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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium
Journal of Animal Breeding and Genetics, Volume 127, No. 5, Year 2010
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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. © 2010 Blackwell Verlag GmbH.
Authors & Co-Authors
Tapio, Miika
Unknown Affiliation
Sonstegard, Tad Stewart
United States, Washington, D.c.
United States Department of Agriculture
Drögemüller, Cord
Switzerland, Bern
University of Bern
Leeb, Tosso
Switzerland, Bern
University of Bern
Simianer, Henner
Germany, Gottingen
Georg-august-universität Göttingen
Hanotte, Olivier H.
United Kingdom, Nottingham
University of Nottingham
Rieder, Stefan
Switzerland, Zollikofen
Swiss College of Agriculture
Statistics
Citations: 77
Authors: 7
Affiliations: 5
Identifiers
Doi:
10.1111/j.1439-0388.2010.00862.x
ISSN:
14390388
Research Areas
Genetics And Genomics
Study Design
Cross Sectional Study