Hostname: page-component-78c5997874-s2hrs Total loading time: 0 Render date: 2024-11-14T13:25:18.343Z Has data issue: false hasContentIssue false
  • English
  • Français

Analysis of genetic diversity of African yam bean using SSR markers derived from cowpea

Published online by Cambridge University Press:  30 March 2015

Ndenum S. Shitta ,
Michael T. Abberton ,
Adenubi I. Adesoye ,
Daniel B. Adewale  and
Olaniyi Oyatomi
Ndenum S. Shitta
Affiliation:
Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Nigeria
Michael T. Abberton*
Affiliation:
Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Nigeria
Adenubi I. Adesoye
Affiliation:
Department of Botany, University of Ibadan, Ibadan, Nigeria
Daniel B. Adewale
Affiliation:
Department of Biological Sciences, Ondo State University of Science and Technology, Okitipupa, Nigeria
Olaniyi Oyatomi
Affiliation:
Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Nigeria
*
*Corresponding author. E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

African yam bean, AYB (Sphenostylis stenocarpa Hochst. ex. A. Rich Harms), is a tuberous legume of tropical Africa. AYB has the potential to significantly boost food security due to its considerable nutritional qualities. However, the crop is underutilized. To efficiently utilize AYB genetic resources for its improvement, it is necessary to understand the crop's diversity. This study investigated the amplification ability of 36 cowpea simple sequence repeat (SSR) primers across AYB genomic DNA, extracted from 67 accessions. Thirteen (36%) of the cowpea SSRs showed transferability in AYB. Eight of these SSRs amplified above 60% of AYB accessions and generated 55 polymorphic fragments with an average of 6.9 per primer. Polymorphic information content ranged from 0.6691 to 0.8857 with an average of 0.7791. This study also assessed the genetic diversity within 67 AYB accessions using eight cowpea (Vigna unguiculata L. Walp)-derived SSR primers. The result revealed a high level of genetic diversity with simple matching coefficient ranging from 0.458 to 1.000. A dendrogram depicting three main clusters was generated based on unweighted pair group method with arithmetic average. Cluster 1 was the most diverse with a dissimilarity range of 0.517–1.000. The level of genetic diversity revealed in this study indicates that the studied AYB germplasm can be exploited for genetic improvement. Additionally, the transferable markers will aid AYB genome research and also make possible the comparative mapping between AYB and cowpea.

