Genetic diversity of weedy rice (Oryza sativa f. spontanea) populations in Sri Lanka: An application of Self Organizing Map (SOM)

Abstract. Weerakoon SR, Somaratne S. 2021. Genetic diversity of weedy rice (Oryza sativa f. spontanea) populations in Sri Lanka: An application of Self Organizing Map (SOM). Asian J Agric 5: 35-43. Weedy rice (WR) (Oryza sativa f. spontanea) has become a major threat in rice cultivation. Discrimination of WR from cultivated rice is difficult since agro-morphology of WR and cultivated rice are overlapping. Molecular markers are useful and can be an informative tool for estimating genetic diversity and relationships in closely related WR eco-types. Self-Organizing Maps (SOM) is an interesting and promising classification tool employing an innovative and data-driven classification method based on unsupervised artificial neural networks. The present study focused on exploring the potential use of SOM to classify WR populations of different eco-climatic zones in Sri Lanka using agro-morphological and molecular data. Separate SOMs for each set of variables, agro-morphological and molecular data were developed. The best SOM was chosen based on the error performance. Findings of SOM analyses showed that certain morphological characters (seedling height, leaf blade width, leaf blade length, culm strength, panicle shattering, seed coat color and leaf angle) and certain molecular characters detected from SSR primers (RM 11, RM 21, RM 14, and RM 280) are important in separation of different WR eco-types satisfactorily. SOM clustering of cultivated, wild, and WR eco-types indicated specific patterns of grouping with respect to climatic conditions of the country. WR eco-types in dry zone and wet zone of the country are closely related to Oryza nivara and O. rufipogon respectively.