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PloS one2013; 8(4); e61544; doi: 10.1371/journal.pone.0061544

Genetic structure and gene flows within horses: a genealogical study at the french population scale.

Abstract: Since horse breeds constitute populations submitted to variable and multiple outcrossing events, we analyzed the genetic structure and gene flows considering horses raised in France. We used genealogical data, with a reference population of 547,620 horses born in France between 2002 and 2011, grouped according to 55 breed origins. On average, individuals had 6.3 equivalent generations known. Considering different population levels, fixation index decreased from an overall species FIT of 1.37%, to an average [Formula: see text] of -0.07% when considering the 55 origins, showing that most horse breeds constitute populations without genetic structure. We illustrate the complexity of gene flows existing among horse breeds, a few populations being closed to foreign influence, most, however, being submitted to various levels of introgression. In particular, Thoroughbred and Arab breeds are largely used as introgression sources, since those two populations explain together 26% of founder origins within the overall horse population. When compared with molecular data, breeds with a small level of coancestry also showed low genetic distance; the gene pool of the breeds was probably impacted by their reproducer exchanges.
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Publication Date: 2013-04-22 PubMed ID: 23630596PubMed Central: PMC3632587DOI: 10.1371/journal.pone.0061544Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research examined the genetic structure and gene flows within horse populations in France. It found that most horse breeds do not have a fixed genetic structure and there is a complex network of gene flow between breeds.

Research Methodology

  • The researchers used genealogical data from a population of 547,620 horses born in France between 2002 and 2011.
  • The horses were grouped according to 55 different breed origins.
  • The researchers assessed the equivalent generations known for each horse and found an average of 6.3 equivalent generations.

Findings:

  • The study found that the fixation index, a measure of genetic diversity within a population, did vary when looking at different populations and level.
  • Across the species as a whole, there was a fixation index (FIT) of 1.37% suggesting some level of genetic structure.
  • However, when viewing the 55 origins or breed groups, this decreased to an average of -0.07% suggesting a lack of genetic structure within breeds.

Gene Flows Among Horse Breeds

  • The research found a complex pattern of gene flow between horse breeds, with few populations being closed off to foreign influence.
  • Most breeds show varying levels of introgression, which refers to the transfer of genetic information from one species to another following periods of interbreeding.
  • Two breeds, the Thoroughbred and Arab, were identified as primary sources of gene introgression accounting for 26% of founder origins within the total horse population.

Comparison with Molecular Data

  • When compared with molecular data, breeds with low levels of coancestry also showed low genetic distance.
  • This suggests that the gene pool of the breeds was likely influenced by the number of exchanges between breeders.

This research provides a comprehensive analysis of the genetic structure and gene flows within horse breeds in France. The results improve our understanding of the genetic complexity of domestic horse populations, which could inform breeding practices and conservation efforts.

Cite This Article

APA
Pirault P, Danvy S, Verrier E, Leroy G. (2013). Genetic structure and gene flows within horses: a genealogical study at the french population scale. PLoS One, 8(4), e61544. https://doi.org/10.1371/journal.pone.0061544

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 8
Issue: 4
Pages: e61544
PII: e61544

Researcher Affiliations

Pirault, Pauline
  • AgroParisTech, Unité Mixte de Recherche 1313 Génétique Animale et Biologie Intégrative, Paris, France.
Danvy, Sophy
    Verrier, Etienne
      Leroy, Grégoire

        MeSH Terms

        • Animals
        • Founder Effect
        • France
        • Gene Flow
        • Genetic Variation
        • Genetics, Population
        • Horses / genetics
        • Inbreeding
        • Models, Genetic
        • Pedigree
        • Phylogeny
        • Probability

        Conflict of Interest Statement

        The authors have declared that no competing interests exist.

