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Preliminary analysis of microsatellite-based genetic diversity of goats in southern Nigeria

Published online by Cambridge University Press:  01 December 2011

M. Okpeku ,
S.O. Peters ,
M.O. Ozoje ,
O.A. Adebambo ,
B.O. Agaviezor ,
M.J. O'Neill  and
I.G. Imumorin
M. Okpeku
Affiliation:
Department of Livestock Production, Niger Delta University, Amassoma, Nigeria Department of Animal Breeding and Genetics, University of Agriculture, Abeokuta, Nigeria
S.O. Peters
Affiliation:
Department of Animal Breeding and Genetics, University of Agriculture, Abeokuta, Nigeria Department of Animal Science, Cornell University, Ithaca, NY 14853, USA
M.O. Ozoje
Affiliation:
Department of Animal Breeding and Genetics, University of Agriculture, Abeokuta, Nigeria
O.A. Adebambo
Affiliation:
Department of Animal Breeding and Genetics, University of Agriculture, Abeokuta, Nigeria
B.O. Agaviezor
Affiliation:
Department of Animal Science and Fisheries, University of Port-Harcourt, Port-Harcourt, Nigeria
M.J. O'Neill
Affiliation:
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
I.G. Imumorin*
Affiliation:
Department of Animal Science, Cornell University, Ithaca, NY 14853, USA
*
Correspondence to: Dr Ikhide G. Imumorin, Department of Animal Science, Cornell University, 267 Morrison Hall, Ithaca, NY 14853, USA. email: [email protected]; tel: 607-255-2850 fax: 607-255-9829
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Summary

To better understand natural genetic variation in indigenous livestock resources, as well as formulate conservation policies, better genetic characterization is required to balance the competing needs of genetic improvement and conservation of native germplasm, primarily in rural agricultural systems in developing countries. Genetic diversity of goats in southern Nigeria was assessed using 295 indigenous goats with ten microsatellite DNA markers. The breeds are West African Dwarf (WAD), Red Sokoto (RS) and Sahel (SA) sampled from farms, market places and rural homesteads. The mean expected heterozygosity (HE) ranged from 0.608 to 0.784 in two sub-populations of WAD goats. Deviations from Hardy–Weinberg equilibrium (HWE) were statistically significant (p < 0.05) indicating that these populations are under various forces stemming from the management choices of rural dwellers. Polymorphic information content of these markers averaged 0.803 and mean GST index was 0.176. The measure of genetic distance between pairs of breeds indicated that the lowest distance was between WAD and RS (0.268) and the highest distance was between WAD and SA (0.662) goats, respectively. The estimated dendogram clustered these Nigerian goats into nine sub-populations and two major genetic groups. The study suggests that indigenous goat populations in southern Nigeria may be collapsed from three breeds into two distinct genetic groups, possibly due to extensive cross-breeding and gene flow between them, which are symptomatic of uncontrolled crossing across much of the country.

Résumé

Afin de mieux comprendre la variation génétique naturelle des ressources des animaux d'élevage indigènes et pour élaborer des politiques de conservation, il est nécessaire d'améliorer la caractérisation génétique qui équilibre les besoins opposés de l'amélioration génétique et de la conservation du matériel génétique local, en particulier dans les systèmes ruraux et agricoles des pays en développement. On a évalué la diversité génétique des chèvres dans le sud du Nigéria en utilisant 295 chèvres indigènes avec 10 marqueurs microsatellites d'ADN. Les races, dont les échantillons ont été saisis dans les exploitations agricoles, dans les marchés et dans les fermes familiales, étaient la West African Dwarf, la Red Sokoto et la Sahel. L'hétérozygotie moyenne prévue dans deux sous-populations de chèvres West African Dwarf variait entre 0,608 et 0,784. Les écarts par rapport à l'équilibre de Hardy-Weinberg ont été significatifs du point de vue statistique (p < 0.05), ce qui indique que ces populations subissent des pressions différentes selon les choix de gestion des habitants des zones rurales. Le contenu d'informations polymorphiques de ces marqueurs a été en moyenne de 0,803 et l'index de GST moyen a été de 0,176. La mesure de la distance génétique entre deux races a indiqué respectivement la distance la plus faible entre les chèvres West African Dwarf et Red Sokoto (0,268) et la plus élevée entre les chèvres West African Dwarf et Sahel (0,662). Le dendrogramme estimé a regroupé ces chèvres nigériennes dans neuf sous-populations et dans deux groupes génétiques majeurs. L'étude suggère que les populations de chèvres indigènes dans le sud du Nigéria proviennent probablement de trois races qui se sont assemblées dans deux groupes génétiques distincts, probablement en raison d'importants croisements et flux de gènes entre ces races, qui révèlent la présence de croisements non maîtrisés dans une grande partie du pays.

