Validation of the 50k Illumina goat SNP chip in the South African Angora goat

Abstract

Tools for the genomic evaluation of goats have generally lagged behind those for other species. However, the recent availability of the goat SNP50 consortium bead chip has marked a positive change for this small ruminant species. Polymorphic loci can differ greatly between breeds of the same species. Exclusion of fibre-producing breeds, such as the Angora goat, during the development of this genotyping array necessitates the validation of SNPs included on the chip to allow for genomic applications that would accelerate genetic progress in mohair yield and quality. Forty eight unrelated Angora goats, displaying phenotypic variation in two important price-determining traits, namely fibre diameter and fleece weight, were genotyped with the goat SNP50 consortium bead chip. Results revealed that 46 983 SNP (88.1%) of the 53 347 called SNPs were polymorphic (MAF>0.05). After quality control, 3 960 SNP were filtered from further analysis for violating Hardy-Weinberg and call-rate parameter thresholds, leaving 43 759 (82%) of the 53 347 SNPs to be validated for downstream analysis. Observed and expected heterozygosity values of 0.365 and 0.370, respectively, were obtained for polymorphic SNPs. A total of 30 357 SNPs in linkage disequilibrium (LD) were removed to obtain a set of independent markers, resulting in a final SNP density of 1 SNP/ ~226 kb. Results indicate that the goat SNP50 bead chip was informative in the Angora goats that were studied, and should be useful in examining the underlying genetic variation

Keywords: Call rate, Hardy-Weinberg equilibrium, linkage disequilibrium, minor allele frequency