Skip to main content
SpringerLink
Log in

SSR marker development, genetic diversity and population structure analysis of Bambara groundnut [Vigna subterranea (L.) Verdc.] landraces

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

We report here the development of 75 SSR markers for Bambara groundnut through various sequencing approaches and the subsequent utilization of these SSR markers and other marker types (DArT Arrays) for the analysis of genetic diversity, population structure and the selection of pure lines from landraces. To assess the level of genetic diversity in Bambara groundnut landrace collections, 68 and 201 polymorphic SSR and DArT markers, respectively, were assayed against 24 single individual seed from a core collection of landraces. Polymorphic information content (PIC) ranged from 0.08 to 0.89 with an average of 0.42 across all SSR polymorphic markers, with observed (Ho) and expected (He) heterozygosity of 0.01 and 0.5 respectively. For the population structure analysis, 12 SSR markers selected as highly polymorphic from the initial screen were assayed against 123 landrace accessions. The average PIC across the 12 SSR was 0.66 with an average Ho of 0.02 and an inbreeding coefficient (f) of 0.98, suggesting that seed derived from a single plant essentially represents an unselected variety. Based on the low level of Ho and high f observed in the landrace samples, a subset of 35 genotypes derived from the landraces were advanced for field trials in Botswana and scored for 37 phenotypic traits. These 35 individual genotypes were ranked for agronomic performance based on yield component factors and other qualitative traits after field evaluation. Five genotypes with good yield potential and adaptability were recommended as potential varieties for Botswanan agro-ecology.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Aliyu S, Massawe FJ (2013) Microsatellites based marker molecular analysis of Ghanaian bambara groundnut (Vigna subterranea (L.) Verdc.) landraces alongside morphological characterization. Genet Resour Crop Evol 60(2):777–787

    Article  Google Scholar 

  • Allard RW (1960) Principles of plant breeding. Wiley, New York

    Google Scholar 

  • Amadou HI, Bebeli PJ, Kaltsikes PJ (2001) Genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm revealed by RAPD markers. Genome 44:995–999

    Article  CAS  PubMed  Google Scholar 

  • Baker DC (1987) Arable farming development priorities in the central agricultural regions, Botswana: a farming system analysis. Dissertation, Michigan States University, USA

  • Basu S, Roberts JA, Azam-Ali SN, Mayes S (2007a) Bambara groundnut. In: Kole C (ed) Genomic mapping and molecular breeding in plants, vol 3., Pulses, sugar and tuber cropsSpringer, New York, pp 159–173

    Google Scholar 

  • Basu S, Roberts JA, Azam-Ali SN, Mayes S (2007b) Development of microsatellite markers for bambara groundnut (Vigna subterranea (L.) Verdc.)—an underutilized African legume crop species. Mol Ecol Notes 7:1326–1328

    Article  CAS  Google Scholar 

  • Basu S, Mayes S, Davey M, Roberts JA, Azam-ali SN, Mithen R, Pasquet RS (2007c) Inheritance of “domestication” traits in bambara groundnut (Vigna subterranea (L.) Verdc.). Euphytica 157:59–68

    Article  CAS  Google Scholar 

  • Blanca J, Cañizares J, Roig C, Ziarsolo P, Nuez F, Picó B (2011) Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genom 12:104

    Article  CAS  Google Scholar 

  • Buso GSC, Amaral ZPS, Brondani RPV, Ferreira EM (2006) Microsatellites markers for the common bean (Phaseolus vulgaris). Mol Ecol Notes 6:252–254

    Article  CAS  Google Scholar 

  • Collard BCY, Jehufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts. Euphytica 142:169–196

    Article  CAS  Google Scholar 

  • Deswarte JC, (2001) Variation in the photosynthetic activity within and between three Bambara groundnut. Dissertation, The University of Nottingham

  • Edwards KJ, Barker JH, Daly A, Jones C, Karp A (1996) Microsatellites libraries enriched for several microsatellites sequences in plants. Biotechniques 5:758–760

