B. Li1, P.M. VanRaden1, D.J. Null1, J.R. O'Connell2 and J.B. Cole1*
1Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, MD 20705-2350
2University of Maryland School of Medicine, Baltimore, MD 21201
*Corresponding author
2020 J. Dairy Sci. (?)
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The goal of this study was to identify potential QTL for 27 production, fitness, and conformation traits of Guernsey cattle through genome-wide association (GWA) analyses, with extra emphasis on BTA19 where major QTL were observed for several traits. Animals’ de-regressed predicted transmitting abilities (PTA) from the December, 2018, official U.S. genomic evaluations were used as phenotypes. All of the Guernsey cattle included in the QTL analyses were predictor animals in the reference population, ranging from 1,077 to 1,685 animals for different traits. Single-trait GWA analyses were carried out by a mixed-model approach for all 27 traits using imputed high-density genotypes. A major QTL was detected on BTA19 influencing several milk production traits, conformation traits, and livability of Guernsey cattle, and the most significant SNP lie in the region of 26.2-28.3 Mb. The MYH10 (myosin heavy chain 10) gene residing within this region was found to be highly associated with milk production and body conformation traits of dairy cattle. After the initial GWA analyses, which suggested that many significant SNP are in linkage with one another, conditional analyses were used for fine-mapping. The top significant SNP on BTA19 were fixed as covariables in the model, one at a time, until no more significant SNP were detected on BTA19. After this fine-mapping approach was applied, only one significant SNP was detected on BTA19 for most traits, but multiple, independent significant SNP were found for protein yield, dairy form, and stature. In addition, the haplotype that hosts the major QTL on BTA19 was traced to a U.S. Guernsey born in 1954. The haplotype is common in the breed, indicating a long-term influence of this QTL on the U.S. Guernsey population.
Key Words: fine-mapping, Guernsey cattle, quantitative trait loci