Hostname: page-component-cd9895bd7-jn8rn Total loading time: 0 Render date: 2024-12-18T15:38:54.587Z Has data issue: false hasContentIssue false

European pig genetic diversity: a minireview*

Published online by Cambridge University Press:  01 July 2009

L. Ollivier*
Affiliation:
Institut National de la Recherche Agronomique-Station de Génétique Quantitative et Appliquée, 78350 Jouy-en-Josas, France
Get access

Abstract

An evaluation of the European pig diversity has been carried on by several countries, with the support of the European Union over the period of 1994 to 2000. This article presents an overview of the results of this investigation, focussing on two genetic marker techniques, namely microsatellites (MS) and amplification of fragment length polymorphism (AFLP). Nearly 200 loci were characterised on about 50 individuals from each of 59 to 71 breeds, according to the marker considered. The analysis of diversity, based on genetic distances, led to similar conclusions for the two marker types (MS and AFLP), in spite of a markedly lower total diversity of AFLP compared to MS. The analysis of the MS loci showed that the allelic diversity pattern among breeds was quasi-independent from the diversity pattern based on allele frequencies. Genetic distances showed no particular clustering of local with international breeds, confirming the genetic uniqueness of the European local breeds compared to mainstream international breeds. The taxonomy of the local breeds revealed a cluster of the Iberian type breeds, in contrast with a wider dispersal of the breeds from other countries. Phylogeny often disagreed with documented breeds’ history, showing the complex migration/admixture patterns which underlie the breeds’ relationships. Methodologies developed in this investigation as well as the database and the DNA depository created should provide support for further innovative research in the field of domestic animal diversity management.

