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Genetic diversity in African yam bean accessions based on AFLP markers: towards a platform for germplasm improvement and utilization

Published online by Cambridge University Press:  19 June 2014

B. D. Adewale ,
I. Vroh-Bi ,
D. J. Dumet ,
S. Nnadi ,
O. B. Kehinde ,
D. K. Ojo ,
A. E. Adegbite  and
J. Franco
B. D. Adewale*
Affiliation:
International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria University of Agriculture, PMB 2240, Abeokuta, Nigeria
I. Vroh-Bi
Affiliation:
International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
D. J. Dumet
Affiliation:
International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
S. Nnadi
Affiliation:
International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria Ebonyi State University, PMB 53, Abakaliki, Nigeria
O. B. Kehinde
Affiliation:
University of Agriculture, PMB 2240, Abeokuta, Nigeria
D. K. Ojo
Affiliation:
University of Agriculture, PMB 2240, Abeokuta, Nigeria
A. E. Adegbite
Affiliation:
University of Agriculture, PMB 2240, Abeokuta, Nigeria
J. Franco
Affiliation:
International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
*
*Corresponding author. E-mail: [email protected]
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Abstract

Accurate knowledge of intra-specific diversity of underutilized crop species is a prerequisite for their genetic improvement and utilization. The diversity of 77 accessions of African yam bean (AYB, Sphenostylis stenocarpa) was assessed by amplified fragment length polymorphism (AFLP) markers. A total of EcoRI/MseI primer pairs were selected and 227 AFLP bands were generated, of which 59(26%) were found to be polymorphic in the 77 accessions of AYB. The most efficient primer combination for polymorphic detection was E-ACT/M-CAG with a polymorphic efficiency of 85.5%, while the least efficient was E-AGC/M-CAG with a polymorphic efficiency of 80.6%. The Jaccard genetic distance among the accessions of AYB ranged between 0.048 and 0.842 with a mean of 0.444. TSs98 and TSs104B were found to be the most similar accessions with a genetic similarity of 0.952. The neighbour-joining dendrogram grouped the 77 accessions of AYB into four distinct clusters comprising 8, 20, 21 and 28 accessions. The major clustering of the accessions was not related to their geographical origin. Cluster I was found to be the most diverse. The mean fixation index (0.203) and the mean expected heterozygosity (0.284) revealed a broad genetic base of the AYB accessions. The same germplasm set was previously evaluated for several agro-morphological traits. As the collection of additional AYB germplasm continues, the phenotypic profile, the clustering of the accessions and the AFLP primer combinations from this study can be used to augment breeding programmes.

Keywords

African yam beanamplified fragment length polymorphismgenetic diversitySphenostylis stenocarpa A. Rich. Harms
Type
Research Article
Information
Plant Genetic Resources , Volume 13 , Issue 2 , August 2015 , pp. 111 - 118
Copyright
Copyright © NIAB 2014 

