Molecular profiling of rice (Oryza sativa L.) genotypes using trait-based SNP markers linked to yield under drought condition

Abstract

Drought is one of the major abiotic stress factors affecting the growth and production of rice globally and it can cause an estimated yield loss up to 90% in rice. With the increasing population around the globe, a comprehensive approach for mitigating drought stress should be taken to develop drought-tolerant rice varieties to meet future food demands. One hundred and eighty-two rice genotypes were evaluated for six critical gene/QTLs associated with drought tolerance using SNP marker data. The results revealed that 172 genotypes carry at least one gene/QTL for drought tolerance. The six gene/QTLs, namely, DTY1.1, qDTY2.2, qDTY3.1, qDTY3.2, qDTY4.1 and qDTY12.1were found in 103, 26, 90, 25, 27 and 45 genotypes corresponding to 57, 49, 14, 14, 15 and 25% of the total screened genotypes, respectively. Remarkably, five genotypes (RL-32, RL-105, RL-110, RL-142 and RL-158) possessed a unique combination three major genes/QTLs and three genotypes (RL-21, RL-41 and RL-188) possessed a unique combination four major gene/QTLs for drought tolerance. Furthermore, both cluster and populationn structure analyses revealedd the distribution of the genotypes into two major clusters. The genotypes carrying valuable gene/QTLs either in single or combination, hold immense potential for deployment in drought tolerance rice breeding programs.