Long non-coding RNA transcriptome landscape of anthers at different developmental stages in response to drought stress in tomato

Abstract

Pollen development is particularly susceptible to drought stress. Long non-coding RNAs (lncRNAs) are known to play a role in plant development and responses to drought stress. However, the expression profile and putative function of lncRNAs in drought-induced male sterility remain largely unknown. In this study, we investigated the lncRNA transcriptome landscape of tomato anthers at early and late stages—tetrad-vacuolated microspore (TED-VUM) and binucleate-mature pollen (BIN-MP) anthers, respectively—in response to drought stress using RNA-sequencing. In total, we identified 67,770 lncRNAs, of which 3053 lncRNAs were drought responsive. Interestingly, there were more differentially expressed (DE) lncRNAs in TED-VUM (2879) than in BIN-MP (174) anthers, which was consistent with the TED-VUM anthers being more drought sensitive. Functional enrichment analysis revealed that the target genes of DE lncRNAs were significantly enriched in diverse metabolic processes, including in carbohydrate metabolism and hormone synthesis. Co-expression analysis also identified 1407 lncRNAs that strongly co-expressed with 8 target genes that are involved in hormone (abscisic acid and jasmonic acid) and carbohydrate (sucrose and starch) metabolisms and tapetum development, highlighting the potential of lncRNA–target–gene modulation of anther development under drought stress. Our results serve as a baseline for future investigations of the potential function of lncRNAs in plant reproductive development under drought stress.