Abstract
BackgroundOur 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 followed by gene identification and in silico functional analyses. The association results were further validated using five scenarios with different numbers of SNPs.ResultsSeven hundred and eighty-two SNPs were significantly associated with calving performance at a genome-wise 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 (30%), 18 (27%), 20 (13%), 6 (6%), 7 (5%), 14 (5%) and 13 (3%). SNP enrichment functional analyses for calving traits at a FDR of 1% suggested potential biological processes including musculoskeletal movement, meiotic cell cycle, oocyte maturation and skeletal muscle contraction. Furthermore, pathway analyses suggested potential pathways associated with calving performance traits including tight junction, oxytocin signaling, and MAPK signaling (P < 0.10). The prediction ability of the 1206 significant SNPs was between 78 and 83% of the prediction ability of the BovineSNP50 SNPs for calving performance traits and between 35 and 79% for body conformation traits.ConclusionsVarious SNPs that are significantly associated with calving performance are located within or nearby genes with potential roles in tight junction, oxytocin signaling, and MAPK signaling. Combining the significant SNPs or SNPs within or nearby gene(s) from the HD panel with the BovineSNP50 panel yielded a marginal increase in the accuracy of prediction of genomic estimated breeding values for all traits compared to the use of the BovineSNP50 panel alone.
Highlights
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
The objectives of our study were to identify genomic regions associated with 10 calving performance and 28 body conformation traits in Holstein cattle, to retrieve information from associated regions to increase the understanding of the underlying biology of these traits, and to test the predictive ability of these regions in young bulls
[46, 47] and would probably have cryptic relationships that are not described by the available pedigree
Summary
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. The Illumina Bovine SNP50 SNP chip (50 K; Illumina Inc., San Diego, USA) [19] has been used to identify significant regions that are associated with calving [20] and conformation traits [21]. Over the last four years, higher-density SNP chip panels have been developed, including the Illumina BovineHD BeadChip (HD; Illumina Inc., San Diego, USA) and, many animals have been sequenced [22]. These HD panels have not had a significant impact on genetic improvement programs, with very minor increases in prediction accuracies over the 50 K panel, either within or across breeds [23, 24]. HD panels can be used to improve the detection of regions that harbor causal mutations and, in which, genes of interest and new SNPs can be identified
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