    Google Scholar 

  • Goli AE, Begemann F, Ng NQ (1995) Characterization and evaluation of IITA’s Bambara groundnut collection. In: Heller J, Begemann F, Mushonga J (eds) Promoting the conservation and use of underutilized and neglected crops. Proceedings of the workshop on conservation and improvement of Bambara groundnut (Vigna subterranea (L.) Verdc.), 14–16 November, 1995, Harare, Zimbabwe, pp 101–118. International Plant Genetic Resources Institute, Rome, Italy

  • Intergovernmental Panel on Climate Change (IPCC), Gitay H, Suarez A, Watson RT (eds) (2002) Climate change and biodiversity. IPCC Technical Paper V

  • IPGRI, IITA, BAMLINK (2000) Descriptors for Bambara groundnut (Vigna subterranea), International Plant Genetic Resources Institute, Rome, Italy; International Institute of Tropical Agriculture, Ibadan, Nigeria; International Bambara Groundnut Network, Germany

  • Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity Arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29:1–7

    Article  Google Scholar 

  • Jaenicke H, Höschle-Zeledon I (eds) (2006) Strategic framework for underutilized plant species research and development, with special reference to Asia and the Pacific, and to Sub-Saharan Africa. International Centre for Underutilised Crops, Colombo, Sri Lanka and Global Facilitation Unit for Underutilized Species, Rome, Italy

  • Kovach W (2006) MVSP-multivariate statistical package, Version 3.1. Kovach Computing Services, Anglesey, Wales

  • Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinf Appl Notes 21(9):2128–2129

    Article  CAS  Google Scholar 

  • Massawe FJ, Dickinson M, Roberts JA, Azam-Ali SN (2002) Genetic diversity in Bambara groundnut (Vigna subtarranea (L.) Verdc) landraces as revealed by AFLP markers. Genome 45:1175–1180

    Article  CAS  PubMed  Google Scholar 

  • Massawe FJ, Roberts JA, Azam-Ali SN, Davey MR (2003) Genetic diversity in Bambara groundnut (Vigna subterranea (L.) Verdc.) landraces assessed by Random Amplified Polymorphic DNA (RAPD) markers. Genet Resour Crop Evol 50:737–741

    Article  CAS  Google Scholar 

  • Massawe FJ, Mwale SS, Roberts JA (2005) Breeding in Bambara groundnut (Vigna subterranea (L.) Verdc.): strategic considerations. Afr J Biotechnol 4:463–471

    Google Scholar 

  • Mayes S, Massawe FJ, Alderson PG, Roberts JA, Azam-Ali SN, Hermann M (2011) The potential for underutilized crops to improve security of food production. J Exp Bot 63(3):1075–1079

    Article  PubMed  Google Scholar 

  • Ntundu WH, Bach IC, Christiansen JL, Andersen SB (2004) Analysis of genetic diversity in Bambara groundnut [Vigna subterranea (L.) Verdc.] landraces using amplified fragment length polymorphism (AFLP) markers. Afr J Biotechnol 3:220–225

    CAS  Google Scholar 

  • Ntundu WH, Shillah SA, Marandu WYF, Christiansen JL (2006) Morphological diversity of Bambara groundnut [Vigna subterranea (L.) Verdc.] landraces in Tanzania. Genet Resour Crop Evol 53:367–378

    Article  Google Scholar 

  • Olukolu BA, Mayes S, Stadler F, Ng NQ, Fawole I, Dominique D, Azam-Ali SN, Abbott AG, Kole C (2012) Genetic diversity in Bambara groundnut (Vigna subterranea (L.) Verdc.) as revealed by phenotypic descriptors and DArT marker analysis. Genet Resour Crop Evol 59:347–358

    Article  Google Scholar 

  • Pasquet RS, Schwedes S, Gepts P (1999) Isozyme diversity in Bambara groundnut. Crop Sci 39:1228–1236

