The BovMAS Consortium : a complete genome scan of Brown Swiss cattle for milk yield and protein percent using selective DNA pooling with milk samples

A selective DNA pooling approach using milk samples was applied to map QTL affecting milk yield (MK) and milk protein percentage (PP). in 10 half sib daughter families of Brown Swiss sires with 1000 to 3600 individuals each. Three families were sampled in Germany, three in Italy, one in Austria and three jointly in Austria and Italy. For each sire-trait combination the 200 high and 200 low daughters, ranked by dam-corrected EBV, were chosen for selective DNA pooling. For each tail two independent pools, each of 100 daughters chosen at random, were constructed. Sire allele frequencies were obtained by densitometry at 139 evenly spaced genome-wide autosomal markers. Significance was at 5% FDR level with nominal value of about 0.04 at the marker level and 0.01 at the sire by marker level. 19 markers were significant for PP, 29 for MK, 80 for both traits, and 11 markers were not significant for either. Out of the 846 (PP) and 844 (MY) sire by marker combinations, 154 and 138 were significant for PP and MK, respectively, and 62 for both traits. From the combinations significant for at least one of the traits, MK and PP showed the same direction of the effect in 162 instances, and opposite effect in 183 instances.