Prioritization of candidate genomic regions for milking speed in Holstein cattle using international evaluations.

Abstract

Milking speed (MSPD) is an economically important trait in dairy cattle affecting labor efficiency, animal welfare and milking parlor productivity. This complex quantitative trait has been investigated to characterize its genetic basis and support genomic selection. Previous genome-wide association studies (GWAS) have reported genomic regions potentially related to MSPD; however, results vary considerably among studies and often provide limited functional interpretation. This study aimed to prioritize candidate genomic regions for MSPD based on the ranking of estimated SNP effects from the InterGenomics Holstein genomic evaluation coordinated by Interbull. The data set included genotypic and estimated breeding value information from 14,668 Holstein bulls, including 486 from Slovenia. Bioinformatic analyses were performed using Variant Effect Predictor, Animal QTLdb, STRING, KEGG and Haploview. The highest-ranked SNPs were selected for downstream genomic characterization and functional analyses. The 30 highest-ranked SNPs were located within protein-coding or long non-coding RNA genes or in intergenic regions. Thirteen SNPs had previously been reported for MSPD, including variants within ANKFN1, TRIM25, NDUFA9, YPEL2 and PPP2R2C, whereas 17 SNPs mapped to regions not previously linked to MSPD, including MAPRE2, MSI2 and ANGPT4. Three SNPs located within or near ANKFN1 were among the 4 highest-ranked variants. The highest number of prioritized SNPs was observed on BTA19, BTA13 and BTA6. Nine of the highest-ranked SNPs overlapped with production, fertility and conformation traits, potentially indicating pleiotropy. These findings provide a prioritized set of candidate genomic regions for further investigation of the genetic basis of MSPD.