**5. Conclusions**

This study provided novel insight into global transcriptional responses in rice under moderate RDS in a DTY-dependent manner and highlighted associated physiological mechanisms that allow DTY-IL to better cope with RDS. In DTY-IL flag-leaves, structural and metabolic integrity associated with cell wall re-organization and active ROS metabolism prevent leaf rolling and allow for maintenance of cellular growth and homeostasis under RDS, which supports sustained rates of photosynthetic activity and consequently provisioning of energy and carbon to developing sinks. In the developing panicles close to anthesis, sustained energy and carbon allocation enables the minimizing of damage to reproductive structures due to RDS through protective mechanisms, including ROS homeostasis, post-transcriptional modifications, detoxification, and secondary metabolite production; ultimately this results in improved fertility and yield under moderate RDS (Figure S21). Assessment of DTY-specific allelic variation within the *qDTY1.1* and *qDTY3.2* regions prioritized two candidate genes in DTY-IL, a predicted auxin-responsive protein with a DOMON\_DOH and a Cyt\_*b561* domain, and a CIPK\_C and SnRK3- domain-containing protein, which might positively affect source-sink regulation under drought.

**Supplementary Materials:** The following are available online at http://www.mdpi.com/2073-4425/11/10/1124/s1, Table S1. Mapping results of RNA-Seq reads of Swarna and DTY-IL in flag-leaf and emerging panicle tissues under RDS and control conditions, Table S2. GO enrichment analysis of the commonly down-regulated genes in DTY-IL and Swarna under RDS in the flag-leaf and emerging panicle tissues, Table S3. Pathway enrichment analysis of Swarna downregulated and DTY-IL upregulated DEGs in flag-leaf under RDS, Table S4. Overrepresented *cis*-acting elements of Swarna downregulated and DTY-IL upregulated DEGs in flag-leaf under RDS, Table S5. GO enrichment analysis of the commonly up-regulated genes in DTY-IL and Swarna under RDS in the flag-leaf and emerging panicle tissues, Table S6. Pathway enrichment analysis of Swarna downregulated and DTY-IL upregulated DEGs in emerging panicle under RDS, Table S7. Overrepresented *cis*-acting elements of Swarna downregulated and DTY-IL upregulated DEGs in emerging panicle under RDS, Table S8. List of different module color and sizes generated in flag-leaf and emerging panicle tissue using WGCNA, Table S9. The top 10 Go terms in biological process, molecular function, and cellular component categories in M1 and M2 in flag-leaf and emerging panicle tissues under RDS, Table S10. The list of 140 and 102 genes with their putative functions and expression profiles in the DTY-IL and Swarna under RDS in the M14 and M16 modules in flag-leaf tissue, Table S11. Identified hub genes in M14 and M16 in flag-leaf with their putative functions and expression profiles between the DTY-IL and Swarna under RDS, Table S12. The list of 138 and 73 with their putative functions and expression profiles in the DTY-IL and Swarna under RDS in the M10 and M15 modules in panicle tissue, Table S13. Identified hub genes in M10 and M15 in panicle with their putative functions and expression profiles between the DTY-IL and Swarna under RDS, Table S14. qRT-PCR primers used in the study, Table S15. Information on the introgressed chromosome segments and the differentially expressed genes in the DTY1.1-IL compared with Swarna under control and reproductive-drought stress conditions and overlapping *qDTY's* in flag-leaf and panicle tissues, Table S16. List of DEGs in the *qDTY1.1* region across the di fferent pairwise comparisons in flag-leaf and emerging panicle transcriptomes under RDS, Table S17. Distinct *cis* regulatory elements in the 2 kb upstream promoter region of LOC\_Os01g67030 in Nipponbare, MH63, and N22 sequences, Figure S1. Climate data and soil water content during water stress treatment. Figure S2. Quality control assessment for 16 flag-leaf tissue samples, Figure S3. Quality control assessment for 15 panicle tissue samples, with one Swarna control outlier removed, Figure S4. Quality control assessment for 16 panicle tissue samples, Figure S5. DEGs identification, Figure S6. Venn diagrams of di fferentially expressed genes (DEGs), Figure S7. Flag-leaf significant GO terms of biological processes that are down-regulated in Swarna (A) and up-regulated in DTY-IL (B) under RDS, Figure S8. Panicle significant GO terms of biological processes that are down-regulated in Swarna (A) and up-regulated in DTY-IL (B) under RDS, Figure S9. Mapman overview of the DEGs of interest in DTY-IL and Swarna under RDS, Figure S10. Identification of gene co-expression modules in the flag-leaf (A-C) and panicle (D-F) transcriptome under RDS, Figure S11. Bar graphs and Heatmaps of M1 and M2 in flag-leaf and panicle tissues under RDS, Figure S12. Major biological processes and over-represented GO Slim descriptions of drought-responsive M14 (A) and M16 (B) in flag-leaf tissue under RDS, Figure S13. Hub genes from the drought-responsive modules in the flag-leaf, Figure S14. Major biological processes and over-represented GO Slim descriptions of drought responsive M10 (A) and M15 (B) in panicle tissue under RDS, Figure S15. Hub genes from the drought-responsive modules in the panicles, Figure S16. The tissue-specific expression under RDS, Figure S17. qRT-PCR validation of candidate genes, Figure S18. Gene structure including the 2 kb upstream region of LOC\_Os01g67030 in the three published reference genomes representing Nipponbare, *indica*, and *ausboro*, Figure S19. Multiple peptide sequence alignment of LOC\_Os01g67030 in Nipponbare, MH63, and N22 sequences, Figure S20. Multiple peptide sequence alignment of LOC\_Os03g03510 in Nipponbare, MH63, and N22 sequences. Figure S21. Model of suggested DTY-IL dependent drought tolerance mechanisms.

**Author Contributions:** J.A.T. and T.K. conceptualized and designed the experiment; J.A.T. and S.C. performed the experiments; J.A.T. conducted the data analyses; R.M., J.D.A., and P.B. supervised on some of the data analyses; J.A.T. and T.K. wrote the manuscript; R.M. and A.K. (Ajay Kohli) contributed to reviewing and editing; S.D. gave the seeds; A.K. (Arvind Kumar) was involved in funding acquisition. All authors have read and agreed to the published version of the manuscript.

**Funding:** This work was supported by the Bill and Melinda Gates Foundation.

**Acknowledgments:** We thank the Bill and Melinda Gates Foundation for the project support.

**Conflicts of Interest:** The authors declare no conflict of interest and 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.
