Status and origin of Egyptian local rabbits in comparison with Spanish common rabbits using mitochondrial DNA sequence analysis

Ahmed Mostafa Emam, Sandra Afonso, Pedro González-Redondo, G.M.K. Mehaisen, A.A.A. Azoz, N.A. Ahmed, N. Fernand


Mitochondrial DNA (mtDNA) and cytochrome b (cyt b) gene sequences were used to determine the status of genetic diversity and phylogeny for 132 individuals from local rabbit breeds in Egypt and Spain. The Egyptian local rabbit breeds were Egyptian Red Baladi (ERB), Egyptian Black Baladi (EBB) and Egyptian Gabali Sinai (EGS). However, the Spanish local rabbit breed was Spanish common rabbit (SCR). Previous breeds were compared with European Wild Rabbit taken from Albacete, Spain (EWR). A total of 353 mutations, 290 polymorphic sites, 14 haplotypes, 0.06126 haplotype diversity and –1.900 (P<0.05) for Tajima’s D were defined in this study. Haplotype A mostly occurred in 83.3% of Egyptian rabbits and 11.7 % of EWR, while haplotype B occurred in 63.8% of Spanish rabbits and 36.2% of the EGS breed. A total of 47 domestic and wild Oryctolagus cuniculus published sequences were used to investigate the origin and relation among the rabbit breeds tested in this study. The most common haplotype (A) was combined with 44.7% of published sequences. However, haplotype B was combined with 8.5%. Haplotypes of Egyptian, SCR and EWR were scattered in cluster 1, while we found only one EGS haplotype with two haplotypes of EWR in cluster 2. Our results assumed that genetic diversity for ERB, EBB and SCR was very low. Egyptian breeds and SCR were introduced from European rabbits. We found that ERB and EBB belong to one breed.


Egyptian rabbits; Spanish common rabbit; genetic diversity; mitochondrial DNA

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Abrantes J., Areal H., Esteves P.J. 2013. Insights into the European rabbit (Oryctolagus cuniculus) innate immune system: genetic diversity of the toll-like receptor 3(TLR3) in wild populations and domestic breeds. BMC Genet., 14: 73.

Achilli A., Olivieri A., Pellecchia M., Uboldi C., Colli L., Al-Zahery N., Accetturo M., Pala M., Kashani B.H., Perego U.A., Battaglia V., Fornarino S., Kalamati J., Houshmand M., Negrini R., Semino O., Richards M., Macaulay V., Ferretti L., Bandelt H.J., Ajmone-Marsan P., Torroni A. 2008. Mitochondrial genomes of extinct aurochs survive in domestic cattle. Curr. Biol., 18: R157-R158.

Alves J.M., Carneiro, M., Afonso S., Lopes S., Garreau H., Boucher S., Allian D., Queney G., Esteves P.J., Bolet J. and Ferrnand N. 2015. Levels and patterns of genetic diversity and population structure in domestic rabbits. PLoS One 10 (12): e0144687.

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 July 2000, Valencia, Spain, pp. 281-315.

Bollback J.P., Huelsenbeck J.P. 2007. Clonal interference is alleviated by high mutation rates in large populations. Mol. Biol. Evol., 24: 1397-1406.

Bortoluzzi C., Bosse M., Derks M.F.L., Crooijmans R., Groenen M.A.M, Megens H.J. 2019. The type of bottleneck matters: Insights into the deleterious variation landscape of small managed populations. Evol Appl., 13: 330-341.

Brook B.W. 2008. Demographics versus genetics in conservation biology. In: Carrol, S.P. and Fox, C.W. (eds). Conservation Biology: Evolution in Action. Oxford University Press: USA. 35-49.

Campos, R., Storz, J.F., Ferrand, N. 2012. Copy number polymorphism in the α-globin gene cluster of European rabbit (Oryctolagus cuniculus). Heredity, 108: 531-536.

Carneiro M., Afonso S., Geraldes A., Garreau H., Bolet G., Boucher S., Tircazes A., Queney G., Nachman M.W., Ferrand N. 2011. The genetic structure of domestic rabbits. Mol. Biol. Evol., 28: 1801-1816.

Carneiro M., Albert F.W., Melo-Ferreira J., Galtier N., Gayral P., Blanco-Aguiar J.A., Villafuerte R., Nachman N.M., Ferrand N. 2012. Evidence for widespread positive and purifying selection across the European rabbit (Oryctolagus cuniculus) genome. Mol. Biol. Evol., 29: 1837-1849.

