Whole-Genome Sequencing Data Reveal New Loci Affecting Milk Production in German Black Pied Cattle (DSN).

German Black Pied (DSN) is considered an ancestral population of the Holstein breed. The goal of the current study was to fine-map genomic loci for milk production traits and to provide sequence variants for selection. We studied genome-wide associations for milk-production traits in 2160 DSN cows. Using 11.7 million variants from whole-genome sequencing of 304 representative DSN cattle, we identified 1980 associated variants (-log() ≥ 7.1) in 13 genomic loci on 9 chromosomes. The highest significance was found for the region affecting milk fat content (-log() = 11.93, MAF = 0.23, substitution effect of the minor allele (ß) = -0.151%). Different from Holstein, was fixed (0.97) for the alanine protein variant for high milk and protein yield. A key gene affecting protein content was (-log() = 8.47, MAF = 049, ß = -0.055%) and the region (-log() = 10.48, MAF = 0.34, ß = 0.054%). Additionally, we suggest the importance of for protein and fat yield, for milk yield, for milk and protein yield, and for milk and fat yield. Selection for favored alleles can improve milk yield and composition. With respect to maintaining the dual-purpose type of DSN, unfavored linkage to genes affecting muscularity has to be investigated carefully, before the milk-associated variants can be applied for selection in the small population.