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Assessment of the genetic diversity in cowpea (Vigna unguiculata L. Walp.) germplasm from Ghana using simple sequence repeat markers

Published online by Cambridge University Press:  13 April 2010

Aaron T. Asare
Department of Molecular Biology and Biotechnology, University of Cape Coast, Cape Coast, Ghana Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
Bhavani S. Gowda
Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
Isaac K. A. Galyuon
Department of Molecular Biology and Biotechnology, University of Cape Coast, Cape Coast, Ghana
Lawrence L. Aboagye
Plant Genetic Resources Research Institute, Bunso, Ghana
Jemmy F. Takrama
Cocoa Research Institute of Ghana, PO Box 8, New Tafo-Akim, Ghana
Michael P. Timko*
Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
*Corresponding author. E-mail:


Genetic diversity and phylogenetic relationships among 141 cowpea (Vigna unguiculata L. Walp.) accessions collected throughout the nine geographical regions of Ghana were evaluated using simple sequence repeat (SSR) molecular markers. Twenty-five primer combinations pre-selected by their ability to polymerase chain reaction amplify SSRs from a set of test cowpea germplasm were evaluated. Of these, 20 primer combinations gave reproducible polymorphisms among 97.2% of the cowpea accessions tested, with the remaining accessions being found to be genetically identical. The informative primer combinations revealed a total of 74 alleles at 20 loci with an average of 3.8 alleles detected per locus. Variation in heterozygosity among cowpea SSRs ranged from 0.01 to 0.84 with an average occurrence of 0.19. The polymorphism information content varied from 0.07 to 0.66 with an average of 0.38. The Ghanaian cowpea accessions clustered into five main branches, each of which was loosely associated with the geographical regions from which samples were obtained. Accession GH2288 was found to be the most divergent cowpea accession compared with all others including the outgroup IT84S-2049, a breeding line from Nigeria. Our results provide a framework for future studies aimed at the conservation and management of cultivated cowpea germplasm in Ghana, and a good starting point for the selection of parental lines for genetic improvement programmes.

Research Article
Copyright © NIAB 2010

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Abe, J, Xu, D, Suzuki, Y, Kanazawa, A and Shimamoto, Y (2003) Soybean germplasm pools in Asia revealed by nuclear SSRs. Theorical and Applied Genetics 106: 445453.CrossRefGoogle ScholarPubMed
Ayres, NM, McClung, AM, Larkin, PD, Bligh, HFJ, Jones, CA and Park, WD (1997) Microsatellite and single nucleotide polymorphism differentiate apparent amylase classes in an extended pedigree of US rice germplasm. Theoretical and Applied Genetics 94: 773784.CrossRefGoogle Scholar
Ba, FS, Pasquet, RE and Gepts, P (2004) Genetic diversity in cowpea [Vigna unguiculata (L.) Walp.] as revealed by RAPD markers. Genetic Resources and Crop Evolution 51: 539550.Google Scholar
Benson, G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research 27: 573580.Google Scholar
Blair, M and McCouch, SR (1997) Microsatellite and sequence-tagged site markers diagnostic for the bacterial blight resistance gene, xa-5. Theoretical and Applied Genetics 94: 773784.Google Scholar
Bowers, J, Boursiquot, J, This, P, Chu, K, Johansson, H and Meredith, C (1999) Historical genetics: the percentage of Chardonnay, Gamay, and other wine grapes of northern France. Science 285: 15621565.Google Scholar
