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Int J Mol Sci. 2019 Jan 8;20(1). pii: E222. doi: 10.3390/ijms20010222.

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

Li W1,2, Jia Y3, Liu F4, Wang F5,6, Fan F7,8, Wang J9,10, Zhu J11,12, Xu Y13,14, Zhong W15,16, Yang J17,18.

Author information

1
Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China. liwenqi@jaas.ac.cn.
2
Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China. liwenqi@jaas.ac.cn.
3
United States Department of Agriculture-Agriculture Research Service, Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA. yulin.jia@ars.usda.gov.
4
Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China. fqliu20011@sina.com.
5
Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China. qiezi324@163.com.
6
Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China. qiezi324@163.com.
7
Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China. weidadefan@sohu.com.
8
Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China. weidadefan@sohu.com.
9
Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China. wangjunjaas@aliyun.com.
10
Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China. wangjunjaas@aliyun.com.
11
Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China. zhujinyanrain@163.com.
12
Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China. zhujinyanrain@163.com.
13
Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China. linkinxy@163.com.
14
Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China. linkinxy@163.com.
15
Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China. wgzhong0503@139.com.
16
Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China. wgzhong0503@139.com.
17
Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China. yangjie@jaas.ac.cn.
18
Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China. yangjie@jaas.ac.cn.

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:

Dickeya zeae; RNA and degradome sequencing; disease resistance; microRNA; rice foot rot disease

PMID:
30626113
PMCID:
PMC6337123
DOI:
10.3390/ijms20010222
[Indexed for MEDLINE]
Free PMC Article

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