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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: [email protected]; tel: 706-368-6919; fax: 706-236-223 and Kumarasamy Thangaraj, CSIR-Centre for Cellular and Molecular Biology Uppal Road, Hyderabad 500007, India. email: [email protected]; tel: +91 040-27192828; fax: +91 040-27160591
Correspondence to: Sunday Peters, Department of Animal Science, Berry College, Mount Berry, GA 30149, USA. email: [email protected]; tel: 706-368-6919; fax: 706-236-223 and Kumarasamy Thangaraj, CSIR-Centre for Cellular and Molecular Biology Uppal Road, Hyderabad 500007, India. email: [email protected]; 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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References

Abdul-Aziz, M. 2010. Present status of the world goat populations and their productivity. Lohmann Inf., 45(2): 42.Google Scholar
Adebambo, O.A. 2003. Animal breeds: a nation's heritage. Abeokuta, Nigeria, An Inaugural Lecture Delivered at University of Agriculture, 102 pp.Google Scholar
Agha, S.H., Pilla, F., Galal, S., Shaat, I., D'Andrea, M., Reale, S., Abdelsalam, A.Z.A. & Li, M.H. 2008. Genetic diversity in Egyptian and Italian goat breeds measured with microsatellite polymorphism. J. Anim. Breed Genet., 125(3): 194–200.Google Scholar
Akis, I., Oztabak, K., Mengi, A. & Un, C. 2014. Mitochondrial DNA diversity of Anatolian indigenous domestic goats. J. Anim. Breed Genet. doi: 10.1111/jbg.12096.Google Scholar
Amills, M., Ramirez, O., Tomas, A., Badaoui, B., Marmi, J., Acosta, J., Sanchez, A. & Capote, J. 2009. Mitochondrial DNA diversity and origins of South and Central American goats. Anim. Genet., 40(3): 315–322.CrossRefGoogle ScholarPubMed
Azor, P.J., Monteagudo, L.V., Luque, M., Tejedor, M.T., Rodero, E., Sierra, I., Herrera, M., Rodero, A. & Arruga, M.V. 2005. Phylogenetic relationships among Spanish goats breeds. Anim. Genet., 36(5): 423–425.Google Scholar
Bandelt, H.J., Forster, P. & Rohl, A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol., 16: 37–38.Google Scholar
Bayer, W. 1986. Traditonal small ruminant production in the sub-humid zone of Nigeria. In von Kaufman, R., Chater, S. & Blench, R., eds. Livestock systems research in Nigeria's sub-humid zone. Proc. Second ILCA/NAPRI Symp., pp. 141–166. Kaduna.Google Scholar
Bradley, D.G., Machugh, D.E., Cunningham, P. & Loftus, R.T. 1996. Mitochondrial diversity and the origins of African and European cattle. Proc. Natl. Acad. Sci. U.S.A., 3: 5131–5135.Google Scholar
Brown, G.G., Gadaleta, G., Pepe, G. & Saccone, C. 1986. Structural conservation and variation in the D loop containing region of vertebrate mitochondrial DNA. J. Mol. Biol., 192: 503–511.Google Scholar
Cerda-Flores, R.M., Villalobos-Torres, M.C., Barrera-Saldaña, H.A., Cortés-Prieto, L.M., Barajas, L.O., Rivas, F., Carracedo, A., Zhong, Y., Barton, S.A. & Chakraborty, R. 2002. Genetic admixture in three Mexican Mestizo populations based on D1S80 and HLA-DQA1 loci. Am. J. Hum. Biol., 14(2): 257–263.Google Scholar
Chen, S.Y., Su, Y.H., Wu, S.F., Sha, T. & Zhang, Y.P. 2005. Mitochondrial diversity and phylogeographic structure of Chinese domestic goats. Mol. Phylogenet. Evol., 37(3): 804–814.Google Scholar
ÇinarKul, B. & Ertugrul, O. 2011. mtDNA diversity and phylogeography of some Turkish native goat breeds. Ankara Üniv. Vet. Fak. Derg., 58: 129–134.Google Scholar
