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Genetic relationships of indigenous goats reared by pastoralists in Kenya based on mitochondria D-loop sequence

Published online by Cambridge University Press:  26 October 2016

E.K. Githui ,
F.M. Kibegwa ,
J.M. Kamau ,
S.K. Mutura ,
Z.A. Okwany ,
D.M. Ngigi  and
E.W. Mwangi
E.K. Githui*
Affiliation:
Molecular Genetics Laboratory, National Museums of Kenya, P. O. Box 40658-00100, Nairobi, Kenya Molecular Biology Laboratory, Institute of Primate Research, P. O. Box 24481-00502 Karen, Kenya
F.M. Kibegwa
Affiliation:
Department of Animal Production, University of Nairobi, P. O. Box 30197-00100, Nairobi, Kenya
J.M. Kamau
Affiliation:
Molecular Genetics Laboratory, National Museums of Kenya, P. O. Box 40658-00100, Nairobi, Kenya Molecular Biology Laboratory, Institute of Primate Research, P. O. Box 24481-00502 Karen, Kenya
S.K. Mutura
Affiliation:
Molecular Genetics Laboratory, National Museums of Kenya, P. O. Box 40658-00100, Nairobi, Kenya Molecular Biology Laboratory, Institute of Primate Research, P. O. Box 24481-00502 Karen, Kenya
Z.A. Okwany
Affiliation:
Molecular Genetics Laboratory, National Museums of Kenya, P. O. Box 40658-00100, Nairobi, Kenya Molecular Biology Laboratory, Institute of Primate Research, P. O. Box 24481-00502 Karen, Kenya
D.M. Ngigi
Affiliation:
Molecular Genetics Laboratory, National Museums of Kenya, P. O. Box 40658-00100, Nairobi, Kenya Molecular Biology Laboratory, Institute of Primate Research, P. O. Box 24481-00502 Karen, Kenya
E.W. Mwangi
Affiliation:
Molecular Genetics Laboratory, National Museums of Kenya, P. O. Box 40658-00100, Nairobi, Kenya
*
Correspondence to: E.K. Githui, Molecular Genetics Laboratory, National Museums of Kenya and Molecular Biology Laboratory, Institute of Primate Research, Kenya. email: kegithui@yahoo.com
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Summary

Kenya indigenous goat breeds (Capra hircus) have not been accurately described. Therefore, there is threat of erosion of unique genotypes such as those associated with adaptability and disease resistance, through indiscriminate crossbreeding. The Kenyan goats classification based on phenotype/morphology identifies three breeds: Small East African (SEA) goats, the Galla goat and crosses of SEA and the Galla. In the present study, we sampled goats from two main geographic regions of Kenya with pastoralist communities, the Maasai and Somali/Boran. DNA was extracted from whole blood and polymerase chain reaction amplified using primers flanking a fragment of Cytocrome-b and D-loop regions of mitochondria DNA. The sequences derived were analysed both within Kenya goat populations and also compared with phylogeographic-related datasets. These data show that the majority of Kenyan indigenous goats are not distinct and their genetic structure is very diverse; however, distinct haplogroups were present. Genetic diversity showed weak positive in Tajima D test for Kenyan indigenous goats, while the Iberian/Mediterranean/Middle-East dataset had a more pronounced negative value indicating that the two populations are under different selection pressure. These analyses enabled phylogenetic relationships between and within species and the comparisons of local goats to related breeds geographically. The information can be applied management of conservation-guided breeding programmes by crossing the indigenous breed's unique genes with high productivity traits from another source.

Résumé

Les races caprines (Capra hircus) indigènes du Kenya n'ont pas été décrites avec précision. Ainsi, il existe une menace d’érosion de génotypes uniques, tels que ceux en rapport avec l'adaptabilité et la résistance aux maladies, du fait des croisements incontrôlés. Le classement des caprins kényans selon le phénotype/morphologie identifie trois races: Naine d'Afrique Orientale (NAO), Galla et les croisements entre NAO et Galla. Dans cette étude, les populations caprines de deux des principales régions géographiques du Kenya présentant des communautés pastorales (les Maasaï et les Somalis/Boran) ont été échantillonnées. De l'ADN a été extrait du sang et amplifié par PCR avec des amorces encadrant un fragment du Cytochrome b et les régions des boucles D de l'ADN mitochondrial. Les séquences obtenues ont été analysées au sein des populations caprines du Kenya, ainsi que comparées avec des ensembles de données phylogéographiques connexes. Les données ont montré que, dans l'ensemble, les populations caprines indigènes du Kenya ne sont pas distinctes et que leur structure génétique est très variée. Pourtant, la présence de différents haplogroupes a été décelée. La diversité génétique a présenté un résultat légèrement positif au test D de Tajima pour ce qui est des caprins indigènes du Kenya, alors que l'ensemble de données Ibérique/Méditerranéen/Proche-Orient a obtenu une valeur négative plus marquée, ce qui indique que les deux populations se trouvent soumises à différentes pressions de sélection. Ces analyses ont permis d’établir les relations phylogénétiques inter- et intra-espèce et de comparer les caprins locaux avec des races géographiquement connexes. Ces informations peuvent être appliquées à la gestion de programmes de conservation cherchant l'amélioration génétique par le croisement de gènes uniques des races indigènes avec des caractères de haute productivité en provenance d'autres sources.

Resumen

Las razas caprinas (Capra hircus) autóctonas de Kenya no han sido descritas con precisión. Por ello, existe un riesgo de erosión de genotipos únicos, tales como los relacionados con la capacidad de adaptación y la resistencia a enfermedades, debido a los cruzamientos indiscriminados. La clasificación de las cabras kenianas en base al fenotipo/morfología distingue tres razas: cabra Enana de África Oriental (EAO), cabra Galla y cruces entre EAO y Galla. En el presente estudio, se muestrearon cabras de dos de las principales regiones geográficas de Kenya con comunidades pastoriles, los Masáis y los Somalíes/Boran. Se extrajo ADN de la sangre y se amplificó mediante PCR usando cebadores contiguos a un fragmento de Citocromo b y a las regiones de los bucles D del ADN mitocondrial. Las secuencias derivadas fueron analizadas en el seno de las poblaciones caprinas de Kenya y comparadas con conjuntos de datos filogeográficos relacionados. Los datos muestran que la mayoría de las cabras autóctonas de Kenya no son distintas y que su estructura genética es muy diversa. Aun así, se detectó la presencia de diferentes haplogrupos. La diversidad genética arrojó un resultado levemente positivo en el test D de Tajima en el caso de las cabras autóctonas kenianas, mientras que el conjunto de datos Ibérico/Mediterráneo/Oriente Próximo dio un valor negativo más pronunciado, lo que indica que las dos poblaciones se hallan bajo distintas presiones selectivas. Estos análisis permitieron establecer las relaciones filogenéticas inter- e intra-especie y comparar las cabras locales con razas geográficamente relacionadas. Esta información puede ser aplicada a la gestión de programas, con la vista puesta en la conservación, que persiguen la mejora genética mediante el cruzamiento de genes únicos de las razas autóctonas con caracteres de alta productividad procedentes de otras fuentes.

Keywords

Indigenous goatsKenyamitochondrial DNAphylogeneticscaprins indigènesKenyaADN mitochondrialphylogéniecabras autóctonasKenyaADN mitocondrialfilogenia
Type
Research Article
Information
Animal Genetic Resources/Resources génétiques animales/Recursos genéticos animales , Volume 59 , December 2016 , pp. 73 - 80
Copyright
Copyright © Food and Agriculture Organization of the United Nations 2016 

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