Type
Full Paper
Copyright
Copyright © The Animal Consortium 2009

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Akey, M, Zhang, G, Zhang, K, Li, J, Shriver, MD 2002. Interrogating a high-density SNP map for signatures of natural selection. Genome Research 12, 18051814.CrossRefGoogle ScholarPubMed
Amaral, AJ, Megens, H-J, Crooijmans, RPMA, Heuven, HCM, Groenen, MAM 2008. Linkage equilibrium decay and haplotype block structure in the pig. Genetics 179, 569579.CrossRefGoogle Scholar
Archibald, AL, Haley, CS, Brown, J et al. 1995. The PiGMaP consortium linkage map of the Pig (Sus scrofa). Mammalian Genome 6, 157175.CrossRefGoogle Scholar
Barker, JSF 2001. Conservation and management of genetic diversity: a domestic animal perspective. Canadian Journal of Forestry Research 31, 588595.CrossRefGoogle Scholar
Barker, JSF, Hill, WG, Bradley, D, Nei, M, Fries, R, Wayne, RK 1993–1998. An integrated global programme to establish the genetic relationships among the breeds of each domestic animal species. FAO report, Rome. Reprinted as: FAO (1998). Secondary Guidelines for Development of National Farm Animal Genetic Resources Management Plans. Measurement of Domestic Animal Diversity (MoDAD): Original Working Group Report. FAO, Rome.Google Scholar
Bataillon, TM, David, JL, Schoen, DJ 1996. Neutral genetic markers and conservation genetics: simulated germplasm collections. Genetics 144, 409417.CrossRefGoogle ScholarPubMed
Beaumont, MA, Balding, DJ 2004. Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology 13, 969980.CrossRefGoogle ScholarPubMed
Blott, S, Andersson, L, Groenen, M, SanCristobal, M, Chevalet, C, Cardellino, R, Li, N, Huang, L, Li, K, Plastow, G, Haley, C 2003. Characterisation of genetic variation in the pig breeds of China and Europe – The PigBioDiv2 project. Archivos de Zootecnia 52, 207217.Google Scholar
Bonin, A, Ehrich, D, Manel, S 2007. Statistical analysis of amplified fragment length polymorphism: a toolbar for molecular ecologists and evolutionists. Molecular Ecology 16, 37373758.CrossRefGoogle Scholar
Chakraborty, R, De Andrade, M, Daiger, SP, Budowle, B 1992. Apparent heterozygote deficiencies observed in DNA typing data and their implications in forensic applications. Annals of Human Genetics 56, 4557.CrossRefGoogle ScholarPubMed
Derban, S, Foulley, J-L, Ollivier, L 2002–2005. WEITZPRO: a software for analysing genetic diversity. INRA, Paris, France. Retrieved May 5, 2008, from http://www-sgqa.jouy.inra.fr/rubrique.php3?id_rubrique=5Google Scholar
Dinklage, H, Gruhn, R 1969. Blutgruppen-and Serumproteinpolymorphisms bei verchiedenen in Deutschland vorhandenen Schweinerassen. Zeitschrift für Tierzüchtung und Züchtungsbiologie 86, 136146.CrossRefGoogle Scholar
El Mousadik, A, Petit, RJ 1996. High level of genetic differentiation for allelic richness among populations of the argan tree (Argania spinosa (L.) Skeels) endemic to Morocco. Theoretical and Applied Genetics 92, 832836.Google Scholar
Foulley, J-L, Ollivier, L 2006. Estimating allelic richness and its diversity. Livestock Science 101, 150158.Google Scholar
Foulley, J-L, van Schriek, MGM, Alderson, L et al. 2006. Genetic diversity analysis using lowly polymorphic dominant markers: the example of AFLP in pigs. Journal of Heredity 97, 244252.CrossRefGoogle ScholarPubMed
Groenen, MAM, Joesten, R, Boscher, M-Y, Amigues, Y, Rattink, A, Harlizius, B, van den Poel, JJ, Crooijmans, R 2003. The use of microsatellites genotyping for population studies in the pig with individual and pooled samples. Archivos de Zootecnia 52, 145155.Google Scholar
Hill, WG, Weir, BS 2004. Moment estimation of population diversity and genetic distance from data on recessive markers. Molecular Ecology 13, 895908.CrossRefGoogle ScholarPubMed
Laval, G, Iannuccelli, N, Legault, C, Milan, D, Groenen, MAM, Giuffra, E, Andersson, L, Niessen, P-H, Jorgensen, C-B, Geldermann, H, Foulley, J-L, Chevalet, C, Ollivier, L 2000. Genetic diversity of eleven European pig breeds. Genetics Selection Evolution 32, 187203.Google Scholar
Le Dour, O, Nordstedt, I, Aguilar, A (ed.) 2000. Examples of demonstration projects in the life sciences programmes, vol. 3. European Commission, Luxembourg.Google Scholar
Lewontin, RC, Krakauer, J 1973. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74, 175195.Google Scholar
Major, F 1968. Untersuchungen über die verwandtschaftlichen Beziehungen zwischen verschiedenen europäischen Landrassepopulationen mit Hilfe von Blutgruppenfaktoren. PhD, University of Göttingen, Göttingen.Google Scholar
Martinez, AM, Delgado, JV, Rodero, A, Vega-Pla, JL 2000. Genetic structure of the Iberian pig breed using microsatellites. Animal Genetics 31, 295301.CrossRefGoogle ScholarPubMed
Maynard Smith, J, Haig, J 1974. The hitch-hiking effect of a favourable gene. Genetical Research 23, 2335.CrossRefGoogle Scholar
