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Comparative analysis of root transcriptomes from two contrasting drought-responsive Williams 82 and DT2008 soybean cultivars under normal and dehydration conditions.

Ha CV, Watanabe Y, Tran UT, Le DT, Tanaka M, Nguyen KH, Seki M, Nguyen DV, Tran LS - Front Plant Sci (2015)

Bottom Line: The higher drought tolerability of DT2008 vs.W82 might be attributed to differential expression in genes encoding osmoprotectant biosynthesis-, detoxification- or cell wall-related proteins, kinases, transcription factors and phosphatase 2C proteins.This research allowed us to identify genetic components that contribute to the improved drought tolerance of DT2008, as well as provide a useful genetic resource for in-depth functional analyses that ultimately leads to development of soybean cultivars with improved tolerance to drought.

View Article: PubMed Central - PubMed

Affiliation: Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science Yokohama, Japan ; National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science Hanoi, Vietnam.

ABSTRACT
The economically important DT2008 and the model Williams 82 (W82) soybean cultivars were reported to have differential drought-tolerant degree to dehydration and drought, which was associated with root trait. Here, we used 66K Affymetrix Soybean Array GeneChip to compare the root transcriptomes of DT2008 and W82 seedlings under normal, as well as mild (2 h treatment) and severe (10 h treatment) dehydration conditions. Out of the 38172 soybean genes annotated with high confidence, 822 (2.15%) and 632 (1.66%) genes showed altered expression by dehydration in W82 and DT2008 roots, respectively, suggesting that a larger machinery is required to be activated in the drought-sensitive W82 cultivar to cope with the stress. We also observed that long-term dehydration period induced expression change of more genes in soybean roots than the short-term one, independently of the genotypes. Furthermore, our data suggest that the higher drought tolerability of DT2008 might be attributed to the higher number of genes induced in DT2008 roots than in W82 roots by early dehydration, and to the expression changes of more genes triggered by short-term dehydration than those by prolonged dehydration in DT2008 roots vs. W82 roots. Differentially expressed genes (DEGs) that could be predicted to have a known function were further analyzed to gain a basic understanding on how soybean plants respond to dehydration for their survival. The higher drought tolerability of DT2008 vs. W82 might be attributed to differential expression in genes encoding osmoprotectant biosynthesis-, detoxification- or cell wall-related proteins, kinases, transcription factors and phosphatase 2C proteins. This research allowed us to identify genetic components that contribute to the improved drought tolerance of DT2008, as well as provide a useful genetic resource for in-depth functional analyses that ultimately leads to development of soybean cultivars with improved tolerance to drought.

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Heatmap analysis of genes from well-known stress-related transcription factor families showing differential expression in various comparisons under well-watered and/or dehydration conditions. DT-C/W-C, DT2008-well-watered control-0 h vs. W82-well-watered control-0 h; DT-D2/W-D2, DT2008-dehydrated-2 h vs. W82-dehydrated-2 h; DT-D10/W-D10, DT2008-dehydrated-10 h vs. W82-dehydrated-10 h; W-D2/W-C, W82-dehydrated-2 h vs. W82-well-watered control-0 h; W-D10/W-C, W82-dehydrated-10 h vs. W82-well-watered control-0 h; DT-D2/DT-C, DT2008-dehydrated-2 h vs. DT2008-well-watered control-0 h; DT-D10/DT-C, DT2008-dehydrated-10 h vs. DT2008-well-watered control-0 h.
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Figure 4: Heatmap analysis of genes from well-known stress-related transcription factor families showing differential expression in various comparisons under well-watered and/or dehydration conditions. DT-C/W-C, DT2008-well-watered control-0 h vs. W82-well-watered control-0 h; DT-D2/W-D2, DT2008-dehydrated-2 h vs. W82-dehydrated-2 h; DT-D10/W-D10, DT2008-dehydrated-10 h vs. W82-dehydrated-10 h; W-D2/W-C, W82-dehydrated-2 h vs. W82-well-watered control-0 h; W-D10/W-C, W82-dehydrated-10 h vs. W82-well-watered control-0 h; DT-D2/DT-C, DT2008-dehydrated-2 h vs. DT2008-well-watered control-0 h; DT-D10/DT-C, DT2008-dehydrated-10 h vs. DT2008-well-watered control-0 h.

Mentions: A closer look at the sets of the DEG sets identified in W82 and DT2008 roots under dehydration revealed a number of common phenomena between their up- and downregulated gene sets, respectively (comparisons W-D/W-C and DT-D/DT-C) (Supplementary Tables S6E,F, S7E,F). Many genes belonging to different TF families, such as the AP2_EREBP-, bZIP-, MYB- and NAC-type TF families, exhibited transcriptional changes by dehydration in both W82 and DT2008 roots, of which more dehydration-inducible genes were found than dehydration-repressible genes (W-D2/W-C, W-D10/W-C, DT-D2/DT-C, and DT-D10/DT-C in Figure 4; Supplementary Figure S2; Supplementary Table S9). For instance, there were 13 and 5 upregulated GmNAC genes, in dehydrated W82 and DT2008 roots, respectively, while there were only 0 and 1 downregulated GmNAC genes detected in the respective root samples (Supplementary Table S9). Another example is that among the AP2_EREBP-type members, 13 and 11 dehydration-induced genes were found in W82 and DT2008 roots, respectively, in comparison with 3 and 4 dehydration-repressed genes in the respective dehydrated roots (Supplementary Table S9). Under our stringently set criteria of the fold change and q-values, the majority of the TF genes of these representative TF families were observed to be induced in either W82 or DT2008 roots by the prolonged 10 h rather than the short 2 h dehydration treatment (Figure 4; Supplementary Table S9).


