Screening for submergence tolerant varieties via association of Sub1 gene related markers in rice (Oryza sativa L.)

Complete submergence from flooding and stagnant water seriously injures the plant’s growth and survival. The aim of the study was to identify local rice varieties that can be used as breeding materials for submergence tolerant varieties development using SSR and CAPS markers. Phenotypic screening revealed a significant difference whereby the mean elongation was higher for susceptible lines compared to tolerant lines. A strong negative correlation at -0.933 existed between survival percentage and elongation height in the submerged group. The elongation for the control group was also higher at 24.541 ± 5.119 cm than the submerged group at 14.806 ± 8.196 cm. Genotypic screening using the GNS2 CAPS marker has revealed the presence of the Sub1 gene and the gene polymorphism in the identified tolerant varieties with SSR markers, RM8303 that showed the highest PIC value (0.5174) and gene diversity (0.5816). It is expected that the results obtained may significantly help the development of better varieties in the upcoming rice breeding programmes.