Hostname: page-component-cd9895bd7-8ctnn Total loading time: 0 Render date: 2024-12-28T01:24:55.127Z Has data issue: false hasContentIssue false
  • English
  • Français

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: [email protected]
Get access

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 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Abate, A., Wanyoike, M.M. & Badamana, M.S. 1989. Towards improving animal production in the range lands of Kenya. In Proceedings of the XVI International Grassland Congress, 4–11 October 1989, Nice – France, 1989, 1613 1614; 8 Ref. Association Francaise pour la Production Fourragere, Centre National de Recherché Agronomique, Versailles, France.Google Scholar
Ajmone-Marsan, P., Colli, L., Han, J.L., Achilli, A., Lancioni, H., Joost, S., Crepaldi, P., Pilla, F., Stella, A., Taberlet, P., Boettcher, P., Negrini, R., Lenstra, J. A. 2014. The characterization of goat genetic diversity: towards a genomic approach. Small Rumin. Res. 121: 58–72.Google Scholar
Bradley, D.G., MacHugh, D.E., Cunningham, P. & Loftus, R.T. 1996. Mitochondrial DNA diversity and the origins of African and European cattle. Proc. Natl. Acad. Sci. USA 93: 5131–5135.CrossRefGoogle ScholarPubMed
Devendra, C. & McLeroy, G.B. 1982. Goat and sheep production in the tropics. Intermediate tropical agriculture series. UK, Longman Group. 271 pp.Google Scholar
Dong, Y., Xie, M., Jiang, Y., Xiao, N., Du, X., Zhang, W., Tosser-Klopp, G., Wang, J., Yang, S., Liang, J., Chen, W., Chen, J., Zeng, P., Hou, Y., Bian, C., Pan, S., Li, Y., Liu, X., Wang, W., Servin, B., Sayre, B., Zhu, B., Sweeney, D., Moore, R., Nie, W., Shen, Y., Zhao, R., Zhang, G., Li, J., Faraut, T., Womack, J., Zhang, Y., Kijas, J., Cockett, N., Xu, X., Zhao, S., Wang, J., Wang, W. 2013. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat. Biotechnol. 31: 135–41.CrossRefGoogle ScholarPubMed
Doro, M.G., Piras, D., Leoni, G.G., Casu, G., Vaccargiu, S., Parracciani, D., Naitana, S., Pirastu, M., Novelletto, A. 2014. Phylogeny and patterns of diversity of goat mtDNA haplogroup a revealed by resequencing complete mitogenomes. PLoS ONE 9(4): e95969.Google Scholar
FAO. 2007. The state of the world's animal genetic resources for food and agriculture. Edited by B. Rischkowsky & D. Pilling. Rome (available at http://www.fao.org/docrep/010/a1250e/a1250e00.htm) (accessed 15 Jan 2015).Google Scholar
FAO. 2012. Status and trends of animal genetic resources. Commission on genetic resources for food and agriculture. 15–19 April 2013. Rome (available at http://www.fao.org/docrep/meeting/027/mg046e.pdf) (accessed 15 Jan 2015).Google Scholar
Felsenstein, J. 1993. PHYLIP (phylogeny inference package). 3.5 c ed. Department of Genetics, University of Washington, Seattle.Google Scholar
Fernandez, H., Hughes, S., Vigne, J.D., Helmer, D., Hodgins, G., Miquel, C., Hanni, C., Luikart, G., Taberlet, P. 2006. Divergent mtDNA lineages of goats in an Early Neolithic site, far from the initial domestication areas. Proc. Natl. Acad. Sci. USA 103: 15375–15379.CrossRefGoogle Scholar
Georgoudis, A. 1995. Animal genetic diversity plays important role in Mediterranean agriculture. Divers.: Mediterran. 11: 16–19.Google Scholar
Georgoudis, A. 1998. Considerations for the mixed production system in the Mediterranean area. In Belhadj, T., Boutonnet, J.P. & DiGiulio, A., eds. Filière des viandes rouges dans les pays méditerranéens, pp. 123–131. Zaragoza, CIHEAM.Google Scholar
Hanotte, O., Toll, J., Iniguez, L. & Rege, J.E.O. 2006. Farm animal genetic resources: why and what do we need to conserve. In Proc. IPGRI–ILRI–FAO–CIRAD Workshop: Option for In situ and Ex situ Conservation of AnGR, 8–11 November 2005, Montpellier, France.Google Scholar
