Mapping QTL affecting milk somatic cell count in the Italian Brown Swiss dairy cattle - the QuaLAT project

A selective DNA pooling approach using milk samples was employed to map QTL affecting milk somatic cells count (MSCC) in the Italian Brown Swiss dairy cattle population. The mapping population consisted of five half sib daughter families of Brown Swiss bulls, sires of 1000 to 3600 daughters. Two hundred highest and 200 lowest daughters, ranked by dam-corrected EBV, were selected from the high and the low tail. Four independent replicate pools, each made of 50 randomly chosen daughters, were prepared for each sire-tail combination. Di-nucleotide microsatellite markers were used to scan the genome. Sire marker allele frequencies were estimated by densitometry and shadow correction analysis. Significance threshold of 10% aFDR was used at the marker level, and resulted in a critical CWER P-value of 0.054. A threshold of 20% aFDR within the significant markers was used at the sire-marker level and resulted in a critical P-values of 0.058. Out of 145 markers, 41 were significant. Out of 122 sire-marker tests, at the significant markers, 58 resulted significant. QTL regions will be selected for further intensive study. This is the first complete genome scan for MSCC in the Brown Swiss breed.