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Article

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

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Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10300, Thailand
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Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10300, Thailand
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Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10300, Thailand
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Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10300, Thailand
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Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10300, Thailand
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National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Phahonyothin Rd. Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
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Genome Center and Department of Plant Biology, UC Davis Genome Center, UC Davis, Davis, CA 95616, USA
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Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
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Author to whom correspondence should be addressed.
Genes 2020, 11(10), 1197; https://doi.org/10.3390/genes11101197
Received: 25 August 2020 / Revised: 9 October 2020 / Accepted: 9 October 2020 / Published: 14 October 2020
(This article belongs to the Special Issue Recent Advances in Genetics and Breeding of Major Staple Food Crops)
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 segment 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. View Full-Text
Keywords: CSSLs; drought stress; ‘KDML105’ rice; co-expression network CSSLs; drought stress; ‘KDML105’ rice; co-expression network
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MDPI and ACS Style

Punchkhon, C.; Plaimas, K.; Buaboocha, T.; Siangliw, J.L.; Toojinda, T.; Comai, L.; De Diego, N.; Spíchal, L.; Chadchawan, S. Drought-Tolerance Gene Identification Using Genome Comparison and Co-Expression Network Analysis of Chromosome Substitution Lines in Rice. Genes 2020, 11, 1197. https://doi.org/10.3390/genes11101197

AMA Style

Punchkhon C, Plaimas K, Buaboocha T, Siangliw JL, Toojinda T, Comai L, De Diego N, Spíchal L, Chadchawan S. Drought-Tolerance Gene Identification Using Genome Comparison and Co-Expression Network Analysis of Chromosome Substitution Lines in Rice. Genes. 2020; 11(10):1197. https://doi.org/10.3390/genes11101197

Chicago/Turabian Style

Punchkhon, Chutarat, Kitiporn Plaimas, Teerapong Buaboocha, Jonaliza L. Siangliw, Theerayut Toojinda, Luca Comai, Nuria De Diego, Lukáš Spíchal, and Supachitra Chadchawan. 2020. "Drought-Tolerance Gene Identification Using Genome Comparison and Co-Expression Network Analysis of Chromosome Substitution Lines in Rice" Genes 11, no. 10: 1197. https://doi.org/10.3390/genes11101197

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