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Maintenance of mtDNA diversity in Kalahari Red goat of South Africa imported to Nigeria

Published online by Cambridge University Press:  08 December 2014

M.N. Bemji ,
E.O. Awotunde ,
O. Olowofeso ,
I.J. James ,
B.O. Oduguwa ,
N. Okwelum  and
O.A. Osinowo
M.N. Bemji*
Affiliation:
Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B. 2240, Abeokuta, Nigeria
E.O. Awotunde
Affiliation:
Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B. 2240, Abeokuta, Nigeria
O. Olowofeso
Affiliation:
Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B. 2240, Abeokuta, Nigeria
I.J. James
Affiliation:
Department of Animal Physiology, Federal University of Agriculture, P.M.B. 2240, Abeokuta, Nigeria
B.O. Oduguwa
Affiliation:
Institute of Food Security, Environmental Resources and Agricultural Research, Federal University of Agriculture, P.M.B. 2240, Abeokuta, Nigeria
N. Okwelum
Affiliation:
Institute of Food Security, Environmental Resources and Agricultural Research, Federal University of Agriculture, P.M.B. 2240, Abeokuta, Nigeria
O.A. Osinowo
Affiliation:
Department of Animal Physiology, Federal University of Agriculture, P.M.B. 2240, Abeokuta, Nigeria
*
Correspondence to: M.N. Bemji, Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B. 2240, Abeokuta, Nigeria. email: [email protected]
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Summary

Analysis of mitochondrial DNA (mtDNA) was carried out using 38 Kalahari Red (KR) goats randomly sampled from a flock imported into Nigeria in 2011 by the Federal University of Agriculture, Abeokuta, as an initial step to investigate the genetic structure of the breed, due to limited information on the breed. Apart from estimating genetic diversities, phylogenetic analysis to elucidate maternal lineages, relationship with wild goats as well as Tajima's D and Fu's Fs statistics were computed to test the departure from constant population size under the neutral model. The first hypervariable (HV1) region of mtDNA (481 bp) sequenced from 38 goats represented 11 haplotypes. Polymorphism of HV1 fragment was high, haplotype and nucleotide diversities were 0.869 ± 0.030 and 0.0299 ± 0.0067, respectively. Maximum-likelihood tree constructed with 11 haplotypes and 22 reference haplotypes representing six haplogroups worldwide revealed that five out of 11 haplotypes belong to haplogroup A, whereas six haplotypes belong to B. KR population clustered with Capra aegagrus as its wild ancestor. There was evidence of mitochondrial footprint that reflected past population decline based on positive and significant Fu's Fs estimate (6.283; P < 0.01). The mtDNA data did not however show that genetic variability of the breed has drastically reduced on account of population reduction. The information obtained is strategic to utilization and conservation of the population.

Résumé

Analyse de l'ADN mitochondrial (ADNmt) a été réalisée à l'aide de 38 chèvres Kalahari rouge prélevés au hasard dans un troupeau importé au Nigéria en 2011 par l'Université fédérale de l'Agriculture, Abeokuta, dans un premier temps pour étudier la structure génétique de la race, en raison du peu de données sur la race. En dehors de l'estimation de la diversité génétique, l'analyse phylogénétique d'élucider des lignées maternelles et origine de la race ainsi que des statistiques D de Tajima et Fu Fs étaient calculés à tester le départ de la taille de la population constante sous le modèle neutre. La première région hypervariable (HV1) de l'ADN mitochondrial (481 bp) séquencée à partir de 38 chèvres représenté 11 haplotypes. Le polymorphisme du fragment HV1 était diversités haute, les haplotypes et les nucléotides respectivement 0.869 ± 0.030 et 0.0299 ± 0.0067. Arbre de maximum de vraisemblance construit avec des 11 haplotypes et 22 haplotypes de référence représentant les 6 haplogroupes dans le monde entier a révélé que 6 des 11 haplotypes appartiennent à haplogroupe A, tandis que 5 haplotypes appartiennent à la population de B. KR en cluster avec Capra aegagrus comme son ancêtre sauvage. Il y avait preuve de l'empreinte mitochondrial qui traduit devant le déclin de la population sur la base Fs estimation positive et significative de Fu (6.283; P < 0.01). Les données de l'ADN mitochondrial ne montrent pas cependant que la variabilité génétique de la race a drastiquement réduit en raison de la réduction de la population. L'information obtenue est stratégique pour l'utilisation et la conservation de la population.

Resumen

Se realizó un análisis de ADN mitocondrial (ADNmt) con 38 cabras de raza Kalahari Roja elegidas al azar en un rebaño importado en Nigeria en 2011 por la Universidad Federal de Agricultura, en Abeokuta, como un primer paso para la investigación de la estructura genética de la raza, ya que es escasa la información que, sobre ella, existe. Además de estimar la diversidad genética, se llevó a cabo un análisis filogenético para determinar los linajes maternos y la relación con las cabras salvajes. Se calcularon también los estadísticos D de Tajima y Fs de Fu para evaluar la situación de partida bajo condiciones de neutralidad y estabilidad demográfica. La primera región hipervariable (HV1) del ADNmt (481 pares de bases) secuenciado en las 38 cabras presentó 11 haplotipos. El fragmento HV1 presentó un elevado polimorfismo, siendo la diversidad de haplotipos y de nucleótidos de 0.869 ± 0.030 y 0.0299 ± 0.0067, respectivamente. El árbol de máxima verosimilitud, construido con 11 haplotipos y 22 haplotipos de referencia, que representaban 6 haplogrupos de todo el mundo, mostró que 5 de los 11 haplotipos pertenecían al haplogrupo A, mientras que 6 haplotipos pertenecían al B. La población Kalahari Roja formó un conglomerado que tenía a Capra aegagrus como antepasado salvaje. Dado el valor positivo y significativo del estadístico Fs de Fu (6.283; P < 0.01), hubo indicios, en la información mitocondrial, de una disminución de la población en el pasado. La información del ADNmt no refleja sin embargo que se haya reducido drásticamente la variabilidad genética de la raza como consecuencia de la reducción de la población. La información obtenida resulta estratégica para la utilización y conservación de la población.

Keywords

demographic historyKalahari Red goatlineagesmtDNA diversitydiversité de l'ADN mitochondriallignéesoriginehistoire démographiquechèvre de Kalahari rougediversidad del ADNmtlinajesorigenhistoria demográficacabra Kalahari Roja
Type
Research Article
Information
Animal Genetic Resources/Resources génétiques animales/Recursos genéticos animales , Volume 55 , December 2014 , pp. 39 - 46
Copyright
Copyright © Food and Agriculture Organization of the United Nations 2014 

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