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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #360064
Research Project: Gene Discovery and Crop Design for Current and New Rice Management Practices and Market Opportunities

Location: Dale Bumpers National Rice Research Center

Title: Genome-wide identifcation and characterization of long non-coding RNAs responsive to Dickeya zeae in rice

Author
item LI, WENQI - Jiangsu Academy Agricultural Sciences
item Jia, Yulin
item WANG, FANQUAN - Jiangsu Academy Agricultural Sciences
item FEI, YUNYAN - Jiangsu Academy Agricultural Sciences
item FAN, FANGJUN - Jiangsu Academy Agricultural Sciences
item WANG, JUN - Jiangsu Academy Agricultural Sciences
item ZHU, JINYAN - Jiangsu Academy Agricultural Sciences
item XU, YANG - Jiangsu Academy Agricultural Sciences
item ZHONG, WELGONG - Jiangsu Academy Agricultural Sciences
item YANG, JIE - Jiangsu Academy Agricultural Sciences

Submitted to: RSC Advances
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/9/2018
Publication Date: 10/8/2018
Citation: Li, W., Jia, Y., Wang, F., Fei, Y., Fan, F., Wang, J., Zhu, J., Xu, Y., Zhong, W., Yang, J. 2018. Genome-wide identifcation and characterization of long non-coding RNAs responsive to Dickeya zeae in rice. RSC Advances. https://doi.org/10.1039/c8ra04993a.
DOI: https://doi.org/10.1039/c8ra04993a

Interpretive Summary: Rice foot rot disease caused by the bacterial pathogen Dickeya zeae is a destructive disease threatening rice yield and quality. Plant non-coding RNAs (lncRNAs) are known to be involved in plant stress response but their relationship to plant disease resistance is unknown. In the present study, whole transcriptome sequencing (RNAseq) was used to investigate the abundance of these plant non-coding RNAs in rice roots in response to infection by the bacterium. A total of 4,709 lncRNAs were identified of which 2,518 were up-regulated (increased) and 2,191 were down-regulated (decreased). Five of the increased lncRNAs were associated with genetic targets that are known stress response genes suggesting that these lncRNAs degrade the transcripts of target genes leading to effective disease resistance. These findings reveal new molecular mechanisms of plant innate defense response to a bacterial pathogen which may help in developing disease resistant rice varieties.

Technical Abstract: Plant long non-coding RNA (lncRNA) is a type of newly emerging epigenetic regulator playing a critical role in plant growth, development, and biotic stress responses. However, it is unknown whether lncRNAs are involved in resistance responses between rice and Dickeya zeae (D. zeae), a bacterial agent causing rice foot rot disease. In this study, RNA-seq was performed to uncover the co-expression regulating networks mediated by D. zeae responsive lncRNAs and their candidate target genes. Of the 4,709 lncRNAs identi'ed, 2,518 and 2,191 were up- and down-regulated in response to D. zeae infection, respectively. Expression changes of 17 selected lncRNAs and their predicted targets with a potential role in defense response were investigated by qPCR. The expression levels of lncRNAs were up-regulated while their cognate candidate target genes were down-regulated upon D. zeae infection. In addition, several lncRNAs were predicted to be target mimics of osa-miR396 and osa-miR156. These results suggest that lncRNAs might play a role in response to D. zeae infection by regulating the transcript levels of their targets and miRNAs in rice.