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Int. J. Mol. Sci. 2017, 18(9), 1975; doi:10.3390/ijms18091975

Complementary RNA-Sequencing Based Transcriptomics and iTRAQ Proteomics Reveal the Mechanism of the Alleviation of Quinclorac Stress by Salicylic Acid in Oryza sativa ssp. japonica

1
Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
2
Institute of Crop Science and Resource Conservation (INRES), Abiotic Stress Tolerance in Crops, University of Bonn, 53115 Bonn, Germany
3
Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
*
Authors to whom correspondence should be addressed.
Received: 9 July 2017 / Revised: 8 September 2017 / Accepted: 12 September 2017 / Published: 14 September 2017
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants 2017)
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Abstract

To uncover the alleviation mechanism of quinclorac stress by salicylic acid (SA), leaf samples of Oryza sativa ssp. Japonica under quinclorac stress with and without SA pre-treatment were analyzed for transcriptional and proteomic profiling to determine the differentially expressed genes (DEGs) and proteins (DEPs), respectively. Results showed that quinclorac stress altered the expression of 2207 DEGs (1427 up-regulated, 780 down-regulated) and 147 DEPs (98 down-regulated, 49 up-regulated). These genes and proteins were enriched in glutathione (GSH) metabolism, porphyrin and chlorophyll metabolism, the biosynthesis of secondary metabolites, glyoxylate and dicarboxylate metabolism, and so on. It also influenced apetala2- ethylene-responsive element binding protein (AP2-EREBP) family, myeloblastosis (MYB) family and WRKY family transcription factors. After SA pre-treatment, 697 genes and 124 proteins were differentially expressed. Pathway analysis showed similar enrichments in GSH, glyoxylate and dicarboxylate metabolism. Transcription factors were distributed in basic helix-loop-helix (bHLH), MYB, Tify and WRKY families. Quantitative real-time PCR results revealed that quinclorac stress induced the expression of glutathion reductase (GR) genes (OsGR2, OsGR3), which was further pronounced by SA pre-treatment. Quinclorac stress further mediated the accumulation of acetaldehyde in rice, while SA enhanced the expression of OsALDH2B5 and OsALDH7 to accelerate the metabolism of herbicide quinclorac for the protection of rice. Correlation analysis between transcriptome and proteomics demonstrated that, under quinclorac stress, correlated proteins/genes were mainly involved in the inhibition of intermediate steps in the biosynthesis of chlorophyll. Other interesting proteins/genes and pathways regulated by herbicide quinclorac and modulated by SA pre-treatment were also discussed, based on the transcriptome and proteomics results. View Full-Text
Keywords: Oryza sativa L.; quinclorac; salicylic acid; RNA sequencing; iTRAQ; differentially expressed genes (DEGs); differentially expressed proteins (DEPs); transcription factor Oryza sativa L.; quinclorac; salicylic acid; RNA sequencing; iTRAQ; differentially expressed genes (DEGs); differentially expressed proteins (DEPs); transcription factor
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Wang, J.; Islam, F.; Li, L.; Long, M.; Yang, C.; Jin, X.; Ali, B.; Mao, B.; Zhou, W. Complementary RNA-Sequencing Based Transcriptomics and iTRAQ Proteomics Reveal the Mechanism of the Alleviation of Quinclorac Stress by Salicylic Acid in Oryza sativa ssp. japonica. Int. J. Mol. Sci. 2017, 18, 1975.

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