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

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    Authors
    Flury, C.
    Tapio, M.
    Sonstegard, T.S.
    Drögemaller, C.
    Leeb, T.
    Simianer, H.
    Hanotte, Olivier H.
    Rieder, S.
    Date
    2010-10
    Language
    en
    Type
    Journal Article
    Accessibility
    Limited Access
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    Citation
    Flury, C.; Tapio, M.; Sonstegard, T.; Drögemüller, 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(5):339-347.
    Permanent link to cite or share this item: https://hdl.handle.net/10568/1822
    DOI: https://dx.doi.org/10.1111/j.1439-0388.2010.00862.x
    Abstract/Description
    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 single nucleotide polymorphism (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. LD-based 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.
    AGROVOC Keywords
    CATTLE; GENETICS
    Subjects
    GENETICS; LIVESTOCK; INDIGENOUS BREEDS;
    Collections
    • ILRI livestock genetics program outputs [344]
    • ILRI articles in journals [5079]

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