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Assessment of genetic diversity in Ethiopian cowpea [Vigna unguiculata (L.) Walp.] germplasm using simple sequence repeat markers

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Abstract

The genetic diversity of cowpea (Vigna unguiculata L. Walp.) in Ethiopia was analyzed using 19 uniform accessions, 62 variable accessions (yielding 185 sub-types), and two mungbean (Vigna radiata) accessions (four subtypes) as outgroup. A set of 23 polymorphic simple sequence repeat (SSR) markers was identified, and polymorphism in the various accessions was scored by determining amplicon variability. Allele frequency, genetic diversity, and polymorphism information content (PIC) were determined for each SSR marker, and a neighbor joining dendrogram was generated to show the genetic relationship among the individual accessions. A total of 75 allelic variants was defined, with the average number of alleles per locus calculated to be three. The average genetic diversity (D) was 0.47, and PIC was 0.4. Three main clusters were identified by phylogenetic analysis, and the clusters and sub-grouping were supported by STRUCTURE and principal component analysis. This grouping had a moderate fixation index value of 0.075 and gene flow (Nm) of 3.176, indicating that the accessions possess wide diversity within individuals and populations. The accessions showed no clustering by geographical origins. Three well-characterized molecular markers (SSR1, C42-2B, and 61RM2) for race specific resistance to Striga gesnerioides in the cowpea cultivar B301 were used to evaluate the accessions for their potential for use in genetic improvement against this pest. Based on this analysis, only two accessions, 222890–2 from Gambela and 286–2 from the Southern Nations, Nationalities, and Peoples (SNNP) region, were found to cluster with B301 and contain the SSR1 resistance allele. These findings will assist in germplasm conservation efforts by the Institute of Biodiversity and Conservation of Ethiopia, and contribute to future studies aimed at the genetic improvement of local germplasm for improved overall agronomic performance as well as Striga resistance in particular.

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References

  • Abe J, Xu D, Suzuki Y, Kanazawa A, Shimamoto Y (2003) Soybean germplasm pools in Asia revealed by nuclear SSRs. Theor Appl Genet 106:445–453

    CAS  PubMed  Google Scholar 

  • Andargie M, Pasquet RS, Gowda BS, Muluvi GM, Timko MP (2011) Construction of a SSR-based genetic map and identification of QTL for domestication traits using recombinant inbred lines from a cross between wild and cultivated cowpea (V. unguiculata (L.) Walp.). Mol Breed 28:413–420

    Article  Google Scholar 

  • Asare AT, Gowda BS, Galyuon IK, Aboagye LL, Takrama JF, Timko MP (2010) Assessment of the genetic diversity in cowpea (Vigna unguiculata L. Walp.) germplasm from Ghana using simple sequence repeat markers. Plant Genet Res 8:142–150

    Article  CAS  Google Scholar 

  • Asare AT, Galyuon IK, Padi FK, Otwe EP, Takrama J (2013) Responses of recombinant inbred lines of cowpea [(Vigna unguiculata (l.) walp] to Striga gesnerioides infestation in Ghana. Eur Sci J 9:503–513

    Google Scholar 

  • Ba FS, Pasquet RS, Gepts P (2004) Genetic diversity in cowpea [Vigna unguiculata (L.) Walp.] as revealed by RAPD markers. Genet Resour Crop Evol 51:539–550

    Article  CAS  Google Scholar 

  • Badiane FA, Diouf D, Sané D, Diouf O, Goudiaby V, Diallo N (2004) Screening cowpea [Vigna unguiculata (L.) Walp.] varieties by inducing water deficit and RAPD analyses. Afr J Biotechnol 3:174–178

    CAS  Google Scholar 

  • Badiane F, Gowda B, Cissé N, Diouf D, Sadio O, Timko M (2012) Genetic relationship of cowpea (Vigna unguiculata) varieties from Senegal based on SSR markers. Genet Mol Res 11:292–304

    Article  CAS  PubMed  Google Scholar 

  • Barrett B, Kidwell K (1998) AFLP-based genetic diversity assessment among wheat cultivars from the Pacific Northwest. Crop Sci 38:1261–1271

