Diversity assessment among native Middle Egypt rabbit populations in North Upper-Egypt province by microsatellite polymorphism
Submitted: 2016-04-17
|Accepted: 2016-10-25
|Published: 2017-03-30
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Keywords:
rabbit, North Upper Egypt, genetic diversity, microsatellite
Supporting agencies:
Abstract:
Safeguarding biodiversity is an important goal for animal production in developed countries. This study investigated genetic diversity among native Middle-Egypt rabbit (NMER) populations in North Upper-Egypt province by using microsatellite polymorphism. Nineteen microsatellite loci were used in the study and an area of 231 km was surveyed, as native rabbits covered 14 points belonging to four Northern Upper Egypt governorates (South Giza, Fayoum, Beni Suef and Minya). Standard statistical parameters of genetic variability within and between populations confirmed that the highest genetic diversity was found towards the south. Among NMER populations, the mean number of alleles per locus was lowest in South Giza (5.32), while it was highest in Minya (6.00). This study found that NMER featured a high number of private alleles ranging between 7 and 11 (mean value was 10.5). Results also showed a high genetic diversity in NMER populations and that heterozygosity ranged between 0.384 and 0.445, strongly indicating extensive genetic variation in the NMER populations. The mean values of observed and expected heterozygosity were 0.405 and 0.612, respectively. Factorial correspondence analysis and neighbour joining trees (NJ) showed 2 main NMER rabbit groups: the Northern group (South Giza and Fayoum) and the Southern group (Beni Suef and Minya). All populations showed a high percentage of assignment in this study (0.913 to 0.946). The structure analysis showed that each population existed in separate clusters. This research provides an overview of genetic diversity of NMER populations in the Northern Upper Egypt province for the first time. In conclusion, results of this study could be used to designate priorities for conservation of NMER populations.
References:
Abdel-Mawgood A. L. 2012. DNA Based Techniques for Studying Genetic Diversity. In Caliskan M. (Eds.) Genetic Diversity in Microorganisms, 95-122, InTechRijeka, Croatia.
Abel-Kafy E. M., Shabaan H. M. A., Azoz, A. A. A., El-Sayed A. F. M. , Abdel-Latif A. M. 2011. Descriptions of native rabbit breeds in Middel-Egypt. In Proc.: 4th Egyptian Conference of Rabbit Science. 30th October, 2011, Giza, Egypt.
Alda F., Doadrio I. 2014. Spatial genetic structure across a hybrid zone between European rabbit subspecies. Peer J., 30: e582.doi:10.7717/peerj.582
Alves J.M., Carneiro M., Afonso S., Lopes S., Garreau H., Boucher S., Allain D., Queney G., Esteves P.J., Bolet J., Ferrand N. 2015. Levels and Patterns of Genetic Diversity and Population Structure in Domestic Rabbits. PLoS ONE, 10: e0144687. doi:10.1371/journal.pone.0144687
Badawy A.G. 1975. Rabbit Raising, 2nd ed. Central Administration for Agricultural Culture, Ministry of Agriculture, Egypt (in Arabic).
Belkhir K., Borsa P., Chikhi L., Raufaste N., Bonhomme F. 1996-2004. GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRSUMR 5171. Université de Montpellier IIed., France. Available from:
http://www.genetix.univ-montp2.fr/genetix/genetix.htm
Ben Larabi M., San-Cristobal M., Chantry-Darmon C., Bolet G. 2012. Genetic diversity of rabbit populations in Tunisia using microsatellites markers. In Proc.: 10th World Rabbit Congress, 3-6 September, 2012, Sharm El-Sheikh, Egypt.
Ben Larabi M., San-Cristobal M., Chantry-Darmon C., Bolet G. 2014. Population structure in Tunisian indigenous rabbit as curtained using molecular information. World Rabbit Sci., 22: 223-230. doi:10.4995/wrs.2014.1468
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, 281-315.
Carneiro M., Baird S.J.E., Afonso S., Ramirez E., Tarroso P., Teotonio H., Villafuerte R., Nachman M.W., Ferrand N. 2013. Steep clines within a highly permeable genome across a hybrid zone between two subspecies of the European rabbit. Mol. Ecol., 22: 2511-2525. doi:10.1111/mec.12272
Emam A.M., Afonso S., Azoz A.A.A., González-Redondo P., Mehaisen G.M.K., Ahmed N.A., Ferrand N. 2016. Microsatellite polymorphism in some Egyptian and Spanish common rabbit breeds. In Proc.: 11th World Rabbit Congress, 15-18 June, 2016, Qingdao, China.
