Quantitative Trait Locus (QTL) Detection For Milk Protein Composition In Dairy Cattle

The Dutch Milk Genomics Initiative aims at identification of genes that contribute to natural genetic variation in quality traits of bovine milk, among which milk-protein composition. The heritabilities, i.e. the proportion of phenotypic variation due to genetics, for the major milk proteins were high and ranged from 0.25 for β-casein to 0.80 for β-lactoglobulin. The heritabilities show that genes contribute to the genetic variation of major milk proteins. However, it is not known which genes cause this genetic variation. The objective of this study, therefore, was to perform a whole genome scan to detect quantitative trait loci (QTL), i.e. DNA region on the genome which has an effect on a quantitative trait, for the milk protein composition in 1,912 Holstein-Friesian cows. One morning milk sample was taken between February and March 2005. All milk samples were analyzed for the major milk proteins using capillary zone electrophoresis. DNA was isolated from blood samples of 849 cows and semen samples of seven bulls. As genetic markers, 1,341 single nucleotide polymorphisms (SNPs) were used. Ten significant chromosomal regions affecting milk protein composition were detected. The chromosomal regions most significantly related to the major milk proteins (Pgenome<0.05) were found on Bos Taurus autosome (BTA) 6 and 11. The QTL on BTA6 was found at about 80 cM and affected αS1-casein, αS2-casein, β-casein and к-casein. The QTL on BTA11 was found at 124 cM and affected β-lactoglobulin. The proportion of phenotypic variance explained by the QTL was 3.6% for β-casein and 7.9% for к-casein on BTA6, and 28.3% for β-lactoglobulin on BTA11. The QTL affecting αS2-casein on BTA6 and 17 showed a significant interaction. We investigated the extent to which the detected QTL on BTA6 and 11 could be explained by known polymorphisms in β-casein, к-casein, or β-lactoglobulin genes. Correction for these known polymorphisms decreased the proportion of phenotypic variance explained by the QTL previously found on BTA6 and 11. Thus, several significant QTL affecting milk protein composition were found, of which some could partially be explained by known polymorphisms in milk protein genes. Fine mapping of the detected QTL regions to reduce confidence intervals of the detected QTL for milk protein composition, to facilitate new candidate genes that affect milk protein composition, is in progress by using the 60K bovine SNP chip.