Validation of Newly Designed SSR Markers for Eight Rice (Oryza sativa L.) Genotypes with Variable Heat Tolerance Responses Based on Agromorphic Data and Pollen Fertility Analysis

Rice is one of the most valuable staple food crops in the world. However, several challenges greatly affect production, one of which is the threat imposed by heat stress. To address this, researchers are developing varieties that are heat stress tolerant with genetic markers aid. In this study, eight rice genotypes, namely Dular, Nagina 22, NSIC Rc 222, Milyang 23, EL15, EL92, EL85, and IR52 were observed for agromorphic data, which included plant height, panicle length, filled and unfilled grains, and grain yield. Flower samples were collected to determine the effect of heat stress on pollen fertility. Molecular markers were designed via in silico analysis based on the nine QTL regions distributed among five chromosomes (1, 3, 4, 5, and 10). Out of the 90 newly developed markers, Markers 3066 and 2503 showed good potential as informative markers among heat tolerance classification. Results showed the genotype-specific responses of varieties during heat stress and non-heat stress conditions. EL15 had the best agromorphic performance and appeared to be the best elite line. Identification of gene-specific SSR markers has proven to be effective in understanding heat tolerance for future marker-assisted selection.