Population structure in Tunisian indigenous rabbit ascertained using molecular information
DOI:
https://doi.org/10.4995/wrs.2014.1468Keywords:
Tunisian rabbit, microsatellite, genetic differentiation, genetic diversityAbstract
Understanding the genetic structure of domestic species provides a window into the process of domestication. This study attempts to offer an insight into the prevailing genetic status of Tunisian indigenous rabbit breeds using molecular markers. Thirty-six microsatellite loci were used to provide a comprehensive insight into the genetic status and relationship among 12 Tunisian indigenous rabbit populations. A total of 264 rabbits from villages of the Tozeur and Kebili regions were studied. Standard statistics parameters of genetic variability within and between populations were calculated. The observed heterozygosity, unbiased expected heterozygosity and the effective number of alleles were used to assess the genetic variation of each indigenous breed. Results show a high genetic diversity and observed heterozygosity ranged between 0.3 and 0.5, which implies that there is an abundant genetic variation stored in Tunisian indigenous rabbit breeds. Significant population differentiation was observed (Fst=0.11), which means that most of the genetic variation resides within breeds. The percentage of individuals correctly classified to their population was 85%. Breeds with more than one breeder origin were divided into subgroups, due to differences in gene frequencies between breeders, which in some cases creates a genetic differentiation even higher than that observed between distinct breeds. The current study is the first detailed analysis of the genetic diversity of Tunisian indigenous rabbit populations. The data generated here provides valuable information about the genetic structure of the 12 rabbit populations and this can be used to designate priorities for their conservation.
Downloads
References
Baldauf S.L. 2003. Phylogeny for the faint of heart: a tutorial. Trends in Genetics, 19: 345-351. doi:10.1016/S0168-9525(03)00112-4
Belkhir K., Borsa P., Chikhi L., Raufaste N., Bonhomme F. 2004. GENETIX v. 4.05, Logiciel sous WindowsTM pour la Génétique des Populations. Laboratoire Génome et Population, Université Montpellier II, Montpellier, France. Available at: http://kimura.univ-montp2.fr/genetix.
Ben Larbi M., Haddad B., Allalout S. 2008. Characterization of traditional rabbit breeding used in the south of Tunisia. In Proc.: 9th World Rabbit Congress, 10-13 June, 2008, Verona, Italy
Berthouly C., Bed’Hom B., Tixier-Boichard M., Chen C.F., Lee Y.P., Laloë D., Legros H., Verrier E., Rognon X. 2008. Using molecular markers and multivariate methods to study the genetic diversity of local European and Asian chicken breeds. Animal Genetics, 39: 121-129. doi:10.1111/j.1365-2052.2008.01703.x
Bolet G., Brun J.M., Monnerot M. , Abeni F., Arnal C., Arnold J., Bell D., Bergoglio G., Besenfelder U., Bosze S., Boucher S., Chanteloup N., Ducourouble M.C., Durand-Tardif M., Esteves P.J., Ferrand N., Gautier A., Haas C., Hewitt G., Jehl N., Joly T., Koehl P.F., Laube T., Lechevestrier S., Lopez M., Masoero G., Menigoz J.J., Piccinin R., Queney G., Saleil G., Surridge A., Van Der Loo W., Vicente J.S., Viudes De Castro M.P., Virag G., Zimmermann J.M. 2000. Evaluation and conservation of European rabbit (Oryctolagus Cuniculus) genetic resources. First results and Inferences, In Proc.: 7th World Rabbit Congress, 4-7 Juillet, 2000, Valencia, Spain, 281-315.
Bolet G., Monnerot M., Besenfelder U., Bosze S., Boucher S., Ferrand N., Hewitt G., Joly T., Lechevestrier S., Lopez M., Masoero G., Van Der Loo W., Vicente J., Virag G. 2002. Inventory, characterisation and conservation of European rabbit genetic resources. 7th World Congress on Genetics Applied to Livestock Production, August 19-23, 2002, Montpellier, France, Communication N° 04-11.