    Article  CAS  Google Scholar 

  • Botanga CJ, Timko MP (2006) Phenetic relationships among different races of Striga gesnerioides (Willd.) Vatke from West Africa. Genome 49:1351–1365

  • Choumane W, Winter P, Weigand F, Kahl G (2000) Conservation and variability of sequence-tagged microsatellite sites (STMSs) from chickpea (Cicer aerietinum L.) within the genus Cicer. Theor Appl Genet 101:269–278

    Article  CAS  Google Scholar 

  • De Vicente M, Lopez C, Fulton T (2004) Genetic diversity analysis with molecular marker data: learning module. International Plant Genetic Resources Institute (IPGRI), Cornell University

  • Dikshit H, Jhang T, Singh N, Koundal K, Bansal K, Chandra N, Tickoo J, Sharma T (2007) Genetic differentiation of Vigna species by RAPD, URP and SSR markers. Biol Plant 51:451–457

    Article  CAS  Google Scholar 

  • Diouf D, Hilu KW (2005) Microsatellites, RAPD markers to study genetic relationships among cowpea breeding lines and local varieties in Senegal. Genet Resour Crop Evol 52:1057–1067

    Article  CAS  Google Scholar 

  • Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing structure output and implementing the evanno method. Conserv Genet Resour 4:359–361

    Article  Google Scholar 

  • Ehlers J, Hall A (1996) Genotypic classification of cowpea based on responses to heat and photoperiod. Crop Sci 36:673–679

    Article  Google Scholar 

  • Fang J, Chao C-CT, Roberts PA, Ehlers JD (2007) Genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] in four West African and USA breeding programs as determined by AFLP analysis. Genet Resour Crop Evol 54:1197–1209

    Article  CAS  Google Scholar 

  • Fatokun C, Danesh D, Young N, Stewart E (1993) Molecular taxonomic relationships in the genus Vigna based on RFLP analysis. Theor Appl Genet 86:97–104

    Article  CAS  PubMed  Google Scholar 

  • Fotso M, Azanza J-L, Pasquet R, Raymond J (1994) Molecular heterogeneity of cowpea (Vigna unguiculata, Fabaceae) seed storage proteins. Plant Syst Evol 191:39–56

    Article  CAS  Google Scholar 

  • Gemechu K, Ali K, Makkouk K, Halila M, Malhotra R, Ahmed S, Surenda B (2003) Food and forage legumes of Ethiopia: progress and prospects. Proceedings of the 13th Annual Research and Extension Review Meeting, Addis Ababa, Ethiopia, pp. 124–130

  • He C, Poysa V, Yu K (2003) Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars. Theor Appl Genet 106:363–373

    CAS  PubMed  Google Scholar 

  • Hegde V, Mishra S (2009) Landraces of cowpea, Vigna unguiculata (L.) Walp., as potential sources of genes for unique characters in breeding. Genet Resour Crop Evol 56:615–627

    Article  CAS  Google Scholar 

  • Kiambi D, Newbury H, Ford-Lloyd B, Dawson I (2005) Contrasting genetic diversity among Oryza longistaminata (A. Chev et Roehr) populations from different geographic origins using AFLP. Afr J Biotechnol 4:308–317

    CAS  Google Scholar 

  • Kumar MD (2011) Pulse Crop production: principles and technologies. PHI Learning, New Delhi

    Google Scholar 

  • Kuruma R, Kiplagat O, Ateka E, Ouoche G (2008) Genetic diversity of Kenya cowpea accessions based on morphological and microsatellite markers. East Afr Agric For J 76:3–4

    Google Scholar 

  • Lane JA, Moore THM, Child DV, Cardwell K (1996) Characterization of virulence and geographic distribution of Striga gesnerioides on cowpea in West Africa. Plant Dis 80:299–301

    Article  Google Scholar 

  • Lane JA, Moore THM, Child DV, Bailey JA (1997) Variation in virulence of Striga gesnerioides on cowpea: new sources of resistance. In: Singh BB, Mohan Raj DR, Dashiell KE, Jackai LEN (eds) Advances in cowpea research. International Institute for Tropical Agricultural Sciences, Ibadan, pp 225–230