Resumen

Análisis preliminar de microsatélites basados en la diversidad genética caprina del sur de Nigeria. Para comprender mejor la variación genética natural en los recursos ganaderos indígenas, así como formular las políticas de conservación, es necesario llevar a cabo una mejor caracterización genética para equilibrar las necesidades competitivas de la mejora genética y conservación de germoplasma nativo, principalmente en los sistemas agrícolas de los países en desarrollo. La diversidad genética de las cabras del sur de Nigeria se evaluó utilizando 295 cabras indígenas con 10 marcadores de microsatélites de ADN. Las razas muestreadas en las explotaciones, en los mercados y en las haciendas fueron la West African Dwarf (WAD), la Red Sokoto (RS) y la Sahel (SA). La heterocigosidad media esperada (HE) varió desde 0,608 hasta 0,784 en dos subpoblaciones de cabras WAD. Las desviaciones del equilibrio Hardy-Weinberg (HWE) fueron estadísticamente significativas (p < 0,05), indicando que estas poblaciones se encuentran bajo diversas fuerzas relacionadas con la gestión de la población rural. El contenido de información polimórfica de estos marcadores fue de un promedio de 0,803 y el índice medio GST fue 0,176. La medida de la distancia genética entre los pares de razas indicó que la menor distancia se encuentra entre los animales WAD y los RS (0.268) y la mayor distancia entre las cabras WAD y las cabras SA (0,662), respectivamente. El dendograma agrupó estas cabras de Nigeria en nueve subpoblaciones y dos grupos genéticos más importantes. El estudio pone de manifiesto que las poblaciones caprinas indígenas del sur de Nigeria podrían venirse abajo como tales tres razas, pasando a formarse dos grupos genéticos diferentes, posiblemente debido al cruzamiento y al flujo genético entre ellas, por el cruzamiento con controlado que está teniendo lugar en.

Keywords

DNAgenetic diversitygoatsmicrosatelliteNigeriaADNdiversité génétiquechèvresmicrosatelliteNigériaANDdiversidad genéticacabrasmicrosatéliteNigeria
Type
Research Article
Information
Animal Genetic Resources/Resources génétiques animales/Recursos genéticos animales , Volume 49 , December 2011 , pp. 33 - 41
Copyright
Copyright © Food and Agriculture Organization of the United Nations 2011

