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Genome-wide identification of microRNAs and phased siRNAs in soybean roots under long-term salt stress

Genes & Genomics 2020년 42권 11호 p.1239 ~ 1249
Wang Qian, Yang Yingxia, Lu Guoqing, Sun Xianjun, Feng Youren, Yan Shuangyong, Zhang Huiyuan, Jiang Qiyan, Zhang Hui, Hu Zheng, Chen Rui,
소속 상세정보
 ( Wang Qian ) - Tianjin Academy of Agricultural Sciences Biotechnology Research Institute
 ( Yang Yingxia ) - Tianjin Academy of Agricultural Sciences Biotechnology Research Institute
 ( Lu Guoqing ) - Tianjin Academy of Agricultural Sciences Biotechnology Research Institute
 ( Sun Xianjun ) - Chinese Academy of Agricultural Sciences Institute of Crop Sciences
 ( Feng Youren ) - Tianjin Academy of Agricultural Sciences
 ( Yan Shuangyong ) - Tianjin Academy of Agricultural Sciences Tianjin Crop Research Institute
 ( Zhang Huiyuan ) - Chinese Academy of Agricultural Sciences Institute of Crop Sciences
 ( Jiang Qiyan ) - Chinese Academy of Agricultural Sciences Institute of Crop Sciences
 ( Zhang Hui ) - Chinese Academy of Agricultural Sciences Institute of Crop Sciences
 ( Hu Zheng ) - Chinese Academy of Agricultural Sciences Institute of Crop Sciences
 ( Chen Rui ) - Tianjin Academy of Agricultural Sciences Biotechnology Research Institute

Abstract


Background: Salinity stress, as the key limiting factor for agricultural productivity, can activate a series of molecular responses and alter gene expression in plants. Endogenous regulatory small RNAs, such as microRNAs (miRNAs) and phased siRNAs (phasiRNAs), play crucial roles during stress adaptation and prevent the injury from environmental circumstances.

Objective: To identify long-term salt stress responsive miRNAs and phasiRNAs as well as their associated genes and pathways in soybean roots.

Methods: Small RNA and degradome sequencing strategies were applied to genome widely investigate miRNAs and phasiRNAs in soybean roots under control and long-term salt stress conditions.

Results: In this study, stringent bioinformatic analysis led to the identification of 253 conserved and 38 novel miRNA candidates. Results of expression profiling, target and endogenous target mimics predictions provided valuable clues to their functional roles. Furthermore, 156 genes were identified to be capable of generating 21 nt and 24 nt phasiRNAs, in which 37 candidates were confirmed by degradome data for miRNA-directed cleavage. Approximately 90% of these phasiRNA loci were protein coding genes. And GO enrichment analysis pointed to “signal transduction” and “ADP binding” entries and reflected the functional roles of identified phasiRNA genes.

Conclusion: Taken together, our findings extended the knowledge of salt responsive miRNAs and phasiRNAs in soybean roots, and provided valuable information for a better understanding of the regulatory events caused by small RNAs underlying plant adaptations to long-term salt stress.

키워드

Long-term salt stress; Soybean roots; MicroRNA; Phased siRNA; Endogenous target mimicry

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