Evaluation of Drought Tolerance in Selected Upland Land Rice Varieties Using Simple Sequence (SSR) Repeat Markers

Rice (Oryza sativa L.) is recognized as one of the most important staple food crops for more than 3.5 billion people in the world, accounting for more than half of human calories intake globally. The devastation caused by drought is one of the most important abiotic stress affecting rice production. The study was undertaken to identify drought tolerance upland rice varieties associated with polymorphic microsatellite (Simple Sequence Repeats (SSRs)) markers. The results on allele frequency, number of alleles and the polymorphic information content (PIC) of each locus among the studied varieties indicated that all the 6 specific primers produced scorable amplification bands in the analysis and all the primers were polymorphic, these polymorphic primers produced 23 alleles. The primer RM390 (0.73) showed higher discriminatory power to distinguish varieties due to its high PIC value and RM36 (0.19) showed lower PIC value. Indicating less discriminatory power of this primer under study. Gene diversity values of 20 rice varieties ranged from 0.19 (RM36) to 0.73 (RM390) with a mean of 0.58. These values showed that the varieties had several different recognized genes related to drought tolerance. The observed heterozygosity ranged from 0 to 0.33 (RM3558) with an average of 0.06 across all loci. The RM3558 and RM390 loci were the only ones that detected heterozygotes in the analyzed varieties. The majority of the SSR markers exhibited observed heterozygosity as zero, indicating that majority of rice cultivars used were pure and completely homozygous for SSR markers used in the study. UPGMA cluster analysis based on Jaccard’s dissimilarity coefficient showing 20 rice varieties generated from 6 SSR markers clustering model approach, distance-based neighbor-joining cluster and principal coordinate analysis using genotypic data grouped the varieties into three sub-populations. Analysis of molecular variance (AMOVA) and pairwise FST values showed significant differentiation among all the pairs of sub-population ranging from 0.152 to 0.222 suggesting that all the three subpopulations were significantly different from each other. Among the markers, RM3558, RM390 and RM170 were validated as markers linked to drought tolerance due to their ability to differentiate tolerant varieties from susceptible ones. Based on the SSRs variation analysis and clustering patterns, the NERICA rice varieties were identified as diverse cultivars and they are suitable and adapted to areas with insufficient rain fall for upland rice production and future breeding program.