Use of SNP markers to conserve genome-wide genetic diversity in livestock

Samenvatting

Conservation of genetic diversity in livestock breeds is important since it is, both within and between breeds, under threat. The availability of large numbers of SNP markers has resulted in new opportunities to estimate genetic diversity in more detail, and to improve prioritization of animals for conservation of genetic diversity. The aim of this thesis was to further explore the potential of SNP markers for estimation and conservation of genetic diversity within livestock breeds. This was evaluated analyzing Holstein cattle populations, genotyped with a commonly used 50k SNP chip. Genetic diversity was estimated with SNP markers and compared to genetic diversity estimated with pedigree information. Both methods could detect differences in overall genetic diversity, even between two closely related populations. With SNP markers, differences in genetic diversity at the chromosomal level could be identified as well. Subsequently, SNP markers and pedigree information were used to prioritize animals for conservation in a gene bank using optimal contributions. SNP based prioritization was slightly more effective than pedigree based information, both over the whole genome and at specific regions of the genome. We extended the optimal contribution method to simultaneously conserve a single allele at a specific frequency and maximize the overall genetic diversity conserved in a gene bank. The loss of overall genetic diversity was larger when the target frequency for animals conserved in the gene bank differed more from the original frequency in the population. It can be concluded that dense SNP data form a powerful tool for estimation and conservation of genetic diversity in livestock breeds. Although pedigree information gives a good representation of the overall genetic diversity, SNP markers can provide more detailed information about the genetic diversity over the genome. Especially for small populations, SNP markers can play an important role in conservation of unique alleles, while simultaneously minimizing the loss of genetic diversity at the rest of the genome.