Summary: | 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<sub>10</sub>(<i>p</i>) ≥ 7.1) in 13 genomic loci on 9 chromosomes. The highest significance was found for the <i>MGST1</i> region affecting milk fat content (−log<sub>10</sub>(<i>p</i>) = 11.93, MAF = 0.23, substitution effect of the minor allele (ß<sub>MA</sub>) = −0.151%). Different from Holstein, <i>DGAT1</i> was fixed (0.97) for the alanine protein variant for high milk and protein yield. A key gene affecting protein content was <i>CSN1S1</i> (−log<sub>10</sub>(<i>p</i>) = 8.47, MAF = 049, ß<sub>MA</sub> = −0.055%) and the <i>GNG2</i> region (−log<sub>10</sub>(<i>p</i>) = 10.48, MAF = 0.34, ß<sub>MA</sub> = 0.054%). Additionally, we suggest the importance of <i>FGF12</i> for protein and fat yield, <i>HTR3C</i> for milk yield, <i>TLE4</i> for milk and protein yield, and <i>TNKS</i> 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.
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