**5. Conclusions**

The KDML105 chromosome substitution line CSSL104 displayed a drought-tolerance phenotype based on photosynthetic maintenance ability. Identification of SNPs between KDML105 and the tolerant CSSL, together with co-expression network analysis, predicted 18 candidate drought-tolerance genes—ten of which were involved in photosynthesis or chloroplast development. Seven of them were selected for the characterization by using *Arabidopsis* mutant lines for the homologous genes. Four out of seven mutants showed a higher growth rate than WT under drought stress. Therefore, *LOC\_Os01g72800*, *LOC\_Os07g37550*, *LOC\_Os07g38300*, and *LOC\_Os10g10170* are proposed to be the drought-tolerance genes in CSSL104 rice.

**Author Contributions:** Conceptualization, S.C. and L.C.; methodology, K.P., T.P., L.C., N.D.D., and L.S.; software, K.P., T.P., N.D.D., and L.S.; validation, C.P.; formal analysis, C.P.; investigation, C.P.; resources, J.L.S. and T.T.; data curation, C.P. and T.B.; writing—original draft preparation, C.P.; writing—review and editing, S.C., T.B., and L.C.; visualization, C.P., S.C.; supervision, S.C., N.D.D., and L.S.; project administration, S.C.; funding acquisition, S.C. All authors have read and agreed to the published version of the manuscript.

**Funding:** C.P. was supported by the 100th Anniversary of Chulalongkorn University Doctoral Scholarship, and this study was supported by the 90th Anniversary of Chulalongkorn University, Rachadapisek Sompote Fund, gran<sup>t</sup> no. GCUGR1125614034D. The collaboration between CEEPP and CRH was supported by the graduate school and the Rachadapisek Sompote Fund, Chulalongkorn University, Thailand. L.S. and N.D.D. acknowledge the ERDF project entitled "Development of Pre-Applied Research in Nanotechnology and Biotechnology" (No. CZ.02.1.01/0.0/0.0/17\_048/0007323).

**Acknowledgments:** We thank Noppakhun Khunpolwattana for rice DNA extraction and Panita Chutimanukul and Thammaporn Kojonna for their kind help.

**Conflicts of Interest:** The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.