Keywords

African yam beancowpeagenetic diversitySSRs
Type
Research Article
Information
Plant Genetic Resources , Volume 14 , Issue 1 , March 2016 , pp. 50 - 56
Copyright
Copyright © NIAB 2015 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Adesoye, AI and Nnadi, NC (2011) Mitotic chromosome studies of some accessions of African yam bean Sphenostylis stenocarpa (Hochst. ex A. Rich.) Harms. African Journal of Plant Science 5: 835–841.Google Scholar
Adewale, BD (2010) African yam bean: a food security crop? IITA R4D Review 4: 54–56.Google Scholar
Adewale, BD and Dumet, DJ (2009) African yam bean: a crop with food security potentials for Africa. African Technology Development Forum 6: 66–71.Google Scholar
Adewale, BD and Dumet, DJ (2011) Descriptors for African yam bean Sphenostylis stenocarpa (Hochst ex. A. Rich.) Harms. Available at: http://old.iita.org/cms/articulefiles/1488-ayb_descriptors.pdf.Google Scholar
Adewale, BD, Vroh-Bi, I, Dumet, DJ, Kehinde, OB, Ojo, DK, Adegbite, AE and Franco, J (2012) Morphological diversity analysis of African yam bean (Sphenostylis stenocarpa Hochst. Ex A. Rich) Harms and prospects for utilization in germplasm conservation and breeding. Genetic Resources and Crop Evolution 59: 927–936.CrossRefGoogle Scholar
Adewale, BD, Vroh-Bi, I, Dumet, DJ, Nnadi, S, Kehinde, OB, Ojo, DK, Adegbite, AE and Franco, J (2014) Genetic diversity in Africa yam bean accessions based on AFLP markers: towards a platform for germplasm improvement and utilization. Plant Genetic Resources Characterization and Utilization: 1–8. DOI:10.1017/S1479262114000707.Google Scholar
Akande, SR (2009) Germplasm characterization of African yam bean from southwest Nigeria. Acta Horticulturae 806: 695–700.Google Scholar
Botstein, D, White, RL, Skolnick, M and Davis, RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32: 314–331.Google Scholar
Brookfield, JF (1996) A simple new method for estimating null allele frequency from heterozygote deficiency. Molecular Ecology 5: 453–455.Google Scholar
Choudhary, S, Sethy, NK, Shokeen, B and Bhatia, S (2008) Development of chickpea EST–SSR markers and analysis of allelic variation across related species. Theoretical and Applied Genetics 118: 591–608.Google Scholar
Datta, S, Kaashyap, M and Kumar, S (2009) Amplification of chickpea-specific SSR primers in Cajanus species and their validity in diversity analysis. Plant Breeding 129: 334–340.CrossRefGoogle Scholar
Dellaporta, SL, Wood, J and Hicks, JB (1983) A plant DNA mini preparation: version II. Plant Molecular Biology Reporter 1: 19–21.Google Scholar
De Vicente, MC, Guzman, FA, Engels, J and Ramanatha, RV (2005) Genetic characterization and its use in decision making for the conservation of crop germplasm. In Proceedings of the international workshop on the role of biotechnology for the characterization and conservation of crop, forestry and fishery genetic resources. Food and Agriculture Organization of the United Nations, Rome.Google Scholar
Gepts, P (1993) The use of molecular and biochemical markers in crop evaluation studies. Evolution Biology 27: 51–94.Google Scholar
Gupta, SK and Gopalakrishna, T (2009) Genetic diversity analysis in blackgram (Vigna mungo (L.) Hepper) using AFLP and transferable microsatellite markers from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi). Genome 52: 120–129.Google Scholar
Gupta, SK and Gopalakrishna, T (2010) Development of unigene-derived SSR markers in cowpea (Vigna unguiculata) and their transferability to other Vigna species. Genome 53: 508–523.Google Scholar
Gupta, S, Sen, GD, Anjum, K, Pratrap, A and Kumar, J (2013) Transferability of simple sequence repeat markers in blackgram (Vigna mungo L. Hepper). Australian Journal Crop Science 7: 345–353.Google Scholar
He, G, Woullard, FE, Marong, I and Guo, BZ (2006) Transferability of soybean SSR markers in peanut (Arachis hypogaea L.). Peanut Science 33: 22–28.Google Scholar
Li, G, Ra, WH, Park, JW, Kwon, SW, Lee, JH, Park, CB and Park, YJ (2011) Developing EST–SSR markers to study molecular diversity in Liriope and Ophiopogon . Biochemical Systematic and Ecology 39: 241–252.Google Scholar
Liu, K and Muse, SV (2005) PowerMarker integrated analysis environment for genetic marker data. Bioinformatics 29: 2128–2129.Google 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
Ojuederie, BO, Morufat, OB, Iyiola, F, David, OI and Mercy, OO (2014) Assessment of the genetic diversity of African yam bean (Sphenostylis stenocarpa Hochst ex. A Rich. Hams) accessions using amplified fragment length polymorphism (AFLP) markers. African Journal of Biotechnology 18: 1850–1858.Google Scholar
Padulosi, S, Thompson, J and Rudebjer, P (2013) Fighting poverty, hunger and malnutrition with neglected and underutilized species (NUS): needs challenges and the way forward. Bioversity International Rome.Google Scholar
Pei, X, Xiaohua, W, Baogen, W, Younghua, L, Dehui, Q, Jeffery, DE, Timothy, JC, Tingting, H, Zhongfu, L and Guoijing, L (2009) 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 25: 675–684.Google Scholar
Popoola, JO, Adegbite, AE, Adewale, BD and Odu, BO (2011) Morphological intraspecific variabilities in African yam bean (Sphenostylis stenocarpa) Hochst. Ex. A. Rich Harms. Scientific Research and Essay 6: 507–515.Google Scholar
Reddy, MR, Rathour, R, Kumar, N, Katoch, P and Sharma, TR (2010) Cross-genera legume SSR markers for analysis of genetic diversity in Lens species. Plant Breeding 129: 514–518.Google Scholar
Rohlf, FJ (1998) NTSYSpc: Numerical Taxonomy and Multivariate Analysis System. Version 2.02. Setauket, NY: Exeter Software.Google Scholar
Ruchi, V, Bhat, KV and Lakhanpaul, S (2009) Transferability of sequence tagged microsatellite sites (STMS) primers to pulse yielding taxa belonging to Phaseolae. International Journal of Integrative Biology 5: 62–66.Google Scholar
Sanjeev, G, Debjyoti, SG, Anjum, KT, Aditya, P and Jitendra, K (2013) Transferability of simple sequence repeat markers in blackgram (Vigna mungo L. Hepper). Australian Journal of Crop Science 7: 345–353.Google Scholar
Somta, P, Chankaew, S, Rungnoi, O and Srinives, P (2011) Genetic diversity of the Bambara groundnut (Vigna subterranea (L.) Verdc.) as assessed by SSR markers. Genome 54: 898–910.Google 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 Products Research Journal 6: 10–19.Google Scholar
Van, OC, Hutchison, WF, Will, DPM and Shipley, P (2004) MICRO-CHECHER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4: 535–538.Google Scholar
Supplementary material: File

Shitta supplementary material

Table S1

Download Shitta supplementary material(File)
File 19.5 KB