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References

Abdul-Aziz, M. 2010. Present status of the world goat populations and their productivity. Lohman Inf., 45: 42–52.Google Scholar
Adebambo, O.A. 2003. Animal breeds: a nation's heritage. An inaugural lecture delivered at University of Agriculture, Abeokuta, Nigeria, 8 October 2003. 102 pp.Google Scholar
Adebambo, O.A., Williams, J.L., Blott, S. & Urquhart, B. 2004. Genetic relationship between native sheep breeds in Nigeria based on microsatellite DNA polymorphism. Anim. Genet. Resour. Inf., 34: 27–39.Google Scholar
Adebambo, A.O., Adebambo, O., Williams, J.L., Blott, S. & Urquart, B. 2011. Genetic distance between two popular Nigerian goat breeds used for milk production. Livestock Res. Rural Dev., 23(2), Article #26. Retrieved October 7, 2011, from http://www.lrrd.org/lrrd23/2/adeb23026.htm.Google Scholar
Adedeji, T.A., Ozoje, M.O., Peters, S.O., Sanusi, A.O., Ojedapo, L.O. & Ige, A.O. 2011. Coat pigmentation and Wattle genes effect on some haematological characteristics of heat stressed and extensively reared West African Dwarf goats. World J. Life Sci. Med. Res., 3: 48–55.Google Scholar
Agha, S.H., Pilla, F., Galal, S., Shaat, I., D'Andrea, M., Reale, S., Abdelsalam, A.Z. & Li, M.H. 2008. Genetic diversity in Egyptian and Italian goat breeds measured with microsatellite polymorphism. J. Anim. Breed. Genet., 125(3): 194–200.CrossRefGoogle ScholarPubMed
Barker, J.S.F., Moore, S.S., Hetzel, D.J.S., Tan, S.G. & Byrne, K. 1997. Genetic diversity of Asian water buffalo (Bubalus bubalis): microsatellite variation and a comparison with protein coding loci. Anim. Genet., 28: 103–115.CrossRefGoogle Scholar
Bruno-de-Sousa, C., Martinez, A.M., Ginja, C., Santos-Silva, F., Carolino, M.I., Delgado, J.V. & Gama, L.T. 2011. Genetic diversity and population structure in Portuguese goat breeds. Livestock Sci., 135: 131–139.CrossRefGoogle Scholar
Buvanendra, V., Sooriyamoorthy, T., Ogunsusi, R.A. & Adu, I.F. 1981. Haemoglobin polymorphism and resistance to helminths in Red Sokoto goats. Trop. Anim. Health Prod., 13: 217–21.CrossRefGoogle Scholar
Cañon, J., García, D., García-Atance, M.A., Obexer-Ruff, G., Lenstra, J.A., Ajmone-Marsan, P., Dunner, S. & ECONOGENE Consortium. 2006. Geographical partitioning of goat diversity in Europe and the Middle East. Anim. Genet., 37(4): 327–34.CrossRefGoogle ScholarPubMed
Cerda-Flores, R.M., Villalobos-Torres, M.C., Barrera-Saldaña, H.A., Cortés-Prieto, L.M., Barajas, L.O., Rivas, F., Carracedo, A., Zhong, Y., Barton, S.A., Chakraborty, R. 2002. Genetic admixture in three Mexican Mestizo populations based on D1S80 and HLA-DQA1 loci. Am. J. Hum. Biol., 14(2): 257–63.CrossRefGoogle ScholarPubMed
Christiansen, F.B., Frydenberg, O., Gyldenholm, A.O. & Simonsen, V. 1974. Genetics of Zoraces populations. VI. Further evidence based on age group samples of a heterozygote deficit EstIII polymorphism. Hereditas, 77: 225–236.CrossRefGoogle ScholarPubMed
Dixit, S.P., Verma, N.K., Ahlawat, S.P.S., Aggarwal, R.A.K., Kumar, S., Chander, R. & Singh, K.P. 2008. Molecular genetic characterization of Kutchi breed of goat. Curr. Sci., 95: 946–951.Google Scholar
Dixit, S.P., Verma, N.K., Aggarwal, R.A.K., Kumar, S., Chander, R., Vyas, M.K., Singh, K.P. 2009. Genetic structure and differentiation of three Indian goat breeds. Asian-Australasian J. Anim. Sci., 22(9): 1234–1240.CrossRefGoogle Scholar
Dixit, S.P., Verma, N.K., Aggarwal, R.A.K., Vyas, M.K., Rana, J., Sharma, A., Tyagi, P., Arya, P. & Ulmek, B.R. 2010. Genetic diversity and relationship among southern Indian goat breeds based on microsatellite markers. Small Ruminant Res., 91: 153–159.CrossRefGoogle Scholar
