Simple sequence repeat (SSR) markers linked to drought tolerant traits in selected Sudanese rice (Oryza sativa L.) genotypes

Abstract

Rice growth and productivity are affected by biotic and abiotic stresses; key among them being drought. Conventional breeding for drought tolerance is slowed down by the complex nature of mechanisms underlying this stress although molecular markers offer a promising approach. Plant exposure to drought stress leads to a significant effect in chlorophyll content and reduction in photosynthesis. In this study, 23 Sudanese rice (Oryza sativa L.) genotypes under greenhouse conditions for drought tolerance were examined. The study focus on tracking changes in chlorophyll content under stress (by withholding water and later rewatering) and further screened them for DNA polymorphisms using simple sequence repeat (SSR) markers. The results showed that genotypes IR11A306, IRRI 154, NERCA 6, IR12N 240, NERICA 4, Wakra and IRRI 150 exhibited high drought tolerance based on the assay. After dehydration, IR11A306 recorded the highest increment in total chlorophyll while IR11A483 showed the highest reduction followed by NERICA 15, IR11 N121, IRRI 168, NERICA 7, NERICA 1, NERICA 14 and Nipponbare. When plants were rehydrated and total chlorophyll measured, the highest increase and best recovery were observed in IR74371-70-1-1 followed by IRRI 168, IRRI 147, Nipponbare, Kosti 2, IAC 165 and Umgar. Genotype IR11A306 showed the least reduction in chlorophyll followed by NERICA 15, IRRI 150, IRRI 122, IR12N 240, IRRI 154, NERICA 16, NERICA 4 and Wakra. Eighteen out of the 19 primers tested showed amplification of the SSR markers generating 569 alleles that ranged between 13 and 113 alleles per marker. These alleles further produced polymorphism information content (PIC) values of 0.51 to 0.99 per marker. The assay helped select genotypes that showed a steady recovery of chlorophyll content following drought stress while the markers studied could be useful for future molecular breeding for drought tolerance in rice.