Genome Wide Analysis for Milk, Fat and Protein Yield, and Milking Speedin Turkish Holstein Dairy Cattle

Abstract

Abstract Genome wide association studies (GWAS), for testing relations between genetic variants with phenotypic differences in a trait, have been comprehensively used in dairy cattle. The main purpose of this study was to determine single nucleotide polymorphism (SNP) variants associated with milk traits in the Turkish Holstein dairy cattle population. Genotypic data from 79 dairy herds and 17 166 cows calved between 2012 and 2019 were obtained from the Cattle Breeders' Association of Turkey (CBAT) and used in GWAS for first lactation milk, fat and protein yield and milking speed. The phenotypes were adjusted for known environmental factors before analysis. The cows were genotyped with Affymetrix Axiom Bovine 54K SNP Chip and the analyses were carried out in R statistical language. After conducting quality control, the data from 15 288 cows with 31 944 SNPs were used in the analysis. In the study, a total of seven SNPs were found, two of them were found to be effective on milk yield (rs109146371, rs109350371) on the BTA14, one was associated with protein yield (rs41718954) on the BTA14, one was associated with fat yield (rs10451141) on the BTA18 and three were associated with milking speed (rs29009916, rs109459144, rs42647772) on the BTA2, BTA11 and BTA12, respectively. Four of them (rs110451141 for fat yield, and rs29009916, rs109459144, rs42647772 for milking speed) were identified for the first time. These findings will be valuable in designing an effective genomic selection program for Holstein dairy cattle populations.