Genetic Diversity Analysis of Tomato Germplasm via RAPD Markers: A Case Study in Bangladesh

Shamima Nasrin *

Bangladesh Jute Research Institute (BJRI), Dhaka-1207, Bangladesh.

Abdul Mannan

Agrotechnology Discipline, Khulna University, Khulna-9208, Bangladesh.

Monirul Islam

Agrotechnology Discipline, Khulna University, Khulna-9208, Bangladesh.

Sabiha Sultana

Agrotechnology Discipline, Khulna University, Khulna-9208, Bangladesh.

Abu Sayem Jiku

Bangladesh Jute Research Institute (BJRI), Dhaka-1207, Bangladesh.

M Al-Mamun

Bangladesh Jute Research Institute (BJRI), Dhaka-1207, Bangladesh.

*Author to whom correspondence should be addressed.


Abstract

This study aimed to assess the genetic diversity of collected tomato germplasm using Random Amplified Polymorphic DNA (RAPD) markers. The relationship between genetic diversity estimates and germplasm collections is important to facilitate effective germplasm collection, evaluation and utilization. RAPD markers are also more effective and efficient than morphological markers in determining recombination variability in genetic diversity assessment. The experiment was conducted at the Laboratory of Molecular Horticulture in Agrotechnology Discipline, Khulna University, Khulna, Bangladesh from October to December 2022. Sixteen isolates were amplified three times with eight primers. RAPD fragments were identified by the name of the primer and the size of the amplified bands. Only well-defined fragments were rated as having two alleles (present and absent) of the putative locus. All tomato Varieties were in two distinct clusters, Cluster I consisted of 6 varieties and Cluster II contained the remaining 10 varieties. BARI Tomato-2 and Suraksa were most distinctly related and Ruma-19 and Guli were most closely related.

Keywords: RAPD markers, germplasm, morphological markers, genetic analysis


How to Cite

Nasrin , Shamima, Abdul Mannan, Monirul Islam, Sabiha Sultana, Abu Sayem Jiku, and M Al-Mamun. 2024. “Genetic Diversity Analysis of Tomato Germplasm via RAPD Markers: A Case Study in Bangladesh”. Asian Journal of Biotechnology and Genetic Engineering 7 (1):112-20. https://journalajbge.com/index.php/AJBGE/article/view/129.

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References

Statista. Global production of vegetables in 2019, by type (in million metric tons) Published by M. Shahbandeh; 2021. Accessed On: 5 March 2021. Available:https://www.statista.com/statistics/264065/global-production-of-vegetables-by-type/

Kumar S, Kumar R, Kumar S, Singh M, Banerjee MK. Rai M. Hybrid seed production of Solanaceous Vegetables. A Practical Manual, IIVR Technical Bulletin. 2003;9:1-34.

Oladosu Y, Rafii MY, Arolu F, Chukwu SC, Salisu MA, Olaniyan BA, Fagbohun IK, Muftaudeen TK. Genetic diversity and utilization of cultivated eggplant germplasm in varietal improvement. Plants. 2021;10 (8):1714.

Poczai P, Varga I, Bell N, Hyvonen J. (). Genetic diversity assessment of bittersweet (Solanum dulcamara, Solanaceae) germplasm using conserved DNA-derived polymorphism and intron-targeting markers. Annals of Applied Biology. 2011;159:141-153. DOI: 10.1111/j.1744-7348.2011.00482.x

Herison C, Sutjahjo SH, Sulastrini I, Rustikawati R, Marwiyah S. (). Genetic diversity analysis in 27 tomato accessions using morphological and molecular markers. Agrivita - Journal of Agricultural Science. 2018;40:36-44.

Korir NK, Han J, Shangguan L, Wang C, Kayesh E, Zhang Y, Fang J. Plant variety and cultivar identification: advances and prospects. Critical Reviews in Biotechnology. 2012;33:111-125.

