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Mitochondrial DNA hypervariable region 1 diversity in Nigerian goats

Published online by Cambridge University Press:  03 January 2017

Moses Okpeku ,
Sunday O. Peters ,
Ikhide G. Imumorin ,
Kyle C. Caires ,
Varun K. Sharma ,
Mathew Wheto ,
Rakesh Tamang ,
Adeyemi S. Adenaike ,
Michael O. Ozoje  and
Kumarasamy Thangaraj
Moses Okpeku
Affiliation:
Department of Animal Science, Niger Delta University, Amasomma, Nigeria CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
Sunday O. Peters*
Affiliation:
Department of Animal Science, Berry College, Mount Berry, GA 30149, USA Department of Animal and Dairy Sciences, University of Georgia, Athens, GA 30602, USA
Ikhide G. Imumorin
Affiliation:
Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 1 4853, USA
Kyle C. Caires
Affiliation:
Department of Animal Science, Berry College, Mount Berry, GA 30149, USA
Varun K. Sharma
Affiliation:
CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India Department of Surgery, Oncology and Gastroenterology, University of Padova, Via Gattamelata 64, 35128, Padova, Italy
Mathew Wheto
Affiliation:
Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 1 4853, USA Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
Rakesh Tamang
Affiliation:
CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata-700019, India
Adeyemi S. Adenaike
Affiliation:
Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
Michael O. Ozoje
Affiliation:
Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
Kumarasamy Thangaraj*
Affiliation:
CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
*
Correspondence to: Sunday Peters, Department of Animal Science, Berry College, Mount Berry, GA 30149, USA. email: speters@berry.edu; tel: 706-368-6919; fax: 706-236-223 and Kumarasamy Thangaraj, CSIR-Centre for Cellular and Molecular Biology Uppal Road, Hyderabad 500007, India. email: thangs@ccmb.res.in; tel: +91 040-27192828; fax: +91 040-27160591
Correspondence to: Sunday Peters, Department of Animal Science, Berry College, Mount Berry, GA 30149, USA. email: speters@berry.edu; tel: 706-368-6919; fax: 706-236-223 and Kumarasamy Thangaraj, CSIR-Centre for Cellular and Molecular Biology Uppal Road, Hyderabad 500007, India. email: thangs@ccmb.res.in; tel: +91 040-27192828; fax: +91 040-27160591
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Summary

Goats make up the largest group of ruminant livestock in Nigeria and are strategic in bridging animal protein supply gap and improving the economy of rural households. The hypervariable region 1 (HVR1) of the caprine mitochondrial genome was investigated to better understand genetic diversity important for improving selection for animal breeding and conservation programs. We sequenced and analysed the mitochondrial DNA (mtDNA) HVR1 in 291 unrelated indigenous Nigerian goats (West African Dwarf (WAD), Red Sokoto (RSO) and Sahel (SAH)), randomly sampled from around the country, and compared them with the HVR1 sequences of 336 Indian goats and 12 other sequences in five different species in the genus Capra (C. falconeri, C. ibex nubiana, C. aegagrus, C. cylindricornis and C. sibirica). A total of 139 polymorphic sites from 291 individuals were captured in 204 haplotypes. Within and among population variations were 77.25 and 22.74 percent, respectively. Nigerian goats showed high genetic diversity (0.87) and high FST values, and separate from Indian goats and other wild species. Haplogroups in WAD separates it from RSO and SAH concomitant with a different demographic history. Clear genetic structure was found among Nigerian goat breeds with appreciable variation in mtDNA HVR1 region. This study grouped Nigerian goat breeds into two major groups suggesting two different demographic origins for Northern and Southern breeds. High genetic admixing denotes different maternal origins and in contrast to evidence from goats from Levant and Central Asia, where goats were originally domesticated.

