Genome-wide association study of meat quality traits using whole-genome sequence data in a multi-breed sheep population

This is the first study showing GWAS results from whole-genome sequence (WGS) data in sheep. The objective of this study was to fine map previously identified QTL and detect new QTL for meat quality traits in a multi-breed sheep population using WGS data. The traits measured were carcass fat depth, intramuscular fat, post-weaning eye muscle depth, post-weaning body weight and SF5. Corrected phenotypes were available on 13,363 to 26,769 Australian sheep depending on the trait. The GWAS for all five traits for the 50K, HD, and WGS identified 18, 52 and 250 QTL regions, respectively based on a 5% FDR threshold. Together, the largest QTLs explained a substantial part of the additive genetic variance (between 10.6 - 14.3%). Previously identified QTL on chromosomes 6 and 18 were confirmed. Single breed analysis for Merino sheep only, showed a reduced significance of the large QTL, but in similar regions. We were able to identify candidate genes involved in meat quality using functional annotation. We conclude that the WGS data provided more and clearer evidence of QTL regions, potentially resulting in more predictive SNPs and more detailed functional analysis of genes underlying the QTL regions.