Christensen N.D., Peng X. 2012. Rabbit genetic and transgenic model. In: The Laboratory Rabbit, Guinea pig, Hamster and other Rodents (Eds. Suckow, M.A., Stevens, K.A. and Wilson, R.P). Elsevier, USA, pp. 165-194.

Christodoulakis M., Golding G.B., Iliopoulos C.S., Pinzón Ardila Y.J., Smyth W.F. 2007. Efficient algorithms for counting and reporting segregating sites in genomic sequences. J. Comput. Biol., 14: 1001-1010.

Emam A.M., Afonso, S., Azoz, A., Mehaisen, G.M.K., Gonzalez, P.; Ahmed, N.A., Ferrnand N. 2016. Microsatellite polymorphism in some Egyptian and Spanish common rabbit breeds. In Proc.: 11th World Rabbit Congress, 15-18 June 2016, Qingdao, China. pp: 31-34.

Emam A.M., Azoz A., Mehaisen G.M.K., Ferrnand N., Ahmed N.A. 2017. Diversity assessment among native middle Egypt rabbit populations in North upper- Egypt province by microsatellite polymorphism. World Rabbit Sci., 25: 9-16.

Ennafaa H., Monnerot M., Gaaied A.E., Mounolou J.C. 1987. Rabbit mitochondrial DNA: preliminary comparison between some domestic and wild animals. Genet. Select. Evol.,19:279-288.

FAO. 2007. Global plan of action for animal genetic resources and the Interlaken declaration. Available at Accessed August 2019.

FAO. 2011. Animal production and health guidelines (9), Molecular genetic characterization of animal genetic resources, Commission on genetic resources for food and agriculture. Food and Agriculture Organization of the United Nations. Rome.

Fu Y.X., Li W.H. 1993. Statistical tests of neutrality of mutations. Genetics,133: 693-709.

Fuller S.J., Wilson, J.C., Mather P.B. 1997. Patterns of differentiation among wild rabbit populations Oryctolagus Cuniculus L. in arid and semiarid ecosystems of North-Eastern Australia. Mol. Eco., 6: 145-153.

Gaggiotti O.E. 2003. Genetic threats to population persistence. Ann. Zool. Fennici, 40: 155-168. Galal E.S.E., Khalil M.H. 1994. Development of rabbit industry in Egypt. Cahiers Options Méditerranéennes, 8: 43-56.

Geraldes A., Ferrand N., Nachman M.W. 2006. Contrasting patterns of introgression at X-linked loci across the hybrid zone between subspecies of the European rabbit (Oryctolagus cuniculus). Genetics, 173, 919-933.

Ghalayini M, Launay A, BridierNahmias A, Clermont O, Denamur E, Lescat M, Tenaillon O. 2018. Evolution of a dominant natural isolate of Escherichia coli in the human gut over the course of a year suggests a neutral evolution with reduced effective population size. Appl. Environ. Microbiol., 84: e02377-17.

González-Redondo P. 2007. Estado de las poblaciones y posibilidades de recuperación del conejo doméstico común Español. In Proc.: IV Jornadas Ibéricas de Razas Autóctonas y sus Productos Tradicionales: Innovación, Seguridad y Cultura Alimentarias. Seville (Spain), pp. 367-372.

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-Sheikh, Egypt, pp. 177-181.

Guo H., Jiao Y., Tan X., Wang X., Huang X., Huizhe X., Jin H. and. Paterson, A.H. 2019. Gene duplication and genetic innovation in cereal genomes. Genome Res. 29: 261-269.

Guo H., Jiao Y., Tan X., Wang X., Huang X., Jin H., Paterson A.H. Gene duplication and genetic innovation in cereal genomes. Genome Res., 29: 261-269.

Gupta A., Bhardwaj A., Supriya, Sharma P., Pal Y., Kumar S. 2015. Mitochondrial DNA- a Tool for Phylogenetic and Biodiversity Search in Equines. J. Biodivers Endanger Species, S1: 006.

Hall S.J.G. 2004. Livestock biodiversity: genetic resources for the farming of the future. Blackwell Science Ltd. Oxford, United Kingdom. 280 pp.

Jayaraman R. 2011. Hypermutation and stress adaptation in bacteria. J. Genet., 90: 383-391.

Kekkonen J., Brommer J.E. 2014. Reducing the loss of genetic diversity associated with assisted colonization-like introductions of animals. Available at Accessed January 2015.

Khalil M.H. 2002. The Baladi Rabbits (Egypt). In: Rabbit genetic resources in Mediterranean Countries. Eds. M. H. Khalil and M. Baselga. Options Mediterranéennes Serie B, 38: 39-50.