Excoffier, L., Smouse, P.E., & Quattiro, J.M. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131: 479–491.CrossRefGoogle ScholarPubMed
FAOSTAT. 2013. Food and Agriculture Organization of the United Nations database, Accessed on 22nd May, 2014.Google Scholar
Fu, X.-Y. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147: 915–925.CrossRefGoogle ScholarPubMed
Jia, Y.-H., Shi, X.-W., Jian, C.-S., Zhu, W.-S., Zhang, Y.-P., He, Z.-Q., Liao, Z.-L., Yu, Y.-H. & Li, T.-Q. 1999. Mitochondrial DNA polymorphism of Guizhou goat breeds. Zool. Res., 20(2): 88–92.Google Scholar
Joshi, M.B., Rout, P.K.., Mandal, A.K., Tyler-Smith, C., Singh, L. & Thangaraj, K. 2004. Phylogeography and origin of Indian domestic goats. Mol. Biol. Evol., 21(3): 454–462.Google Scholar
Kim, S.Y., Li, Y., Guo, Y., Li, R., Holmkvist, J., Hansen, T., Pedersen, O., Wang, J. & Nielsen, R. 2010. Design of association studies with pooled or un-pooled next-generation sequencing data. Genet. Epidemiol., 34(5): 479–491.Google Scholar
Kryazhimskiy, S. & Plotkin, J.B. 2008. The population genetics of dN/dS. PLoS Genet., 4(12): e1000304.CrossRefGoogle ScholarPubMed
Li, X., Zhang, Y., Chen, S., Zeng, F., Qiu, X. & Liu, X. 1997. Study on the mtDNA RFLP of goat breeds. Zool. Res., 18(4): 421–428.Google Scholar
Li, X.L. & Valentini, A. 2004. Genetic diversity of Chinese indigenous goat breeds based on microsatellite markers. J. Anim. Breed Genet., 121(5): 350–355.Google Scholar
Librado, P. & Rozas, J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinf. Appl. Note, 25(11): 1451–1452.Google Scholar
Lira, J., Linderholm, A., Olaria, C., Brandstrom Durling, M., Gilbert, M.T., Ellegren, H., Willerslev, E., Liden, K., Arsuaga, J.L. & Gotherstrom, A. 2010. Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses. Mol. Ecol., 19: 64–78.Google Scholar
Liu, Y.P., Wu, G.S., Yao, Y.G., Miao, Y.W., Luikart, G., Baig, M., Beja-Pereira, A., Ding, Z.L., Palanichamy, M.G. & Zhang, Y.P. 2006. Multiple maternal origins of chickens: out of the Asian jungle. Mol. Phylogenet. Evol., 38: 12–19.Google Scholar
Liu, Y.P., Cao, S.X., Chen, S.Y., Yao, Y.G. & Liu, T. Z. 2009. Genetic diversity of Chinese domestic goat based on the mitochondrial DNA sequence variation. J. Anim. Breed Genet., 126(1): 80–89.Google Scholar
Luikart, G., Giellly, L., Excoffier, J.D., Vigne, J., Bouuvet, J. & Taberlet, V. 2001. Multiple maternal origins and weak phylogeographic structure in domestic goats. Proc. Natl. Acad. Sci. U.S.A., 98: 5927–5932.Google Scholar
MacHugh, D.E. & Bradley, D.G. 2001. Livestock genetic origins: goats buck the trend. Proc. Natl. Acad. Sci. U.S.A., 98: 5382–94.Google Scholar
Mannen, H., Nagata, Y., & Tsuji, S. 2001. Mitochondrial DNA reveal that domestic goat (Capra hircus) are genetically affected by two subspecies of bezoar (Capra aegagurus). Biochem. Genet., 39: 145–154.Google Scholar
Muema, E.K., Wakhungu, J.W., Hanotte, O. & Jianlin, H. 2009. Genetic diversity and relationship of indigenous goats of sub-Saharan Africa using microsatellite DNA markers. Livest. Res. Rural Dev., 21(2): Article #28. Retrieved October 7, 2013 (available at http://www.lrrd.org/lrrd21/2/muem21028.htm).Google Scholar
Naderi, S., Rezaei, H.R., Taberlet, P., Zundelm, S., Rafat, S.A., Naghashm, H.R., el-Barody, M.A.A., Ertugrul, O. & Pompanon, F. 2007. Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS ONE, 2(10): e1012.Google Scholar
Niu, D., Fu, Y., Luo, J., Ruan, H., Yu, X.P., Chen, G. & Zhang, Y.P. 2002. The origin and genetic diversity of Chinese native chicken breeds. Biochem. Genet., 40: 163–174.Google Scholar
