Genome-Wide Association Study for Milk Somatic Cell Score in Holstein Friesian Cows in Slovenia

Mastitis is a serious challenge for the dairy industry, leading to economic losses and affecting milk quality. The aim of this study is to identify genetic factors associated with mastitis resistance by conducting a genome-wide association study (GWAS) for the somatic cell score (SCS). Phenotypic records of 350 Holstein Friesian cows were obtained from the Slovenian Cattle Recording Scheme Database and consisted of around 1500 lactation data from 2012 to 2023 collected on a single farm in Slovenia. Corresponding genotypic data were also retrieved from the same database and genotyped using the Illumina BovineSNP50 BeadChip (Illumina, Inc., San Diego, CA, USA). For the association study, three SCS parameters were considered, including lactation mean somatic cell score (LM_SCS), maximum SCS value (SCSMAX), and top three mean value of SCS (TOP3). After performing a GWAS using FarmCPU and BLINK models, five significant SNPs associated with the TOP3 trait were found on BTA 14, 15, 22, and 29. The identified SNP markers were closely linked to six known candidate genes (<i>DNASE1L3</i>, <i>SLC36A4</i>, <i>ARMC1</i>, <i>PDE7A</i>, <i>MMP13</i>, CD44). These results indicate potential genetic markers associated with SCS in the Slovenian Holstein Friesian population.