Confirmation and fine‐mapping of clinical mastitis and somatic cell score QTL in N ordic H olstein cattle

Summary A genome‐wide association study of 2098 progeny‐tested N ordic H olstein bulls genotyped for 36 387 SNP s on 29 autosomes was conducted to confirm and fine‐map quantitative trait loci ( QTL ) for mastitis traits identified earlier using linkage analysis with sparse microsatellite markers in the same population. We used linear mixed model analysis where a polygenic genetic effect was fitted as a random effect and single SNP s were successively included as fixed effects in the model. We detected 143 SNP ‐by‐trait significant associations ( P  < 0.0001) on 20 chromosomes affecting mastitis‐related traits. Among them, 21 SNP ‐by‐trait combinations exceeded the genome‐wide significant threshold. For 12 chromosomes, both the present association study and the previous linkage study detected QTL , and of these, six were in the same chromosomal locations. Strong associations of SNP s with mastitis traits were observed on bovine autosomes 6, 13, 14 and 20. Possible candidate genes for these QTL were identified. Identification of SNP s in linkage disequilibrium with QTL will enable marker‐based selection for mastitis resistance. The candidate genes identified should be further studied to detect candidate polymorphisms underlying these QTL .