Department of Animal Sciences, Washington State University, Pullman WA 99164; Division of Animal Sciences, University of Missouri, Columbia MO 65211; Department of Animal and Veterinary Sciences, University of Idaho, Caldwell ID 83605
Title:
Genome-Wide association analysis and gene set enrichment analysis-SNP identify genes associated with 305-day milk yield in Holstein dairy cows
Milk production traits, such as 305-day milk yield (305MY), have been under direct selection to improve production in dairy cows. Over the past 50 years, the average milk yield has nearly doubled, and over 56% of the increase is attributable to genetic improvement. As such, additional improvements in milk yield are still possible as new loci are identified. The objectives of this study were to detect SNPs and gene sets associated with 305MY in order to identify new candidate genes contributing to variation in milk production. A population of 781 primiparous Holstein cows from six central Washington dairies with records of 305MY and energy corrected milk (ECM) were used to perform a genome-wide association analysis (GWAA) using the Illumina BovineHD BeadChip (777,962 SNPs) to identify QTL associated with 305MY (P < 1.0 × 10-5). A gene set enrichment analysis with SNP data (GSEA-SNP) was performed to identify gene sets (normalized enrichment score (NES) > 3.0) and leading edge genes (LEGs) influencing 305MY. The GWAA identified 3 QTL comprised of 34 SNPs and 30 positional candidate genes. In the GSEA-SNP, 5 gene sets with 59 unique and 47 shared LEGs contributed to 305MY. Identification of QTL and LEGs associated with 305MY can provide additional targets for genomic selection to continue to improve 305MY in dairy cattle.