Development of a Diversity Panel for Traditional Rice (Oryza Sativa L.)Accessions/Varieties in Sri Lanka

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Oryza sativa L. varieties grown in Sri Lanka from ancient times to the middle of the last century are known as traditional rice varieties and a collection of over 2000 traditional rice accessions conserved at Gene Bank, Plant Genetics Resource Center (PGRC), Peradeniya, Sri Lanka. Farmers preferred traditional rice varieties for their adaptability to biotic and abiotic stresses and are an important component of the biodiversity of Sri Lanka. A detailed understanding of the genetic structure and diversity of traditional rice varieties is essential for the effective utilization of rice genetic resources and identification of potential parents possessing valuable genetic traits for future crop improvement in rice breeding programmes. The objective of the present study was phenotypic and molecular characterization of one hundred (100) traditional rice accession/varieties collected from PGRC, Sri Lanka and identification of a broad diversity panel for these traditional rice accessions/varieties. Rice varieties were grown in a plant house following Randomized Complete Block design with 4 replicates and 5 plants per each replicate. Thirty-two (32) agro-morphological characters were observed. Green leaves of rice varieties were individually collected from 20 day-old seedlings for gDNA extraction using Plant genomic DNA kit followed by the CTAB protocol. Thirty‐three microsatellite (Simple Sequence Repeat – SSR) primer pairs were used to assay genetic variation. DNA amplification was carried out using a thermal cycler and PCR products were subjected to fragment analysis by capillary electrophoresis. Descriptive statistics and basic inferential statistical analyses were performed to access the variation of agro-morphological characters among rice varieties. Data were subjected to cluster analysis (CA) to examine the grouping tendencies and supplemented with Multidimensional scaling (MDS) to explore the procedural differences in the outcome. CA and MDS produced seven (07) groups which were further analyzed using Classification and Regression Analysis (CART) to extract the diagnostic agro-morphological features. Based on CART result, groups of rice varieties were characterized by lemma–palea color, presence or absence of awn, seedling height, and flag-leaf angle. Traditional rice accessions/varieties represent distant clusters on agro-morphological features. Molecular analyses revealed, all 33 loci displayed polymorphism (66.7-96.9 %) among 100 traditional rice accessions/varieties with a total of 387 alleles identified with an average of 11.72 alleles per accession. AMOVA results showed that 34% of the variation distributed among accessions/varieties, 59% of among individuals and 7% within individual indicating a comparatively high level of genetic differentiation among individuals of selected rice accessions/varieties. Structure analysis results illustrated that all 100 accessions/varieties were genetically structured into fifteen well-separated groups, high ΔK peak was recorded at K=15, K= 5, K= 19 and K= 2 respectively. UPGMA analysis based on Jaccard's similarity separated the accessions into five (5) major clusters. A cophenetic correlation with r=0.786 strongly supported the clustering pattern of UPGMA dendrogram. A principal coordinate analysis (PCoA) also confirmed the UPGMA clusters. The genetic diversity information obtained will be useful in efficient use of Sri Lankan rice germplasm collection in breeding programmes. This information will also be useful in management of in situ and ex situ germplasm collections in conservation programs for traditional rice varieties.