Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 355017
Title Genetic diversity analysis using lowly polymorphic dominant markers: The example of AFLP in pigs.
Author(s) Foulley, J.L.; Schriek, M. van; Groenen, M.A.M.; Heuven, H.C.M.
Source Journal of Heredity 97 (2006)3. - ISSN 0022-1503 - p. 244 - 252.
Department(s) Animal Breeding and Genomics
Publication type Refereed Article in a scientific journal
Publication year 2006
Keyword(s) dierveredeling - varkens - varkensrassen - rasverschillen - genetische diversiteit - genetische afstand - genetische analyse - genetische merkers - dna-fingerprinting - genfrequentie - dna-vermenigvuldiging - genetische polymorfie - genetische bronnen van diersoorten - aflp - animal breeding - pigs - pig breeds - breed differences - genetic diversity - genetic distance - genetic analysis - genetic markers - dna fingerprinting - gene frequency - dna amplification - genetic polymorphism - animal genetic resources - amplified fragment length polymorphism - population diversity - selective neutrality - distance - frequency
Categories Animal Breeding and Genetics (General) / Pigs
Abstract DNA markers are commonly used for large-scale evaluation of genetic diversity in farm animals, as a component of the management of animal genetic resources. AFLP markers are useful for such studies as they can be generated relatively simply; however, challenges in analysis arise from their dominant scoring and the low level of polymorphism of some markers. This paper describes the results obtained with a set of AFLP markers in a study of 59 pig breeds. AFLP fingerprints were generated using four primer combinations (PC), yielding a total of 148 marker loci, and average harmonic mean of breed sample size was 37.3. The average proportion of monomorphic populations was 63% (range across loci: 3%-98%). The moment-based method of Hill and Weir (2004, Mol Ecol 13:895-908) was applied to estimate gene frequencies, gene diversity (F ST), and Reynolds genetic distances. A highly significant average FST of 0.11 was estimated, together with highly significant PC effects on gene diversity. The variance of FST across loci also significantly exceeded the variance expected under the hypothesis of AFLP neutrality, strongly suggesting the sensitivity of AFLP to selection or other forces. Moment estimates were compared to estimates derived from the square root estimation of gene frequency, as currently applied for dominant markers, and the biases incurred in the latter method were evaluated. The paper discusses the hypotheses underlying the moment estimations and various issues relating to the biallelic, dominant, and lowly polymorphic nature of this set of AFLP markers and to their use as compared to microsatellites for measuring genetic diversity
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