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Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium
Author(s) -
Flury C.,
Tapio M.,
Sonstegard T.,
Drögemüller C.,
Leeb T.,
Simianer H.,
Hanotte O.,
Rieder S.
Publication year - 2010
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/j.1439-0388.2010.00862.x
Subject(s) - effective population size , linkage disequilibrium , breed , population size , biology , population , sample size determination , statistics , genetics , disequilibrium , demography , single nucleotide polymorphism , evolutionary biology , genetic variation , mathematics , genotype , medicine , sociology , gene , ophthalmology
Summary 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.