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Title: Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium

item FLURY, C - Swiss College Of Agriculture
item TAPIO, M - International Livestock Research Institute (ILRI) - Kenya
item Sonstegard, Tad
item DROGEMULLER, C - University Of Berne
item LEEB, T - University Of Berne
item SIMIANER, H - Georg August University
item HANOTTE, O - International Livestock Research Institute (ILRI) - Kenya
item RIEDER, S - Swiss College Of Agriculture

Submitted to: Journal of Animal Breeding and Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/21/2010
Publication Date: 10/1/2010
Citation: Flury, C., Tapio, M., Sonstegard, T.S., Drogemuller, C., Leeb, T., Simianer, H., Hanotte, O., Rieder, S. 2010. Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium. Journal of Animal Breeding and Genetics. 127:339-347.

Interpretive Summary: An important parameter to consider when selecting breeds of cattle for germplasm preservation is effective population size, which helps assess genetic diversity within a livestock population. This is important in determining how much germplasm from a single breed would have to be captured to preserve a breed. In this study, we performed an analysis of genetic diversity on a breed of Swiss cattle that have not undergone intensive selection for any production traits like most popular breeds currently in commercial production. In this scenario, which would be similar to most rare breeds, one could then have a better general idea how many animals would be needed for a population presumed to have more diversity than a breed under intense selection. We also used molecular genetic data for determining relationships rather than pedigrees, which can be erroneous. The results based on linkage disequilibrium calculations from DNA marker data revealed that the actual effective population size ranged fromf 87 – 149 whereas pedigree-based effective population size was much higher. High-density SNP-based genetic characterization of a population is effective at determining a more accurate population size relative to pedigree based analyses.

Technical Abstract: Effective population size is an important parameter for the assessment of genetic diversity within a livestock population and its development over time. If pedigree information is not available, linkage disequilibrium (LD) analysis might offer an alternative perspective for the estimation of effective population size. In this study, 128 individuals of the Swiss Eringer breed were genotyped using the Illumina BovineSNP50 beadchip. We set bin size at 50 kb for LD analysis, assuming that LD for proximal SNP-pairs reflects distant breeding history while LD from distal SNP-pairs would reflect near history. Recombination rates varied among different regions of the genome. The use of physical distances as an approximation of genetic distances (e.g. setting 1 Mb = 0.01 Morgan) led to an upward bias in LD-based estimates of effective population size for generations beyond 50, while estimates for recent history were unaffected. Correction for restricted sample size did not substantially affect these results. LDbased actual effective population size was estimated in the range of 87 – 149 whereas pedigree-based effective population size resulted in 321 individuals. For conservation purposes requiring knowledge of recent history (< 50 generations), approximation assuming constant recombination rate seemed adequate.