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Open AccessArticle

Comparison between the Transcriptomes of ‘KDML105’ Rice and a Salt-Tolerant Chromosome Segment Substitution Line

1
Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10300, Thailand
2
Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
3
Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
4
Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10300, Thailand
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Rice Gene Discovery Unit, National Center for Genetic Engineering and Biotechnology, Kasetsart University, Kamphangsaen Campus, Nakhonpathom 73140, Thailand
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Department of Plant Biology, UC Davis Genome Center, UC Davis, Davis, CA 95616, USA
*
Author to whom correspondence should be addressed.
Genes 2019, 10(10), 742; https://doi.org/10.3390/genes10100742
Received: 7 August 2019 / Revised: 17 September 2019 / Accepted: 20 September 2019 / Published: 24 September 2019
(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)
‘KDML105’ rice, known as jasmine rice, is grown in northeast Thailand. The soil there has high salinity, which leads to low productivity. Chromosome substitution lines (CSSLs) with the ‘KDML105’ rice genetic background were evaluated for salt tolerance. CSSL18 showed the highest salt tolerance among the four lines tested. Based on a comparison between the CSSL18 and ‘KDML105’ transcriptomes, more than 27,000 genes were mapped onto the rice genome. Gene ontology enrichment of the significantly differentially expressed genes (DEGs) revealed that different mechanisms were involved in the salt stress responses between these lines. Biological process and molecular function enrichment analysis of the DEGs from both lines revealed differences in the two-component signal transduction system, involving LOC_Os04g23890, which encodes phototropin 2 (PHOT2), and LOC_Os07g44330, which encodes pyruvate dehydrogenase kinase (PDK), the enzyme that inhibits pyruvate dehydrogenase in respiration. OsPHOT2 expression was maintained in CSSL18 under salt stress, whereas it was significantly decreased in ‘KDML105’, suggesting OsPHOT2 signaling may be involved in salt tolerance in CSSL18. PDK expression was induced only in ‘KDML105’. These results suggested respiration was more inhibited in ‘KDML105’ than in CSSL18, and this may contribute to the higher salt susceptibility of ‘KDML105’ rice. Moreover, the DEGs between ‘KDML105’ and CSSL18 revealed the enrichment in transcription factors and signaling proteins located on salt-tolerant quantitative trait loci (QTLs) on chromosome 1. Two of them, OsIRO2 and OsMSR2, showed the potential to be involved in salt stress response, especially, OsMSR2, whose orthologous genes in Arabidopsis had the potential role in photosynthesis adaptation under salt stress. View Full-Text
Keywords: phototropin; pyruvate dehydrogenase kinase; two‐component signaling system phototropin; pyruvate dehydrogenase kinase; two‐component signaling system
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Khrueasan, N.; Chutimanukul, P.; Plaimas, K.; Buaboocha, T.; Siangliw, M.; Toojinda, T.; Comai, L.; Chadchawan, S. Comparison between the Transcriptomes of ‘KDML105’ Rice and a Salt-Tolerant Chromosome Segment Substitution Line. Genes 2019, 10, 742.

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