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

Wenqi Li,Weigong Zhong,Fengquan Liu,Jun Wang,Fangjun Fan,Jie Yang,Yulin Jia,Jinyan Zhu,Fangquan Wang,Yang Xu

doi:10.3390/ijms20010222

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.

Highlights

Plant microRNAs are non-protein coding RNAs with 21–24 nucleotides
Through these efforts we demonstrated that a set of candidate miRNAs and relevant targets including miR396 and predicted target may play an important role in the defense responses to D. zeae
At 48 hpi, 26 miRNAs were up-regulated and 39 miRNAs were down-regulated (Figure 2B; Table S3). These results suggest that certain miRNAs were expressed at some time points after D. zeae infection in an incompatible interaction suggesting that they may play an important role during pathogen infection

Summary

Introduction

Plant microRNAs (miRNAs) are non-protein coding RNAs with 21–24 nucleotides (nt). Most recently, miRNAs were demonstrated to be a critical component of sophisticated plant defense system [1,2,3]. Plant immunity is involved in two tiers of defenses where the first tier is a pathogen-associated molecular pattern (PAMP) trigged immunity (PTI) [4,5]. The second tier of defense is often involved in pathogen effector-triggered immunity (ETI) mediated mostly by R proteins with leucine rich repeat and nucleotide binding site (NLR) [4,5]. It was predicted that targets of plant miRNAs can be NLR genes, or genes involved in PTI [2,3]. In Arabidopsis, bacterial flagellin flg22-induced miR393 promoted resistance response to virulent Pseudomonas syringae pv. Three bacterial flagellin flg22-induced miRNAs, miR160, miR398b and miR773 were shown to be involved in resistance responses via regulating PAMP-induced callose deposition in Arabidopsis [11,12].

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