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References

Adewale, BD (2011) Genetic diversity, stability and reproductive biology of African yam bean (Sphenostylis stenocarpa Hochst. ex A. Rich.) Harms . PhD Thesis, University of Agriculture, Abeokuta. Google Scholar
Adewale, BD, Aremu, CO and Amazue, UE (2012a) Intra-specific variability and diversity analysis of African yam bean by seed size parameters. ARPN Journal of Agricultural and Biological Science 7: 454–461.Google Scholar
Adewale, BD, Dumet, DJ, Vroh-Bi, I, Kehinde, OB, Ojo, DK, Adegbite, AE and Franco, J (2012b) Morphological diversity analysis of African yam bean (Sphenostylis stenocarpa Hochst. ex A. Rich.) and prospects for utilization in germplasm conservation and breeding. Genetic Resources and Crop Evolution 59: 927–936.Google Scholar
Ajibade, SR, Balogun, MO, Afolabi, OO, Ajomale, KO and Fasoyiro, SB (2005) Genetic variation in nutritive and anti nutritive content of African yam bean (Sphenostylis stenocarpa). Tropical Science 45: 144–148.CrossRefGoogle Scholar
Arbelbide, M, Yu, J and Bernardo, R (2006) Power of mixed-model QTL mapping from phenotypic, pedigree and marker data in self-pollinated crops. Theoretical and Applied Genetics 112: 876–884.Google Scholar
Asare, AT, Gowda, BS, Galyuon, IKA, Aboagye, LL, Takrama, JF and Timko, MP (2010) Assessment of the genetic diversity in cowpea (Vigna unguiculata L. Walp.) germplasm from Ghana using simple sequence repeat markers. Plant Genetic Resources: Characterization and Utilization 8: 142–150.Google 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: 539–550.Google Scholar
Beyene, Y, Botha, A and Myburg, AA (2005) A comparative study of molecular and morphological methods of describing genetic relationships in traditional Ethiopian highland maize. African Journal of Biotechnology 4: 586–595.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: 358–366.Google Scholar
Dellaporta, SL, Wood, J and Hicks, JB (1983) A plant DNA minipreparation: version II. Plant Molecular Biology Report 1: 19–21.Google Scholar
Dolinsk, C, Kamitani, FL, Machado, IR and Winter, CE (2008) Molecular and morphological characterization of heterorhabditid entomopathogenic nematodes from the tropical rainforest in Brazil. Memórias do Instituto Oswaldo Cruz 103: 150–159.Google Scholar
Du, XY, Zhang, QL and Luo, Z-R (2009) Comparison of four molecular markers for genetic analysis in Diospyros L. (Ebenaceae). Plant Systematic and Evolution 281: 171–181.CrossRefGoogle Scholar
Edem, DO, Amugo, CI and Eka, OU (1990) Chemical composition of yam bean (Sphenostylis stenocarpa). Tropical Science 30: 59–63.Google Scholar
Ekpo, AS (2006) Changes in amino acid composition of African yam beans (Sphenostylis stenocarpa) and African locust beans (Parkia filicoida) on cooking. Pakistan Journal of Nutrition 5: 254–256.Google Scholar
Emadzade, K, Lehnebach, C, Lockhart, P and Hörandl, E (2010) A molecular phylogeny, morphology and classification of genera of Ranunculeae (Ranunculaceae). Taxon 59: 809–828.Google Scholar
Excoffier, L, Laval, G and Schneider, S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolution and Bioinformatics Online 1: 47–50.Google Scholar
Kornerup, A and Wanscher, JH (1978) Methuen Hand Book of Colour. London: Methuen.Google Scholar
Martos, V, Royo, C, Rharrabti, Y and Garcia del Moral, LF (2005) Using AFLPs to determine phylogenetic relationships and genetic erosion in durum wheat cultivars released in Italy and Spain throughout the 20th century. Field Crops Research 92: 107–116.CrossRefGoogle Scholar
McKay, GJ, Egan, D, Morris, E, Scott, C and Brown, AE (1999) Genetic and morphological characterization of Cladobotryum species causing cobweb disease of mushrooms. Applied Environmental and Microbiology 65: 606–610.Google Scholar
Mohammadi, SA and Prasanna, BM (2003) Analysis of genetic diversity in crop plants – salient statistical tools and considerations. Crop Science 43: 1235–1248.Google Scholar
Mondini, L, Noorani, A and Pagnotta, MA (2009) Assessing plant genetic diversity by molecular tools. Diversity 1: 19–35.Google Scholar
