Cradock Merino) and 0.002 (Grootfontein Merino). The expected heterozygosity was 0.363 for the Afrino and 0.369 for both Merino populations. All three sheep populations had low inbreeding levels and moderate genetic variation. The population genetic substructure, ancestry proportion and genetic relatedness between the populations were investigated via principal component analysis (PCA) and admixture plots. These plots corresponded to the populations’ selection practises and breeding programs as well as to the geographical locations where the individuals were kept. The GWAS was applied to each dataset separately and per trait using the efficient mixed model association eXpedited (EMMAX) software and visualised by Manhattan plots. Nine suggestive SNPs were identified to be in possible association with the traits. Of these nine, seven SNP were identified to be in close proximity or linked to previously annotated genes. Seven genes were identified which were in association with growth and reproduction traits. The genes SIX6, C14orf13 and TRPS1 showed the most promise for body weight and growth traits. For reproduction and fertility traits the genes LIG1, CABP5, GRIK3 and HDAC9 warrants further investigation.