Submitted to: World Congress of Genetics Applied in Livestock Production
Publication Type: Proceedings
Publication Acceptance Date: May 9, 2010
Publication Date: August 1, 2010
Citation: Flury, C., Tapio, M., Sonstegard, T.S., Drogemuller, C., Leeb, T., Hanotte, O., Simianer, H., Rieder, S. 2010. The use of SNP data for the monitoring of genetic diversity in cattle breeds. World Congress of Genetics Applied in Livestock Production.
Interpretive Summary: The first step in understanding genetic diversity in a breed of cattle is to estimate the effective population size of that breed. This is done by looking at the shared genetic structure observed at SNP-based DNA markers across the genomes of animals sampled from that breed. These types of tools and studies are essential “first steps” for deriving methods to evaluate conservation of rare and native breeds for nations in need where pedigree and phenotype information are often lacking.
LD between SNPs contains information about effective population size. In this study, we investigate the use of genome-wide SNP data for marker based estimation of effective population size for two taurine cattle breeds of Africa and two local cattle breeds of Switzerland. Estimated recombination rates for BTA10 are presented for all four breeds. Recombination rates vary along different chromosomal regions, however no obvious differences among breeds were found. Using estimated genetic map distances for derivation of Ne compared to using physical map distances directly led to differences in past effective population size. SNP data allow for the assessment of genetic diversity within breed under the absence of pedigree information.