Morris, JB (2009) Characterization of butterfly pea (Clitoria ternatea L.) accessions for morphology, phenology, reproduction and potential nutraceutical, pharmaceutical trait utilization. Genetic Resources and Crop Evolution 56: 421–427.CrossRefGoogle Scholar
Moyib, OK, Gbadegesin, MA, Aina, OO and Odunola, AO (2008) Genetic variation within a collection of Nigerian accessions of African yam bean (Sphenostylis stenocarpa) revealed by RAPD primers. African Journal of Biotechnology 7: 1839–1846.Google Scholar
National Research Council(1979) Tropical Legumes: Resources for the Future. Washington, DC: National Academy of Sciences, p.246.Google Scholar
Nwokolo, E (1996) The need to increase consumption of pulses in the developing world. In: Nwokolo, E and Smart, J (eds) Food and Feed from Legumes and Oilseeds. London: Chapman and Hall, pp. 3–11.CrossRefGoogle Scholar
Obiagwu, CJ (1997) Screening process for ideal food legume cover crops in the tropical ecosystem: (II) application of selection method for grain legume crops of the Benue River Basins of Nigeria (BRBN). Journal of Sustainable Agriculture 10: 15–31.Google Scholar
Okigbo, BN (1973) Introducing the yam bean Sphenostylis stenocarpa (Hochst. ex A. Rich.) Harms. In: Proceedings of the First IITA Grain Legume Improvement Workshop. 29 October–2 November 1973, Ibadan, Nigeria, pp. 224–238.Google Scholar
Pasquet, RS (2000) Allozyme diversity of cultivated cowpea Vigna unguiculata (L.) Walp. Theoretical and Applied Genetics 101: 211–219.Google Scholar
Perrier, X and Jacquemoud-Collet, JP (2006) DARwin software . Available at: http://darwin.cirad.fr/darwin.Google Scholar
Popoola, JO, Adegbite, AE, Obembe, OO, Adewale, BD and Odu, BO (2011) Morphological intraspecific variabilities in African yam bean (AYB) (Sphenostylis stenocarpa Ex. A. Rich) Harms. Scientific Research and Essay 6: 507–515.Google Scholar
Potter, D and Doyle, JJ (1992) Origins of the African yam bean (Sphenostylis stenocarpa, Leguminosae): evidence from morphology, isozymes, chloroplast DNA, and linguistics. Economic Botany 46: 276–292.CrossRefGoogle Scholar
Potter, D and Doyle, JJ (1994) Phylogeny and systematics of Sphenostylis and Nesphostylis (Leguminoseae: Phaseoleae) based on morphological and chloroplast DNA data. Systematic Botany 19: 389–406.Google Scholar
Saitou, N and Nei, M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406–425.Google Scholar
Sarutayophat, T, Nualsri, C, Santipracha, Q and Saereeprasert, V (2007) Characterization and genetic relatedness among 37 yardlong bean and cowpea accessions based on morphological characters and RAPD analysis. Songklanakarin Journal of Science and Technology 29: 591–600.Google Scholar
Siezen, RJ, Starrenburg, MJC, Boekhorst, J, Renckens, B, Douwe Molenaar, D and van Hylckama Vlieg, JET (2008) Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche. Applied and Environmental Microbiology 74: 424–436.Google Scholar
Tero, N, Aspi, J, Siikamaki, P, Jakalaniemi, A and Tuomi, J (2003) Genetic structure and gene flow in a metapopulation of an endangered plant species, Silene tatarica . Molecular Ecology 12: 2073–2085.CrossRefGoogle Scholar
Uguru, MI and Madukaife, SO (2001) Studies on the variability in agronomic and nutritive characteristics of African yam bean (Sphenostylis stenocarpa Hochst ex. A. Rich. Harms). Plant Production Research Journal 6: 10–19.Google Scholar
Varshney, RK, Chabane, K, Hendre, PS, Aggarwal, RK and Graner, A (2007) Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Science 173: 638–649.Google Scholar
Venkatesha, SC, Ramanjini, GPH, Ganapathy, KN, Gowda, MB, Ramachandra, R, Girish, G, Channamallikarjuna, V, Shantala, L and Gowda, TKS (2010) Genetic fingerprinting in Dolichos bean using AFLP markers and morphological traits. International Journal of Biotechnology and Biochemistry 6: 395–404.Google Scholar
Vos, P, Hogers, R, Bleeker, M, Reijans, M, Van de Lee, T, Hornes, M, Fritjers, A, Pot, J, Pelema, J, Kuiper, M and Zabeau, M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acid Research 23: 4407–4414.Google Scholar
Vroh-Bi, I, Anagbogu, C, Nnadi, S and Tenkouano, A (2010) Genomic characterization of natural and somaclonal variations in bananas (Musa spp.). Plant Molecular Biology Report 29: 440–448.Google Scholar
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