Development of a core collection from Sri Lankan traditional rice (Oryza sativa) varieties for phenotypic and genetic diversity




Abstract. Weerakoon SR, Somaratne S. 2021. Development of a core collection from Sri Lankan traditional rice (Oryza sativa) varieties for phenotypic and genetic diversity. Nusantara Bioscience 13: 61-67. A collection of over 2000 traditional rice varieties are conserved at Gene Bank, Plant Genetics Resource Center, Sri Lanka. Oryza sativa varieties grown in Sri Lanka from ancient times to the middle of the last century are known as traditional rice. These varieties show adaptability to biotic and abiotic stresses and, an important component of biodiversity of Sri Lanka. A detailed understanding of the diversity of traditional rice varieties is essential for effective utilization of rice genetic resources and identification of potential parents possessing valuable genetic traits for future crop improvement. Study objectives were phenotypic and molecular characterization of one-hundred traditional rice varieties and to identify a core collection for phenotypic and genetic diversity. Rice varieties were grown in a plant house following RCBD with 4 replicates and 5 plants per replicate. Thirty-two agro-morphological characters were observed/collected. Genomic DNA was extracted from 20-days-old seedlings. Thirty?three microsatellite (Simple Sequence Repeat-SSR) primer pairs were used to assay genetic variation and PCR products were subjected to fragment analysis by capillary electrophoresis. Descriptive statistics and basic inferential statistical analyses were performed to access variation of agro-morphological characters among rice varieties. Cluster analysis and Multidimensional scaling produced 07 groups which were further analyzed using Classification and Regression Analysis to extract the diagnostic agro-morphological features. Groups of rice varieties were characterized by lemma palea color, awn color at maturity, seedling height, and flag-leaf angle. Traditional varieties represent distant clusters on agro-morphological features. Molecular analyses revealed all 33 loci displayed polymorphism (66.7-96.9%) among 100 traditional rice varieties with a total of 387 alleles identified with an average of 11.72 alleles per variety. All varieties were genetically structured into fifteen well-separated groups. UPGMA analysis based on Jaccard's similarity separated varieties into 05 major clusters. Genetic diversity information is useful in the efficient use of Sri Lankan rice germplasm and managing in situ and ex situ germplasm collections in conserving traditional rice varieties.


Abeyratne EF. 1956. Dry land farming in Ceylon. Tropical Agriculturalist 112(3): 191-229.
Atwell BJ, Wang H, Scafaro AP. 2014. Could abiotic stress tolerance in wild relatives of rice be used to
improve Oryza sativa? Plant Science 215-216: 48-58.
Bentota AP, Weerasinghe BGDS. 2005. Iron toxicity tolerance in some traditional rice varieties of Sri
Lanka, Annals of the Sri Lanka Department of Agriculture, Department of Agriculture, Peradeniya, Sri Lanka. 7:337-340.
Camacho Villa TC, Maxted N, Scholten M, Ford-Lloyd B. 2005. Defining and identifying crop landraces.
Plant Genetic Resources: Characterisation and Evaluation 3(3): 373-384.
Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S. 2000.
Diversity of microsatellites derived from genomic libraries and GeneBank sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100:713–722.
Crop Recommendations. 2014. Department of Agriculture, Sri Lanka.
Choudhury B, Khan ML. Dayanandan S. 2013. Genetic structure and diversity of indigenous rice (Oryza
sativa) varieties in the Eastern Himalayan region of Northeast India. SpringerPlus 2(1): 228.
Efisue A, Tongoona P, Derera J, Langyintuo A, Laing M, Ubi B. 2008. Farmers' perceptions on rice
varieties in Sikasso region of Mali and their implications for rice breeding. Journal of Agronomy and Crop Science 194(5): 393-400.
Kobayashi N, Ikeda R, Vaughan DA. Shigenaga S. 1991. Resistance to tungro in some wild relatives
of rice. International Rice Research Newsletter 16(4): 13.
Lin CS, Binns MR. 1985. Procedural approach 12. for assessing cultivar-location data: pair wise genotype-
environment interactions of test cultivars with checks. Canadian Journal of Plant Science 65(4):1065-1071.
Lin CS, Binns MR, Lefkovitch LP. 1986. Stability analysis: where do we stand? Crop Science 26(5):
Mandal AB, Pramanik SC, Chowdhury B, Bandyopadhyay AK. 1999. Salt-tolerant Pokkali
somaclones: performance under normal and saline soils in Bay Islands. Field Crops Research 61(1): 13-21.
Madurangi SAP, Ranawake AL, Dahanayake N. 2012. Evaluation of level of drought tolerance in
traditional rice cultivars in Sri Lanka at the seedling stage. Proceedings of the International Symposium on Agriculture and Environment 2012, Ruhuna, Sri Lanka, 29 November, 2012 pp.325-327.
Munasinghe SP, Somaratne S, Weerakoon SR. 2017. Screening of Sri Lankan Rice (Oryza sativa
L.) Landraces for Drought tolerance. Tropical Agricultural Research 28 (2): 183-191.
Pan abokke CR. 1996. Soils and Agro-ecological Environments of Sri Lanka. Natural Resources Series - 2
pp 31. Natural Resources and Energy Authority, 47/5, Maitland Place, Colombo 7.
PGRC Characterization Catalogue on Rice Germplasm. 199). Plant Genetics Resource Center (PGRC),
Gannoruwa, Sri Lanka.
Ranawake AL, Amarasinghe UGS. 2014. Relationship of Yield and Yield Related Traits of Some
Traditional Rice Cultivars in Sri Lanka as Described by Correlation Analysis. Journal of Scientific Research and Reports 3(18): 2395-2403.
Rajkumar G, Weerasena J, Fernando K, Liyanage A, Silva R. 2011. Genetic differentiation among Sri
Lankan traditional rice (Oryza sativa ) varieties and wild rice species by AFLP markers. NORDIC Journal of Botany.,
Ren F, Lu BR, Li S, Huang J, Zhu Y. 2005. A comparative study of genetic relationships among the AA-
genome Oryza species using RAPD and SSR markers. TAG Theoretical and Applied Genetics 108(1): 113-120.
Roa AC, Chavarriaga-Aguirre P, Duque MC, Maya MM, Bonierbale MW, Iglesias C, Tohme J. 2000. Cross-
species amplification of Cassava (Manihot esculenta) (Euphorbicaceae) microsatellites: allelic poplymorphism and degree of relationship. Am J Bot. 87:1647–1655.
Samita S, Anputhas M, Abeysiriwardena DS de Z. 2005. Accounting for multi traits in recommending
rice varieties for diverse environments. Experimental Agriculture 41(2): 213-225.
Shishido R, Kikuchi M. Nomura K, Ikehash, H. 2006. Evaluation of genetic diversity of wild rice (Oryza
rufipogon Griff.) in Myanmar using simple sequence repeats (SSRs). Genetic Resources and Crop Evolution 53(1): 179-186.
Thomson M, Septiningsih E, Suwardjo F, Santoso T, Silitonga T, McCouch S. 2007. Genetic diversity
analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. TAG Theoretical and Applied Genetics 114(3): 559-568.
Yu SB, Xu WJ, Vijayakumar CHM, Ali J, Fu BY, Xu JL, Jiang YZ, Marghirang R, Domingo J, Aqino C, Virmani
SS, Li ZK. 2003. Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program. TAG Theoretical and Applied Genetics 108(1): 131-140.
Wickramasinghe HAM, Noda T. 2008. Physicochemical properties of starches from Sri Lankan rice
varieties. Food Science and Technology Research 14(1): 49-54.