3.11 BPH infestation affected m6A modification of genes involved in growth-related phytohormones pathways
The overall m6A methylation position in rice was significantly attenuated by the BPH treatment (Figure 1f,g; Supporting Information: S4). However, the defense-related pathways were activated by BPH infestation which was accompanied by a large proportion of upregulated transcripts and m6A methylation sites (Figure 4, 5; Table S11, S15). Plant defense against herbivores is costly and is often associated with growth repression (Deng et al., 2020). We then explored m6A modification and transcriptional regulation of genes involved in plant growth-related phytohormones pathways especially auxin and gibberellin (GA).
Among the selected 32 genes containing m6A modification sites, 11 up- and 79 down-directed m6A modification positions were present in BPH-infested plants compared with those in the un-infected plants. A total of 27 genes were found to have down-directed m6A sites, among which 26 genes showed down-trending m6A methylation; that is, the number of down-directed m6A sites was higher than up-directed m6A sites (Supporting Information: Table S20). For transcriptome regulation, 27 of these 32 transcripts were significantly downregulated in BPH-infested plants, 25 of which displayed down-trending m6A methylation (Figure 6a-d, Supporting Information: Table S20-S22). This indicated a positive correlation between m6A modifications and the expression of key genes responsible for rice growth. In contrast, for the GA metabolic process, three of the five candidate genes were upregulated in the BPH-infested group. There were 9 up- and 5 down-directed m6A modification positions in the BPH-infected plants compared to those in the un-infected plants. m6A modifications and gene expression were also positively correlated (Figure 6e, Supporting Information: Table S20, S22). The m6A modification levels of auxin pathway- and GA biosynthesis-related genes were significantly attenuated under BPH attack. This was accompanied by the downregulated expression of these transcripts. Meanwhile, m6A modification was involved in the activation of GA catabolism-related genes. Thus, rice growth was restricted during BPH attack to optimize resource allocation for plant defense though affecting m6A modification of genes involved in defense- and growth-related phytohormones pathways.