Brown, SM, Hopkins, MS, Mitchell, SE, Senior, ML, Wang, TY, Duncan, RR, Gonzalez-Candelas, F and Kresovich, S (1996) Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum [Sorghum bicolor (L.) Moench]. Theoretical and Applied Genetics 93: 190198.Google ScholarPubMed
Chen, X, Temnykh, S, Xu, Y, Cho, YG and McCouch, SR (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theoretical and Applied Genetics 95: 553567.Google Scholar
Chen, XF, Laudeman, TW, Rushton, PJ, Thomas, TA and Timko, MP (2007) CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences. BMC Bioinformatics 8: 129.CrossRefGoogle ScholarPubMed
Choumane, W, Winter, P, Weigand, F and Kahl, G (2000) Conservation and variability of sequence tagged microsatellites sites (STMS) from chickpea (Cicer aerietinum L.) within the genus Cicer. Theoretical and Applied Genetics 101: 269278.Google Scholar
Coulibaly, S, Pasquet, RS, Papa, R and Gepts, P (2002) AFLP analysis of the phenetic organization and genetic diversity of Vigna unguiculata L. Walp. reveals extensive gene flow between wild and domesticated types. Theoretical and Applied Genetics 104: 358366.CrossRefGoogle ScholarPubMed
Doebley, J (1989) Isozymic evidence and the evolution of crop plants. In: Soltis, DE and Soltis, PS (eds) Isozymes in Plant Biology. Portland, OR: Dioscorides Press, pp. 165191.Google Scholar
Dib, C, Faure, S, Fizames, C, Samson, D, Drouot, N, Vignal, A, Millasseau, P, Mare, S, Hazan, J, Seboun, E, Lathrop, G, Gyapay, G, Morisselte, J and Weissenbach, J (1996) A comprehensive genetic map of the human genome based on 5264 microsatellites. Nature 380: 152154.Google Scholar
Diouf, D and Hilu, KW (2005) Microsatellite and RAPD markers to study genetic relationships among cowpea breeding lines and local varieties in Senegal. Genetic Resources and Crop Evolution 52: 19571967.CrossRefGoogle Scholar
Ehlers, JD and Hall, AE (1996) Genotypic classification of cowpea based on responses to heat and photoperiod. Crop Science 36: 673679.CrossRefGoogle Scholar
Ehlers, JD and Hall, AE (1997) Cowpea (Vigna unguiculata L. Walp.). Field Crops Research 53: 187204.CrossRefGoogle Scholar
Eloward, HOA and Hall, AE (1987) Influence of early and late nitrogen fertilization on yield and nitrogen fixation of cowpeas under well-watered and dry field conditions. Field Crops Research 15: 229244.Google Scholar
Fall, L, Diouf, D, Fall-Ndiaye, MA, Badiane, FA and Gueye, M (2003) Genetic diversity in cowpea [Vigna unguiculata (L.) Walp.] varieties determined by ARA and RAPD techniques. African Journal of Biotechnology 2: 4850.Google Scholar
Fang, J, Chao, C-CT, Roberts, OA and Ehlers, JD (2007) Genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] in four West African and USA breeding programs as determined by AFLP analysis. Genetic Resources and Crop Evolution 54: 11971209.CrossRefGoogle Scholar
Fatokun, CA, Danesh, D and Young, ND (1993) Molecular taxonomic relationships in the genus Vigna based on the RFLP analysis. Theoretical and Applied Genetics 86: 97104.CrossRefGoogle ScholarPubMed
Fatokun, CA, Mignouna, HD, Knox, MR and Ellis, THN (1997) AFLP variation among cowpea varieties. Agronomy Abstracts. Madison, WI: ASA, p. 156.Google Scholar
Fery, RL (1985) The genetics of cowpea: a review of the world literature. In: Singh, SR and Rachie, KO (eds) Cowpea Research, Production and Utilization. Chichester/New York: John Wiley and Sons, Ltd, pp. 2562.Google Scholar
Fotso, M, Azanza, JL, Pasquet, R and Raymond, J (1994) Molecular homogeneity of cowpea (Vigna unguiculata, Fabaceae) seed storage proteins. Plant Systematics and Evolution 191: 3956.CrossRefGoogle Scholar
Hall, AE (2004) Breeding for adaptation to drought and heat in cowpea. European Journal of Agronomy 21: 447454.Google Scholar
