Transcriptome profile reveals heat response mechanism at molecular and metabolic levels in rice flag leaf

• Time course microarray analysis of rice flag leaf under heat stress was carried out.
• Heat-responsive genes were identified and analyzed by HCL, KMC, GO, MapMan, etc.
• Genes from Hsf, Hsp, glycolysis and UPS were generally enhanced under heat.
• TCA, specific secondary metabolisms and light-reaction were repressed by heat stress.
• Heat response mode in rice flag leaf was postulated based on the expression patterns.

Flag leaf is one of the key photosynthesis organs during rice reproductive stage. A time course microarray analysis of rice flag leaf was done after 40 °C treatment for 0 min, 20 min, 60 min, 2 h, 4 h, and 8 h. The identified significant heat responsive genes were mainly involved in transcriptional regulation, transport, protein binding, antioxidant, and stress response. KMC analysis discovered the time-dependent gene expression pattern under heat. MapMan analysis demonstrated that, under heat treatment, Hsp genes and genes involved in glycolysis and ubiquitin-proteasome were enhanced, and genes involved in TCA, carotenoid, dihydroflavonol and anthocyanin metabolisms and light-reaction in the photosynthesis were widely repressed. Meanwhile, some rate-limiting enzyme genes in shikimate, lignin, and mevalonic acid metabolisms were up-regulated, revealing the importance of maintaining specific secondary metabolites under heat stress. The present study increased our understanding of heat response in rice flag leaf and provided good candidate genes for crop improvement.