Exploring novel QTLs for drought tolerance traits using a new rice genetic resource would be valuable to dissect the mechanisms underlying the complexity of the trait. Here, we used a recombinant inbred line population to detect the QTL associated with agro-physiological traits under drought stress, in particular incorporating the SNPs and 147 phenotype data, analyzed the transcript expression of genes within QTL using differential gene expression meta-analysis and qRT-PCR technique. Composite interval mapping analysis allowed the detection of 154 QTLs distributed into 66 regions, which included a large QTL cluster called ‘hotspot QTL’ that strongly associated with drought tolerance on rice chromosome 8. We found several genes within the QTL-containing regions that were highly expressed based on the meta-analysis approach. In the future, the QTL reported here may be utilized for marker-assisted breeding and the candidate drought-responsive genes could be characterized for dissecting a comprehensive molecular mechanism of drought tolerance in rice.