Advertisement

Conservation Genetics

, Volume 6, Issue 5, pp 729–741 | Cite as

An assessment of European pig diversity using molecular markers: Partitioning of diversity among breeds

  • Louis OllivierEmail author
  • Lawrence Alderson
  • Gustavo C. Gandini
  • Jean-Louis Foulley
  • Chris S. Haley
  • Ruth Joosten
  • Annemieke P. Rattink
  • Barbara Harlizius
  • Martien A. M. Groenen
  • Yves Amigues
  • Marie-Yvonne Boscher
  • Geraldine Russell
  • Andy  Law
  • Roberta Davoli
  • Vincenzo Russo
  • Donato Matassino
  • Céline Désautés
  • Erling Fimland
  • Meena Bagga
  • Juan-Vicente Delgado
  • Jose L. Vega-Pla
  • Amparo  M. Martinez
  • Antonio M. Ramos
  • Peter Glodek
  • Johann-Nikolaus Meyer
  • Graham S. Plastow
  • Kenneth W. Siggens
  • Alan L. Archibald
  • Denis Milan
  • Magali San Cristobal
  • Guillaume Laval
  • Keith Hammond
  • Ricardo Cardellino
  • Claude Chevalet
Article

Abstract

Genetic diversity within and between breeds (and lines) of pigs was investigated. The sample comprised 68 European domestic breeds (and lines), including 29 local breeds, 18 varieties of major international breeds, namely Duroc, Hampshire, Landrace, Large White and Piétrain, and 21 commercial lines either purebred or synthetic, to which the Chinese Meishan and a sample of European wild pig were added. On average 46 animals per breed were sampled (range 12–68). The genetic markers were microsatellites (50 loci) and AFLP (amplified fragment length polymorphism, 148 loci). The analysis of diversity showed that the local breeds accounted for 56% of the total European between-breed microsatellite diversity, and slightly less for AFLP, followed by commercial lines and international breeds. Conversely, the group of international breeds contributed most to within-breed diversity, followed by commercial lines and local breeds. Individual breed contributions to the overall European between- and within-breed diversity were estimated. The range in between-breed diversity contributions among the 68 breeds was 0.04–3.94% for microsatellites and 0.24–2.94% for AFLP. The within-breed diversity contributions varied very little for both types of markers, but microsatellite contributions were negatively correlated with the between-breed contributions, so care is needed in balancing the two types of contribution when making conservation decisions. By taking into account the risks of extinction of the 29 local breeds, a cryopreservation potential (priority) was estimated for each of them.

Keywords

biodiversity conservation genetic marker pig 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Notes

Acknowledgements

This work has received support from several programmes of the European Union (contracts BI02-CT94-3044, RESGEN-CT95-012 and BIO4-CT98-0188), which are gratefully acknowledged. Thanks are also due to the providers of the PiGMaP data not involved in PigBioDiv, namely Luc Peelman (Ghent, Belgium), Hermann Geldermann (Stuttgart, Germany), Merete Fredholm (Copenhagen, Denmark), and Leif Andersson (Uppsala, Sweden), and to Henner Simianer (Göttingen) for useful comments and suggestions. We also gratefully acknowledge the constructive comments provided by an anonymous referee.