Bowcock A.M., Ruiz-Linares A., Tomfohrde J., Minch E., Kidd J.R., Cavalli-Sforza L.L. 1994. High resolution of human evolutionary trees with polymorphic microsatellites. Nature, 368, 455-457. doi:10.1038/368455a0
Branco M., Ferrand N., Monnerot M. 2000. Phylogeography of the European rabbit (Oryctolagus cuniculus) in the Iberian Peninsula inferred from RFLP analysis of the cytochrome b gene. Heredity, 85: 307-317. doi:10.1046/j.1365-2540.2000.00756.x
Carneiro M., Afonso S., Geraldes A., Garreau H., Bolet G., Boucher S., Tircazes A., Queney G., Nachman W., Ferrand N. 2011. The Genetic Structure of Domestic Rabbits. Mol. Biol. Evol., 28: 1801-1816. doi:10.1093/molbev/msr003
Chantry-Darmon C., Urien C., Hayes H., Bertaud M., Chadi-Taourit S., Chardon P., Vaiman D., Rogel-Gaillard C. 2005 Construction of a cytogenetically anchored microsatellite map in rabbit. Mamm. Genome, 16: 442-459. doi:10.1007/s00335-005-2471-z
Felsenstein, J. 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
Ferrand, N. 2008. Inferring the evolutionary history of the European rabbit (Oryctolagus cuniculus) from molecular markers. Lagomorph Biology 1: 47-65. doi:10.1007/978-3-540-72446-9_4
Grimal A., Safaa H.M., Saenz-de-Juano M.D., Viudes-de-Castro M.P., Mehaisen G.M.K., Elsayed D.A.A., Lavara R., Marco-Jiménez F., Vicente J.S. 2012. Phylogenetic relationship among four Egyptian and one Spanish rabbit populations based on microsatellite markers. In Proc.: 10th World Rabbit Congress, 3-6 September, 2012, Sharm El Shikh, Egypte.
Monnerot M., Vigne J.-D., Biju-Duval C., Casane D., Callou C., Hardy C., Mougel F., Soriguer R., Dennebouy N., Mounolou J.C. 1994. Rabbit and man: genetic and historic approach. Genetics Selection Evolution 26: 167s-182s. doi:10.1186/1297-9686-26-S1-S167
Mougel F. 1997. Variation de trois types de marqueurs génétiques dans l’évolution de l’espèce Oryctolagus cuniculus: Aspects moléculaires et relations avec la biologie et la structure des populations. Thèse de Doctorat, Université Paris- Sud, Orsay, France, pp. 306.
Mounolou J.C, Queney G., Bolet G., Dennebouy N., Monnerot M. 2003. Integrative Biology and Genetic Resources Management. Integr. Comp. Biol., 43: 271-275. doi:10.1093/icb/43.2.271
Muchadeyi F.C., Eding H., Wollny C.B.A., Groeneveld E., Makuza S.M., Shamseldin R., Simianer H., Weigend S. 2007. Absence of population substructuring in Zimbabwe chicken ecotypes inferred using microsatellite analysis. Animal Genetics, 38: 332-339. doi:10.1111/j.1365-2052.2007.01606.x
Nei M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York.
Pritchard J.K., Stephens M., Donnely P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
Queney G., Ferrand N., Weiss S., Mougel F., Monnerot M. 2001. Stationary distributions of microsatellite loci between divergent population groups of the European rabbit (Oryctolagus cuniculus). Mol. Biol. Evol., 18: 2169-2178. doi:10.1093/oxfordjournals.molbev.a003763
Raymond M., Rousset F. 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Hered., 86, 248-249er H. 1973
Reynolds J., Weir B.S., Cockerman C.C. 1983, Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105: 767-779.
Rogel-Gaillard C., Ferrand N, Hayes H. 2009. Rabbit in Genome Mapping and Genomics in Domestic Animals. Cockett N.E., Kole C. (Eds.). Springer-Verlag Berlin Heidelberg, 165-230. doi:10.1007/978-3-540-73835-0_7
Rousset F. 2008. Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resour., 8: 103-106. doi:10.1111/j.1471-8286.2007.01931.x
Saitou N., Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol. 4: 406-25.
Weir B.S., Cockerham C.C., 1984. Estimating F-statistics with special regard to system of mating. Evolution, 38, 1358-1370. doi:10.2307/2408641
Downloads
Published
Issue
Section
License
This journal is licensed under a "Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)".