Comparative analysis of root transcriptomes from two contrasting drought-responsive Williams 82 and DT2008 soybean cultivars under normal and dehydration conditions.

Ha CV, Watanabe Y, Tran UT, Le DT, Tanaka M, Nguyen KH, Seki M, Nguyen DV, Tran LS - Front Plant Sci (2015)

Heatmap analysis of genes from well-known stress-related transcription factor families showing differential expression in various comparisons under well-watered and/or dehydration conditions. DT-C/W-C, DT2008-well-watered control-0 h vs. W82-well-watered control-0 h; DT-D2/W-D2, DT2008-dehydrated-2 h vs. W82-dehydrated-2 h; DT-D10/W-D10, DT2008-dehydrated-10 h vs. W82-dehydrated-10 h; W-D2/W-C, W82-dehydrated-2 h vs. W82-well-watered control-0 h; W-D10/W-C, W82-dehydrated-10 h vs. W82-well-watered control-0 h; DT-D2/DT-C, DT2008-dehydrated-2 h vs. DT2008-well-watered control-0 h; DT-D10/DT-C, DT2008-dehydrated-10 h vs. DT2008-well-watered control-0 h.
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Figure 4: Heatmap analysis of genes from well-known stress-related transcription factor families showing differential expression in various comparisons under well-watered and/or dehydration conditions. DT-C/W-C, DT2008-well-watered control-0 h vs. W82-well-watered control-0 h; DT-D2/W-D2, DT2008-dehydrated-2 h vs. W82-dehydrated-2 h; DT-D10/W-D10, DT2008-dehydrated-10 h vs. W82-dehydrated-10 h; W-D2/W-C, W82-dehydrated-2 h vs. W82-well-watered control-0 h; W-D10/W-C, W82-dehydrated-10 h vs. W82-well-watered control-0 h; DT-D2/DT-C, DT2008-dehydrated-2 h vs. DT2008-well-watered control-0 h; DT-D10/DT-C, DT2008-dehydrated-10 h vs. DT2008-well-watered control-0 h.
Mentions: A closer look at the sets of the DEG sets identified in W82 and DT2008 roots under dehydration revealed a number of common phenomena between their up- and downregulated gene sets, respectively (comparisons W-D/W-C and DT-D/DT-C) (Supplementary Tables S6E,F, S7E,F). Many genes belonging to different TF families, such as the AP2_EREBP-, bZIP-, MYB- and NAC-type TF families, exhibited transcriptional changes by dehydration in both W82 and DT2008 roots, of which more dehydration-inducible genes were found than dehydration-repressible genes (W-D2/W-C, W-D10/W-C, DT-D2/DT-C, and DT-D10/DT-C in Figure 4; Supplementary Figure S2; Supplementary Table S9). For instance, there were 13 and 5 upregulated GmNAC genes, in dehydrated W82 and DT2008 roots, respectively, while there were only 0 and 1 downregulated GmNAC genes detected in the respective root samples (Supplementary Table S9). Another example is that among the AP2_EREBP-type members, 13 and 11 dehydration-induced genes were found in W82 and DT2008 roots, respectively, in comparison with 3 and 4 dehydration-repressed genes in the respective dehydrated roots (Supplementary Table S9). Under our stringently set criteria of the fold change and q-values, the majority of the TF genes of these representative TF families were observed to be induced in either W82 or DT2008 roots by the prolonged 10 h rather than the short 2 h dehydration treatment (Figure 4; Supplementary Table S9).

Bottom Line: The higher drought tolerability of DT2008 vs.W82 might be attributed to differential expression in genes encoding osmoprotectant biosynthesis-, detoxification- or cell wall-related proteins, kinases, transcription factors and phosphatase 2C proteins.This research allowed us to identify genetic components that contribute to the improved drought tolerance of DT2008, as well as provide a useful genetic resource for in-depth functional analyses that ultimately leads to development of soybean cultivars with improved tolerance to drought.

View Article: PubMed Central - PubMed

Affiliation: Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science Yokohama, Japan ; National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science Hanoi, Vietnam.

ABSTRACT
The economically important DT2008 and the model Williams 82 (W82) soybean cultivars were reported to have differential drought-tolerant degree to dehydration and drought, which was associated with root trait. Here, we used 66K Affymetrix Soybean Array GeneChip to compare the root transcriptomes of DT2008 and W82 seedlings under normal, as well as mild (2 h treatment) and severe (10 h treatment) dehydration conditions. Out of the 38172 soybean genes annotated with high confidence, 822 (2.15%) and 632 (1.66%) genes showed altered expression by dehydration in W82 and DT2008 roots, respectively, suggesting that a larger machinery is required to be activated in the drought-sensitive W82 cultivar to cope with the stress. We also observed that long-term dehydration period induced expression change of more genes in soybean roots than the short-term one, independently of the genotypes. Furthermore, our data suggest that the higher drought tolerability of DT2008 might be attributed to the higher number of genes induced in DT2008 roots than in W82 roots by early dehydration, and to the expression changes of more genes triggered by short-term dehydration than those by prolonged dehydration in DT2008 roots vs. W82 roots. Differentially expressed genes (DEGs) that could be predicted to have a known function were further analyzed to gain a basic understanding on how soybean plants respond to dehydration for their survival. The higher drought tolerability of DT2008 vs. W82 might be attributed to differential expression in genes encoding osmoprotectant biosynthesis-, detoxification- or cell wall-related proteins, kinases, transcription factors and phosphatase 2C proteins. This research allowed us to identify genetic components that contribute to the improved drought tolerance of DT2008, as well as provide a useful genetic resource for in-depth functional analyses that ultimately leads to development of soybean cultivars with improved tolerance to drought.

No MeSH data available.


Related in: MedlinePlus