References

  1. Alderson L (2003) Criteria for the recognition and prioritisation of breeds of special genetic importance. Animal Genetic Resources Information 33:1–9Google Scholar
  2. Barker JSF (2001) Conservation and management of genetic diversity: a domestic animal perspective. Can. J. For. Res. 31:588–595CrossRefGoogle Scholar
  3. Barker JSF, (2002). Relevance of animal genetic resources and differences to the plant sector. In: Groeneveld E, Glodek P, (eds), Animal Breeding and Animal Genetic Resources. Federal Agricultural Research Centre (FAL), Mariensee and Institute of Animal Genetics, Göttingen, Braunschweig, Germany, pp. 15–21Google Scholar
  4. Barker JSF, Hill WG, Bradley D, Nei M, Fries R, Wayne RK (1998) Measurement of domestic animal diversity (MoDAD): original working group report. FAO, RomeGoogle Scholar
  5. Barker JSF, Tan SG, Moore SS, Mukherjee TK, Matheson JL, Selvaraj OS (2001) Genetic variation within and relationships among populations of Asian goats. J. Anim. Breed. Genet. 118:213–233CrossRefGoogle Scholar
  6. Bataillon TM, David JL, Schoen DJ (1996) Neutral genetic markers and conservation genetics: simulated germplasm collections. Genetics 144:409–417PubMedGoogle Scholar
  7. Caballero A, Toro MA (2002) Analysis of genetic diversity for the management of conserved subdivided populations. Conserv Genet. 3:289–299CrossRefGoogle Scholar
  8. Canon J, Alexandrino P, Bessa I, Carlos C, Carretero Y, Dunner S, Ferran N, Garcia D, Jordana D, Laloë D, Pereira A, Sanchez A, Moazami-Goudarzi K (2001) Genetic diversity measures of local European beef cattle breeds for conservation purposes. Genet. Sel. Evol. 33:311–322CrossRefPubMedGoogle Scholar
  9. Chaiwong N, Kinghorn BP (1999) Use of genetic markers to aid conservation decisions for groups of rare domestic breeds. Proc. Assoc. Advmt. Anim. Breed. Genet. 13:365–368Google Scholar
  10. Derban S, Foulley JL, Ollivier L (2002) WEITZPRO: a software for analysing genetic diversity. INRA, ParisGoogle Scholar
  11. EAAP – Working Group on Animal Genetic Resources (1998) Assessment of the degree of endangerment of livestock breeds. Book of Abstracts of the 49th Annual Meeting of the European Association for Animal Production, 40Google Scholar
  12. Eding H, Meuwissen THE (2001) Marker-based estimates of between and within population kinship for the conservation of genetic diversity. J. Anim. Breed. Genet. 118:141–159CrossRefGoogle Scholar
  13. Felsenstein J (2000) PHYLIP (Phylogeny Inference Package). Department of Genome Sciences University of Washington, SeattleGoogle Scholar
  14. Gandini GC, Ollivier L, Danell B, Distl O, Georgoudis A, Groeneveld E, Martyniuk E, van Arendonk JAM, Woolliams J (2004) Criteria to assess the degree of endangerment of livestock breeds in Europe. Livest. Prod. Sci. 91:173–182CrossRefGoogle Scholar
  15. Groenen MAM, Joesten R, Boscher MY, 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. Arch. Zootec. 52:145–155CrossRefGoogle Scholar
  16. Jones GF (1998). Genetic aspects of domestication, common breeds and their origin. In: Rothschild MF, Ruvinsky A (eds) The Genetics of the Pig. CAB International, Wallingford, Oxon, UK, pp. 17–50Google Scholar
  17. Laval G, Iannuccelli N, Legault C, Milan D, Groenen MAM, Giuffra E, Andersson L, Nissen PH, Joergensen CB, Beeckmann P, Geldermann H, Foulley JL, Chevalet C, Ollivier L (2000) Genetic diversity of eleven European pig breeds. Genet. Sel. Evol. 32:187–203CrossRefPubMedGoogle Scholar
  18. Li K, Chen Y, Moran C, Fan B, Zhao S, Peng Z, (2000) Analysis of diversity and genetic relationship between four Chinese indigenous pig breeds and one Australian commercial pig breed. Anim. Genet. 31:322–325CrossRefPubMedGoogle Scholar
  19. Lynch M, Pfrender M, Spitze K, Lehman N, Hicks J, Allen D, Latta l, Ottene M, Bogue F, Colbourne J (1999) The quantitative and molecular genetic architecture of a subdivided species. Evolution 53:100–110CrossRefGoogle Scholar
  20. Martinez AM, Delgado JV, Rodero A, Vega-Pla JL, (2000) Genetic structure of the Iberian pig breed using microsatellites. Anim. Genet. 31:295–301CrossRefPubMedGoogle Scholar
  21. Mason JL (1988) A World Dictionary of Livestock Breeds Types and Varieties. CAB International, Wallingford, Oxon, UKGoogle Scholar
  22. Nei M (1972) Genetic distances between populations. Am. Nat. 106:283–292CrossRefGoogle Scholar
  23. Nei M (1973) Analysis of gene diversity in subdivided populations. Proc. Nat. Acad. Sci. 70:3321–3323PubMedCrossRefGoogle Scholar
  24. Nunney L (2000) The limits to knowledge in conservation genetics. The value of effective population size. Evol. Biol. 32:179–194Google Scholar