He, C, Poysa, V and Yu, K (2003) Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars. Theoretical and Applied Genetics 106: 363373.Google ScholarPubMed
Hegde, VS and Mishra, SK (2009) Landraces of cowpea, Vigna unguiculata (L.) Walp., as potential sources of genes for unique characters in breeding. Genetic Resources and Crop Evolution 56: 615627.Google Scholar
Langyintuo, AS, Lowenberg-DeBoer, J, Faye, M, Lambert, D, Ibro, G, Moussa, B, Kergna, A, Kushwaha, S, Musa, S and Ntoukam, G (2003) Cowpea supply and demand in West Africa. Field Crops Research 82: 215231.CrossRefGoogle Scholar
Li, CD, Fatokun, CA, Ubi, B, Singh, BB and Scoles, GJ (2001) Determining genetic similarities and relationships among cowpea breeding lines and cultivars by microsatellite primers. Crop Science 41: 189197.CrossRefGoogle Scholar
Liu, K and Muse, S (2005) PowerMarker. An integrated analysis environment for genetic marker analysis. Bioinformatics 21: 21282129.CrossRefGoogle ScholarPubMed
Mengoni, A, Gori, A and Bazzicalupo, M (2000) Use of RAPD and microsatellite (SSR) variation to assess genetic relationships among population of tetraploid alfalfa, Medicago sativa. Plant Breeding 118: 17.Google Scholar
Mignouna, HD, Ng, NQ, Ikca, J and Thottapilly, G (1998) Genetic diversity in cowpea as revealed by random amplified polymorphic DNA. Journal of Genetics and Breeding 52: 151159.Google Scholar
Nei, M and Li, WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences (USA) 76: 52695273.CrossRefGoogle ScholarPubMed
Nkongolo, KK (2003) Genetic characterization of Malawian cowpea (Vigna unguiculata (L.) Walp.) landraces: diversity and gene flow among accessions. Euphytica 129: 219228.CrossRefGoogle Scholar
Ogunkanmi, LA, Ogundipe, OT, Ng, NQ and Fatokun, CA (2008) Genetic diversity in wild relatives of cowpea (Vigna unguiculata) as revealed by simple sequence repeats (SSR) markers. Journal of Food Agriculture and Environment 6: 253268.Google Scholar
Panella, L and Gepts, P (1992) Genetic relationships with Vigna unguiculata (L.) Walp. based on isozyme analyses. Genetic Resources and Crop Evolution 39: 7188.Google Scholar
Pasquet, RS (1993) Variation at isoenzyme loci in wild Vigna unguiculata (L.) Walp. (Fabaceae, Phaseoleae). Plant Systematics and Evolution 186: 157173.Google Scholar
Pasquet, RS (1999) Genetic relationships among subspecies of Vigna unguiculata (L.) Walp. based on allozyme variation. Theoretical and Applied Genetics 98: 11041119.CrossRefGoogle Scholar
Pasquet, RS (2000) Allozyme diversity of cultivated cowpea Vigna unguiculata (L.) Walp. Theoretical and Applied Genetics 101: 211219.CrossRefGoogle Scholar
Perrino, P, Laghetti, G, Spagnoletti Zeuli, PL and Monti, LM (1993) Diversification of cowpea in the Mediterranean and other centers of cultivation. Genetic Resources and Crop Evolution 40: 121132.CrossRefGoogle Scholar
Quaye, W, Adofo, K, Madode, YE and Abizari, A-R (2009) Exploratory and multidisciplinary survey of the cowpea network in Tolon-Kumbungu district of Ghana: a food sovereignty perspective. African Journal of Agricultural Research 4: 311320.Google Scholar
Rongwen, J, Akkaya, MS, Bhagwat, AA, Lavi, U and Cregan, PB (1995) The use of microsatellite DNA markers for soybean genotype identification. Theoretical and Applied Genetics 90: 4348.CrossRefGoogle ScholarPubMed
Sanginga, N, Dashiell, KE, Diels, J, Vanlauwe, B, Lyasse, O, Carsky, RJ, Tasawali, S, Asafo-Adjei, B, Menkir, A, Schulz, S, Singh, BB, Chikoye, D, Keatinge, D and Ortiz, R (2003) Sustainable resource management coupled to resilient germplasm to provide new intensive cereal-grain-legume-livestock systems in the dry savanna. Agriculture, Ecosystystems & Environment 100: 305314.Google Scholar
