Improved genome-wide associations using a breed-specific 200K SNP chip for German Black Pied (DSN) cattle

Summary

The DSN200K chip was specifically designed for German Black Pied cattle (DSN ‘Deutsches Schwarzbuntes Niederungsrind’) to improve genome-wide association analyses (GWAS) in DSN. Here, we performed GWAS with 2,099 DSN cows and 20 milk performance traits using 131,273 SNPs from the DSN200K chip. We compared those GWAS results to results obtained with the Illumina BovineSNP50 BeadChip (Illumina 50K) and in silico randomly generated SNP chips. Those random SNP chips had the same number of SNPs as on the DSN200K chip selected from a prefiltered set of 2.6 million sequence variants. We identied 13-15 times more associated SNPs with the DSN200K chip than with the Illumina 50K and 2.7-3.2 times more than with random SNP chips. With the DSN200K chip, we associated DSN-unique SNPs and SNPs with impact on gene transcripts which could potentially be causal mutations. These SNPs were seldom identied with the Illumina 50K or the random SNP chips.