AUTHOR=Sun Xiaochuan , Tang Mingjia , Xu Liang , Luo Xiaobo , Shang Yutong , Duan Weike , Huang Zhinan , Jin Cong , Chen Guodong 

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

JOURNAL=Frontiers in Genetics

VOLUME=Volume 14 - 2023

YEAR=2023

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2023.1232363

DOI=10.3389/fgene.2023.1232363

ISSN=1664-8021

ABSTRACT=Long non-coding RNAs (lncRNAs) are increasingly recognized as cis-and transacting 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, genome-wide identification of lncRNAs using strand-specific RNA sequencing (ssRNA-seq) was performed, from radish fleshy root samples subjected to varying time points of salinity treatment. A total of 7709 novel lncRNAs were identified, with 363 of them displaying significant differential expression in response to salt application. Furthermore, though target gene prediction, 5006 cis-and 5983 trans-target genes were obtained for the differentially expressed (DE)-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 (ROS) scavenging, photosynthesis, phytohormone regulation, and kinase activity. Notably, the current study represents the first comprehensive genome-wide analysis of salt-responsive lncRNAs in radish, as far as our knowledge extends. 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.