Genetic relationships between six eastern Pyrenean sheep breeds assessed using microsatellites

Ainhoa Ferrando, Félix Goyache, Pere-Miquel Parés, Carlos Carrión, Jordi Miró, Jordi Jordana


The knowledge of the genetic composition and relationships among livestock breeds is a necessary step for the implementation of management and conservation plans. This study aims to characterise the genetic diversity and relationships among six sheep breeds of meat aptitude that are spread through the eastern Pyrenees: Tarasconnaise, Castillonnaise and Rouge du Roussillon from France, and Aranesa, Xisqueta and Ripollesa from Spain. All but Tarasconnaise are catalogued as endangered. These breeds do not share the same ancestral origin but commercial trades and gene flow between herds are known to have occurred for centuries. Additionally, two outgroup breeds were included: the Guirra, from a different geographical location, and the Lacaune, a highly selected breed of dairy aptitude. A total of 410 individuals were typed using a panel of 12 microsatellite markers. Statistical, phylogenetic and Bayesian analyses showed that eastern Pyrenean breeds retained high levels of genetic diversity and low, but significant, levels of genetic differentiation (FST = 4.1%). While outgroups were clearly differentiated from other breeds, Pyrenean breeds tended to form two clusters. The first encompassed Tarasconnaise and Aranesa, which probably descend from a common meta-population. The second tended to group the other four breeds. However, none reached high mean Q-values of membership to a discrete cluster. This is consistent with the recent past gene flow between breeds, despite different ancestral genetic origins. The genetic characterisation carried out of the eastern Pyrenean sheep populations provides useful information to support decision making on their conservation and focusing efforts and resources to more singular breeds.


genetic diversity; genetic resources; endangered breeds; European sheep

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Ajmone-Marsan P, Globaldiv Consortium, 2010. A global view of livestock biodiversity and conservation. Anim Genet 41: 1-5.

Alvarez I, Royo LJ, Fernández I, Gutiérrez JP, Gómez E, Goyache F, 2004. Genetic relationships and admixture among sheep breeds from Northern Spain assessed using microsatellites. J Anim Sci 82: 2246-2252.

Arranz JJ, Bayón Y, San Primitivo F, 2001. Genetic differentiation among Spanish sheep breeds using microsatellites. Genet Sel Evol 33: 529-542.

Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K, 1989. Currents Protocols in Molecular Biology. Vol. 2. John Wiley and Sons Inc., New York. 1600 pp.

Avellanet R, 2006. Conservación de recursos genéticos ovinos en la raza Xisqueta: caracterización estructural, racial y gestión de la diversidad en programas "in situ". Doctoral thesis. Universidad Autónoma de Barcelona, Barcelona.

Babo D, 2000. Races ovines et caprines françaises, Edits. France Agricole, Paris. 204 pp.

Baumung R, Cubric-Curik V, Schwend K, Achmann R, Söelkner J, 2006. Genetic characterisation and breed assignment in Austrian sheep breeds using microsatellite marker information. J Anim Breed Genet 123: 265-271.

Buchanan FC, Crawford AM, 1993. Ovine microsatellites at the OarFCB11, OarFCB128, OarFCB193, OarFCB266 and OarFCB304 loci. Anim Genet 24: 145.

Buchanan FC, Swarbrick PA, Crawford AM, 1992. Ovine dinucleotide repeat polymorphism at the MAF65 locus. Anim Genet 23: 85.

Calvo JH, Alvarez-Rodríguez J, Marcos-Carcavilla A, Serrano M, Sanz A, 2011. Genetic diversity in the Churra tensina and Churra lebrijana endangered Spanish sheep breeds and relationship with other Churra group breeds and Spanish mouflon. Small Rumin Res 95: 34-39.

Ciani E, Ciampolini B, D'Andrea M, Castellana E, Cecchi F, Incoronato C, D'Angelo F, Albenzio M, Pilla F, Matassino D, Cianci D, 2013. Analysis of genetic variability within and among Italian sheep breeds reveals population stratification and suggests the presence of a phylogeographic gradient. Small Rumin Res 112: 21-27.

Cinkulov M, Popovski Z, Porcu K, Tanaskovska B, Hodzic A, Bytyqi H, Mehmeti H, Margeta V, Djedovic R, Hoda A, et al., 2008. Genetic diversity and structure of the West Balkan Pramenka sheep types as revealed by microsatellite and mitochondrial DNA analysis. J Anim Breed Genet 125: 417-426.

Earl DA, vonHoldt BM, 2012. Structure Harvester: a website and program for visualizing Structure output and implementing the Evanno method. Conservation Genet Resour 4: 359-361.

Ede AJ, Pierson CA, Crawford AM, 1995. Ovine microsatellites at the OarCP34, OarCP38, OarCP43, OarCP49, OarCP73, OarCP79 and OarCP99 loci. Anim Genet 26: 130-131.

El Mousadik A, Petit RJ, 1996. High level of genetic differentiation for allelic richness among populations of the argan tree (Argania spinosa (L) Skeel) endemic to Morocco. Theor Appl Genet 92: 832-839.

Esteban C, 2003. Razas ganaderas españolas. II. Ovinas. Ed. FEAGAS y Ministerio de Agricultura, Pesca y Alimentación, Madrid. 470 pp.

Evanno G, Regnaut S, Goudet J, 2005. Detecting the number of clusters of individuals using the software Structure: a simulation study. Mol Ecol 4: 2611-2620.

FAO, 2009. Preparation of national strategies and action plans for animal genetic resources. FAO Animal Production and Health Guidelines, No. 2, Rome. 70 pp.

Glowatzki-Mullis ML, Muntwyler J, Baeumle E, Gaillard C, 2009. Genetic diversity of Swiss sheep breeds in the focus of conservation research. J Anim Breed Genet 126: 164-175.