Hughes, S., Fernàndez, H., Cucchi, T., Duffraisse, M., Casabianca, F., Istria, D., Pompanon, F., Vigne, J.D., Hanni, C., Taberlet, P. 2012. A dig into the past mitochondrial diversity of Corsican goats reveals the influence of secular herding practices. PLoS ONE 7: e30272.CrossRefGoogle ScholarPubMed
Joshi, M.B., Rout, P.K., Mandal, A.K., Tyler-Smith, C., Singh, L. & Thangaray, K. 2004. Phylogeography and origins of Indian domestic goats. Mol. Biol. Evol. 21: 454–462.CrossRefGoogle ScholarPubMed
Kibegwa, F.M., Githui, K.E., Jung'a, J.O., Badamana, M.S. and Nyamu, M.N. 2016. Mitochondrial DNA variation of indigenous goats in Narok and Isiolo counties of Kenya. J. Anim. Breed. Genet. 133:238–247.Google Scholar
Kibegwa, F.M., Githui, E.K., Jung'a, J.O., Badamana, M.S. & Nyamu, M.N. 2015. Mitochondrial DNA variation of indigenous goats in Narok and Isiolo counties of Kenya. J. Anim. Breed Genet. doi: 10.1111/jbg.12182.Google Scholar
Librado, P. & Rozas, J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451–1452.CrossRefGoogle ScholarPubMed
Luikart, G., Gielly, L., Excoffier, L., Vigne, J.D., Bouvet, J. & Taberlet, P. 2001. Multiple maternal origins and weak phylogeographic structure in domestic goats. Proc. Natl. Acad. Sci. USA 98: 5927–5932.CrossRefGoogle ScholarPubMed
MacHugh, D. & Bradley, D. 2001. Livestock genetic origins: goats buck the trend. Proc. Natl. Acad. Sci. USA 98: 5382–5384.Google Scholar
Manceau, V., Despres, L., Bouvet, J. & Taberlet, P. 1999. Systematics of the genus Capra inferred from mitochondrial DNA sequence data. Mol. Phylogenet. Evol. 13: 504–510.CrossRefGoogle ScholarPubMed
Naderi, S., Rezaei, H.R., Taberlet, P., Zundel, S., Rafat, S.A., Naghash, H.R., el-Barody, M.A., Ertugrul, O., Pompanon, F., Econogene Consortium. 2007. Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS ONE 2(10): e1012. doi: 10.1371/journal.pone.0001012.Google Scholar
Naderi, S., Rezaei, H.R., Pompanon, F., Blum, M.G., Negrini, R., Naghash, H.R., Balkiz, O., Mashkour, M., Gaggiotti, O.E., Ajmone-Marsan, P., Kence, A., Vigne, J.D., Taberlet, P. 2008. The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals. Proc. Natl. Acad. Sci. USA 105: 17659–17664.Google Scholar
Nei, M. & Kumar, S. 2000. Molecular evolution and phylogenetics. New York, Oxford University Press.Google Scholar
Pereira, F. & Amorim, A. 2010. Origin and Spread of Goat Pastoralism. In Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0022864, pp 1–10.Google Scholar
Pieter, E., ed. Africa A to Z. 2013. Continental and Country Profiles. 3. ed. Pretoria: Africa Institute of South Africa. pp 40–52.Google Scholar
Porter, V. 1996. Goats of the world. Ipswich, UK, Farming Press.Google Scholar
Pringle, H. 1998. Neolithic agriculture: reading the signs of ancient animal domestication. Science, 282: 1448.Google Scholar
Sambrook, J., Maniatis, T. & Fritsch, E.F. 1987. Molecular cloning. A laboratory manual. Cold spring harbor, 14th Printing.Google Scholar
Taberlet, P., Valentini, A., Rezaei, H.R., Naderi, S., Pompanon, F., Negrini, R. & Ajmone-Marsan, P. 2008. Are cattle, sheep, and goats endangered species? Mol. Ecol. 17: 275–284.Google Scholar
Tajima, F. 1989. Statistical methods to test for nucleotide mutation hypothesis by DNA polymorphism. Genetics 123: 585–595.Google Scholar
Tamura, K., Nei, M. & Kumar, S. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl. Acad. Sci. USA 101: 11030–11035.Google Scholar
Tamura, K., Stecher, G., Peterson, D., Alan Filipski, A. & Kumar, S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30: 2725–2729.Google Scholar
Zeder, M.A. & Hesse, B. 2000. The initial domestication of goats (Capra hircus) in the Zagros mountains 10,000 years ago. Science 287(5461): 2254–2257.Google Scholar