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Assessing priorities for conservation in Tuscan cattle breeds using microsatellites

Published online by Cambridge University Press:  22 August 2011

R. Bozzi*
Dipartimento di Biotecnologie Agrarie – Sezione Scienze Animali, Via delle Cascine 5, 50144 Firenze, Italy
I. Álvarez
SERIDA-Deva, Camino de Rioseco 1225, E-33394 Gijón (Asturias), Spain
A. Crovetti
Dipartimento di Biotecnologie Agrarie – Sezione Scienze Animali, Via delle Cascine 5, 50144 Firenze, Italy
I. Fernández
SERIDA-Deva, Camino de Rioseco 1225, E-33394 Gijón (Asturias), Spain
D. De Petris
Dipartimento di Biotecnologie Agrarie – Sezione Scienze Animali, Via delle Cascine 5, 50144 Firenze, Italy
F. Goyache
SERIDA-Deva, Camino de Rioseco 1225, E-33394 Gijón (Asturias), Spain
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Preservation of rare genetic stocks requires assessment of within-population genetic diversity and between-population differentiation to make inferences on their degree of uniqueness. A total of 194 Tuscan cattle (44 Calvana, 35 Chianina, 25 Garfagnina, 31 Maremmana, 31 Mucca Pisana and 28 Pontremolese) individuals were genotyped for 34 microsatellite markers. Moreover, 56 samples belonging to Argentinean Creole and Asturiana de la Montaña cattle breeds were used as an outgroup. Genetic diversity was quantified in terms of molecular coancestry and allelic richness. STRUCTURE analyses showed that the Tuscan breeds have well-differentiated genetic backgrounds, except for the Calvana and Chianina breeds, which share the same genetic ancestry. The between-breed Nei's minimum distance (Dm) matrices showed that the pair Calvana–Chianina was less differentiated (0.049 ± 0.006). The endangered Tuscan breeds (Calvana, Garfagnina, Mucca Pisana and Pontremolese) made null or negative contributions to diversity, except for the Mucca Pisana contribution to allelic richness (CT = 1.8%). The Calvana breed made null or negative within-breed contributions (W = 0.0%; CW = −0.4%). The Garfagnina and Pontremolese breeds made positive contributions to between-breed diversity but negative and high within-breed contributions, thus suggesting population bottleneck with allelic losses and increase of homozygosity in the population. Exclusion of the four endangered Tuscan cattle breeds did not result in losses in genetic diversity (T = −0.7%; CT = −1.2%), whereas exclusion of the non-endangered breeds (Chianina and Maremmana) did (T = 2.1%; CT = 3.9%); the simple exclusion of the Calvana breed from the former group led to losses in genetic diversity (T = 0.47%; CT = 2.34%), indicating a diverse significance for this breed. We showed how quantifying both within-population diversity and between-population differentiation in terms of allelic frequencies and allelic richness provides different and complementary information on the genetic backgrounds assessed and may help to implement priorities and strategies for conservation in livestock.

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Copyright © The Animal Consortium 2011

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These authors contributed equally to this work and shall share the first authorship.