Goudet J, 2001. FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Updated from Goudet (1995). Available in [25 April, 2012].

Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay K, Jianlin H, Groeneveld E, et al., 2010. Genetic diversity in farm animals-A review. Anim Genet 41: 6-31.

Handley LJL, Byrne K, Santucci F, Townsend S, Taylor M, Bruford MW, Hewitt GM, 2007. Genetic structure of European sheep breeds. Heredity 99: 620-631.

Hoffmann I, 2011. Livestock biodiversity and sustainability. Livest Sci 139: 69-79.

Hulme DJ, Silk JP, Redwin J, Barense WR, Beh KJ, 1994. Ten polymorphic ovine microsatellites. Anim Genet 25: 434-435.

Hulme DJ, Davies KP, Beh KJ, Maddox JF, 1996. Ovine dinucleotide repeat polymorphism at the McM218, McM150 and McM138 loci. Anim Genet 26: 57.

Kusza S, Nagy I, Sasvári Z, Stágel A, Németh T, Molnár A, Kume K, Bósze Z, Jávor A, Kukovics S, 2008. Genetic diversity and population structure of Tsigai and Zackel type of sheep breeds in the Central-, Eastern- and Southern-European regions. Small Rumin Res 78: 13-23.

Kusza S, Gyarmathy E, Dubravska J, Nagy I, Jávor A, Kukovics S, 2009. Study of genetic differences among Slovak Tsigai populations using microsatellite markers. Czech J Anim Sci 54: 468-474.

Langella O, 1999. Populations 1.2.31. CNRS UPR9034. Available in [7 May, 2012].

Ligda C, Altarayrah J, Georgoudis A, Econogene Consortium, 2009. Genetic analysis of Greek sheep breeds using microsatellite markers for setting conservation priorities. Small Rumin Res 83: 42-48.

Luikart G, Alendorf F.W, Sherwin B, Cornuet JM, 1998. Distortion of allele frequency distributions provide a test of recent population bottlenecks. J Hered 12: 238-247.

Nei M, Tajima R, Tateno Y, 1983. Accuracy of estimated phylogenetic threes from molecular data. J Mol Evol 19: 153-170.

Parés PM, 2008. Caracterització estructural i racial de la raça ovina Aranesa. Doctoral thesis. Universitat Autònoma de Barcelona, Barcelona. [In Catalan].

Parés PM, Perezgrovas R, Jordana J, 2011. Comparison of four European endangered red sheep based on fleece characteristics. Anim Genet Resour 48: 85-91.

Peter C, Bruford M, Perez T, Dalamitra S, Hewitt G, Erhardt G, Econogene Consortium, 2007. Genetic diversity and subdivision of 57 European and Middle-Eastern sheep breeds. Anim Genet 38: 37-44.

Piry S, Luikart G, Cornuet J.M, 1999. Bottleneck: A computer program for detecting recent reductions in effective population size from allele frequency data. J Hered 90: 502-503.

Pritchard J, Stephens M, Donnelly P, 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.

Salamon D, Gutiérrez-Gil B, Arranz J.J, Barreta J, Batinic V, Dzidic A, 2014. Genetic diversity and differentiation of 12 eastern Adriatic and western Dinaric native sheep breeds using microsatellites. Animal 8: 200-207.

Sánchez-Belda A, Sánchez-Trujillano MC, 1986. Razas ovinas españolas. Ed. FEAGAS y Ministerio de Agricultura, Pesca y Alimentación, Madrid. 877 pp.

Santos-Silva F, Ivo RS, Sousa MCO, Carolino MI, Ginja C, Gama LT, 2008. Assessing genetic diversity and differentiation in Portuguese coarse-wool sheep breeds with microsatellite markers. Small Rumin Res 78: 32-40.

Schneider S, Kueffer JM, Roessli D, Excoffier L, 1997. Arlequin: a software for population genetics data analysis, vers. 1.1. Genetics and Biometry Laboratory, Dept. of Anthropology, University of Geneva, Switzerland. 174 pp.

Scott PC, Maddox JF, Gogolin-Ewens KJ, Brandon MR, 1991. Inmunogenetics 34: 80-87.

Reynolds J, Weir BS, Cockerham CC, 1983. Estimation of the coancestry coefficient: Basis for a short-term genetic distance. Genetics 105: 767-779.

Takezaki N, Nei M, 1996. Genetic distance and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144: 389-399.

Tapio M, Tapio I, Grislis Z, Holm LE, Jeppsson S, Kantanen J, Miceikiene I, Olsaker I, Viinalass H, Eythorsdottir E, 2005. Native breeds demonstrate high contributions to the molecular variation in northern European sheep. Mol Ecol 14: 3951-3963.

Tapio M, Ozerov M, Tapio I, Toro MA, Marzanov N, Ćinkulov M, Goncharenko G, Kiselyova T, Murawski M, Kantanen J, 2010. Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia. BMC Genetics 11: 76.

Tolone M, Mastrabgelo S, Rosa AJM, Portolano B, 2012. Genetic diversity and population structure of Sicilian sheep breeds using microsatellite markers. Small Rumin Res 102: 18-25.

Vainman D, Mercier D, Moazami-Goudarzi K, Eggen A, Ciampolini R, Lépingle A, Velmala R, Kaukinen J, Varvio SL, Martin P, 1994. A set of 99 cattle microsatellites: characterization, synteny mapping and polymorphism. Mammalian 5: 288-297.

Weir BS, Cockerham CC, 1984. Estimating F statistics for the analyses of population structure. Evolution 38: 1358-1370.

Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, et al., 1999. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol 10: 42.

DOI: 10.5424/sjar/2014124-6173