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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #347344
Research Project: Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals

Location: Animal Genomics and Improvement Laboratory

Title: Large-scale GWAS reveals reason for the DGAT1 significance and identifies new SNP effects in Holstein cattle

Author
item MA, LI - University Of Maryland
item JIANG, JICAI - University Of Maryland
item PRAKAPENKA, DZIANIS - University Of Minnesota
item Tooker, Melvin
item Vanraden, Paul
item Cole, John
item DA, YANG - University Of Minnesota

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 11/13/2017
Publication Date: 11/13/2017
Citation: Ma, L., Jiang, J., Prakapenka, D., Tooker, M.E., Van Raden, P.M., Cole, J.B., Da, Y. 2017. Large-scale GWAS reveals reason for the DGAT1 significance and identifies new SNP effects in Holstein cattle. Livestock High-Throughput Phenotyping and Big Data Analytics, Beltsville, MD. Nov. 13-14.

Interpretive Summary:

Technical Abstract: The U.S. dairy genomic database provides unprecedented large sample size to identify genetic variants associated with dairy traits and to estimate the size and direction of the genetic effects. The DGAT1 gene has been widely confirmed to have the most significant effects on fat, milk and protein yields but it was unclear why DGAT1 was so significant. We conducted a large-scale GWAS for seven traits using 294,079 first lactation Holstein cows with genotypic data of 60,671 SNPs. The results of the only DGAT1 SNP available in this study, rs109421300, revealed that the DGAT1 significance was due to the extreme antagonistic pleiotropy effects of the ‘G’ allele of rs109421300. Specifically, the DGAT1 significance was due to the extremely large positive effect for fat yield but was due to the extremely large negative effects of the ‘G’ allele for milk and protein yields. Genes with the most favorable alleles included C6 and the LY6E-ARC region for high milk yield, ADAMTSL1 for high protein yield, the ‘G’ allele of DGAT1 for fat yield, and CEP97 for low somatic cell score. Genes with the most unfavorable alleles included COX17 and SIPA1L3 for low daughter pregnancy rate and cow conception rate, AFF1 for low heifer conception rate, the GC-ADAMTS3 region for high somatic cell score, and the ‘G’ allele of DGAT1 for low milk and protein yields. The three fertility traits, daughter pregnancy rate, cow and heifer conception rates, lacked strikingly positive effects. The 24.06-27.13 Mb region of chromosome 5 had highly significant dominance effects on milk, fat and protein yields. Four genes of chromosome 23 had dominance effects on milk yield, DGAT1 had dominance effect on fat yield, and AFF1 had dominance effect on heifer conception rate.