Agenzia Regionale Sviluppo e Innovazione Agricoltura (ARSIA) 2006. Risorse genetiche animali autoctone della Toscana. (Autochthonous animal genetic resources of Tuscany). Press Service srl, Sesto Fiorentino, Italy.Google Scholar
Álvarez, I, Gutiérrez, JP, Royo, LJ, Fernández, I, Goyache, F 2009. Quantifying diversity losses due to selection for scrapie resistance in three endangered Spanish sheep breeds using microsatellite information. Preventive Veterinary Medicine 91, 172178.CrossRefGoogle ScholarPubMed
Álvarez, I, Royo, LJ, Pérez-Pardal, L, Fernández, I, Lorenzo, L, Goyache, F 2011. Assessing diversity losses due to selection for coat colour in the endangered bay-Asturcón pony using microsatellites. Livestock Science 135, 199204.CrossRefGoogle Scholar
Álvarez, I, Gutiérrez, JP, Royo, LJ, Fernández, I, Gómez, E, Arranz, JJ, Goyache, F 2005. Testing the usefulness of the molecular coancestry information to assess genetic relationships in livestock using a set of Spanish sheep breeds. Journal of Animal Science 83, 737744.CrossRefGoogle ScholarPubMed
Balducci, A 1920. Per il miglioramento e la diffusione della razza bovina della Calvana. In Proceedings of the X Congresso degli Allevatori della Regione Toscana, Firenze, 20–22 maggio 1920.Google Scholar
Beja-Pereira, A, Caramelli, D, Lalueza, C, Vernesi, C, Ferrand, N, Sampietro, L, Casoli, A, Goyache, F, Royo, LJ, Conti, S, Lari, M, Martini, A, Ouragh, L, Magid, A, Atash, A, Boscato, P, Triantophylidis, C, Ploumi, K, Sineo, L, Mallegni, F, Taberlet, P, Erhardt, G, Bertranpetit, J, Barbujani, G, Luikart, G, Bertorelle, G 2006. Genetic evidence for multiple origins of European cattle in Near-East, Africa, and Europe. Proceedings of the National Academy of Sciences of the USA 21, 81138118.CrossRefGoogle Scholar
Caballero, A, Toro, MA 2002. Analysis of genetic diversity for the management of conserved subdivided populations. Conservation Genetics 3, 289299.CrossRefGoogle Scholar
Caballero, A, Rodríguez-Ramilo, ST 2010. A new method for the partition of allelic diversity within and between subpopulations. Conservation Genetics 11, 22192229.CrossRefGoogle Scholar
Ciampolini, R, Cetica, V, Ciani, E, Mazzanti, E, Fosella, X, Marroni, F, Biagetti, C, Sebastiani, M, Papa, P, Filippini, G, Cianci, D, Presciuttini, S 2006. Statistical analysis of individual assignment tests among four cattle breeds using fifteen STR loci. Journal of Animal Science 84, 1119.CrossRefGoogle Scholar
Domestic Animal Diversity Information System 2010. Domestic Animal Diversity Information System (DADIS), Food and Agriculture Organization of the United Nations. Retrieved November 10, 2010, from Scholar
Eding, H, Meuwissen, THE 2001. Marker-based estimates of between and within population kinships for the conservation of genetic diversity. Journal of Animal Breeding and Genetics 118, 141159.CrossRefGoogle Scholar
Evanno, G, Regnaut, S, Goudet, J 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14, 26112620.CrossRefGoogle ScholarPubMed
Food and Agriculture Organization 2009. Preparation of national strategies and action plans for animal genetic resources. FAO Animal Production and Health Guidelines, No. 2, Rome.Google Scholar
Gandini, G, Villa, E 2003. Analysis of the cultural value of local livestock breeds: a methodology. Journal of Animal Breeding and Genetics 120, 111.CrossRefGoogle Scholar
Gandini, G, Ollivier, L, Danell, B, Distl, O, Georgoudis, A, Groeneveld, E, Martyniuk, E, van Arendonk, JAM, Woolliams, JA 2004. Criteria to assess the degree of endangerment of livestock breeds in Europe. Livestock Production Science 91, 173182.CrossRefGoogle Scholar
Ginja, C, Gama, LT, Penedo, MCT 2010a. Analysis of STR markers reveals high genetic structure in Portuguese native cattle. Journal of Heredity 101, 201210.CrossRefGoogle ScholarPubMed
Ginja, C, Penedo, MCT, Sobral, MF, Matos, J, Borges, C, Neves, D, Rangel-Figuereido, T, Cravador, A 2010b. Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed. Genetics Selection Evolution 42, 1828.CrossRefGoogle ScholarPubMed
Gutiérrez, JP, Royo, LJ, Álvarez, I, Goyache, F 2005. MolKin v2.0: a computer program for genetic analysis of populations using molecular coancestry information. Journal of Heredity 96, 718721.CrossRefGoogle ScholarPubMed
Hurlbert, SH 1971. The non concept of species diversity: a critique and alternative parameters. Ecology 52, 577586.CrossRefGoogle Scholar
Jakobsson, M, Rosenberg, NA 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 18011806.CrossRefGoogle ScholarPubMed
Jordana, J, Alexandrino, P, Beja-Pereira, A, Bessa, I, Cañon, J, Carretero, Y, Dunner, S, Laloë, D, Moazami-Goudarzi, K, Sanchez, A, Ferrand, N 2003. Genetic structure of eighteen local south European beef cattle breeds by comparative F-statistics analysis. Journal of Animal Breeding and Genetics 120, 7387.CrossRefGoogle Scholar
