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Journal of Heredity Advance Access originally published online on June 1, 2006
Journal of Heredity 2006 97(3):244-252; doi:10.1093/jhered/esj038
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© The American Genetic Association. 2006. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org.

Genetic Diversity Analysis Using Lowly Polymorphic Dominant Markers: The Example of AFLP in Pigs

J-L Foulley, MGM van Schriek, L Alderson, Y Amigues, M Bagga, M-Y Boscher, B Brugmans, R Cardellino, R Davoli, JV Delgado, E Fimland, GC Gandini, P Glodek, MAM Groenen, K Hammond, B Harlizius, H Heuven, R Joosten, AM Martinez, D Matassino, J-N Meyer, J Peleman, AM Ramos, AP Rattink, V Russo, KW Siggens, JL Vega-Pla, and L Ollivier

From INRA, Station de Génétique Quantitative et Appliquée, 78352 Jouy-en-Josas cedex, France (Foulley and Ollivier); Keygene N.V., PO Box 216, 6700 AE Wageningen, The Netherlands (van Schriek, Brugmans, Heuven, and Peleman); Rare Breeds Survival Trust, 6 Harnage, Shrewsbury, Shropshire SY5 6EJ, United Kingdom (Alderson); Labogena, Domaine de Vilvert, 78352 Jouy-en-Josas cedex, France (Amigues and Boscher); Sygen International, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, United Kingdom (Bagga and Siggens); the Animal Genetic Resources Group, FAO, Viale delle Terme di Caracalla, Roma 00100, Italy (Cardellino and Hammond); DIPROVAL, Universita di Bologna, Via Rosselli 107, 42100 Coviolo-Reggio Emilia, Italy (Davoli and Russo); the Facultad de Veterinaria, Universidad de Cordoba, Avda Medina Azahara 9, 14005 Cordoba, Spain (Delgado and Martinez); Nordic Gene Bank Farm Animals, Pb 5003, 1432 Aas, Norway (Fimland); the Department VSA, Universita degli Studi di Milano, Via Celoria 10, 20133 Milano, Italy (Gandini); the Animal Genetics Institute, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany (Glodek and Meyer); Wageningen University, PO Box 338, 6700 AH Wageningen, The Netherlands (Groenen, Harlizius, Heuven, Joosten, and Rattink); ConSDABI-NFP.I-FAO, Centro di Genomica e di Proteomica per la Qualità e per l'Eccellenza alimentare, Località Piano Cappelle, 82020 Benevento, Italy (Matassino); Universidade de Tras-os-Montes e Alto Douro, 5001 Vila Real Codex, Portugal (Ramos); and Laboratorio de Genetica Molecular, FESSCR, Apartado Oficial Sucursal 2, 14071 Cordoba, Spain (Vega-Pla). B. Brugmans is now at EasyGene Nieuw Kanaal 7E, 6709 PA Wageningen, The Netherlands

Address correspondence to L. Ollivier at the address above, or e-mail: louis.ollivier{at}jouy.inra.fr.

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 (FST), 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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A. A. Vicente, M. I. Carolino, M. C. O. Sousa, C. Ginja, F. S. Silva, A. M. Martinez, J. L. Vega-Pla, N. Carolino, and L. T. Gama
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