A large-scale genome-wide association study in U.S. Holstein cattle

Authors: JIANG, JICAI - University Of Maryland; MA, LI - University Of Maryland; PRAKAPENKA, DZIANIS - University Of Minnesota; Vanraden, Paul; Cole, John; DA, YANG - University Of Minnesota

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/15/2019
Publication Date: 5/14/2019
Citation: Jiang, J., Ma, L., Prakapenka, D., Van Raden, P.M., Cole, J.B., Da, Y. 2019. A large-scale genome-wide association study in U.S. Holstein cattle. Frontiers in Genetics. 10:412. https://doi.org/10.3389/fgene.2019.00412.
DOI: https://doi.org/10.3389/fgene.2019.00412

Interpretive Summary: Genome-wide association studies help identify genomic regions that may control various traits of economic importance in dairy cattle by associating differences in an individual’s’ DNA with differences in animal performance. This study used the large U.S. Holstein population, which includes 294,079 genotyped cows, to study nine health and fitness traits. The results validated some genomic regions with large effects identified in previous research, and identified new regions of the genome with effects on cow production and fitness. The new regions will be studied in follow-up research to see if the specific DNA changes that cause differences in production can be identified.

Technical Abstract: Genome-wide association study (GWAS) is a powerful approach to identify genetic variants associated with phenotypes. However, only limited mutual confirmation from different studies was available. The rapid growth in single nucleotide polymorphism (SNP) data and phenotypic observations in U.S. Holstein cattle provides an opportunity of large-scale GWAS for the discovery of new effects and genetic mechanisms towards building consensus of genetic variants associated with dairy traits. The GWAS using 294,079 first lactation Holstein cows identified new additive and dominance effects on three yield traits, two percentage traits, three fertility traits and somatic cell score. This study revealed DGAT1 had extreme antagonistic pleiotropy effects on milk production with the largest positive effect on fat yield and the largest negative effects on milk and protein yields, and these extreme positive and negative effects were responsible for DGAT1’s most significant effects on milk production. The SLC4A4-GC-NPFFR2-ADAMTS3 region of Chr06 had multiple highly significant effects for milk production, fertility and somatic cell score. The GHR-PRLR region of Chr20 had significant effects on milk yield and the largest positive allelic effects on milk yield. A Chr05 region had significant effects on fat yield, and another Chr05 region had the most significant dominance effects on milk, fat and protein yields. COX17 of Chr01, GC of Chr06 and SIPA1L3 of Chr18 had the most significant effects on daughter pregnancy rate and cow conception rate, AFF1 of Chr06 had the most significant dominance effect on heifer conception rate, and SIPA1L3 and AFF1 had the most significant dominance effects on daughter pregnancy rate and cow conception rate. These fertility effects were primarily due to their negative allelic effects. For somatic cell score, GC of Chr06 and PRLR of Chr20 had the most significant additive effects, and CEP97 of Chr01 had the lowest somatic cell score. The large-scale GWAS identified new additive and dominance effects associated with dairy traits and new genetic mechanism of SNP effects, and provided a large-sample prospective of dairy SNP effects. Results from this large-scale GWAS are a significant contribution towards building consensus on genetic variants associated with dairy phenotypes.