Kim J.H., Byun M.J., Kim M.J., Suh S.W., Ko Y.G., Lee C.W., Jung K.S., Kim E.S., Yu D.J., Kim W.Y., Choi S.B. 2013. MtDNA diversity and phylogenetic state of Korean cattle breed, Chikso. Asian-Australas. J. Anim. Sci., 26: 163-170.

Librado P., Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25: 1451-1452.

Long J.R., Qiu X.P., Zeng F.T., Tang L.M., Zhang Y.P. 2003. Origin of rabbit (Oryctolagus cuniculus) in China: evidence from mitochondrial DNA control region sequence analysis. Anim. Genet., 34: 82-87.

Martin-Burriel, I., Marcos, S., Osta R., García-Muro, E., Zaragoza, P. 1996. Genetic characteristics and distances amongst Spanish and French rabbit population. World Rabbit Sci., 4: 121-126.

Ministry of Agriculture and Land Reclamation in Egypt, FAO (2003). First Report on the state of animal Genetic Resources in the Arab Republic of Egypt. FAO, Rome, pp. 23.

Monnerot M., Vigne J.D., Biju-Duval C., Casane D., Callou C., Hardy C., Mougel F., Soriguer R., Dennebouy N., Mounolou J. (1994) Rabbit and man: genetic and historic approach. Genet. Select. Evol., 26: 167s-182s.

Mougel F., Gautier A, Queney G., Sanchez M., Dennebouy N., Monnerot M. 2002. History of European rabbit populations in France: advantage and disadvantage of mtDNA. Available at Accessed August 2019.

Nguyen N., Brajkovic V., Cubric-Curik V., Ristov S., Veir Z., Szendrő Z., Nagy I., Curik, I. 2018. Analysis of the impact of cytoplasmic and mitochondrial inheritance on litter size and carcass in rabbits. World Rabbit Science, 26: 287-298.

Owuor S.A., Mamati E.G., Kasili R.W. 2019. Origin, Genetic Diversity, and Population Structure of Rabbits (Oryctolagus cuniculus) in Kenya. BioMed. Res. Internat., 2019: 7056940.

Park G., Pichugin Y., Huang W., Traulsen A. 2019. Population size changes and extinction risk of populations driven by mutant interactors. Phys. Rev., E 99, 022305.

Peischl S., Excoffier L. 2015. Expansion load: recessive mutations and the role of standing genetic variation. Mol. Ecol., 24: 2084-2094.

Sakthivel M., Tamilmani G., Abdul Nazar A.K., Jayakumar R., Sankar M., Rameshkumar P., Anikuttan K.K., Samal A.K., Anbarasu M., Gopakumar G. 2018. Genetic variability of a small captive population of the cobia (Rachycentron canadum) through pedigree analyses. Aquaculture, 498: 435-443.

Schmidt D., Pool J. 2002. The effect of population history on the distribution of Tajima’s D statistics. Available at Accessed March 2019.

Schumer M., Xu C., Powell D.L., Durvasula A., Skov L., Holland C., Blazier J.C., Sankararaman S., Andolfatto P., Rosenthal G.G., Przeworski M. 2018. Natural selection interacts with recombination to shape the evolution of hybrid genomes. Science, 360: 656-660

Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol., 30: 2725-2729.

Valvo M., Russo R., Mancuso F.P. 2017. mtDNA diversity in a rabbit population from Sicily (Italy). Turk. J. Zool. 41: 645-653.

van der Loo W., Mougel F., Sanchez M.S., Bouton C., Castien E., Soriguer R., Hamers R., Monnerot M. 1997. Evolutionary patterns at the antibody constant region in rabbit (Oryctolagus cuniculus): characterization of endemic b-locus haplotypes and their frequency correlation with major mitochondrial gene types in Spain. Gibier Faune Sauvage, 14: 427-449.

Wares J.P. 2010. Natural distributions of mitochondrial sequence diversity support new null hypotheses. Evolution 64: 1136-1142.

Watson J.P.N., Davis S.J.M. 2019. Shape differences in the pelvis of the rabbit, Oryctolagus cuniculus (L.), and their genetic associations. Available at Accessed March 2019.

Yu Yeh S., Hsuan Song C., Llu-lin T., Chung Chou C. 2019. The effects of crossbreeding, age, and sex on erythrocyte indices and biochemical variables in crossbred pet rabbits (Oryctolagus cuniculus). Vet. Clin. Pathol., 48: 469-480.

Zaragoza P., Arana A., Zaragoza I., Amorena B. 1987. Blood biochemical polymorphisms in rabbits presently bred in Spain: Genetic variation and distances amongst populations. Aust. J. Biol. Sci., 40: 275-286.

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