Abstract
An association analysis was carried out using raw (intensity, colour) SNP data from SNPs on the Illumina OvineSNP50 BeadChip that could not be genotyped, and growth and meat yield traits in sheep. Seventeen associations were detected and validated in independent datasets. The heritability of the significant SNP terms were on average (h2=0.38) moderately heritable, suggesting that they may represent heritable genetic units and could be targets for selection. Two SNPs were in copy number variant regions. Associations between these non-normal SNPs and traits remained significant after fitting SNPs used in genomic selection from a 1Mbp region around each non-normal SNP. This suggests that these associations are not currently well accounted for in genomic selection, and that including information from these “non-normal” SNPs could improve the accuracy of EBVs, contributing to genetic improvement of growth and meat yield traits in the NZ sheep industry.