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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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Distribution of genes differentially expressed in roots of W82 and DT2008 by dehydration treatment into functional categories. Genes upregulated or downregulated in W82 (A) or DT2008 (B) roots by at least one dehydration treatment were classified into functional categories using MapMan. W-D/W-C represents W-D2/W-C and/or W-D10/W-C (W82-dehydrated-2 and/or 10 h vs. W82-well-watered control-0 h); DT-D/DT-C represents DT-D2/DT-C and/or DT-D10/DT-C (DT2008-dehydrated-2 and/or 10 h vs. DT2008-well-watered control-0 h).
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Figure 3: Distribution of genes differentially expressed in roots of W82 and DT2008 by dehydration treatment into functional categories. Genes upregulated or downregulated in W82 (A) or DT2008 (B) roots by at least one dehydration treatment were classified into functional categories using MapMan. W-D/W-C represents W-D2/W-C and/or W-D10/W-C (W82-dehydrated-2 and/or 10 h vs. W82-well-watered control-0 h); DT-D/DT-C represents DT-D2/DT-C and/or DT-D10/DT-C (DT2008-dehydrated-2 and/or 10 h vs. DT2008-well-watered control-0 h).

Mentions: As a means to understand the molecular mechanisms underlying root responses that soybean plants develop to increase their adaptation to drought, we used MapMan to classify the dehydration-responsive genes detected in W82 and DT2008 into various functional categories. Lists of unique genes with putatively predicted function (Supplementary Tables S6E,F, S7E,F), which were found to be upregulated or downregulated in W82 or DT2008 roots by at least one dehydration treatment, either 2 or 10 h treatment, were assembled and subjected to MapMan analyses for assignment of each gene into functional category (Figure 3). Our data indicated that among the 20 most abundant categories, in both W82 and DT2008 roots, the upregulated genes of the TF category were the most highly enriched genes, whereas the downregulated genes were enriched in “protein synthesis, targeting, modification, etc” category.


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)

Distribution of genes differentially expressed in roots of W82 and DT2008 by dehydration treatment into functional categories. Genes upregulated or downregulated in W82 (A) or DT2008 (B) roots by at least one dehydration treatment were classified into functional categories using MapMan. W-D/W-C represents W-D2/W-C and/or W-D10/W-C (W82-dehydrated-2 and/or 10 h vs. W82-well-watered control-0 h); DT-D/DT-C represents DT-D2/DT-C and/or DT-D10/DT-C (DT2008-dehydrated-2 and/or 10 h vs. DT2008-well-watered control-0 h).
© Copyright Policy
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4528160&req=5

Figure 3: Distribution of genes differentially expressed in roots of W82 and DT2008 by dehydration treatment into functional categories. Genes upregulated or downregulated in W82 (A) or DT2008 (B) roots by at least one dehydration treatment were classified into functional categories using MapMan. W-D/W-C represents W-D2/W-C and/or W-D10/W-C (W82-dehydrated-2 and/or 10 h vs. W82-well-watered control-0 h); DT-D/DT-C represents DT-D2/DT-C and/or DT-D10/DT-C (DT2008-dehydrated-2 and/or 10 h vs. DT2008-well-watered control-0 h).
Mentions: As a means to understand the molecular mechanisms underlying root responses that soybean plants develop to increase their adaptation to drought, we used MapMan to classify the dehydration-responsive genes detected in W82 and DT2008 into various functional categories. Lists of unique genes with putatively predicted function (Supplementary Tables S6E,F, S7E,F), which were found to be upregulated or downregulated in W82 or DT2008 roots by at least one dehydration treatment, either 2 or 10 h treatment, were assembled and subjected to MapMan analyses for assignment of each gene into functional category (Figure 3). Our data indicated that among the 20 most abundant categories, in both W82 and DT2008 roots, the upregulated genes of the TF category were the most highly enriched genes, whereas the downregulated genes were enriched in “protein synthesis, targeting, modification, etc” category.

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