    Article  CAS  Google Scholar 

  • Roven S, Skaletsky HJ (2000) Primer3 on WWW for general users and for biologists programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386

    Google Scholar 

  • Rungnoi O, Suwanprasert J, Somta P, Srinives P (2012) Molecular genetic diversity of Bambara groundnut (Vigna subterranea L. Verdc.) revealed by RAPD and ISSR marker analysis. SABRAO J Breed Genet 44:87–101

    Google Scholar 

  • Schuelke M (2000) An economic method for the fluorescent labelling of PCR fragments. Nat Biotehnol 18:233–234

    Article  CAS  Google Scholar 

  • Singh RK, Chaudhary SD (1985) Biometrical methods in quantitative genetic analysis. Kalian publishers, New Delhi

    Google Scholar 

  • Singrün C, Schenkel W (2003) Fingerprinting of Bambara groundnut germplasm with molecular marker. In: Proceedings of the international Bambara groundnut symposium, Botswana college of Agriculture, Botswana 8–12 August, 2003, Gaborone, Botswana, pp 161–170

  • Somta P, Chankaew S, Rungnoi O, Srinives P (2011) Genetic diversity of the Bambara groundnut (Vigna subterranea (L.) Verdc.) as assessed by SSR markers. Genome 54:898–910

    Article  CAS  PubMed  Google Scholar 

  • Stadler F (2009) Analysis of differential expression under water-deficit stress and genetic diversity in Bambara groundnut (Vigna subterranea (L.) Verdc.) using novel high-throughput technologies. Dissertation, Technische Universität München (TUM)

  • VSN International (2011) GenStat for Windows, 13th edn. VSN International, Hemel Hempstead

    Google Scholar 

  • Wagner AP, Creel S, Kalinowski ST (2006) Estimating relatedness and relationships using microsatellites loci with null alleles. Heredity 97:336–345

    Article  CAS  PubMed  Google Scholar 

  • Yang S, Pang W, Ash G, Harpe J, Carling J, Wenzel P, Huttner E, Zong X, Kilian A (2006) Low level of genetic diversity in cultivated pigeon pea compared to its wild relatives revealed by diversity arrays technology. Theor Appl Genet 113:585–595

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This project was funded by European Union INCO-DEV: Sixth framework programme through the BAMLINK project.

Author information

Authors and Affiliations

  1. School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK

    Odireleng O. Molosiwa, Siise Aliyu, Katie Mayes & Sean Mayes

  2. School of Biosciences, The University of Nottingham Malaysia Campus, Jalan Broga, Semenyih, 43500, Selangor, Malaysia

    Siise Aliyu, Festo Massawe & Sean Mayes

  3. Crops for the Future (CFF), Block B, UNMC, Jalan Broga, Semenyih, 43500, Selangor, Malaysia

    Siise Aliyu & Sean Mayes

  4. CSIR-Savannah Agricultural Research Institute, Nyankpala, N/R, Ghana

    Siise Aliyu

  5. Centre of Life and Food Sciences Weihenstephan, Technische Universitaet Muenchen, Liesel-Beckmann-Str. 2, 85354, Freising, Germany

    Florian Stadler

  6. Diversity Arrays Technology Pty Ltd, Bldg 3, Level D, University of Canberra, LPO Box 5067, Bruce, ACT, 2617, Australia

    Andrzej Kilian

Authors
  1. Odireleng O. Molosiwa
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Siise Aliyu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Florian Stadler
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Katie Mayes
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Festo Massawe
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Andrzej Kilian
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Sean Mayes
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Siise Aliyu.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 23 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Molosiwa, O.O., Aliyu, S., Stadler, F. et al. SSR marker development, genetic diversity and population structure analysis of Bambara groundnut [Vigna subterranea (L.) Verdc.] landraces. Genet Resour Crop Evol 62, 1225–1243 (2015). https://doi.org/10.1007/s10722-015-0226-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-015-0226-6

Keywords

Search

Navigation