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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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