Journal Article

LncRNA regulates tomato fruit cracking by coordinating gene expression via a hormone-redox-cell wall network

Yu, Qinghui, Xue, Lingzi, Wu, Zhen, Sun, Mintao, Tang, Yaping, Jiang, Fangling, Yu, Lu

2020

Overview

Background Fruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanisms and regulatory networks that respond to abiotic stress, which involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. Fruit cracking is also a physiological disease caused by abiotic stress. It has been reported that a single or several genes may regulate fruit cracking. However, almost none of these reports have involved cracking regulatory networks. Results Here, RNA expression in 0 h, 8 h and 30 h saturated irrigation-treated fruits from two contrasting tomato genotypes, ‘LA1698’ (cracking-resistant, CR) and ‘LA2683’ (cracking-susceptible, CS), was analysed by mRNA and lncRNA sequencing. The GO pathways of the differentially expressed mRNAs were mainly enriched in the ‘hormone metabolic process’, ‘cell wall organization’, ‘oxidoreductase activity’ and ‘catalytic activity’ categories. According to the gene expression analysis, significantly differentially expressed genes included Solyc02g080530.3 ( Peroxide, POD ), Solyc01g008710.3 ( Mannan endo-1,4-beta-mannosidase, MAN ), Solyc08g077910.3 ( Expanded, EXP ), Solyc09g075330.3 ( Pectinesterase, PE ), Solyc07g055990.3 ( Xyloglucan endotransglucosylase-hydrolase 7, XTH7 ), Solyc12g011030.2 ( Xyloglucan endotransglucosylase-hydrolase 9, XTH9 ), Solyc10g080210.2 ( Polygalacturonase-2, PG2 ), Solyc08g081010.2 ( Gamma-glutamylcysteine synthetase, gamma-GCS ), Solyc09g008720.2 ( Ethylene receptor, ER ), Solyc11g042560.2 ( Ethylene-responsive transcription factor 4, ERF4 ) etc. In addition, the lncRNAs (XLOC_16662 and XLOC_033910, etc) regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing tomato cracking. Conclusions This study provides insight into the responsive network for water-induced cracking in tomato fruit. Specifically, lncRNAs regulate the hormone-redox-cell wall network, including plant hormone (auxin, ethylene) and ROS (H 2 O 2 ) signal transduction and many cell wall-related mRNAs ( EXP, PG, XTH ), as well as some lncRNAs (XLOC_16662 and XLOC_033910, etc.).

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Abiotic stress / Agriculture / Analysis / Anopheles / auxins / Biomedical and Life Sciences / Catalytic activity / Cell walls / Cellular signal transduction / Crop production / Environmental conditions / Enzymes / Ethylene / Ethylenes - metabolism / Fruit - genetics / Fruit - physiology / Fruit cracking / Fruits / Gene expression / gene expression regulation / Gene Expression Regulation, Plant / Gene sequencing / Genes / Genomics and evolution / Genotypes / glutamate-cysteine ligase / Glycosyltransferases - metabolism / Hormones / Hydrogen peroxide / Hydrolase / Hydrolases / Indoleacetic Acids - metabolism / Irrigation / Life Sciences / Ligases / LncRNA / Mannan / Mannosidase / Metabolism / Metabolites / mRNA / Network / Oxidation-Reduction / Oxidoreductase / Pectinesterase / Physiological aspects / Plant hormones / Plant Sciences / Polygalacturonase / Proteins / Research Article / RNA / RNA, Long Noncoding - genetics / RNA, Long Noncoding - physiology / RNA, Messenger - metabolism / Signal transduction / Solanum lycopersicum - genetics / Solanum lycopersicum - physiology / Stress, Physiological - genetics / Tomato / Tomatoes / transcription factors / Transcriptome / Tree Biology / Trends / Xyloglucan / xyloglucans / γ-Glutamylcysteine