Expression of root-related transcription factors associated with flooding tolerance of soybean (Glycine max)

Abstract

Much research has been conducted on the changes in gene expression of the model plant Arabidopsis to low-oxygen stress. Flooding results in a low oxygen environment in the root zone. However, there is ample evidence that tolerance to soil flooding is more than tolerance to low oxygen alone. In this study, we investigated the physiological response and differential expression of root-related transcription factors (TFs) associated with the tolerance of soybean plants to soil flooding. Differential responses of PI408105A and S99-2281 plants to ten days of soil flooding were evaluated at physiological, morphological and anatomical levels. Gene expression underlying the tolerance response was investigated using qRT-PCR of root-related TFs, known anaerobic genes, and housekeeping genes. Biomass of flood-sensitive S99-2281 roots remained unchanged during the entire 10 days of flooding. Flood-tolerant PI408105A plants exhibited recovery of root growth after 3 days of flooding. Flooding induced the development of aerenchyma and adventitious roots more rapidly in the flood-tolerant than the flood-sensitive genotype. Roots of tolerant plants also contained more ATP than roots of sensitive plants at the 7th and 10th days of flooding. Quantitative transcript analysis identified 132 genes differentially expressed between the two genotypes at one or more time points of flooding. Expression of genes related to the ethylene biosynthesis pathway and formation of adventitious roots was induced earlier and to higher levels in roots of the flood-tolerant genotype. Three potential flood-tolerance TFs which were differentially expressed between the two genotypes during the entire 10-day flooding duration were identified. This study confirmed the expression of anaerobic genes in response to soil flooding. Additionally, the differential expression of TFs associated with soil flooding tolerance was not qualitative but quantitative and temporal. Functional analyses of these genes will be necessary to reveal their potential to enhance flooding tolerance of soybean cultivars.

Figure 1

Root growth as measured by seminal root biomass (A) and adventitious root biomass (B) of control and flooded PI408105A and S99-2281 plants. Lower-case letters denote comparison between genotype/treatment at the same flooding duration (in days). The upper-case letters denote comparison within each genotype/treatment across different flooding duration. Means at each flooding duration with the same lower-case letter were not significantly different at p < 0.05. Means of each genotype/treatment with the same upper-case letters were not significantly different across different flooding duration.

Figure 2

Root ATP concentration of control and flooded PI408105A and S99-2281 plants. Lower-case letters denote comparison between genotype/treatment at the same flooding duration (in days). The upper-case letters denote comparison within each genotype/treatment across different flooding duration. Means at each flooding duration with the same lower-case letter were not significantly different at p < 0.05. Means of each genotype/treatment with the same upper-case letters were not significantly different across different flooding duration.

Figure 3

Aerenchyma development in roots of PI408105A (A–D) and S99-2281 plants (E–H) at one day (A and E), three days (B and F), seven days (C and G), and ten days (D and H) of soil flooding. Reproducible photomicrographs of PI408105A roots at the 10th day flooding treatment (D) were not available due to damages caused by sectioning of this highly porous segment. The scale bar is 100 μm.

Figure 4

Venn diagram showing the number of differentially expressed genes (p < 0.05) between the two genotypes, whose expression was either unique or overlapping at 1, 3, 7 and 10 days of soil flooding stress.

Figure 5

Expression matrix of genes that were differentially expressed in roots of PI408105A and S99-2281 genotypes at the 1st day (17 genes), the 1st and 3rd days (10 genes), the 1st, 3rd and 7th days (three genes), and the 1st, 3rd, 7th and 10th days (four genes) of soil flooding stress. The red color indicates genes up-regulated by flooding. The green color indicates down-regulation. Gray color indicates no significant difference in expression. Gene function in bold type indicates known anaerobic genes. The scale above the expression image shows the log₂ (flooding/control).

Figure 6

Expression of known anaerobic genes in roots of PI408105A relative to S99-2281 roots at 1, 3, 7 and 10 days of soil flooding stress. The red color indicates that expression in PI408105A roots was higher than in S99-2281 roots. The green color indicates that expression in PI408105 roots was lower than in S99-2281 roots. The scale above the expression image shows the ratio in log₂ (flooding/control) of PI408105A relative to S99-2281 roots.