**Drought-Tolerance Gene Identification Using Genome Comparison and Co-Expression Network Analysis of Chromosome Substitution Lines in Rice**

**Chutarat Punchkhon 1,2, Kitiporn Plaimas 3,4, Teerapong Buaboocha 4,5, Jonaliza L. Siangliw 6, Theerayut Toojinda 6, Luca Comai 7, Nuria De Diego 8, Lukáš Spíchal 8 andSupachitraChadchawan 2,5,\***



Received: 25 August 2020; Accepted: 9 October 2020; Published: 14 October 2020

**Abstract:** Drought stress limits plant growth and productivity. It triggers many responses by inducing changes in plant morphology and physiology. KDML105 rice is a key rice variety in Thailand and is normally grown in the northeastern part of the country. The chromosome segmen<sup>t</sup> substitution lines (CSSLs) were developed by transferring putative drought tolerance loci (QTLs) on chromosome 1, 3, 4, 8, or 9 into the KDML105 rice genome. CSSL104 is a drought-tolerant line with higher net photosynthesis and leaf water potential than KDML105 rice. The analysis of CSSL104 gene regulation identified the loci associated with these traits via gene co-expression network analysis. Most of the predicted genes are involved in the photosynthesis process. These genes are also conserved in *Arabidopsis thaliana*. Seven genes encoding chloroplast proteins were selected for further analysis through characterization of *Arabidopsis* tagged mutants. The response of these mutants to drought stress was analyzed daily for seven days after treatment by scoring green tissue areas via the PlantScreen™ XYZ system. Mutation of these genes affected green areas of the plant and stability index under drought stress, suggesting their involvement in drought tolerance.

**Keywords:** CSSLs; drought stress; 'KDML105' rice; co-expression network
