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Drought Response in Rice: The miRNA Story
Article

Genome-Wide Transcriptome Analysis of Rice Seedlings after Seed Dressing with Paenibacillus yonginensis DCY84T and Silicon

1
Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
2
Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin 17104, Korea
*
Author to whom correspondence should be addressed.
These authors contributed equally to this research.
Int. J. Mol. Sci. 2019, 20(23), 5883; https://doi.org/10.3390/ijms20235883
Received: 16 October 2019 / Revised: 19 November 2019 / Accepted: 19 November 2019 / Published: 23 November 2019
(This article belongs to the Special Issue Underground Mechanism to Enhance Stress Tolerance in Rice)
Plant-growth-promoting bacteria (PGPB) are beneficial microorganisms that can also protect against disease and environmental stress. Silicon (Si) is the second most abundant element in soil, and is known to increase plant growth, grain yield, resistance to biotic stress, and tolerance to abiotic stress. Combined treatment of PGPB and Si has been shown to further enhance plant growth and crop yield. To determine the global effects of the PGPB and Si on rice growth, we compared rice plants treated with Paenibacillus yonginensis DCY84T (DCY84T) and Si with untreated rice. To identify the genes that respond to DCY84T+Si treatment in rice, we performed an RNA-Seq transcriptome analysis by sampling treated and untreated roots on a weekly basis for three weeks. Overall, 576 genes were upregulated, and 394 genes were downregulated in treated roots, using threshold fold-changes of at least 2 (log2) and p-values < 0.05. Gene ontology analysis showed that phenylpropanoids and the L-phenylalanine metabolic process were prominent in the upregulated genes. In a metabolic overview analysis using the MapMan toolkit, pathways involving phenylpropanoids and ethylene were strongly associated with upregulated genes. The functions of seven upregulated genes were identified as being associated with drought stress through a literature search, and a stress experiment confirmed that plants treated with DCY84T+Si exhibited greater drought tolerance than the untreated control plants. Furthermore, the predicted protein–protein interaction network analysis associated with DCY84T+ Si suggests mechanisms underlying growth promotion and stress tolerance. View Full-Text
Keywords: Paenibacillus yonginensis DCY84T; PGPB; RNA-Seq; Root; silicon; rice; drought stress Paenibacillus yonginensis DCY84T; PGPB; RNA-Seq; Root; silicon; rice; drought stress
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MDPI and ACS Style

Yoo, Y.-H.; Kim, M.; Chandran, A.K.N.; Hong, W.-J.; Ahn, H.R.; Lee, G.T.; Kang, S.; Suh, D.; Kim, J.-O.; Kim, Y.-J.; Jung, K.-H. Genome-Wide Transcriptome Analysis of Rice Seedlings after Seed Dressing with Paenibacillus yonginensis DCY84T and Silicon. Int. J. Mol. Sci. 2019, 20, 5883. https://doi.org/10.3390/ijms20235883

AMA Style

Yoo Y-H, Kim M, Chandran AKN, Hong W-J, Ahn HR, Lee GT, Kang S, Suh D, Kim J-O, Kim Y-J, Jung K-H. Genome-Wide Transcriptome Analysis of Rice Seedlings after Seed Dressing with Paenibacillus yonginensis DCY84T and Silicon. International Journal of Molecular Sciences. 2019; 20(23):5883. https://doi.org/10.3390/ijms20235883

Chicago/Turabian Style

Yoo, Yo-Han, Minjae Kim, Anil K.N. Chandran, Woo-Jong Hong, Hye R. Ahn, Gang T. Lee, Sungju Kang, Dabin Suh, Jin-O Kim, Yeon-Ju Kim, and Ki-Hong Jung. 2019. "Genome-Wide Transcriptome Analysis of Rice Seedlings after Seed Dressing with Paenibacillus yonginensis DCY84T and Silicon" International Journal of Molecular Sciences 20, no. 23: 5883. https://doi.org/10.3390/ijms20235883

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