        References

        This article includes 30 references
        1. Porter V, Mason L. A World Dictionary of Livestock Breeds, Types, and Varieties, 5th edition.. 2002.
        2. Moureaux S, Verrier E, Ricard A, Meriaux JC. Genetic variability within French race and riding horse breeds from genealogical data and blood marker polymorphisms.. Genet Sel Evol 28: 83–102.
        3. Cervantes I, Gutiérrez JP, Molina A, Goyache F, Valera M. Genealogical analyses in open populations: the case of three Arab-derived Spanish horse breeds.. J Anim Breed Genet 2009 Oct;126(5):335-47.
          pubmed: 19765160doi: 10.1111/j.1439-0388.2008.00797.xgoogle scholar: lookup
        4. Bartolomé E, Cervantes I, Valera M, Gutiérrez JP. Influence of foreign breeds on the genetic structure of the Spanish Sport Horse population.. Livest Sci 142: 70–79.
        5. Aberle K, Wrede J, Distl O. Analysis of relationships between German heavy horse breeds based on pedigree information.. Berl Munch Tierarztl Wochenschr 2004 Jan-Feb;117(1-2):72-5.
          pubmed: 14964127
        6. Achmann R, Curik I, Dovc P, Kavar T, Bodo I, Habe F, Marti E, Sölkner J, Brem G. Microsatellite diversity, population subdivision and gene flow in the Lipizzan horse.. Anim Genet 2004 Aug;35(4):285-92.
          pubmed: 15265067doi: 10.1111/j.1365-2052.2004.01157.xgoogle scholar: lookup
        7. Leroy G, Callède L, Verrier E, Mériaux JC, Ricard A, Danchin-Burge C, Rognon X. Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism.. Genet Sel Evol 2009 Jan 5;41(1):5.
          pmc: PMC3225878pubmed: 19284689doi: 10.1186/1297-9686-41-5google scholar: lookup
        8. Plante Y, Vega-Pla JL, Lucas Z, Colling D, de March B, Buchanan F. Genetic diversity in a feral horse population from Sable Island, Canada.. J Hered 2007 Sep-Oct;98(6):594-602.
          pubmed: 17855732doi: 10.1093/jhered/esm064google scholar: lookup
        9. Prystupa JM, Juras R, Cothran EG, Buchanan FC, Plante Y. Genetic diversity and admixture among Canadian, Mountain and Moorland and Nordic pony populations.. Animal 2012 Jan;6(1):19-30.
          pubmed: 22436150doi: 10.1017/s1751731111001212google scholar: lookup
        10. Petersen JL, Mickelson JR, Cothran EG, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P, da Câmara Machado A, Distl O, Felicetti M, Fox-Clipsham L, Graves KT, Guérin G, Haase B, Hasegawa T, Hemmann K, Hill EW, Leeb T, Lindgren G, Lohi H, Lopes MS, McGivney BA, Mikko S, Orr N, Penedo MC, Piercy RJ, Raekallio M, Rieder S, Røed KH, Silvestrelli M, Swinburne J, Tozaki T, Vaudin M, M Wade C, McCue ME. Genetic diversity in the modern horse illustrated from genome-wide SNP data.. PLoS One 2013;8(1):e54997.
          pmc: PMC3559798pubmed: 23383025doi: 10.1371/journal.pone.0054997google scholar: lookup
        11. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data.. Genetics 2000 Jun;155(2):945-59.
          pmc: PMC1461096pubmed: 10835412doi: 10.1093/genetics/155.2.945google scholar: lookup
        12. Mucha S, Windig JJ. Effects of incomplete pedigree on genetic management of the Dutch Landrace goat.. J Anim Breed Genet 2009 Jun;126(3):250-6.
          pubmed: 19646154doi: 10.1111/j.1439-0388.2008.00757.xgoogle scholar: lookup
        13. Boichard D, Maignel L, Verrier E. Value of using probabilities of gene origin to measure genetic variability in a population.. Genet SelEvol 29: 5–23.
        14. Leroy G, Baumung R. Mating practices and the dissemination of genetic disorders in domestic animals, based on the example of dog breeding.. Anim Genet 2011 Feb;42(1):66-74.
          pubmed: 20528847doi: 10.1111/j.1365-2052.2010.02079.xgoogle scholar: lookup
        15. Malécot G. Les mathématiques de l'hérédité.. 1948.
        16. Caballero A, Toro MA. Analysis of genetic diversity for the management of conserved subdivided populations.. Conserv Genet 3: 289–299.
        17. Cervantes I, Goyache F, Molina A, Valera M, Gutiérrez JP. Estimation of effective population size from the rate of coancestry in pedigreed populations.. J Anim Breed Genet 2011 Feb;128(1):56-63.
