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Genetic Diversity of a Large Set of Horse Breeds Raised in France

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Genetic Diversity of a Large Set of Horse Breeds Raised in France Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism Grégoire Leroy, Lucille Callède, Etienne Verrier, J-Claude Meriaux, Anne Ricard, Coralie Danchin-Burge, Xavier Rognon To cite this version: Grégoire Leroy, Lucille Callède, Etienne Verrier, J-Claude Meriaux, Anne Ricard, et al.. Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism. Genetics Selection Evolution, BioMed Central, 2009, 41, online (january), Non paginé. 10.1186/1297- 9686-41-5. hal-02667090 HAL Id: hal-02667090 https://hal.inrae.fr/hal-02667090 Submitted on 31 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Genetics Selection Evolution BioMed Central Research Open Access Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism Grégoire Leroy*1,2, Lucille Callède1,2, Etienne Verrier1,2, Jean- Claude Mériaux3, Anne Ricard4, Coralie Danchin-Burge1,2 and Xavier Rognon1,2 Address: 1AgroParisTech, UMR1236 Génétique et Diversité Animales, 16 rue Claude Bernard F-75321 Paris, France, 2INRA, UMR1236 Génétique et Diversité Animales, 78352 Jouy-en-Josas, France, 3LABOGENA, F-78352 Jouy-en-Josas, France and 4INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan, France Email: Grégoire Leroy* - [email protected]; Lucille Callède - [email protected]; Etienne Verrier - [email protected]; Jean-Claude Mériaux - [email protected]; Anne Ricard - [email protected]; Coralie Danchin-Burge - [email protected]; Xavier Rognon - [email protected] * Corresponding author Published: 5 January 2009 Received: 16 December 2008 Accepted: 5 January 2009 Genetics Selection Evolution 2009, 41:5 doi:10.1186/1297-9686-41-5 This article is available from: http://www.gsejournal.org/content/41/1/5 © 2009 Leroy et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract The genetic diversity and structure of horses raised in France were investigated using 11 microsatellite markers and 1679 animals belonging to 34 breeds. Between-breed differences explained about ten per cent of the total genetic diversity (Fst = 0.099). Values of expected heterozygosity ranged from 0.43 to 0.79 depending on the breed. According to genetic relationships, multivariate and structure analyses, breeds could be classified into four genetic differentiated groups: warm-blooded, draught, Nordic and pony breeds. Using complementary maximisation of diversity and aggregate diversity approaches, we conclude that particular efforts should be made to conserve five local breeds, namely the Boulonnais, Landais, Merens, Poitevin and Pottok breeds. Introduction in general expensive. Therefore, it would be useful to iden- During the twentieth century, horse breeding has under- tify priorities among conservation purposes and this gone large changes in Europe. Previously considered as an requires characterising diversity and genetic relations agricultural, industrial and war tool, horse is now essen- between breeds [1]. tially bred for hobby riding. Draught horses, in particular, have been less and less used as utility horses, and many During the last fifteen years, microsatellite markers have draught breeds have undergone a dramatic decrease in frequently been used to evaluate genetic distances and to population size: according to the Haras Nationaux, out of characterise local breeds, [2-10]. Some methods have the nine French draught breeds, six have annual births recently been developed to evaluate the genetic contribu- below 1000. Measures for in situ conservation have been tion of populations to within-breed and between-breed applied in France for several years but such measures are diversities [11,12]. Page 1 of 12 (page number not for citation purposes) Genetics Selection Evolution 2009, 41:5 http://www.gsejournal.org/content/41/1/5 With about 800 000 animals belonging to 50 different French origin, or having been bred in France for at least breeds (source: Haras Nationaux), France shows a large 100 years (PS, AA and AR breeds). In this approach, 50 diversity of horse populations. Among these breeds, 21 animals were randomly sampled among the four and have a French origin or have been bred in France for at three AA and SF subpopulations, respectively, to consti- least a