Genetic diversity analysis of ninety traditional rice (Oryza sativa L.) varieties from Cu Long Rice Research Institute genebank, Vietnam

Analysis of the level of diversity among the 90 traditional varieties is useful in breeding programs as this influences parental selection in varietal development. The diversity of the 90 traditional varieties were assessed using SSR [simple sequence repeat] and quantitative morphological characters. The study aims to evaluate the genetic diversity of traditional rice varieties in the genebank of Cuu Long Rice Research Institute (CLRRI), Vietnam, analyse correlation of characters for application in plant breeding and relate the results between morphological characters and molecular markers. In agro-morphology based analysis, ANOVA showed highly significant differences among the 90 traditional rice varieties, correlation coefficients showed that all the traits were significantly correlated with each other except yield. The standardized Shannon-Weaver diversity indices for the quantitative morphological characters ranged from 0.68 to 0.95 with a mean of H'=0.88. Cluster analysis using UPGMA grouped the 90 traditional varieties into six major clusters. Varieties collected from same collecting site were grouped together in the same cluster. Molecular diversity analysis using 30 polymorphic SSR markers revealed genetic diversity among the 90 traditional varieties. The 90 traditional varieties generated eight clusters at 0.61 similarity coefficient. Some with the same variety names were grouped into different clusters. Though they belong to the same cluster based on morphological markers, molecular analysis showed that they were actually genetically different. Most of the varieties (84 percent) belong to the same cluster (cluster 7). This indicates that these varieties are closely related. Rainfed and deepwater varieties were grouped separately (cluster 4 for deep water rice and cluster 6 for rainfed rice). Both the morphological and SSR markers were able to classify the rice varieties into these agro-ecological groups.