The Genetic diversity of Dahanala traditional red rice and molecular markers associated with trichome density on adaxial surfaces

Main Article Content

Vidyamali Koodalugodaarachchi
Deepthika S. Kekulandara
Dikkumburage R. Gimhani


Oryza sativa 'Dahanala' is a traditional red rice variety acknowledged for its thrips resistance. This study focused on the genetic diversity assessment of Dahanala accessions in Sri Lanka. Twenty-six Dahanala accessions conserved at the genebank of the Plant Genetic Resources Centre and six accessions from the Rice Research and Development Institute, Batalagoda, were analyzed using seven seed morphology characters followed by molecular characterization with 31 simple sequence repeat markers, showing a significant genetic variation of the accessions. Accessions 003924/003327 and 0010160/006165 were reported as two potential pairs of duplicates. The polymorphic information content values varied between 0 (RM255) and 0.697 (RM412). Genetic distance ranged within 0.0 and 0.94 revealing considerable genetic variance. Sixteen closely related accessions were selected as a representative set of Dahanala, including accessions 003924, 003327, 006376, 010160, 006165, 006378, 004968, 003304, 006739, 005386, 004507, 003149, 003131, 627, 626 and 629. To assess the variation of trichome phenotypes among Dahanala accessions, leaf trichome density as well as RM277 and RM279 markers, which carry a putative relationship with thrips resistance, were used as morphological and molecular markers, respectively. Results revealed a variation of trichome density from 6.7 to 30.83 trichomes/mm2. According to the molecular marker analysis, both markers revealed polymorphism in thrips-resistant Dahanala accessions and susceptible Oryza sativa ‘Suduru Samba’ accessions, but no clear linkage between the markers and trichome phenotypes within the selected Dahanala accessions could be found. Further studies are needed to dissect the relationship between trichome phenotype and thrips resistance in red rice.

Article Details

How to Cite
Koodalugodaarachchi, V., Kekulandara, D. and Gimhani, D. (2022) “The Genetic diversity of Dahanala traditional red rice and molecular markers associated with trichome density on adaxial surfaces”, Genetic Resources, 3(5), pp. 10-23. doi: 10.46265/genresj.AVEO9374.
Original Articles

Ananthakrishnan, T N (1979). “Biosystematics of Thysonoptera”. Annual Review of Entomology 24, pp. 159–183. DOI:

Bioversity International, IRRI and WARDA (2007). Descriptors for wild and cultivated rice (Oryza spp.) Rome, Italy: Bioversity International. DOI:

Gimhani, D R (2010). Identification of Microsatellite Marker Linked to Thrips (Stenchaetothrips biformis) Resistance in Rice Using Bulk Segregant Analysis. Sri Lanka.

Gramene. Introduction to Rice. URL:

Gramene Microsat. All SSRs. URL:

Jeffreys, A J, J F Brookfield, and R Semeonoff (1985). “Positive identification of an immigration test-case using human DNA fingerprints”. Nature 317, pp. 818–819. DOI:

Karunadasa, R M S P and W L G Samarasinghe (2017). “Genetic diversity analysis of traditional rice variety ‘Kuruluthuda’ using SSR markers”. In: Proceeding of the International Research Symposium. Sri Lanka: Uva Wellassa University.

Korzun, V (2002). “Use of molecular markers in cereal breeding”. Cellular and molecular biology letters 2, pp. 811–820. URL: Korzun/publication/11082462_Use_of_molecular_markers_in_cereal_breeding/links/ 09e41507f31792683b000000/Use-of-molecular-markers-in-cereal-breeding.pdf.

