ARS | Publication request: GENOME-WIDE ASSOCIATION ANALYSIS IDENTIFIES LOCI FOR PRODUCTIVE TRAITS IN JERSEY BREED

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 5, 2009
Publication Date: January 12, 2009
Citation: Silva, M.V., Van Raden, P.M., Van Tassell, C.P., Sonstegard, T.S., Matukumalli, L.K., Schroeder, S.G., Wiggans, G.R. 2009. GENOME-WIDE ASSOCIATION ANALYSIS IDENTIFIES LOCI FOR PRODUCTIVE TRAITS IN JERSEY BREED. Plant and Animal Genome Conference.

Technical Abstract: A major objective of genomic research in dairy cattle at present is to identify, map, and characterize individual quantitative trait loci (QTL) that affects production traits. A genome scan was conducted in the US Jersey population to identify QTL affecting milk, fat and protein production. Data used at this study were DHI records from the national database of the Animal Improvement Programs Laboratory, USDA (Beltsville, MD). DNA for genetic analysis has been acquired for 1,386 animals from the US Jersey population and May 2008 genetic evaluations for 1,244 animals were used for the whole-genome association. Genotyping was performed using Illumina’s BovineSNP50. For GWA analysis, any SNP with low call rate (<99%), departure from Hardy-Weinberg equilibrium (exact test p<0.01), and minor allele frequency below 5 percent, were excluded from the final analysis (28,403 markers retained). Empirical p-values were corrected for the genome-wide testing and maximization across genetic models, and a genome-wide significance level of 0.05 (two-sided) and Bonferroni corrected level of 0.01 were used. Five genetic models (codominant, dominant, recessive, overdominant and log-additive) were analyzed. For all traits, significant SNPs were found on many chromosomes, especially on chromosomes 1, 2, 6, 14, 19, 23 and 24. Most parts of the significant SNPs were located in similar positions on the chromosomes for milk, fat and protein production. Some of them localized within a single linkage disequilibrium (LD) block.