Comparative transcriptome analysis of two common wheat varieties induced by 7Li-ion beam irradiation reveals mutation hotspot regions and associated pathways

Abstract

Heavy-ion beam irradiation is an effective approach for mutation breeding. Understanding the damage effects and molecular variation induced by mutagenesis is of great significance for improving mutation breeding efficiency. The molecular changes induced by 7Li-ion beam irradiation in wheat have been scarcely reported. In this study, we compared the biological damage effects of different doses of 7Li-ion beam irradiation on the M1 seedlings of two wheat varieties with different γ irradiation sensitivities, Jing411 and Heyou1, and found that doses of 25, 50, 75 and 100 Gy significantly decreased the germination rate and seedling height. Moreover, transcriptome sequencing of three biological replicates of each irradiated sample and unirradiated control revealed that more single-nucleotide variants (SNVs) than small insertions and deletions (indels) were induced by various doses of 7Li-ion beam irradiation in both varieties. Substantially elevated frequencies of mutations relative to gene density were observed on 0–10 Mb of chromosome 1A, 80–90 Mb of chromosome 1B, 720–730 Mb of chromosome 2B, 280–290 Mb of chromosome 3B, 580–590 Mb of chromosome 3D, and 150–160 Mb of chromosome 5D, indicating that mutation hotspots existed in these regions. In addition, KEGG enrichment analysis of differentially expressed genes (DEGs) between control and irradiated wheat revealed pathways significantly enriched in both Jing411 and Heyou1, including “Phenylpropanoid biosynthesis”, “Phenylalanine metabolism” and “Photosynthesis-antenna proteins”. These pathways may play key roles in the response to 7Li-ion beam irradiation. The analysis of genes commonly upregulated under various doses of irradiation indicated that genes involved in antioxidant processes are active in the response to 7Li-ion beam irradiation. This transcriptome dataset provides a valuable public information platform for investigating the transcriptome sequence variation induced by 7Li-ion beam-induced mutagenesis and offers a basis for crop mutation breeding.