Kakoi, H, Tozaki, T, Gawahara, H 2008. Molecular analysis using mitochondrial DNA and microsatellites to infer the formation process of Japanese native horse populations. Biochemical Genetics 46, 101104.CrossRefGoogle Scholar
Lirón, JP, Bravi, CM, Mirol, PM, Peral-García, P, Giovambattista, G 2006. African matrilineages in American Creole cattle: evidence of two independent continental sources. Animal Genetics 37, 379382.CrossRefGoogle ScholarPubMed
Martín-Burriel, I, Rodellar, C, Lenstra, JA, Sanz, A, Cons, C, Osta, R, Reta, M, De Argüello, S, Sanz, A, Zaragoza, P 2007. Genetic diversity and relationships of endangered Spanish cattle breeds. Journal of Heredity 98, 687691.CrossRefGoogle ScholarPubMed
Meuwissen, THE 2009. Towards consensus on how to measure neutral genetic diversity? Journal of Animal Breeding and Genetics 126, 333334.CrossRefGoogle ScholarPubMed
Negrini, R, Milanesi, E, Bozzi, R, Pellecchia, M, Ajmone-Marsan, P 2006. Tuscany autochthonous cattle breeds: an original genetic resource investigated by AFLP markers. Journal of Animal Breeding and Genetics 123, 1016.CrossRefGoogle ScholarPubMed
Negrini, R, Nijman, IJ, Milanesi, E, Moazami-Goudarzi, K, Williams, JL, Erhardt, G, Dunner, S, Rodellar, C, Valentini, A, Bradley, DG, Olsaker, I, Kantanen, J, Ajmone-Marsan, P, Lenstra, JA 2007and European Cattle Genetic Diversity ConsortiumDifferentiation of European cattle by AFLP fingerprinting. Animal Genetics 38, 6066.CrossRefGoogle Scholar
Nei, M 1987. Molecular evolutionary genetics. Columbia University Press, New York.CrossRefGoogle Scholar
Ollivier, L, Foulley, JL 2005. Aggregate diversity: new approach combining within- and between-breed genetic diversity. Livestock Production Science 95, 247254.CrossRefGoogle Scholar
Pellecchia, M, Negrini, R, Colli, L, Patrini, M, Milanesi, E, Achilli, A, Bertorelle, G, Cavalli-Sforza, L, Piazza, A, Torroni, A, Ajmone-Marsan, P 2007. The mystery of Etruscan origins: novel clues from Bos taurus mitochondrial DNA. Proceedings of the Royal Society B: Biological Science 274, 11751179.CrossRefGoogle Scholar
Pérez-Pardal, L, Royo, LJ, Beja-Pereira, A, Curik, I, Traoré, A, Fernández, I, Sölkner, J, Alonso, J, Álvarez, I, Bozzi, R, Chen, S, Ponce de León, FA, Goyache, F 2010b. Y-specific microsatellites reveal an African subfamily in taurine (Bos taurus) cattle. Animal Genetics 41, 232241.CrossRefGoogle ScholarPubMed
Pérez-Pardal, L, Royo, LJ, Beja-Pereira, A, Chen, S, Cantet, RJC, Traoré, A, Curik, I, Sölkner, J, Bozzi, R, Fernández, I, Álvarez, I, Gutiérrez, JP, Gómez, E, Ponce de León, FA, Goyache, F 2010a. Multiple paternal origins of domestic cattle revealed by Y-specific interspersed multilocus microsatellites. Heredity 105, 511519.CrossRefGoogle Scholar
Pertoldi, C, Bijlsma, R, Loeschcke, V 2007. Conservation genetics in a globally changing environment: present problems, paradoxes and future challenges. Biodiversity and Conservation 16, 41474163.CrossRefGoogle Scholar
Petit, RJ, El Mousadik, A, Pons, O 1998. Identifying populations for conservation on the basis of genetic markers. Conservation Biology 12, 844855.CrossRefGoogle Scholar
Petrucci, A 1926. La razza bovina Calvana. Bollettino Speciale. XXVIII. Ed. Consorzio Zootecnico di Prato.Google Scholar
Pritchard, JK, Stephens, M, Donnelly, P 2000. Inference of population structure using multilocus genotype data. Genetics 155, 945959.CrossRefGoogle ScholarPubMed
Rousset, F 2008. Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Molecular Ecology Resources 8, 103106.CrossRefGoogle ScholarPubMed
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. Conservation Biology 17, 12991311.CrossRefGoogle Scholar
Royo, LJ, Pajares, G, Álvarez, I, Fernández, I, Goyache, F 2007. Genetic variability and differentiation in the Spanish roe deer (Capreolus capreolus): a phylogeographic reassessment in the European framework. Molecular Phylogenetics and Evolution 42, 4761.CrossRefGoogle ScholarPubMed
Sambrook, J, Fritsch, EF, Maniatis, T 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, USA.Google Scholar
Sargentini, C, Bozzi, R, Lorenzini, G, Degl'Innocenti, P, Martini, A, Giorgetti, A 2010. Productive performances of Maremmana young bulls reared following organic rules and slaughtered at 18 and 24 months of age. Italian Journal of Animal Science 9, 163168.CrossRefGoogle Scholar
Simianer, H, Reist-Marti, SB, Gibson, J, Hanotte, O, Rege, JEO 2003. An approach to the optimal allocation of conservation funds to minimise loss of genetic diversity between livestock breeds. Ecological Economics 45, 377392.CrossRefGoogle Scholar
Thaon d'Arnoldi, C, Foulley, JL, Ollivier, L 1998. An overview of the Weitzman approach to diversity. Genetics Selection and Evolution 30, 149161.CrossRefGoogle Scholar
Weitzman, ML 1992. On diversity. Quarterly Journal of Economics 107, 363405.CrossRefGoogle Scholar