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Article

Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant Rice

by
Wenqi Li
1,2,
Yulin Jia
3,
Fengquan Liu
4,
Fangquan Wang
1,2,
Fangjun Fan
1,2,
Jun Wang
1,2,
Jinyan Zhu
1,2,
Yang Xu
1,2,
Weigong Zhong
1,2 and
Jie Yang
1,2,*
1
Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China
2
Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
3
United States Department of Agriculture-Agriculture Research Service, Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA
4
Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(1), 222; https://doi.org/10.3390/ijms20010222
Submission received: 28 November 2018 / Revised: 26 December 2018 / Accepted: 31 December 2018 / Published: 8 January 2019
(This article belongs to the Section Molecular Plant Sciences)
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Abstract

Rice foot rot disease caused by the pathogen Dickeya zeae (formerly known as Erwinia chrysanthemi pv. zeae), is a newly emerging damaging bacterial disease in China and the southeast of Asia, resulting in the loss of yield and grain quality. However, the genetic resistance mechanisms mediated by miRNAs to D. zeae are unclear in rice. In the present study, 652 miRNAs including osa-miR396f predicted to be involved in multiple defense responses to D. zeae were identified with RNA sequencing. A total of 79 differentially expressed miRNAs were detected under the criterion of normalized reads ≥10, including 51 known and 28 novel miRNAs. Degradome sequencing identified 799 targets predicted to be cleaved by 168 identified miRNAs. Among them, 29 differentially expressed miRNA and target pairs including miRNA396f-OsGRFs were identified by co-expression analysis. Overexpression of the osa-miR396f precursor in a susceptible rice variety showed enhanced resistance to D. zeae, coupled with significant accumulation of transcripts of osa-miR396f and reduction of its target the Growth-Regulating Factors (OsGRFs). Taken together, these findings suggest that miRNA and targets including miR396f-OsGRFs have a role in resisting the infections by bacteria D. zeae.
Keywords: rice foot rot disease; Dickeya zeae; microRNA; RNA and degradome sequencing; disease resistance rice foot rot disease; Dickeya zeae; microRNA; RNA and degradome sequencing; disease resistance

Share and Cite

MDPI and ACS Style

Li, W.; Jia, Y.; Liu, F.; Wang, F.; Fan, F.; Wang, J.; Zhu, J.; Xu, Y.; Zhong, W.; Yang, J. Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant Rice. Int. J. Mol. Sci. 2019, 20, 222. https://doi.org/10.3390/ijms20010222

AMA Style

Li W, Jia Y, Liu F, Wang F, Fan F, Wang J, Zhu J, Xu Y, Zhong W, Yang J. Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant Rice. International Journal of Molecular Sciences. 2019; 20(1):222. https://doi.org/10.3390/ijms20010222

Chicago/Turabian Style

Li, Wenqi, Yulin Jia, Fengquan Liu, Fangquan Wang, Fangjun Fan, Jun Wang, Jinyan Zhu, Yang Xu, Weigong Zhong, and Jie Yang. 2019. "Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant Rice" International Journal of Molecular Sciences 20, no. 1: 222. https://doi.org/10.3390/ijms20010222

APA Style

Li, W., Jia, Y., Liu, F., Wang, F., Fan, F., Wang, J., Zhu, J., Xu, Y., Zhong, W., & Yang, J. (2019). Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant Rice. International Journal of Molecular Sciences, 20(1), 222. https://doi.org/10.3390/ijms20010222

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