Simon, MV, Benko-Iseppon, AM, Resende, LV, Winter, P and Kahl, G (2007) Genetic diversity and phylogenetic relationships in Vigna Savi germplasm revealed by DNA amplification fingerprinting. Genome 50: 538547.CrossRefGoogle ScholarPubMed
Senior, ML, Murphy, JP, Goodman, MM and Stuber, CW (1998) Utility of SSRs for determining genetic similarities and relationships in maize using an agarose gel system. Crop Science 38: 10881098.Google Scholar
Tarawali, SA, Singh, BB, Gupta, SC, Tabo, R, Harris, F, Nokoe, S, Fernandez-Rivera, S, Bationo, A, Manyong, VM, Makinde, K and Odion, EC (2002) Cowpea as a key factor for a new approach to integrated crop–livestock systems research in the dry Savanna of West Africa. In: Fatokun, CA, Tarawali, SA, Singh, BB, Kormawa, PM and Tamo, M (eds) Challenges and Opportunities for Enhancing Sustainable Cowpea Production. Ibadan: IITA, pp. 233251.Google Scholar
Timko, MP and Singh, BB (2008) Cowpea, a multifunctional legume. In: Moore, PH and Ming, R (eds) Genomics of Tropical Crop Plants. New York, NY: Springer Science+Business Media, LLC, pp. 227258.CrossRefGoogle Scholar
Timko, MP, Ehlers, JD and Roberts, PA (2007) Cowpea. In: Kole, C (ed.) Pulses, Sugar and Tuber Crops, Genome Mapping and Molecular Breeding in Plants. vol. 3. Berlin/Heidelberg: Springer-Verlag, pp. 4967.CrossRefGoogle Scholar
Timko, MP, Rushton, PJ, Laudeman, TW, Bokowiec, MT, Chipumuro, E, Foo Cheung, F, Town, CD and Chen, XF (2008) Sequencing and analysis of the gene-rich space of cowpea. BMC Genomics 9: 103.CrossRefGoogle ScholarPubMed
Uma, MS, Hittalamani, S, Murthy, BCK and Viswanatha, KP (2009) Microsatellite DNA marker aided diversity analysis in cowpea [Vigna unguiculata (L.) Walp.]. Indian Journal of Genetics and Plant Breeding 69: 3543.Google Scholar
Vaillancourt, RE and Weeden, NF (1992) Chloroplast DNA polymorphism suggests a Nigerian centre of domestication for the cowpea Vigna unguiculata (Leguminisae). American Journal of Botany 79: 11941199.Google Scholar
Vaillancourt, RE, Weeden, NF and Barnard, J (1993) Isozyme diversity in the cowpea species complex. Crop Science 33: 606613.Google Scholar
Wang, ML, Barkley, NA, Gillaspie, GA and Pederson, GA (2008) Phylogenetic relationships and genetic diversity of the USDA Vigna germplasm collection revealed by gene-derived markers and sequencing. Genetic Resarch 90: 467480.CrossRefGoogle ScholarPubMed
Weising, K, Winter, P, Huttel, B and Kahl, G (1998) Microsatellite marker for molecular breeding. Journal of Crop Production 1: 113143.Google Scholar
Winter, P, Pfaff, T, Udupa, SM, Huttel, B, Sharma, PC, Sahi, S, Arreguin-Espinoza, R, Weigand, F, Muehlbauer, FJ and Kahl, G (1999) Characterisation and mapping of sequence-tagged microsatellites sites in the chickpea (Cicer arietinum L.) genome. Molecular and General Genetics 262: 90101.CrossRefGoogle ScholarPubMed
Xavier, GR, Martins, LMV, Rumjanek, NG and Filho, FRF (2005) Variabilidade genética em acessos de caupi analisada por meio de marcadores RAPD. Pesquisa Agropecuaria Brasileira (Brasília) 40: 353359.CrossRefGoogle Scholar
Xu, P, Wu, X, Wang, B, Liu, Y, Quin, D, Ehlers, JD, Close, TJ, Hu, T, Lu, Z and Li, G (2010) Development and polymorphism of Vigna unguiculata ssp. unguiculata microsatellite markers used for phylogenetic analysis in asparagus bean (Vigna unguiculata ssp. sesquipedialis (L.) Verdc.). Molecular Breeding doi:10.1007/s11032-009-9364-x.CrossRefGoogle Scholar
Zannou, A, Kossou, DK, Ahanchédé, A, Zoundjihékpon, J, Agbicodo, E, Struik, PC and Sanni, A (2008) Genetic variability of cultivated cowpea in Benin assessed by random amplified polymorphic DNA. African Journal of Biotechnology 7: 44074414.Google Scholar
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