Combining Transcriptomics and Metabolomics to Uncover the Effects of High-Energy Lithium-Ion Beam Irradiation on Capsicum annuum L.

Hot pepper (Capsicum annuum L.) is consumed as one of the oldest domesticated crops all over the world. Although mutation breeding using radiation has been performed in hot peppers, little is known about the comparative analysis of mutagenic effects at the molecular level by ion beam irradiation. To comprehend the response mechanism of hot pepper to the ion beam, we used a mutant with favorable economic characteristics induced by lithium-ion beam irradiation to investigate the biological effects. The results indicated that the lithium-ion beam had a positive effect on important agronomic traits, particularly yield unit, but had a negligible effect on the photosynthetic rate of hot pepper, with a specific influence on chlorophyll b rather than chlorophyll a. By RNA-Seq analysis, 671 up-regulated and 376 down-regulated genes were identified as differentially expressed genes (DEGs) between irradiated and unirradiated hot pepper. Based on GO and KEGG network analysis, the auxin metabolic process was the common pathway in these two networks. A total of 118 potential reactive oxygen species (ROS) scavenging genes and 262 signal transduction genes were identified, suggesting a balance between antioxidant enzymes and enhanced ROS transduction. The amounts of 15 metabolite, involved in GABA pathways, secondary metabolism, carbohydrate metabolism, shikimate pathways, TCA cycles, nitrogen metabolism, glycerol metabolism and acetate pathways, were significantly changed in the ion beam irradiated sample. These results highlighted that the enriched pathways could play important roles in response to ion beam irradiation in hot pepper plants. In summary, these data provide valuable information for future research on ion beam irradiation and genomic studies in hot pepper.