Résumé

Les caprins constituent le plus grand groupe de ruminants domestiques au Nigéria et jouent un rôle stratégique dans l'approvisionnement en protéines animales et dans l'amélioration de l'économie des ménages ruraux. Une recherche a été menée à propos de la région hypervariable 1 (HVR1) du génome mitochondrial caprin dans le but de mieux comprendre l'importance de la diversité génétique pour améliorer la sélection dans les programmes d'amélioration génétique et de conservation des animaux. La région hypervariable 1 de l'ADN mitochondrial (HVR1) a été séquencée et analysée chez 291 chèvres indigènes du Nigéria, sans rapport entre elles (Naine d'Afrique Occidentale (NAO), Rouge de Sokoto (RS) et Sahel (S)), échantillonnées de manière aléatoire à travers le pays et comparées avec les séquences HVR1 de 336 chèvres indiennes et avec 12 autres séquences de 5 espèces différentes du genre Capra (C. falconeri, C. ibex nubiana, C. aegagrus, C. cylindricornis et C. sibirica). Un total de 139 sites polymorphes de 291 individus a été rassemblé en 204 haplotypes. La variation intra- et inter-populationnelle a été de 77,25 pour cent et de 22,74 pour cent, respectivement. Les caprins nigérians ont montré une grande diversité génétique (0,87) et des valeurs de FST élevées et différentes de celles des chèvres indiennes et de celles des autres espèces sauvages. D'après les haplogroupes, la chèvre NAO serait à séparer des populations concomitantes de RS et S avec une histoire démographique différente. Une structure génétique claire a été décelée entre les races caprines du Nigéria, avec une variation substantielle dans la région HVR1 de l'ADN mitochondrial. Cette étude a regroupé les races caprines nigérianes en deux groupes principaux, ce qui suggère deux origines démographiques différentes pour les races du Nord et du Sud. Le fort degré de mélange génétique dénote des origines maternelles différentes, contrairement à ce qui a été observé chez les chèvres du Levant et d'Asie Centrale, où les caprins furent d'abord domestiqués.

Resumen

Las cabras constituyen el mayor grupo de ganado rumiante en Nigeria y desempeñan un papel estratégico en el aporte de proteína animal y en la mejora de la economía de los hogares rurales. Se investigó acerca de la región hipervariable 1 (HVR1) del genoma mitocondrial caprino con el fin de comprender mejor la importancia de la diversidad genética para mejorar la selección en los programas de mejora y conservación animal. Se secuenció y se analizó la región hipervariable 1 del ADN mitocondrial (HVR1) en 291 cabras autóctonas de Nigeria no relacionadas (Enana de África Occidental (EAO), Roja de Sokoto (RS) y Sahel (S)), seleccionadas aleatoriamente a lo largo del país y comparadas con las secuencias HVR1 de 336 cabras indias y con otras 12 secuencias de 5 especies diferentes del género Capra (C. falconeri, C. ibex nubiana, C. aegagrus, C. cylindricornis y C. sibirica). Un total de 139 sitios polimórficos de 291 individuos se concentraron en 204 haplotipos. La variación intra- e interpoblacional fue de 77,25 por ciento y de 22,74 por ciento, respectivamente. Las cabras nigerianas mostraron una elevada diversidad genética (0,87) y unos valores de FST elevados, distintos de los de las cabras indias y de los de las otras especies salvajes. De acuerdo con los haplogrupos, la cabra EAO se desliga de poblaciones concomitantes de RS y S con una historia demográfica diferente. Se identificó una estructura genética clara entre las razas caprinas de Nigeria, con una variación apreciable en la región HVR1 del ADN mitocondrial. Este estudio agrupó las razas caprinas nigerianas en dos grupos principales, sugiriendo así dos orígenes demográficos distintos para las razas septentrionales y meridionales. El alto grado de mezcla genética denota orígenes maternos distintos, a diferencia de lo observado en cabras del Levante y Asia Central, donde se domesticaron originalmente las cabras.

Keywords

genetic diversitygoatshypervariable regionmitochondrial DNANigeriadiversité génétiquecaprinsrégion hypervariableADN mitochondrialNigériadiversidad genéticacabrasregión hipervariableADN mitocondrialNigeria
Type
Research Article
Information
Animal Genetic Resources/Resources génétiques animales/Recursos genéticos animales , Volume 59 , December 2016 , pp. 47 - 54
Copyright
Copyright © Food and Agriculture Organization of the United Nations 2016 

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