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Genome-wide identification of long non-coding RNAs and their potential functions in radish response to salt stress

文献类型： 外文期刊

作者： Sun, Xiaochuan 1 ; Tang, Mingjia 2 ; Xu, Liang 3 ; Luo, Xiaobo 4 ; Shang, Yutong 4 ; Duan, Weike 1 ; Huang, Zhinan 1 ; Jin, Cong 1 ; Chen, Guodong 1 ;

作者机构： 1.Huaiyin Inst Technol, Sch Life Sci & Food Engn, Huaian, Peoples R China

2.Zhejiang Univ, Dept Hort, Hangzhou, Peoples R China

3.Nanjing Agr Univ, Coll Hort, Natl Key Lab Crop Genet & Germplasm Enhancement &, Key Lab Hort Crop Biol & Genet Improvement East Ch, Nanjing, Peoples R China

4.Guizhou Prov Acad Agr Sci, Guizhou Inst Biotechnol, Guiyang, Peoples R China

关键词： lncRNA; salt stress; Raphanus sativus L.; RNA-seq; target genes; Gene Ontology and pathway analyses

期刊名称：FRONTIERS IN GENETICS （ 影响因子：3.7； 五年影响因子：4.3 ）

ISSN：

年卷期： 2023 年 14 卷

页码：

收录情况： SCI

摘要： Long non-coding RNAs (lncRNAs) are increasingly recognized as cis- and trans-acting regulators of protein-coding genes in plants, particularly in response to abiotic stressors. Among these stressors, high soil salinity poses a significant challenge to crop productivity. Radish (Raphanus sativus L.) is a prominent root vegetable crop that exhibits moderate susceptibility to salt stress, particularly during the seedling stage. Nevertheless, the precise regulatory mechanisms through which lncRNAs contribute to salt response in radish remain largely unexplored. In this study, we performed genome-wide identification of lncRNAs using strand-specific RNA sequencing on radish fleshy root samples subjected to varying time points of salinity treatment. A total of 7,709 novel lncRNAs were identified, with 363 of them displaying significant differential expression in response to salt application. Furthermore, through target gene prediction, 5,006 cis- and 5,983 trans-target genes were obtained for the differentially expressed lncRNAs. The predicted target genes of these salt-responsive lncRNAs exhibited strong associations with various plant defense mechanisms, including signal perception and transduction, transcription regulation, ion homeostasis, osmoregulation, reactive oxygen species scavenging, photosynthesis, phytohormone regulation, and kinase activity. Notably, this study represents the first comprehensive genome-wide analysis of salt-responsive lncRNAs in radish, to the best of our knowledge. These findings provide a basis for future functional analysis of lncRNAs implicated in the defense response of radish against high salinity, which will aid in further understanding the regulatory mechanisms underlying radish response to salt stress.

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