  25. Ollivier L (1998) Animal genetic resources in Europe: Present situation and future prospects for conservation. 8th World Conference on Animal Production, Seoul, Korea, Proceedings Symposium Series I, pp. 237–244Google Scholar
  26. Ollivier L, Foulley JL (2004) Objectives in livestock diversity preservation: the European pig example. In: Wissenschaftliches Kolloquium “Nutztierzüchtung im Wandel der Zeit”. Cuvilier Verlag, Göttingen, 87–106Google Scholar
  27. Ollivier L, Foulley JL (2005) Aggregate diversity: New approach combining within- and between-breed genetic diversity. Livest. Prod. Sci., 95, 247–254Google Scholar
  28. Ollivier L, James JW (2004) Predicting the annual effective size of livestock populations. Genet. Res. 84:41–46CrossRefPubMedGoogle Scholar
  29. Ollivier L, Caritez JC, Foulley JL, Legault C, San Cristobal-Gaudy M, Labroue F, Amigues Y, Brandt H, Clemens R, Glodek P, Ludwig P, Kaltwasser C, Meyer J.-N, Davoli R, Gandini G, Martinez A, Vega-Pla JL, Delgado JV (2001) Evaluation of genetic diversity from immunological, biochemical and DNA polymorphisms. In: Ollivier L, Labroue F, Glodek P, Gandini G, Delgado JV (eds) Pig genetic resources in Europe. Characterisation and conservation EAAP publication n°104, Wageningen Pers, Wageningen, The Netherlands, pp. 87–97Google Scholar
  30. Ollivier L, Amigues Y, Boscher MY (2003) An EC-funded project on characterisation of genetic variation in the European pig. Objectives, organisation, breed sampling, DNA preparation and circulation. Arch. Zootec. 52:137–144Google Scholar
  31. Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv. Biol., 12, 844–855CrossRefGoogle Scholar
  32. Pfrender ME, Spitze K, Hicks J, Morgan K, Latta L, Lynch M (2000) Lack of concordance between genetic diversity estimation at the molecular and quantitative-trait levels. Conserv. Genet. 1:263–269CrossRefGoogle Scholar
  33. Piyasatian N, Kinghorn BP, (2003) Balancing genetic diversity, genetic merit and population viability in conservation programmes. J. Anim. Breed. Genet. 120:137–149CrossRefGoogle Scholar
  34. Plastow G, Siggens K, Bagga M, Brugmans B, Heuven H, Peleman J (2003) Utilization of AFLP for genetic distance analysis in pigs. Arch. Zootec. 52:157–164Google Scholar
  35. Reist-Marti SB, Simianer H, Gibson J, Hanotte O, Rege JEO (2003) Weitzman’s approach and conservation of breed diversity: an application to African cattle breeds. Conserv. Biol., 17, 1299–1311CrossRefGoogle Scholar
  36. Reynolds J, Weir BS, Cockerham CC (1983) Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics, 105, 767–779PubMedGoogle Scholar
  37. Ruane J (2000) A framework for prioritizing domestic animal breeds for conservation purposes at the national level: a Norwegian case study. Conserv. Biol. 14:1385–1393CrossRefGoogle Scholar
  38. Russell GA, Archibald AL, Haley CS, Law AS (2003) The pig genetic database and the WWW. Arch. Zootec. 52:165–172Google Scholar
  39. SanCristobal M, Chevalet C, Foulley JL, Ollivier L (2003) Some methods for analysing genetic markers data in a biodiversity setting. Example of the pigbiodiv data. Arch. Zootec. 52:173–183Google Scholar
  40. Simianer H, Marti SB, Gibson J, Hanotte O, Rege JEO (2003) An approach to the optimal allocation of conservation funds to minimize loss of genetic diversity between livestock breeds. Ecological Economics 45:377–392CrossRefGoogle Scholar
  41. Simon DE, Buchenauer D (1993) Genetic diversity of European livestock breeds. EAAP publication n°66, Wageningen Pers, WageningenGoogle Scholar
  42. Sun F, Zhang Y, Wang Z, Yang S (2002) Study on the genetic relationship among 18 Chinese local pig breeds using microsatellite DNA markers. World Congr. Genet. Appl. Livest. Prod. 33:529–532Google Scholar
  43. Thaon d’Arnoldi C, Foulley JL, Ollivier L (1998) An overview of the Weitzman approach to diversity. Genet. Sel. Evol. 30:149–161CrossRefGoogle Scholar
  44. Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucl. Acids Res. 23:4407–4414PubMedCrossRefGoogle Scholar
  45. Weitzman ML (1992) On diversity. Quart. J. Econ. 107, 363–405CrossRefGoogle Scholar
  46. Weitzman ML (1993) What to preserve ? An application of diversity theory to crane conservation. Quart. J. Econ. 108:157–183CrossRefGoogle Scholar
  47. Weitzman ML (1998) The Noah’s ark problem. Econometrica 66:1279–1298CrossRefGoogle Scholar
  48. Wright S (1931) Evolution in Mendelian populations. Genetics 16:97–159PubMedGoogle Scholar
  49. van Zeveren A, Peelman L, van de Weghe A, Bouquet Y (1995) A genetic study of Belgian pig populations by means of seven microsatellites. J. Anim. Breed. Genet. 112:191–204Google Scholar