          pubmed: 21214645doi: 10.1111/j.1439-0388.2010.00881.xgoogle scholar: lookup
        18. Reynolds J, Weir BS, Cockerham CC. Estimation of the coancestry coefficient: basis for a short-term genetic distance.. Genetics 1983 Nov;105(3):767-79.
          pmc: PMC1202185pubmed: 17246175doi: 10.1093/genetics/105.3.767google scholar: lookup
        19. Boichard D. PEDIG: a fortran package for pedigree analysis suited for large populations. 2002 19–23 August 2002; Montpellier.
        20. Druml T, Curik I, Baumung R, Aberle K, Distl O, Sölkner J. Individual-based assessment of population structure and admixture in Austrian, Croatian and German draught horses.. Heredity (Edinb) 2007 Feb;98(2):114-22.
          pubmed: 17035951doi: 10.1038/sj.hdy.6800910google scholar: lookup
        21. Bigi D, Perrotta G. Genetic structure and differentiation of the Italian catria horse.. J Hered 2012 Jan-Feb;103(1):134-9.
          pubmed: 22156056doi: 10.1093/jhered/esr121google scholar: lookup
        22. van de Goor LH, van Haeringen WA, Lenstra JA. Population studies of 17 equine STR for forensic and phylogenetic analysis.. Anim Genet 2011 Dec;42(6):627-33.
          pubmed: 22035004doi: 10.1111/j.1365-2052.2011.02194.xgoogle scholar: lookup
        23. McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, Binns MM, Distl O, Guérin G, Hasegawa T, Hill EW, Leeb T, Lindgren G, Penedo MC, Røed KH, Ryder OA, Swinburne JE, Tozaki T, Valberg SJ, Vaudin M, Lindblad-Toh K, Wade CM, Mickelson JR. A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies.. PLoS Genet 2012 Jan;8(1):e1002451.
          pmc: PMC3257288pubmed: 22253606doi: 10.1371/journal.pgen.1002451google scholar: lookup
        24. Danchin-Burge C, Leroy G, Brochard M, Moureaux S, Verrier E. Evolution of the genetic variability of eight French dairy cattle breeds assessed by pedigree analysis.. J Anim Breed Genet 2012 Jun;129(3):206-17.
          pubmed: 22583325doi: 10.1111/j.1439-0388.2011.00967.xgoogle scholar: lookup
        25. Fernández J, Villanueva B, Pong-Wong R, Toro MA. Efficiency of the use of pedigree and molecular marker information in conservation programs.. Genetics 2005 Jul;170(3):1313-21.
          pmc: PMC1451183pubmed: 15879510doi: 10.1534/genetics.104.037325google scholar: lookup
        26. Leroy G. Genetic diversity, inbreeding and breeding practices in dogs: results from pedigree analyses.. Vet J 2011 Aug;189(2):177-82.
          pubmed: 21737321doi: 10.1016/j.tvjl.2011.06.016google scholar: lookup
        27. Leroy G, Mary-Huard T, Verrier E, Danvy S, Charvolin E, Danchin-Burge C. Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse.. Genet Sel Evol 2013 Jan 2;45(1):1.
          pmc: PMC3599586pubmed: 23281913doi: 10.1186/1297-9686-45-1google scholar: lookup
        28. Hamann H, Distl O. Genetic variability in Hanoverian warmblood horses using pedigree analysis.. J Anim Sci 2008 Jul;86(7):1503-13.
          pubmed: 18310493doi: 10.2527/jas.2007-0382google scholar: lookup
        29. Lauvie A, Danchin-Burge C, Audiot A, Brives H, Casabianca F. A controversy about crossbreeding in a conservation programme: The case study of the Flemish Red cattle breed.. Livest Sci 118: 113–122.
        30. Quignon P, Herbin L, Cadieu E, Kirkness EF, Hédan B, Mosher DS, Galibert F, André C, Ostrander EA, Hitte C. Canine population structure: assessment and impact of intra-breed stratification on SNP-based association studies.. PLoS One 2007 Dec 19;2(12):e1324.
          pmc: PMC2129117pubmed: 18091995doi: 10.1371/journal.pone.0001324google scholar: lookup

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        5. Winton CL, McMahon R, Hegarty MJ, McEwan NR, Davies-Morel MCG, Morgan C, Nash DM. Genetic diversity within and between British and Irish breeds: The maternal and paternal history of native ponies. Ecol Evol 2020 Feb;10(3):1352-1367.
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        8. Farmer K, Krüger K, Byrne RW, Marr I. Sensory laterality in affiliative interactions in domestic horses and ponies (Equus caballus). Anim Cogn 2018 Sep;21(5):631-637.
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