Abstract
BackgroundGerman Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd size of around 2500 animals. The ability to track sequence variants specific to DSN could help to support the conservation of DSN’s genetic diversity and to provide avenues for genetic improvement.ResultsWhole-genome sequencing data of 304 DSN cattle were used to design a customized DSN200k SNP chip harboring 182,154 variants (173,569 SNPs and 8585 indels) based on ten selection categories. We included variants of interest to DSN such as DSN unique variants and variants from previous association studies in DSN, but also variants of general interest such as variants with predicted consequences of high, moderate, or low impact on the transcripts and SNPs from the Illumina BovineSNP50 BeadChip. Further, the selection of variants based on haplotype blocks ensured that the whole-genome was uniformly covered with an average variant distance of 14.4 kb on autosomes. Using 300 DSN and 162 animals from other cattle breeds including Holstein, endangered local cattle populations, and also a Bos indicus breed, performance of the SNP chip was evaluated. Altogether, 171,978 (94.31%) of the variants were successfully called in at least one of the analyzed breeds. In DSN, the number of successfully called variants was 166,563 (91.44%) while 156,684 (86.02%) were segregating at a minor allele frequency > 1%. The concordance rate between technical replicates was 99.83 ± 0.19%.ConclusionThe DSN200k SNP chip was proved useful for DSN and other Bos taurus as well as one Bos indicus breed. It is suitable for genetic diversity management and marker-assisted selection of DSN animals. Moreover, variants that were segregating in other breeds can be used for the design of breed-specific customized SNP chips. This will be of great value in the application of conservation programs for endangered local populations in the future.
Highlights
German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield
Deutsches Schwarzbuntes Niederungsrind (DSN) sequence variants from whole‐genome sequencing For the design of the DSN200k Single Nucleotide Polymorphism (SNP) chip, a representative dataset of DSN sequence variants was needed
Concordance rate of 99.60 ± 0.41 was found comparing results from our pipeline with calls for 57 DSN included in the 1000 Bull Genomes project (Run 8) which were overlapping between the two datasets
Summary
German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd size of around 2500 animals. German Black Pied cattle (DSN, Deutsches Schwarzbuntes Niederungsrind) are a dual-purpose breed that has been selected for milk and beef production. While the modern Holstein breed became the most commonly used breed for milk production worldwide, DSN cattle were kept as a Neumann et al BMC Genomics (2021) 22:905 genetic resource population without strong selection and maintained its dual-purpose character. To conserve its genetic diversity and maintain the DSN-typical characteristics in the breeding program, it is crucial to study its genetics at the populational level
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