Nomura, K., Yonezawa, T., Mano, S., Kawakami, S., Shedlock, A.M., Hasegawa, M. & Amano, T. 2013. Domestication process of the goat revealed by an analysis of the nearly complete mitochondrial protein-encoding genes. PLoS ONE, 8(8): e67775. doi: 10.1371/journal.pone.0067775.Google Scholar
Okpeku, M., Ozoje, M.O., Adebambo, O.A., Agaviezor, B.O., O'Neill, M.J. & Imumorin, I.G. 2011a. Preliminary analysis of microsatellite-based genetic diversity of goats in southern Nigeria. Anim. Genet. Res., 49: 33–41.Google Scholar
Okpeku, M., Yakubu, A., Peters, S.O., Ozoje, M.O., Ikeobi, C.O.N., Adebambo, O.A. & Imumorin, I.G. 2011b. Application of multivariate principal component analysis to morphological traits of goats in southern Nigeria. Acta Agric. Slov., 98: 101–109.Google Scholar
Pereira, F., Pereira, L., Van Asch, B., Bradley, D.G. & Amorim, A. 2005. The mtDNA catalogue of all Portuguese autochthonous goat (Capra hircus) breeds: high diversity of female lineages at the western fringe of European distribution. Mol. Ecol., 14(8): 2313–2318.Google Scholar
Rogers, A.R. & Harpending, H. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol., 9: 552–569.Google Scholar
Rout, P.K., Thangara, K., Mandal, A. & Roy, R. 2012. Genetic variation and population structure in Jamunapari goats using microsatellites, mitochondrial DNA, and milk protein genes. Sci. World J. , 2012: 618909.Google Scholar
Schneider, S., Kueffer, J.M., Roessli, D. & Excoffier, L. 1999. Arlequin 2.001 A software for population genetic data analysis. Switzerland, Genetics and Biometry Laboratory, University of Geneva.Google Scholar
Sultana, S., Mannen, H. & Tsuji, S. 2003. Mitochondrial DNA diversity of Pakistani goats. Anim. Genet., 34: 417–421.Google Scholar
Taberlet, P., Coissac, E., Pansu, J. & Pompanon, F. 2011. Conservation genetics of cattle, sheep, and goats. C. R. Biol., 334: 247–254.Google Scholar
Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol., 30(12): 2725–2729. doi: 10.1093/molbev/mst197.Google Scholar
Thompson, J.D., Higgins, D.G. & Gibson, T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalities and weight matrix choice. Nucl. Acids Res., 22: 4673–4680.Google Scholar
Troy, C.S., Machugh, D.E., Bailey, J.F., Magee, D.A., Loftus, R.T., Cunningham, P., Chamberlain, A.T., Sykes, B.C. & Bradley, D.G. 2001. Genetic evidence for near-Eastern origins of European cattle. Nature, 410: 1088–1091.Google Scholar
Vahidi, S.M., Tarang, A.R., Naqvi, A.U., Falahati Anbaran, M., Boettcher, P., Joost, S., Colli, L., Garcia, J.F. & Ajmone-Marsan, P. 2014. Investigation of the genetic diversity of domestic Capra hircus breeds reared within an early goat domestication area in Iran. Genet. Sel. Evol., 46(1): 27.Google Scholar
Vilà, C., Leonard, J.A., Götherström, A., Marklund, S., Sandberg, K., Lidén, K., Wayne, R.K. & Ellegren, H. 2001. Widespread origins of domestic horse lineages. Science, 291: 474–477.Google Scholar
Zhao, W., Zhong, T., Wang, L.J., Li, L. & Zhang, H.P. 2014. Extensive female-mediated gene flow and low phylogeography among seventeen goat breeds in southwest china. Biochem. Genet., 52(7–8): 355–364.Google Scholar
Zhong, T., Zhao, Q.J., Niu, L.L., Wang, J., Jin, P.F., Zhao, W., Wang, L.J., Li, L., Zhang, H.P. & Ma, Y.H. 2013. Genetic phylogeography and maternal lineages of 18 Chinese black goat breeds. Trop. Anim. Health Prod., 45(8): 1833–1837.Google Scholar