    Google Scholar 

  • Langyintuo A, Lowenberg-Deboer J, Faye M, Lambert D, Ibro G, Moussa B, Kergna A, Kushwaha S, Musa S, Ntoukam G (2003) Cowpea supply and demand in West and Central Africa. Field Crop Res 82:215–231

    Article  Google Scholar 

  • Li Wang M, Barkley NA, Gillaspie GA, Pederson GA (2008) Phylogenetic relationships and genetic diversity of the USDA Vigna germplasm collection revealed by gene-derived markers and sequencing. Genet Res 90:467–480

    Article  Google Scholar 

  • Li J, Timko MP (2009) Gene-for-gene resistance in striga-cowpea associations. Science 325:1094–1094

    Article  CAS  PubMed  Google Scholar 

  • Li C-D, Fatokun CA, Ubi B, Singh BB, Scoles GJ (2001) Determining genetic similarities and relationships among cowpea breeding lines and cultivars by microsatellite markers. Crop Sci 41:189–197

    Article  CAS  Google Scholar 

  • Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129

    Article  CAS  PubMed  Google Scholar 

  • Nkongolo K (2003) Genetic characterization of Malawian cowpea (Vigna unguiculata (L.) Walp) landraces: diversity and gene flow among accessions. Euphytica 129:219–228

    Article  CAS  Google Scholar 

  • O’Neill R, Snowdon R, Köhler W (2003) Population genetics: aspects of biodiversity. Prog Bot 64:115–137

    Article  Google Scholar 

  • Ogunkanmi L, Ogundipe O, Ng N, Fatokun C (2008) Genetic diversity in wild relatives of cowpea (Vigna unguiculata) as revealed by simple sequence repeats (SSR) markers. J Food Agric Environ 6:253–268

    Google Scholar 

  • Pasquet RS (1993) Variation at isozyme loci in wild Vigna unguiculata (Fabaceae, Phaseoleae). Plant Syst Evol 186:157–173

    Article  CAS  Google Scholar 

  • Pasquet R (1999) Genetic relationships among subspecies of Vigna unguiculata (L.) Walp. based on allozyme variation. Theor Appl Genet 98:1104–1119

    Article  CAS  Google Scholar 

  • Pasquet R (2000) Allozyme diversity of cultivated cowpea Vigna unguiculata (L.) Walp. Theor Appl Genet 101:211–219

    Article  CAS  Google Scholar 

  • Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in excel population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Article  Google Scholar 

  • Pejic I, Ajmone-Marsan P, Morgante M, Kozumplick V, Castiglioni P, Taramino G, Motto M (1998) Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theor Appl Genet 97:1248–1255

    Article  CAS  Google Scholar 

  • Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Enfield, Plymouth, pp 43–76

    Google Scholar 

  • Plaschke J, Ganal M, Röder M (1995) Detection of genetic diversity in closely related bread wheat using microsatellite markers. Theor Appl Genet 91:1001–1007

    CAS  PubMed  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Riahi K, Krey V, Rao S, Chirkov V, Fischer G, Kolp P, Kindermann G, Nakicenovic N, Rafai P (2011) RCP-8.5: exploring the consequence of high emission trajectories. Clim Chang 109:33–57. doi:10.1007/s10584-011-0149-y

    Article  CAS  Google Scholar 

  • Rongwen J, Akkaya M, Bhagwat A, Lavi U, Cregan P (1995) The use of microsatellite DNA markers for soybean genotype identification. Theor Appl Genet 90:43–48

    Article  CAS  PubMed  Google Scholar 

  • Sawadogo M, Ouedraogo JT, Gowda BS, Timko MP (2010) Genetic diversity of cowpea (Vigna unguiculata L. Walp) cultivars in Burkina Faso resistant to Striga gesnerioides. Afr J Biotechnol 9:8146–8153

    Article  CAS  Google Scholar 

  • Scoles G, Simon M, Benko-Iseppon A-M, Resende L, Winter P, Kahl G (2007) Genetic diversity and phylogenetic relationships in Vigna Savi germplasm revealed by DNA amplification fingerprinting. Genome 50:538–547

