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Molecular insight into genetic differentiation, population structure and banding pattern analysis of Bambara groundnut (Vigna subterranea [L.] Verdc.) linked with inter simple sequence repeats (ISSR)

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Abstract

Background

A set of 44 selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions was sampled from 11 distinct populations of four geographical zones to assess the genetic drift, population structure, phylogenetic relationship, and genetic differentiation linked with ISSR primers.

Methods and results

The amplification of genomic DNA with 32 ISSR markers detected an average of 97.64% polymorphism while 35.15% and 51.08% polymorphism per population and geographical zone, respectively. Analysis of molecular variance revealed significant variation within population 75% and between population 25% whereas within region 84% and between region 16%. The Bidillali exposed greater number of locally common band i.e., NLCB (≤ 25%) = 25 and NLCB (≤ 50%) = 115 were shown by Cancaraki while the lowest was recorded as NLCB (≤ 25%) = 6 and NLCB (≤ 50%) = 72 for Roko and Maibergo, accordingly. The highest PhiPT value was noted between Roko and Katawa (0.405*) whereas Nei’s genetic distance was maximum between Roko and Karu (0.124). Based on Nei’s genetic distance, a radial phylogenetic tree was constructed that assembled the entire accessions into 3 major clusters for further confirmation unrooted NJ vs NNet split tree analysis based on uncorrected P distance exposed the similar result. Principal coordinate analysis showed variation as PC1 (15.04%) > PC2 (5.81%).

Conclusions

The current study leads to prompting the genetic improvement and future breeding program by maximum utilization and better conservation of existing accessions. The accessions under Cancaraki and Jatau are population documented for future breeding program due to their higher genetic divergence and homozygosity.

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Data availability

All data generated or analysed during this study are included in this article and full length of gel or blots are represented in supplementary file.

Abbreviations

DNA:

Deoxy ribonucleic acid

RNA:

Ribonucleic acid

ISSR:

Inter simple sequence repeat

NJ:

Neighbour joining

NNet:

Neighbour network

PCR:

Polymerase chain reaction

RAPD:

Random amplified polymorphic DNA

RFLP:

Restriction fragment length polymorphism

AFLP:

Amplified fragment length polymorphism

GPS:

Global positioning system

CATB:

Cetyl trimethylammonium bromide

EDTA:

Ethylenediaminetetraacetic acid

PCoA:

Principal coordinate analysis

MVSP:

Multivariate statistical packages

UPGMA:

Unweighted Pair Group Method with Arithmetic Mean

MEGA:

Molecular evolutionary genetic analysis

AMOVA:

Analysis of molecular variance

MCMC:

Markov Chain Monte Carlo

CLUMPAK:

Cluster Markov Packager Across K

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Acknowledgements

The Bangladesh Agricultural Research Council (BARC-Project of NATP Phase-II) and Bangladesh Agricultural Research Institute (BARI) of the People’s Republic of Bangladesh are gratefully acknowledged by the writers. Another deserving of praise is Malaysia’s University Putra Malaysia (UPM).

Funding

Bangladesh Agricultural Research Council (BARC- Project of NATP Phase-II), The People’s Republic of Bangladesh, World Bank, IFAD, and Universiti Putra Malaysia (Research Grant: Vote number 6282518).

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Authors and Affiliations

  1. Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security (ITAFoS), Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia

    Md Mahmudul Hasan Khan, Mohd Y. Rafii & Md Al Mamun

  2. Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia

    Mohd Y. Rafii, Shairul Izan Ramlee & Mashitah Jusoh

  3. Bangladesh Agricultural Research Institute (BARI), Gazipur, 1701, Bangladesh

    Md Mahmudul Hasan Khan & Bimal Chandra Kundu

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  1. Md Mahmudul Hasan Khan
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Contributions

MMHK and MYR created the paper’s concept, design, and methodology. MMHK collected the data. MMHK performed statistical analysis, used software, and interpreted the results. MMHK wrote the first draft and prepared the text. MYR is in charge of supervision. SIR and MJ investigate the situation. MMHK, BCK, and MAM wrote the article; they also reviewed and edited it. The final published version of the paper has been reviewed and approved by all authors.

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Correspondence to Md Mahmudul Hasan Khan.

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Khan, M.M.H., Rafii, M.Y., Ramlee, S.I. et al. Molecular insight into genetic differentiation, population structure and banding pattern analysis of Bambara groundnut (Vigna subterranea [L.] Verdc.) linked with inter simple sequence repeats (ISSR). Mol Biol Rep 50, 7619–7637 (2023). https://doi.org/10.1007/s11033-023-08693-x

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