Genome-Wide Association Analysis to Identify Loci for Milk Yield in Gyr Breed

Authors: SILVA, MARCOS - Embrapa; VERNEQUE, RUI - Embrapa; MACHADO, MARCO - Embrapa; PEIXOTA, MARIA - Embrapa; GUIMARAES, MARTA - Embrapa; ARBEX, WAGNER - Embrapa; GUEDES, ELIZANGELA - Embrapa; Van Tassell, Curtis - Curt; Sonstegard, Tad

Submitted to: Animal Genetics International Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 5/27/2010
Publication Date: 7/25/2010
Citation: Silva, M., Verneque, R.S., Machado, M.A., Peixota, M.G., Guimaraes, M.M., Arbex, W.A., Guedes, E., Van Tassell, C.P., Sonstegard, T.S. 2010. Genome-Wide Association Analysis to Identify Loci for Milk Yield in Gyr Breed. Animal Genetics International Conference Proceedings.

Interpretive Summary:

Technical Abstract: A genome scan was conducted to identify QTL affecting milk yield in a Brazilian Gyr population of progeny test bulls (N=319). Data used in this study was derived from traditional genetic evaluation records computed by the Embrapa Dairy Cattleand released in May/2009 (http://www.cnpgl.embrapa.br/nova/informacoes/melhoramento/Gir/artigos/classificacao_geral_2009.pdf/). Genotyping was performed using Illumina’s BovineSNP50 BeadChip with approximately 54,000 SNPs. For analysis, any SNP with low call rate (<90%), departure from Hardy-Weinberg equilibrium (exact test p<0.01), and minor allele frequency below 5 percent, were excluded from the final analysis (24,532 markers retained). The Bonferroni correction threshold was 0.01. ITSNBN software, which uses a linear model and pedigree information was used in order to detect associations. For all traits, significant SNP were found on BTA 3, 4, 5, 6, 10, 14, 23, and 25. Most significant SNP were localized to specific chromosomal regions and oftern within a single linkage disequilibrium block. Results suggest that marker solutions from genomic evaluations may be useful for identifying genomic regions that merit further study to identify causal mutations.