Ebozoje, M.O. & Ngere, L.O. 1995. Genetic analysis of preweaning growth in West African Dwarf goats and their half-breds. Int. J. Anim. Sci., 10: 247–251.Google Scholar
FAOSTAT. 2011. Food and Agricultural Organization of the United Nations (available at http://faostat.fao.org/default.aspx; accessed 19 July 2011).Google Scholar
FDLPCS. 2007. Federal Department of Livestock and Pest Control Services. FLDPCS Nigerian. Livestock Resources. National Synthesis, 440 pp.Google Scholar
Fitzhugh, H.A., Ehui, S.K., & Lahlou-Kassi, A. 1992. Research strategies for development of animal agriculture. World Anim. Rev., 72: 9–19.Google Scholar
Goudet, J. 2001. FSTAT, a programme to estimate and test gene diversities and fixation indices (version 2.9.3) (available at http://www.unilch/izea/softwares/fstat.html).Google Scholar
Groeneveld, L.F., Lenstra, J.A., Eding, H., Toro, M.A., Scherf, B., Pilling, D., Negrini, R., Finlay, E.K., Jianlin, H., Groeneveld, E., Weigend, S. & GLOBALDIV Consortium. 2010. Genetic diversity in farm animals – a review. Anim. Genet., 41(Suppl. 1): 6–31.CrossRefGoogle ScholarPubMed
Guo, S.W. & Thompson, E.A. 1992. Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics, 48: 361–372.CrossRefGoogle ScholarPubMed
Hoarau, G., Boon, E., Jongma, D.N, Ferber, S., Palsson, J., Van der Veer, H.W., Rijnsdorp, A.D., Stam, W.T. & Olsen, J.L. 2005. Low effective population size and evidence for inbreeding in an overexploited flatfish, plaice (Pleuronectes platessa L.). Proc. R. Soc. B, 272: 497–503.CrossRefGoogle Scholar
Hoffmann, I., Marsan, P.A., Barker, J.S.F., Cothran, E.G., Hanotte, O., Lenstra, J.A., Milan, D., Weigend, S. & Simianer, H. 2004. New MoDAD marker sets to be used in diversity studies for the major farm animal species: recommendations of a joint ISAG/FAO working group. Proc. 29th International Conference on Animal Genetics, 11–16 September 2004, Tokyo, Japan. p. 107.Google Scholar
Imumorin, I.G., Ologun, A.G. & Oyeyemi, M.O. 1999. Preliminary observations on effects of hemoglobin genotype and estimate of genetic distance at the Hb locus in West African Dwarf and Red Sokoto goats. Trop. J. Anim. Sci., 1: 1–9.Google Scholar
Jandurova, O.M., Kott, T., Kottova, B. & Czernekova, V. 2004. Seven microsatellite markers useful for determining genetic variability in white and brown short-haired goat breeds. Small Ruminant Res., 52: 271–274.CrossRefGoogle Scholar
Laval, G., Iannuccelli, N., Legault, C., Milan, D., Groenen, M.A.M., Giuffra, E., Andersson, L., Nissen, P.H., Jorgensen, C.B., Beeckmann, P., Geldermann, H., Foulley, J.L., Chevalet, C. & Ollivier, L. 2000. Genetic diversity of eleven European pig breeds. Genet. Select. Evol., 32: 187–203.CrossRefGoogle ScholarPubMed
Luikart, G., Biju-Duval, M.P., Ertugrul, O., Zagdsuren, Y., Maudet, C. & Taberlet, P. 1999. Power of 22 microsatellite markers in fluorescent multiplexes for parentage testing in goats (Capra hircus). Anim. Genet., 30: 431–438.CrossRefGoogle ScholarPubMed
Mahmoudi, B., Bayat, M., Sadeghi, R., Babayev, M. & Abdollahi, H. 2010. Genetic diversity among three goat populations assessed by microsatellite DNA markers in Iran. Global Vet., 4(2): 118–124.Google Scholar
Marshall, T. 1998. CERVUS v.2.0. University of Edinburgh 1998–2001.Google Scholar
Martínez, A.M., Acosta, J., Vega-Pla, J.L. & Delgado, J.V. 2006. Analysis of the genetic structure of the canary goat populations using microsatellites. Livestock Sci., 102: 140–145.CrossRefGoogle Scholar