El-Hentati H., Mhamdi N., Ben Hamouda M., Chriki A. 2013. Analysis of genetic variability within Tunisian Barbarine and Western thin Tail sheep using RAPD-PCR Method. Life Sci. J., 10: 2003-2009.
Evanno G., Regnaut S., Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol. Ecol., 14: 2611-2620.
doi:10.1111/j.1365-294X.2005.02553.x
FAO. 2007. The state of the world’s animal genetic resources for food and agriculture, edited by Rischkowsky and Pilling. Rome.
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. Ecol., 6: 145-53.
doi:10.1046/j.1365-294X.1997.00167.x
Galal E.S.E., Khalil M.H. 1994. Development of rabbit industry in Egypt. Options Méditerranéennes, Series Cahiers, 8: 43-56.
Galal O.A., Medhat R., Ragaa E. Abd El-Karim. 2013. Analysis of genetic diversity within and among four rabbit genotypes using biochemical and molecular genetic markers. Afr. J. Biotechnol., 12, 2830-2839. doi:10.5897/AJB2013.12332
Glaubitz J.C. 2004. CONVERT: A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol. Ecol. Notes, 4: 309-310. doi:10.1111/j.1471-8286.2004.00597.x
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.
Kalinowski S.T., Taper M.L., Marshall T.C. 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol. Ecol., 16:1099-1106. doi:10.1111/j.1365-294X.2007.03089.x
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.
Ligda C., Zjalic M. 2011. Conservation of animal genetic resources in Europe: overview of the policies, activities, funding and expected benefits of conservation activities. Anim. Genet. Resour., 49: 75-86. doi:10.1017/S2078633611000075
Lowe W.H., Allendorf F.W. 2010. What can genetics tell us about population connectivity? Mol. Ecol., 19: 3038-3051. doi:10.1111/j.1365-294X.2010.04688.x
Liu K., Muse S.V. 2005. PowerMarker: integrated analysis environment for genetic marker analysis. Bioinformatics, 21: 2128-2129. doi:10.1093/bioinformatics/bti282
Martín Collado D. 2013. Integration of socioeconomic and genetic aspects involved in the conservation of animal genetic. Thesis (PhD). University of Biotechnica de Madrid.
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, 23.
Morin P.A., Leduc R.G., Archer F.I., Martien K.K., Huebinger R., Bickham J.W., Taylor B.L. 2009. Significant deviations from Hardy–Weinberg equilibrium caused by low levels of microsatellite genotyping errors. Mol. Ecol. Res., 9: 498-504. doi:10.1111/j.1755-0998.2008.02502.x
Nei M, Maruyama T, Chakraborty R. 1975. The bottleneck effect and genetic variability in populations. Evolution, 29: 1-10. doi:10.2307/2407137
Ormandy E.H., Dale J., Griffin G. 2011. Genetic engineering of animals: Ethical issues, including welfare concerns. Can. Vet. J., 52: 544-550.
Pellegrino I., Cucco M., Follestad A., Boos M. 2015. Lack of genetic structure in greylag goose (Anser anser) populations along the European Atlantic flyway. PeerJ, 3: e1161. doi:10.7717/peerj.1161
Pritchard J.K., Stephens M., Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155: 945-959.
Queney G., Ferrand N., Marchandeau S., Azevedo M., Mougel F., Branco M., Monnerot M. 2000. Absence of a genetic bottleneck in a wild rabbit (Oryctolagus cuniculus) population exposed to a severe viral epizootic. Mol. Ecol., 9: 1253-1264. doi:10.1046/j.1365-294x.2000.01003.x
Schwartz M.K., Pilgrim K.L., McKelvey K.S., Rivera P.T., Ruggiero L.F. 2007. DNA Markers for Identifying Individual Snowshoe Hares Using Field collected Pellets. Northwest Sci., 81: 316-322. doi:10.3955/0029-344X-81.4.316
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. doi:10.1093/molbev/mst197
Wellek S. 2010. Testing statistical hypothesis of equivalence and non inferiority, 2nd ed. Boca Raton, FL: Chapman & Hall/CRC. doi:10.1201/EBK1439808184
Wu X., Wu T., Zhao H., Cheng G., Xu Q., Cheng J., Zhu X., Chen G. 2008. Correlation analysis of wool yield in wan line Angora Rabbits Using microsatellite DNA markers. J. Biol. Sci., 8: 679-682. doi:10.3923/jbs.2008.679.682
Yeh F.C., Yang R.C., Boyle T. 1999. Popgene version 1.31. Microsoft window-based freeware for population genetic analysis. Quick user guide. Department of Renewable Resources ed., University of Alberta, Canada.
