Comprehensive gene expression analysis of submergence stress response in nucleus-cytoplasm hybrid wheat

Submergence and waterlogging stresses inhibit wheat growth and cause yield loss by affecting photosynthesis, respiration, and transpiration through changing antioxidant systems and reducing accumulation and remobilization of photosynthetic products. Nucleus-cytoplasm (NC) interactions have been shown to affect sensitivity to submergence stress in wheat. We performed RNA-seq analysis of genes that show differential expression in response to submergence stress imposed during imbibition and germination of wheat seeds. W employed NC hybrids with low (T-type plasmon) and high (U-type plasmon) sensitivity and their wheat nuclear donor cv. CS. In addition, gene ontology (GO) enrichment analysis was performed on differentially expressed genes (DEGs) to estimate their transcriptional characteristics. Among DEGs down-regulated by submergence stress, ones with GO terms such as “response to oxygen-containing compound”, “response to acid chemical” and “response to jasmonic acid” were significantly enriched in all lines. On the other hand, GO terms “related to cell wall” were highly enriched in genes up-regulated in NC hybrid with U-type plasmon. Our results revealed comprehensive gene expression patterns induced under submergence stress in what. It was also suggested that the expressions of different groups of genes were differentially regulated depending on different cytoplasm types in response to submergence stress in wheat.