Genome-wide association study for dairy traits in Slovenian Brown Swiss breed.

Genome-wide association studies (GWAS) based on thousands of single nucleotide polymorphisms (SNPs) allows exploring genes associated with economically important traits. The objective of this study was to perform GWAS in small population of genotyped bulls of Slovenian Brown Swiss (BSW) breed to identify SNP markers associated with dairy traits: milk yield (MY), fat yield (FY), and protein yield (PY). The daughter yield deviations of 182 progeny tested bulls were used as phenotypes. For each bull, genotypes were scored for 34,450 SNPs across the whole genome. Single SNP analysis was performed to detect significant associations among SNPs and dairy traits across the genome. Two models were considered: 1) linear regression model considering one marker at a time, and 2) linear regression model with admixture components for accounting population stratification. The Bonferroni correction resulted in 52 significant SNPs using model 1). Correction for population stratification based on selected criteria was shown to have great impact on the analysis and then no significant associations among SNPs and dairy traits have been detected. Therefore, the results were sensitive to population stratification and together with the small data set did not give much power to accurately estimate associations. Further improvements should be made on the enlargement of number of genotyped bulls in order to detect association signals and the identification of genes associated with dairy traits in Slovenian BSW breed.