Megens, H-J, Crooijmans, RPMA, San Cristobal, M, Hui, Xing, Li, N, Groenen, MAM 2008. Biodiversity of pig breeds from China and Europe estimated from pooled DNA samples: differences in microsatellite variation between two areas of domestication. Genetics Selection Evolution 40, 103128.Google Scholar
Nsengimana, J, Baret, P, Haley, CS, Visscher, PM 2004. Linkage disequilibrium in the domestic pig. Genetics 166, 13951904.CrossRefGoogle Scholar
Ollivier, L (co-ordinator) 2002. BIO4-CT98-0188. Characterisation of genetic variation in the European pig to facilitate the maintenance and exploitation of biodiversity. Report prepared for the European Commission, Brussels.Google Scholar
Ollivier, L, Sellier, P 1983. Pig genetics: a review. Annales de Génétique et Sélection Animale 14, 481544.CrossRefGoogle Scholar
Ollivier, L, Foulley, J-L 2005. Aggregate diversity: new approach combining within- and between-breed diversity. Livestock Production Science 95, 247254.CrossRefGoogle Scholar
Ollivier, L, Foulley, J-L 2009. Managing genetic diversity, fitness and adaptation of farm animal genetic resources. In Adaptation and fitness in animal populations: evolutionary and breeding perspectives on genetic resource management (ed. JHJ van der Werf, R Frankham, H-U Graser and C Gondro), pp. 201227. Springer, Berlin, Germany.Google Scholar
Ollivier, L, Caritez, J-C, Foulley, J-L et al. 2001a. Evaluation of genetic diversity from immunological, biochemical and DNA polymorphisms. In Pig genetic resources in Europe (ed. L Ollivier, F Labroue, P Glodek, G Gandini and JV Delgado), pp. 8797. Wageningen Pers, Wageningen, The Netherlands.Google Scholar
Ollivier, L, Labroue, F, Glodek, P, Gandini, G, Delgado, JV (ed.) 2001b. Pig genetic resources in Europe. Wageningen Pers, Wageningen, The Netherlands.Google Scholar
Ollivier, L, Amigues, Y, Boscher, M-Y 2003. An EC-funded project on characterisation of genetic variation in the European pig. Objectives, organisation, breed sampling, DNA preparation and circulation. Archivos de Zootecnia 52, 137144.Google Scholar
Ollivier, L, Alderson, L, Gandini, GC et al. 2005. An assessment of the European pig diversity using molecular markers: partitioning of diversity among breeds. Conservation Genetics 6, 729741.CrossRefGoogle Scholar
Plastow, G, Siggens, K, Bagga, M, Brugmanns, B, Heuven, H, Peleman, J 2003. Utilization of AFLP for genetic distance analysis in pigs. Archivos de Zootecnia 52, 157164.Google Scholar
Porter, V 1993. A handbook to the breeds of the world. Helm Information Ltd, The Banks, Mountfield, Near Robertsbridge, UK.Google Scholar
Reynolds, J, Weir, BS, Cockerham, CC 1983. Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105, 767779.Google Scholar
Robertson, A 1975. Gene frequency distributions as a test of selective neutrality. Genetics 81, 775785.Google Scholar
Roslin Institute 2005. A pig diversity database. In 100 technology offers stemming from Biotechnology RTD results (ed. KT Ingemansson and N Knezevic), pp. 7274. European Commission, Luxembourg.Google Scholar
SanCristobal, M, Chevalet, C, Haley, CS et al. 2006a. Genetic diversity within and between European pig breeds using microsatellite markers. Animal Genetics 37, 189198.CrossRefGoogle ScholarPubMed
SanCristobal, M, Chevalet, C, Haley, CS et al. 2006b. Genetic diversity in European pigs utilising AFLP markers. Animal Genetics 37, 232238.Google Scholar
Schlötterer, C 2002. A microsatellite-based multilocus screen for the identification of local selective sweeps. Genetics 160, 753763.CrossRefGoogle ScholarPubMed
Schlötterer, C, Vogl, C, Tautz, D 1997. Polymorphism and locus-specific effects on polymorphism at micosatellite loci in natural Drosophila melanogaster populations. Genetics 146, 309320.CrossRefGoogle Scholar
Skalski, GT, Couch, CR, Garher, AF, Weir, BS, Sullivan, CV 2006. Evaluation of DNA pooling for the estimation of microsatellite allele frequencies: a case study using striped bass (Morone saxatilis). Genetics 173, 863875.CrossRefGoogle ScholarPubMed
Smouse, PE 1998. To tree or not to tree. Molecular Ecology 7, 399412.Google Scholar
Storz, JF 2005. Using genome scans of DNA polymorphism to infer adaptive population divergence. Molecular Ecology 14, 671688.Google Scholar
Tapio, I, Varv, S, Bennewitz, J, Maleviute, J, Fimland, E, Grislis, Z, Meuwissen, THE, Miceikine, I, Olsaker, I, Viinalas, H, Vilkki, J, Kantanen, J 2006. Prioritization for conservation of northern European cattle breeds based on analysis of microsatellite. Conservation Biology 20, 17681779.Google Scholar
Thaon d’Arnoldi, C, Foulley, J-L, Ollivier, L 1998. An overview of the Weitzman approach to diversity. Genetics Selection Evolution 30, 149161.CrossRefGoogle Scholar
Weitzman, ML 1992. On diversity. Quarterly Journal of Economics 107, 363405.CrossRefGoogle Scholar
Weitzman, ML 1993. What to preserve? An application of diversity theory to crane conservation. Quarterly Journal of Economics 108, 157183.Google Scholar