Phenotypic and Genotypic Screening of Green Super Rice Genotypes for Submergence Tolerance at Seedling Stage

Climate change threatens rice-based systems, especially in areas where crops are sensitive to temperature fluctuations. Rice production is significantly impacted by extreme weather events, and persistent and heavy rainfalls which cause floods lead to submergence stress. The primary focus of this research was the evaluation of rice genotypes under controlled flooding conditions. The study included nine green super rice lines and one local control variety based on better tolerance against submergence stress. Using genotyping based on SSR markers, the goal was to better understand how rice germplasm responded to submergence stress at the seedling stage. The treatments included: T0, the control without submergence stress; T1, submergence for 10 days with ethylene treatment; and T2, submergence for 10 days without ethylene treatment. Ten genotypes were tested under complete seedling submergence. Submergence-tolerant genotypes were identified using the RM23877 SSR marker for genotyping. The results highlighted significant genotypic variations (alleles and genetic markers associated with submergence tolerance) in response to submergence stress affected by ethylene treatment, with variable effects observed for different genotypes. Most genotypes had zero survival except for GSR-4 and GSR-61, followed by GSR-5, GSR-13, GSR-2, and Chenab basmati. SSR marker-based genotyping further revealed that six out of ten genotypes present the submergence tolerance allele. We observed significant genotypic variations in the alleles associated with submergence tolerance, including differences in the Sub1A-1, Sub1B, and Sub1C genes among the GSR genotypes. These findings lay the groundwork for marker-assisted selection in breeding programs to develop rice varieties with enhanced submergence tolerance.