Copyright information

© springer 2005

Authors and Affiliations

  • Louis Ollivier
    • 1
    Email author
  • Lawrence Alderson
    • 2
  • Gustavo C. Gandini
    • 3
  • Jean-Louis Foulley
    • 1
  • Chris S. Haley
    • 4
  • Ruth Joosten
    • 5
  • Annemieke P. Rattink
    • 5
  • Barbara Harlizius
    • 5
  • Martien A. M. Groenen
    • 5
  • Yves Amigues
    • 6
  • Marie-Yvonne Boscher
    • 6
  • Geraldine Russell
    • 4
  • Andy  Law
    • 4
  • Roberta Davoli
    • 11
  • Vincenzo Russo
    • 11
  • Donato Matassino
    • 12
  • Céline Désautés
    • 9
  • Erling Fimland
    • 15
  • Meena Bagga
    • 7
  • Juan-Vicente Delgado
    • 13
  • Jose L. Vega-Pla
    • 14
  • Amparo  M. Martinez
    • 13
  • Antonio M. Ramos
    • 16
  • Peter Glodek
    • 10
  • Johann-Nikolaus Meyer
    • 10
  • Graham S. Plastow
    • 7
  • Kenneth W. Siggens
    • 7
  • Alan L. Archibald
    • 4
  • Denis Milan
    • 17
  • Magali San Cristobal
    • 17
  • Guillaume Laval
    • 18
  • Keith Hammond
    • 8
  • Ricardo Cardellino
    • 8
  • Claude Chevalet
    • 17
  1. 1.INRA, Station de Génétique Quantitative et AppliquéeJouy en Josas CedexFrance
  2. 2.Rare Breeds Survival TrustShrewsbury, ShropshireUnited Kingdom
  3. 3.Deparment VSAUniversità degli Studi di MilanoMilanoItaly
  4. 4.Roslin InstituteMidlothianUnited Kingdom
  5. 5.Wageningen UniversityWageningenThe Netherlands
  6. 6.Labogena, Domaine de VilvertJouy-en-Josas CedexFrance
  7. 7.PIC International GroupKingston BackpuizeOxonUnited Kingdom
  8. 8.Animal Genetic Resources Group, FAOViale delle Terme di CaracallaRomaItaly
  9. 9.Agence de la Sélection PorcineParis Cedex 12France
  10. 10.Animal Genetics InstituteGöttingenGermany
  11. 11.DIPROVAL, Universita di BolognaCovioloReggio EmiliaItaly
  12. 12.ConsDABI-NFP.I-FAOLocalità Piano CappelleBeneventoItaly
  13. 13.Facultad de VeterinariaUniversidad de CordobaCordobaSpain
  14. 14.Laboratorio de Genetica MolecularFESSCRCordobaSpain
  15. 15.Nordic Gene Bank Farm AnimalsAasNorway
  16. 16.Universidade de Tras-os-Montes e Alto DouroVila Real CodexPortugal
  17. 17.INRA, Laboratoire de Génétique CellulaireCastanet Tolosan CedexFrance
  18. 18.Computational and Molecular Population Genetics LaboratoryBernSwitzerland

Personalised recommendations