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

Flury, C; Tapio, M; Sonstegard, T; Drögemüller, Cord; Leeb, Tosso; 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), pp. 339-47. Berlin: Wiley-Blackwell 10.1111/j.1439-0388.2010.00862.x

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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.

Item Type:	Journal Article (Original Article)
Division/Institute:	05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Institute of Genetics 05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH)
UniBE Contributor:	Drögemüller, Cord, Leeb, Tosso
Subjects:	500 Science > 590 Animals (Zoology) 600 Technology > 630 Agriculture
ISSN:	0931-2668
Publisher:	Wiley-Blackwell
Language:	English
Submitter:	Factscience Import
Date Deposited:	04 Oct 2013 14:33
Last Modified:	05 Dec 2022 14:10
Publisher DOI:	10.1111/j.1439-0388.2010.00862.x
Web of Science ID:	000281713200005
URI:	https://boris.unibe.ch/id/eprint/12793 (FactScience: 219265)