Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle

Mohammed K. Abo-Ismail, Luiz F. Brito, Stephen P. Miller, Mehdi Sargolzaei, Daniela A. Grossi, Steve S. Moore, Graham Plastow, Paul Stothard, Shadi Nayeri, Flavio S. Schenkel
2017 Genetics Selection Evolution  
Our aim was to identify genomic regions via genome-wide association studies (GWAS) to improve the predictability of genetic merit in Holsteins for 10 calving and 28 body conformation traits. Animals were genotyped using the Illumina Bovine 50 K BeadChip and imputed to the Illumina BovineHD BeadChip (HD). GWAS were performed on 601,717 real and imputed single nucleotide polymorphism (SNP) genotypes using a single-SNP mixed linear model on 4841 Holstein bulls with breeding value predictions and
more » ... e predictions and followed by gene identification and in silico functional analyses. The association results were further validated using five scenarios with different numbers of SNPs. Results: Seven hundred and eighty-two SNPs were significantly associated with calving performance at a genomewise false discovery rate (FDR) of 5%. Most of these significant SNPs were on chromosomes 18 (71.9%), 17 (7.4%), 5 (6.8%) and 7 (2.4%) and mapped to 675 genes, among which 142 included at least one significant SNP and 532 were nearby one (100 kbp). For body conformation traits, 607 SNPs were significant at a genome-wise FDR of 5% and most of them were located on chromosomes 5
doi:10.1186/s12711-017-0356-8 pmid:29115939 fatcat:wkxikyh3zbairlf6zqr3foqvti