**Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of** *qDTYs* **to Reproductive-Stage Drought Stress in Rice (***Oryza sativa* **L.)**

**Jeshurun Asher Tarun 1,2, Ramil Mauleon 3, Juan David Arbelaez 1, Sheryl Catausan 2, Shalabh Dixit 2, Arvind Kumar 2, Patrick Brown 4, Ajay Kohli 2 and Tobias Kretzschmar 3,\***


Received: 14 August 2020; Accepted: 22 September 2020; Published: 24 September 2020

**Abstract:** Rice (*Oryza sativa* L.) is more sensitive to drought stress than other cereals. To dissect molecular mechanisms underlying drought-tolerant yield in rice, we applied di fferential expression and co-expression network approaches to transcriptomes from flag-leaf and emerging panicle tissues of a drought-tolerant yield introgression line, DTY-IL, and the recurrent parent Swarna, under moderate reproductive-stage drought stress. Protein turnover and e fficient reactive oxygen species scavenging were found to be the driving factors in both tissues. In the flag-leaf, the responses further included maintenance of photosynthesis and cell wall reorganization, while in the panicle biosynthesis of secondary metabolites was found to play additional roles. Hub genes of importance in di fferential drought responses included an expansin in the flag-leaf and two peroxidases in the panicle. Overlaying di fferential expression data with allelic variation in DTY-IL quantitative trait loci allowed for the prioritization of candidate genes. They included a di fferentially regulated auxin-responsive protein, with DTY-IL-specific amino acid changes in conserved domains, as well as a protein kinase with a DTY-IL-specific frameshift in the C-terminal region. The approach highlights how the integration of di fferential expression and allelic variation can aid in the discovery of mechanism and putative causal contribution underlying quantitative trait loci for drought-tolerant yield.

**Keywords:** co-expression network; drought-tolerant-yield; reproductive-stage drought; *qDTY*s; rice; transcriptomics
