genome-wide association study for milk production traits in Danish Jersey cattle using a 50K single nucleotide polymorphism chip

Quantitative trait loci for milk production traits in Danish Jersey cattle were mapped by a genome-wide association analysis using a mixed model. The analysis incorporated 1,039 bulls and 33,090 SNP and resulted in 98 detected combinations of QTL and traits on 27 BTA. These QTL comprised 30 for milk index, 50 for fat index, and 18 for protein index. The evidence presents 33 genome-wide QTL on 14 BTA. Of these, 7 had effects on milk index, 21 on fat index, and 5 on protein index. Among the genome-wide QTL, 26 have been previously reported, 2 on BTA4 and BTA5 were new for milk index, and 5 on BTA4, BTA5, BTA13, BTA20, and BTA29 were new QTL for fat index. We found 7 pleiotropic or very closely linked QTL. Most of the QTL were associated with polymorphisms within narrow regions and several may represent the effects of polymorphisms of genes: DGAT1, casein, ARFGAP3, CYP11B1, and CDC-like kinase 4. By a chromosome-wide threshold, 65 additional QTL were detected. Many of them are likely to represent QTL. The results are interesting from a breeding perspective and contribute to the search for the genes causing the polymorphisms important for milk production traits.