2.1.3. LT-Responsive Genes

The identification of LT-responsive genes was not the main objective of this study, but associations between cold- and heat-stress signaling through calcium signaling, ROS signaling, and protein degradation have been reported [18–20], and changes in DNA methylation were also shown to be involved in heat tolerance [21]. In addition, we wanted to examine the possible association between LT treatment and the warming response. We identified 5205 LT-responsive genes, for which more genes were upregulated in Kenshin and downregulated in Chiifu (Figure 4; Table S5), implying that Kenshin is more sensitive to LT exposure than Chiifu. Many GO categories were identified as enriched among upregulated genes in both lines, including "response to cold", "response to stress", and "lipid transport and metabolic process". Although similar GO categories were enriched among LT-responsive genes and genes in the two categories mentioned above (warming and minor warming), the expression *Int. J. Mol. Sci.*  of warming- and minor warming-responsive genes might not be influenced by LT treatment (Table S5). **2018**, *19*, x FOR PEER REVIEW 6 of 22

**Figure 4.** Analysis of LT-responsive genes from two contrasting inbred lines, Chiifu and Kenshin. (**A**) Venn diagram of DEGs with over 2-fold differences in expression; a–h indicate the groups of genes in each category; (**B**) Heatmap of DEGs in each group based on fold change; (**C**) GO enrichment analysis of DEGs in each group, with *p* values obtained using the agriGO tool (http://bioinfo.cau.edu.cn/agriGO/index.php). C and K of figure 4B indicate Chiifu and Kenshin, **Figure 4.** Analysis of LT-responsive genes from two contrasting inbred lines, Chiifu and Kenshin. (**A**) Venn diagram of DEGs with over 2-fold differences in expression; a–h indicate the groups of genes in each category; (**B**) Heatmap of DEGs in each group based on fold change; (**C**) GO enrichment analysis of DEGs in each group, with *p* values obtained using the agriGO tool (http://bioinfo.cau.edu. cn/agriGO/index.php). C and K of Figure 4B indicate Chiifu and Kenshin, respectively.
