Genome-wide association studies for milk traits in New Zealand dairy sheep

The New Zealand dairy sheep industry has grown markedly in the last decades. With better genetics and management, companies have been able to improve key production traits. This study aimed to identify single nucleotide polymorphisms (SNPs) associated with milk traits in dairy sheep. We performed genome-wide association (GWA) analyses for milk yield, fat and protein content using data from commercial farms. We used 54,698 milk yield records and 24,891 fat and protein records from 4,590 and 2,823 ewes, respectively. Phenotypes were collected between August 2018 and April 2021 across three locations in New Zealand. They were adjusted for flock, age, lactation, lambing date, weeks in milk and permanent environment. Animals were genotyped with commercial SNP chips with 13,759 markers available after quality control. GWA models included the genomic relationship matrix, three principal components and genomic inflation correction for the p-values. We found four genome-wide significant associations for milk yield. These variants were mapped to eight genes, PDZRN4 (intron), EDEM2, PROCR, MMP24 (intron), EIF6, FAM83C, UQCC1, and HDAC9 (intron). Of these, PDZRN4, HDAC9 and MMP24 were associated with milk traits in previous studies. No significant associations were found for fat and protein content. Genes shown here are promising candidate genes, requiring validation in independent samples.