Genetic and Genomic Estimation for Somatic Cell Score in Relation with Milk Production Traits of Russian Holstein Dairy Cattle

Monitoring of udder health status is an important element in herd management and selection success for complex fitness traits. Identification of metabolic pathways and QTL responsible for the synthesis of amino acids and fatty acids in milk allows identification of missense mutations that are also associated with high fat, protein content and somatic cell count. The aim of our research was to evaluate genetic correlations between milk production traits and somatic cell score in relation to assessing crucial SNPs. The calculation of variance and covariance components was performed by REML. Breeding value estimates for average daily milk yield (MY), fat (FP) and protein percentage (PP), fat (FY) and protein yield (PY), somatic cell count (SCC) and somatic cell score (SCS) were based on multiple-trait mixed model using BLUPF90 family programs. The genomic relationship matrix was calculated by GBLUP approach. GWAS analysis was carried out using Plink 1.07. The total number of genotyped Holstein bulls (Illumina Bovine SNP50) with DGV values was 466, from which 247 had 8935 daughters’ records. Genomic values were used for GWAS as pseudo phenotype data. Genetic parameters for milk production traits were calculated based on records of 845 sires with 21540 daughters. Heritability coefficients were 0.152, 0.213, 0.204, 0.101, 0.127, 0.050 and 0.055 for MY, FP, PP, FY, PY, SCC and SCS, respectively. Genetic correlations between SCS and MY, FP, PP were -0.059, 0.024 and 0.197, respectively. GWAS analysis performed for FP showed the strong association of SNPs localized on BTA14 while the highest value of the additive variability was observed for DGAT1 mutation (ARS-BFGL-NGS-4939, P=1.1E×10^-11, R²=9.5%). In total, we identified 52 SNPs associated with SCS at P-value more than 1.24×10^-6. The coefficient of determination ranged from 5.9 to 9.2%. The greatest number of SNPs were found on BTA1, 4, 5, 8 and 17. Some of them were localized in the following key genes: rs110754403 (STXBP6, P=2.5E×10^-11), rs43072965 (KCNMB4, PTPRB, TRNAC-GCA, P=2.3E×10^-9), rs42600512 and rs42600489 (CNOT2, P=3.0E×10^-9), rs29019947 (117.6-117.9Mb, MED12L, P2RY12, P2RY13, P2RY14, IGSF10, LOC104971001, GPR87, GPR171, P=5.3E×10^-8...7.4E×10^-9), rs29020595 (CALD1, P=1.2E×10^-7). Our findings will be the basis for the development of the genomic evaluation concept for udder health and milk quality traits for the Russian Holstein and Black-and-White cattle population. Supported by the Russian Scientific Foundation, project number 15-16-00020.