DOI: 10.3109/07388551.2012.675314

Alam SS, Ishrat E, Zaman MY, Habib MA. Comparative karyotype and RAPD analysis for characterizing three varieties of Lycopersicon esculentum Mill. Bangladesh Journal of Botany. 2012;41(2): 149‐154.

Singh PK, Sharma H, Srivastava N, Bhagyawant SS. Analysis of genetic diversity among wild and cultivated chickpea genotypes employing ISSR and RAPD markers. American Journal of Plant Sciences; 2014.

Rai N, Kumar S, Singh RK, Rai KK, Tiwari G, Kashyap SP, Singh M, Rai AB. Genetic diversity in Indian bean (Lablab purpureus) accessions as revealed by quantitative traits and cross-species transferable SSR markers. Indian J Agric Sci. 2016;86(9) :654-660.

Biswas MS, Akhond AAY, Alamin M, Khatun M, Kabir MR. Genetic relationship among ten promising eggplant varieties using RAPD markers. Plant Tissue Culture and Biotechnology, 2009;19(2):119-126.

Paul A, Bandyopadhyay S, Acharyya P, Raychaudhuri SS. Studies on genetic diversity of twelve accessions of Momordica charantia L. using morphological, RAPD and SCAR markers. Asian Journal of Plant Sciences. 2010;9 (8):471-478. DOI:10.3923/ajps.2010.471.478.

Kuras A, Korbin M, Zurawicz E. Comparison of suitability of RAPD and ISSR Techniques for determination of Strawberry (Fragaria × Ananassa Duch.) relationship, Plant Cell, Tissue and Organ Culture. 2004;79:189‐193.

Kandan A. Molecular and phenotypic characterization of Ganoderma lucidum infecting palms and forest trees in India. Journal of Plant Research & Biotechnology. 2013;26(2):344-352.

Sneath PH, Sokal RR. (Numerical Taxonomy: The Principles and Practice of Numerical Classification. 1st Edition, W. H. Freeman, San Francisco; 1973.

Saitou, N, Nei, M. The Neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 1987;4:406-425.

Moonmoon S. Random amplified polymorphic DNA markers (RAPD) for genetic vacation study among tomato varieties. M.S. Thesis. Department of Biotechnology. Bangladesh Agricultural University, Mymensingh. 2006; 34‐51.

Shah MA, Khan AI, Awan FS, Sadaqat HA, Bahadur S, Rasheed A, Baloch FS. Genetic diversity of some tomato cultivars and breeding lines commonly used in Pakistani breeding program. Turkish Journal of Agriculture-Food Science and Technology. 2015;3:126-132.

Paul M, Saha SR. Assessment of genetic diversity of different tomato genotypes using RAPD markers, Progressive Agriculture. 2018;29(4):276-283.

El-Hady EAAA, Haiba, AAA, Abd, NR, Rizkalla A. Phylogenetic diversity and relationships of some tomato varieties by electrophoretic protein and RAPD analysis. Journal of American Science. 2010;6(11): 434-441.

Tabassum N, Sony S, Bhajan S, Islam MN. (). Analysis of Genetic Diversity in Eleven Tomato (Lycopersicon esculentum Mill.) Varieties using RAPD Markers. Plant Tissue Culture and Biotechnology. 2013; 23:49-57.

DOI:10.3329/ptcb.v23i1.15559

Clarck AG, Lanigan CM. (). Prospects for estimating nucleotide divergence with RAPDs. Molecular Biology and Evolution. 1993;10:1069- 1111.

Elham AA, Atef HAA, Abd El-Hamid NR, Rizkalla AA. Phylogenetic diversity and relationships of some tomato varieties by electrophoretic protein and RAPD analysis. Journal of American Science. 2010;11: 434-441.

Naz S, Zafrullah A, Shahzadhi K, Munir N. Assessment of genetic diversity within germplasm accessions in tomato using morphological and molecular markers; 2013.