Physiological, Epigenetic, and Transcriptome Analyses Provide Insights into the Responses of Wheat Seedling Leaves to Different Water Depths under Flooding Conditions

Abstract

Flooding stress, including waterlogging and submergence, is one of the major abiotic stresses that seriously affects the growth and development of plants. In the present study, physiological, epigenetic, and transcriptomic analyses were performed in wheat seedling leaves under waterlogging (WL), half submergence (HS), and full submergence (FS) treatments. The results demonstrate that FS increased the leaves’ hydrogen peroxide (H2O2) and malondialdehyde (MDA) contents and reduced their chlorophyll contents (SPAD), photosynthetic efficiency (Fv/Fm), and shoot dry weight more than HS and WL. In addition, FS increased catalase (CAT) and peroxidase (POD) activities more than HS and WL. However, there were no significant differences in the contents of H2O2, MDA, SPAD, and Fv/Fm, and the activities of superoxide dismutase (SOD) and POD between the HS and WL treatments. The changes in DNA methylation were related to stress types, increasing under the WL and HS treatments and decreasing under the FS treatment. Additionally, a total of 9996, 10,619, and 24,949 genes were differentially expressed under the WL, HS, and FS treatments, respectively, among which the ‘photosynthesis’, ‘phenylpropanoid biosynthesis’, and ‘plant hormone signal transduction’ pathways were extensively enriched under the three flooding treatments. The genes involved in these pathways showed flooding-type-specific expression. Moreover, flooding-type-specific responses were observed in the three conditions, including the enrichment of specific TFs and response pathways. These results will contribute to a better understanding of the molecular mechanisms underlying the responses of wheat seedling leaves to flooding stress and provide valuable genetic and epigenetic information for breeding flood-tolerant varieties of wheat.

Transcriptomic analysis reveals the regulatory mechanisms of messenger RNA (mRNA) and long non-coding RNA (lncRNA) in response to waterlogging stress in rye (Secale cereale L.)

“…This finding suggests that the U-box domain may also contribute to the ethylene signaling pathway by regulating early responses to WS. Studies conducted by Li et al [ 40 ] and Yu et al [ 6 ] on maize and wheat identified several upregulated TFs involved in flooding stress, including bHLH, NAC, MYB-related, WRKY, C2H2, and AP2/ERF. Interestingly, these results are not consistent with the findings of our present study.…”

“…These findings suggest that under WS, lncRNAs induce interconnected responses that involves lipid breakdown, ROS detoxification, and hormone signaling in rye. A study by Li et al [ 40 ] revealed that various pathways, including flavonoid biosynthesis, biosynthesis of secondary metabolites, taurine and hypotaurine metabolism, cutin, suberine and wax biosynthesis, and glutathione metabolism, were significantly enriched by DEGs under different flooding conditions. In line with these findings, our study also showed enrichment of upregulated DE-mRNAs in these pathways (Fig.…”

The Changes of Amino-Acid Metabolism between Wheat and Rice during Early Growth under Flooding Stress

“…In wheat, DNA demethylation significantly increases waterloggingrelated gene expression in tolerant genotypes under hypoxic stress [21]. Both waterlogging and half submergence increase the total DNA methylation level, but this is decreased under full submergence in wheat [22]. However, the potential mechanisms of epigenetic regulation under flooding stress remain largely unknown in rice and wheat.…”