Kudagamage, C (1977). “Varietal resistance to the rice thrips, Baliothrips biformis”. International Rice Research Newsletter 2, pp. 11–11. URL:

Liu, K and S V Muse (2005). “PowerMarker: an integrated analysis environment for genetic marker analysis”. Bioinformatics 21(9), pp. 2128–2129. DOI:

Manatunga, M M S L et al. (2019). “Genetic diversity analysis of ‘Murungakayan’ Rice accessions based on seed morphology and molecular characterization”. Tropical Agricultural Research 30(2), pp. 65–73. DOI:

Matsui, T and H Kagata (2003). “Characteristics of floral organs related to reliable self-pollination in rice (Oryza sativa L.)” Annals of Botany 91(4), pp. 473–477. DOI:

McCouch, S R et al. (2001). “Microsatellite markers in rice: abundance, diversity, and applications”. In: Rice genetics IV. Proceedings of the Fourth International Rice Genetics Symposium, 22-27 October 2000, Los Baños, Philippines. Ed. by G S Khush, D S Brar, B Hardy, et al. Enfield, NH, USA.: Science Publishers, Inc., pp. 117–135. DOI:

Minitab (1991). Minitab reference Manual (Release 7.1). State College, PA 16801, USA: Minitab Inc.

Murray, M G and W F Thompson (1980). “Rapid isolation of high molecular weight plant DNA”. Nucleic Acids Research 8(19), pp. 4321–4326. DOI:

Nei, M, F Tajima, and Y Tateno (1983). “Accuracy of estimated phylogenetic trees from molecular data”. Journal of Molecular Evolution 19, pp. 153–170. DOI:

Nugaliyadde, L and E A Heinrichs (1984). “Resistance of Oryza spp. to thrips, Stenchaetothrips biformis (Bagnall) (Thysanoptera: Thripidae)”. Crop Protection 3, pp. 305–313. DOI:

Panda, N and G B Khush (1995). Host Plant Resistance of Insects: Mechanisms of Resistance. United Kingdom: Biddles Ltd.

Semagn, K (2002). “Genetic relationships among ten endod types as revealed by a combination of morphological, RAPD and AFLP markers”. Hereditas 137(2), pp. 149–156. DOI:

Shahbandeh, M (2022). “Rice - statistics & facts”. In: ed. by and others. Statista. URL:

Siriwardhana, S M, W L G Samarasinghe, and D R Gimhani (2016). “Molecular characterization of a traditional rice variety ‘Kaluheenati’ (Oryza sativa L.) using Simple Sequence Repeats markers”. In: Proceedings of 15th Agricultural Research Symposium, pp. 135–139.

Suriyagoda, L D B et al. (2011). “Morphological variation in selected rice (Oryza sativa L.) germplasm of Sri Lanka”. Journal of the National Science Foundation of Sri Lanka 39, pp. 129–137. DOI:

Tamura, K et al. (2013). “MEGA6: molecular evolutionary genetics analysis version 6.0”. Molecular Biology and Evolution 30(12), pp. 2725–2729. DOI:

Thotagodawatta, T M N B K et al. (2017). “Genetic diversity analysis of traditional rice variety ‘Pokkali’ using Simple Sequence Repeat markers (SSR)”. In: Proceedings of the International Research Symposium. Uva Wellassa University, Sri Lanka, p. 190. URL:

Warusawithana, T M et al. (2017). “Genetic Diversity Analysis of Traditional Rice Variety ’Pachchaperumal‘ Using SSR Markers ”. International Journal of Scientific and Technology Research 6(8), pp. 229–237. URL: Diversity-Analysis-Of-Traditional-Rice-Variety-pachchaperumal-Using-Ssr-Markers.pdf.

Wickramasinghe, H A M and T Noda (2008). “Physicochemical properties of starches from Sri Lankan rice varieties”. Food Science and Technology Research 14, pp. 49–54. DOI:

Wickramasinghe, K S et al. (2007). “Effect of leaf trichomes to thrips resistance in rice”. Annals of Sri Lanka Department of Agriculture 9, pp. 189–198. URL:

Author Biographies

Deepthika S. Kekulandara, Plant Genetic Resources Centre, Gannoruwa, Peradeniya, 20400, Sri Lanka

Assistant Director of Agriculture (Research)


Dikkumburage R. Gimhani, Faculty of Agriculture and Plantation Management, Wayamba University of Sri Lanka, Gonawila (NWP), 60170, Makandura, Sri Lanka

Head, Department of Biotechnology