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Autotoxicity mechanism of Oryza sativa: transcriptome response in rice roots exposed to ferulic acid.

Chi WC, Chen YA, Hsiung YC, Fu SF, Chou CH, Trinh NN, Chen YC, Huang HJ - BMC Genomics (2013)

Bottom Line: Genes associated with signaling and biosynthesis for ethylene and jasmonic acid were upregulated with ferulic acid.The results of a transcriptome analysis suggest the molecular mechanisms of plants in response to FA, including toxicity, detoxicification and signaling machinery.FA may have a significant effect on inhibiting rice root elongation through modulating ET and JA hormone homeostasis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Life Sciences, National Cheng Kung University, No, 1 University Rd, 701, Tainan, Taiwan, ROC. haojen@mail.ncku.edu.tw.

ABSTRACT

Background: Autotoxicity plays an important role in regulating crop yield and quality. To help characterize the autotoxicity mechanism of rice, we performed a large-scale, transcriptomic analysis of the rice root response to ferulic acid, an autotoxin from rice straw.

Results: Root growth rate was decreased and reactive oxygen species, calcium content and lipoxygenase activity were increased with increasing ferulic acid concentration in roots. Transcriptome analysis revealed more transcripts responsive to short ferulic-acid exposure (1- and 3-h treatments, 1,204 genes) than long exposure (24 h, 176 genes). Induced genes were involved in cell wall formation, chemical detoxification, secondary metabolism, signal transduction, and abiotic stress response. Genes associated with signaling and biosynthesis for ethylene and jasmonic acid were upregulated with ferulic acid. Ferulic acid upregulated ATP-binding cassette and amino acid/auxin permease transporters as well as genes encoding signaling components such as leucine-rich repeat VIII and receptor-like cytoplasmic kinases VII protein kinases, APETALA2/ethylene response factor, WRKY, MYB and Zinc-finger protein expressed in inflorescence meristem transcription factors.

Conclusions: The results of a transcriptome analysis suggest the molecular mechanisms of plants in response to FA, including toxicity, detoxicification and signaling machinery. FA may have a significant effect on inhibiting rice root elongation through modulating ET and JA hormone homeostasis. FA-induced gene expression of AAAP transporters may contribute to detoxicification of the autotoxin. Moreover, the WRKY and Myb TFs and LRR-VIII and SD-2b kinases might regulate downstream genes under FA stress but not general allelochemical stress. This comprehensive description of gene expression information could greatly facilitate our understanding of the mechanisms of autotoxicity in plants.

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Genes up- or down-regulated by FA stress. MapMan was used to visualize the detoxification enzyme (A), transporter (B), and phytohormone (C) genes. Each BIN or subBIN is represented as a block, within which upregulated transcripts are displayed as red squares and downregulated transcripts as blue squares. Functional bins identified by the Wilcoxon rank sum statistic as being significantly changed by FA are outlined in blue.
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Figure 2: Genes up- or down-regulated by FA stress. MapMan was used to visualize the detoxification enzyme (A), transporter (B), and phytohormone (C) genes. Each BIN or subBIN is represented as a block, within which upregulated transcripts are displayed as red squares and downregulated transcripts as blue squares. Functional bins identified by the Wilcoxon rank sum statistic as being significantly changed by FA are outlined in blue.

Mentions: These observations were further supported by comparison of metabolism genes with use of MapMan. The genes encoding enzymes related to detoxification were cytochrome P450, UDP glycosyltransferases, and glutathione-S-transferases (FigureĀ 2A). RT-PCR validated the microarray findings (Additional file 6: Figure S4).


Autotoxicity mechanism of Oryza sativa: transcriptome response in rice roots exposed to ferulic acid.

Chi WC, Chen YA, Hsiung YC, Fu SF, Chou CH, Trinh NN, Chen YC, Huang HJ - BMC Genomics (2013)

Genes up- or down-regulated by FA stress. MapMan was used to visualize the detoxification enzyme (A), transporter (B), and phytohormone (C) genes. Each BIN or subBIN is represented as a block, within which upregulated transcripts are displayed as red squares and downregulated transcripts as blue squares. Functional bins identified by the Wilcoxon rank sum statistic as being significantly changed by FA are outlined in blue.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4008027&req=5

Figure 2: Genes up- or down-regulated by FA stress. MapMan was used to visualize the detoxification enzyme (A), transporter (B), and phytohormone (C) genes. Each BIN or subBIN is represented as a block, within which upregulated transcripts are displayed as red squares and downregulated transcripts as blue squares. Functional bins identified by the Wilcoxon rank sum statistic as being significantly changed by FA are outlined in blue.
Mentions: These observations were further supported by comparison of metabolism genes with use of MapMan. The genes encoding enzymes related to detoxification were cytochrome P450, UDP glycosyltransferases, and glutathione-S-transferases (FigureĀ 2A). RT-PCR validated the microarray findings (Additional file 6: Figure S4).

Bottom Line: Genes associated with signaling and biosynthesis for ethylene and jasmonic acid were upregulated with ferulic acid.The results of a transcriptome analysis suggest the molecular mechanisms of plants in response to FA, including toxicity, detoxicification and signaling machinery.FA may have a significant effect on inhibiting rice root elongation through modulating ET and JA hormone homeostasis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Life Sciences, National Cheng Kung University, No, 1 University Rd, 701, Tainan, Taiwan, ROC. haojen@mail.ncku.edu.tw.

ABSTRACT

Background: Autotoxicity plays an important role in regulating crop yield and quality. To help characterize the autotoxicity mechanism of rice, we performed a large-scale, transcriptomic analysis of the rice root response to ferulic acid, an autotoxin from rice straw.

Results: Root growth rate was decreased and reactive oxygen species, calcium content and lipoxygenase activity were increased with increasing ferulic acid concentration in roots. Transcriptome analysis revealed more transcripts responsive to short ferulic-acid exposure (1- and 3-h treatments, 1,204 genes) than long exposure (24 h, 176 genes). Induced genes were involved in cell wall formation, chemical detoxification, secondary metabolism, signal transduction, and abiotic stress response. Genes associated with signaling and biosynthesis for ethylene and jasmonic acid were upregulated with ferulic acid. Ferulic acid upregulated ATP-binding cassette and amino acid/auxin permease transporters as well as genes encoding signaling components such as leucine-rich repeat VIII and receptor-like cytoplasmic kinases VII protein kinases, APETALA2/ethylene response factor, WRKY, MYB and Zinc-finger protein expressed in inflorescence meristem transcription factors.

Conclusions: The results of a transcriptome analysis suggest the molecular mechanisms of plants in response to FA, including toxicity, detoxicification and signaling machinery. FA may have a significant effect on inhibiting rice root elongation through modulating ET and JA hormone homeostasis. FA-induced gene expression of AAAP transporters may contribute to detoxicification of the autotoxin. Moreover, the WRKY and Myb TFs and LRR-VIII and SD-2b kinases might regulate downstream genes under FA stress but not general allelochemical stress. This comprehensive description of gene expression information could greatly facilitate our understanding of the mechanisms of autotoxicity in plants.

Show MeSH
Related in: MedlinePlus