Whole-genome association study for energy balance and fat/protein ratio in German Holstein bull dams

Summary The metabolic status of cows is important to health and fertility, especially in early lactation, and energy balance (EB) and fat/protein ratio (FPR) are considered as appropriate indicators for metabolic disorders. The aim of this study was to detect SNPs (single nucleotide polymorphisms) associated with EB and FPR in German Holstein bull dams belonging to the research herd Karkendamm. Bull dams were genotyped using the Illumina Bovine SNP 50K Bead chip® comprising 54 001 SNPs. A total of 43 593 SNPs and 586 (EB) and 668 (FPR) bull dams passed the quality control criteria. Phenotypes were deregressed breeding values estimated via random regression animal models for lactation days 11, 20, 30, and 42 for EB and FPR. Whole‐genome association analyses were carried out fitting principal components as covariates to adjust for genetic substructure. Permutation tests were applied to estimate genome‐wise significance. Across all observed lactation days, 19 SNPs located in four different intervals on chromosomes 1, 14, 16, and 27 were detected. For EB, seven markers across four chromosomes were identified. There was no overlap between markers associated with FPR and EB. SNPs associated with FPR were mostly located in QTL regions for milk production traits, especially in the region of DGAT1, whereas SNPs associated with EB mainly showed positional relationships to previously described QTL regions affecting functional traits, especially fertility.