Miller, M.P. 1997. TFPGA – tools for populations genetics analyses, version 1.3. A windows programme for the analysis of allozyme and molecular population genetic data. Department of Biological Sciences, Northern Arizona University, Flagstaff, 53 pp.Google Scholar
Moruppa, S.M. 1985. A comparative study of Borno White and Red Sokoto (Maradi) goat breeds. University of Ibadan, Ibadan, Nigeria. (MSc thesis)Google Scholar
Muema, E.K., Wakhungu, J.W., Hanotte, O. & Jianlin, H. 2009. Genetic diversity and relationship of indigenous goats of sub-Saharan Africa using microsatellite DNA markers. Livestock Res. Rural Dev, 21(2), Article #28. Retrieved October 7, 2011, from http://www.lrrd.org/lrrd21/2/muem21028.htm.Google Scholar
Mujibi, N.F. 2005. Genetic characterization of West African Dwarf (WAD) goats using microsatellite markers. Kenyatta University, Nairobi, Kenya. (MSc Thesis)Google Scholar
Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89: 583–590.CrossRefGoogle ScholarPubMed
Odubote, I.K. 1994a. Characterization of the West African Dwarf goat for certain qualitative traits. Nigerian J. Anim. Prod., 2: 37–41.Google Scholar
Odubote, I.K. 1994b. Genetic analysis of the reproductive performance of West African Dwarf goats in the humid tropics. In: Small Ruminant Research and Development in Africa (eds. Lebbie, S.H.B. & Kagwini, E.). Proceedings Third Biennial Conference of African Small Ruminant Research Network, Kampala, Uganda. 5–9 December, 1994. pp. 33–36. International Livestock Research Institute, Nairobi, Kenya.Google Scholar
Odubote, I.K. & Akinokun, J.O. 1992. Estimates of genetic parameters for economic traits in West African Dwarf goat. Nigerian J. Anim. Prod., 19: 114–19.CrossRefGoogle Scholar
Ozoje, M.O. 1998. Coat colour genes in West African Dwarf sheep and goats: a theoretical appraisal. In Proc. Sixth World Congress of Genetics Applied to Livestock Production Vol. 26, pp. 54–57.Google Scholar
Peakall, R. & Smouse, P.E. 2006. GENALEX 6.3: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes, 6: 288–295.CrossRefGoogle Scholar
Qi, Y., Luo, J., Han, X-F., Zhu, Y-Z., Chen, Ca, Liu, J-X, & Sheng, H-J. 2009. Genetic diversity and relationships of 10 Chinese goat breeds in the Middle and Western China. Small Ruminant Res., 82: 88–93.CrossRefGoogle Scholar
Rout, P.K., Joshi, M.B., Mandal, A., Laloe, D., Singh, L. & Thangaraj, K. 2008. Microsatellite-based phylogeny of Indian domestic goats. BMC Genet., 9: 11.CrossRefGoogle ScholarPubMed
Salako, A.E. 2004. Maturity rate of some morphometric traits in the West African Dwarf sheep of Nigeria. Trop. J. Anim. Sci., 7(1): 51–55.Google Scholar
Serrano, M., Calvo, J.H., Martínez, M., Marcos-Carcavilla, A., Cuevas, J., González, C., Jurado, J.J., de Tejada, P.D. 2009. Microsatellite based genetic diversity and population structure of the endangered Spanish Guadarrama goat breed. BMC Genet., 29: 61.Google Scholar
Takezaki, N. & Nei, M. 1996. Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics, 144: 389–399.CrossRefGoogle ScholarPubMed
Toro, M. & Maki-Tanila, A. 2007. Genomics reveals domestication history and facilitates breed development. In Oldenbroek, K., ed. Utilization and conservation of farm animal genetic resources, pp. 75–102. Wageningen, The Netherlands, Wageningen Academic Publishers.CrossRefGoogle Scholar
Visser, C., Hefer, C.A., van Marle-Köster, E. & Kotze, A. 2004. Genetic variation of three commercial and three indigenous goat populations in South Africa. South African J. Anim. Sci., 34(Suppl. 1): 24–27.Google Scholar