century. According to the FAO, at least 15 popula- tute two populations. tions have disappeared during the last 50 years, and eight indigenous breeds are still considered as endangered or Eleven microsatellite markers were used to perform the endangered-maintained. Among those breeds, the major- analysis (AHT4, AHT5, ASB2, HMS1, HMS3, HMS6, ity are draught breeds, namely the Ardennais, Auxois, HMS7, HTG4, HTG6, HTG10, VHL20), with all but two Boulonnais, Poitevin and Trait du Nord breeds, the other (HMS1 and HTG6) being recommended by the Interna- ones being the Merens warm-blooded breed and the tional Society of Animal Genetics for parentage testing Landais and Pottock pony breeds. Information on the and used in similar studies (except HMS1) [7,9,10]. For genetic diversity of French endangered breeds could help the entire sample, amplifications and analyses were per- breeders and providers, decide where they should place formed by the same laboratory, using a capillary more emphasis. sequencer (ABI PRISM 3100 Genetic Analyzer, Applied Biosystems). In the present study, we first analysed the genetic diversity of 39 horse populations reared in France: within-breed Statistical analysis diversity, breed relationship and population structure Allele frequencies, mean number of alleles (MNA), were investigated, using microsatellite data. Then, we observed (Ho) and non-biased expected heterozygosity focussed on 19 breeds of French origin or having been (He), were calculated using GENETIX [13]. Wright Fis, Fit raised in France for at least a century, and evaluated the and Fst coefficients were also computed using the same conservation priorities between these populations, using software. GENEPOP [14] was used to evaluate pairwise different approaches to evaluate within, between and total genetic differentiation between breeds [15] and departure diversity. from Hardy-Weinberg equilibrium, using exact tests and sequential Bonferonni correction [16] on loci. Global Methods tests on Hardy-Weinberg equilibrium were also per- Populations sampled and microsatellite analysis formed using GENEPOP. Allelic richness was computed French nomenclature divides horse breeds into three using FSTAT [17]. groups: warm-blooded, draught horses and ponies. In this study, 39 populations were considered (Table 1). These The matrix of Reynolds unweighted distances DR [18] was 39 populations comprised 31 recognised breeds (includ- computed using POPULATION (Olivier Langella; http:// ing 13 warm-blooded breeds, nine draught breeds, and bioinformatics.org/~tryphon/populations/). Regarding nine pony breeds), the primitive Przewalski horse (used the DR distance, a NeighborNet tree was drawn using as an outgroup), and seven populations originating from SPLITSTREE 4.8 [19]. A factorial correspondence analysis the splitting of two recognised breeds, namely the Anglo- (without the Przewalsky horse) was also performed using Arab (AA) and Selle Français (SF) breeds (divided into GENETIX. Finally, the genetic structure of the populations four and three groups, respectively). The 2005 studbook was assessed using Bayesian clustering methods devel- rules define those groups according to the proportion of oped by Pritchard (STRUCTURE, [20]): using a model foreign genes that can be found from genealogical analy- with admixture and correlated allele frequencies, we made sis: AA6 and AA9 are considered as pure AA, whereas AA5 20 independent runs for each value of the putative and AA10 can have ancestors from another origin, the number of sub-populations (K) between 1 and 22, with a proportion of Arab origin being higher for AA5 and AA6 burn-in period of 20 000 followed by 100 000 MCMC than the others. SF8 has a large proportion of PS origin repetitions. Pairwise similarities (G) between runs were and can therefore be used to produce AA, SFA97 consti- computed using CLUMPP [21]. tutes a group closed to direct foreign influences, whereas SFB98 individuals can have a parent from another breed To evaluate the conservation priorities in a set of popula- (under some conditions). tions, taking into account contributions to within-popula- tion and between-population genetic diversity, Ollivier For each of the 39 populations, 23 to 50 animals born and Foulley [12] have proposed the following method. between 1996 and 2005, were
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