Involvement of long non-coding RNAs in selenium-mediated alleviation of cadmium stress by regulating antioxidant system in pepper

The prevalent heavy metal pollutant cadmium (Cd) threatens agricultural safety and public health. Although selenium (Se) can alleviate Cd phytotoxicity, the role of lncRNA-mediated regulatory networks in this process remains poorly understood in pepper (Capsicum annuum L.). Here, we demonstrate that Se application alleviates Cd-induced growth inhibition in pepper by reducing Cd accumulation across tissues while increasing Se content. Moreover, Se supplementation enhanced the activities of antioxidant enzymes (SOD, CAT, APX, GR) and the GSH content. Cd downregulated the transcript levels of CAT, GR, and GPX, whereas Se co-application restored GR and GPX transcripts and upregulated CAT, thereby alleviating Cd-induced oxidative damage and improving plant growth parameters. Through transcriptome profiling, we identified 14,391 lncRNAs characterized by fewer exons, shorter transcripts, and shorter open reading frames (ORFs). Among these, the key 517 differentially expressed lncRNAs (DELs) were identified, with the putative target genes enriched in carbon metabolism, glycolysis, and amino acid metabolism. Notably, three lncRNAs (MSTRG.44999.1, MSTRG.34872.1, and MSTRG.39896.2) were upregulated under Cd stress but downregulated upon Se supplementation, exhibiting expression patterns consistent with their putative target genes (MGL, BCAT2, TPRA, PFK5, UGT86A1, ENO, and GLO). Conversely, MSTRG.11441.1 and its putative target gene SGAT showed opposite trends. These candidate DELs and their putative target genes participate in interconnected metabolic modules, including glycolysis, amino acid metabolism, and the glyoxylate and dicarboxylate pathway. Our findings support a tentative model where exogenous Se alleviates Cd toxicity by modulating specific candidate lncRNA-mRNA pairs that potentially regulate these pathways, thereby enhancing antioxidant capacity. These findings not only reveal critical lncRNA-mediated mechanisms of Se in Cd detoxification in pepper but also provide potential molecular targets for breeding or engineering crops with improved resilience to heavy metal stress.