    Article  Google Scholar 

  • Singh B (2005) Cowpea [Vigna unguiculata (L.) Walp.]. In: Singh RJ, Jauhar PP (eds) Genetic resources, chromosome engineering and crop improvement, vol 1. CRC, Boca Raton, pp 117–162

    Chapter  Google Scholar 

  • Timko MP, Singh B (2008) Cowpea, a multifunctional legume. In: Moore PH, Ming R (eds) Genomics of tropical crop plants. Springer, New York, pp 227–258

    Chapter  Google Scholar 

  • Timko MP, Ehlers JD, Roberts PA (2007) Cowpea. In: Berlin KC (ed) Genome mapping and molecular breeding in plants, pulses, sugar and tuber crops, vol 3. Springer, Berlin, pp 49–68

    Chapter  Google Scholar 

  • Tosti N, Negri V (2002) Efficiency of three PCR-based markers in assessing genetic variation among cowpea (Vigna unguiculata subsp. unguiculata) landraces. Genome 45:268–275

    Article  CAS  PubMed  Google Scholar 

  • Uma M, Hittalamani S, Murthy B, Viswanatha K (2009) Microsatellite DNA marker aided diversity analysis in cowpea [Vigna unguiculata (L.) Walp]. Indian J Genet Plant Breeding 69:35–43

    CAS  Google Scholar 

  • Vaillancourt R, Weeden N (1992) Chloroplast DNA polymorphism suggests Nigerian center of domestication for the cowpea, Vigna unguiculata (Leguminosae). Am J Bot 79:1194–1199

    Article  CAS  Google Scholar 

  • Wright S (1984) Evolution and the genetics of populations, vol 3: experimental results and evolutionary deductions. The University of Chicago Press, London

  • Xavier GR, Martins LMV, Rumjanek NG, Freire Filho FR (2005) Variabilidade genética em acessos de caupi analisada por meio de marcadores RAPD. Pesq Agrop Brasileira 40:353–359

    Article  Google Scholar 

  • Xu P, Wu X, Wang B, Liu Y, Qin D, Ehlers JD, Close TJ, Hu T, Lu Z, 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.). Mol Breed 25:675–684

    Article  CAS  Google Scholar 

  • Yang Z, Goldman N, Friday A (1994) Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol Biol Evol 11:316–324

    CAS  PubMed  Google Scholar 

  • Zannouou A, Kossou D, Ahanchédé A, Zoundjihékpon J, Agbicodo E, Struik P, Sanni A (2008) Genetic variability of cultivated cowpea in Benin assessed by random amplified polymorphic DNA. Afr J Biotechnol 7:4407–4414

    Google Scholar 

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Acknowledgments

The authors wish to thank the members of the Timko lab for their help in various aspects of this work and for helpful suggestions on this manuscript, especially Sory Diallo, Frederick Awuku, Yu Wang and Tatyana Katova. These studies were supported by funds from the Kirkhouse Trust. While the research reported here was funded by the Kirkhouse Trust, the design, execution, and interpretation of the research remains wholly the responsibility of the authors.

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Authors and Affiliations

  1. Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia

    Belayneh A. Desalegne & Kifle Dagne

  2. Department of Biology, University of Virginia, Gilmer Hall 044, Charlottesville, VA, 22904, USA

    Belayneh A. Desalegne, Suheb Mohammed & Michael P. Timko

  3. Gambela Regional Research Institute (GARI), PO Box 62, Gambela, Ethiopia

    Belayneh A. Desalegne

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  1. Belayneh A. Desalegne
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  2. Suheb Mohammed
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  3. Kifle Dagne
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  4. Michael P. Timko
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Correspondence to Michael P. Timko.

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Desalegne, B.A., Mohammed, S., Dagne, K. et al. Assessment of genetic diversity in Ethiopian cowpea [Vigna unguiculata (L.) Walp.] germplasm using simple sequence repeat markers. Plant Mol Biol Rep 34, 978–992 (2016). https://doi.org/10.1007/s11105-016-0979-x

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