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title: "14.5.3.1 An example of genomic selection in an endangered breed (2024)"
canonical: "https://wiki.groenkennisnet.nl/space/TAB/299467290/14.5.3.1%20An%20example%20of%20genomic%20selection%20in%20an%20endangered%20breed%20(2024)"
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DSN cattle are kept in Germany as a dual purpose breed and as a genetic reserve with a current herd size of around 2500 animals. Whole-genome sequencing data of 304 DSN cattle were used to design a SNP chip with 182,154 variants usable for genomic selection in the DSN breed. The chip included DSN unique variants and variants from previous association studies in DSN. Variants of interest in other breeds were also included. Haplotype blocks were included to ensure 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, other endangered local cattle populations, and also a Bos indicus breed, the performance of the SNP chip was evaluated. The 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 genomic selection of DSN animals. Moreover, variants that were segregating in other breeds can also 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.

Source: G.B. Neumann et al., 2021. Design and performance of a bovine 200k SNP chip developed for endangered German Black Pied cattle (DSN). BMC Genomics: 22:905