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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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Experimental design and summary of the results of the microarray analysis. (A) Diagrams showing experimental design and comparisons. (B) Relative water content of W82 and DT2008 plants exposed to a dehydration treatment. Data represent the mean and SE (n = 5). Asterisks indicate significant differences as determined by a Student's t-test (*P < 0.05; **P < 0.01 and ***P < 0.001). (C) Upregulated and downregulated genes identified in each comparison from 34097 genes that were assigned with a putative function. Data were obtained from the results of three independent microarray experiments of three biological repeats. (D) Effect of stress intensity on gene expression in roots of W82 and DT2008 as indicated by Venn analysis of differentially expressed gene sets identified in (C). 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; W-D/W-C represents W-D2/W-C and/or W-D10/W-C (W82-dehydrated-2 h and/or 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; DT-D/DT-C represents DT-D2/DT-C and/or DT-D10/DT-C (DT2008-dehydrated-2 h and/or 10 h vs. DT2008-well-watered control-0 h).
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Figure 1: Experimental design and summary of the results of the microarray analysis. (A) Diagrams showing experimental design and comparisons. (B) Relative water content of W82 and DT2008 plants exposed to a dehydration treatment. Data represent the mean and SE (n = 5). Asterisks indicate significant differences as determined by a Student's t-test (*P < 0.05; **P < 0.01 and ***P < 0.001). (C) Upregulated and downregulated genes identified in each comparison from 34097 genes that were assigned with a putative function. Data were obtained from the results of three independent microarray experiments of three biological repeats. (D) Effect of stress intensity on gene expression in roots of W82 and DT2008 as indicated by Venn analysis of differentially expressed gene sets identified in (C). 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; W-D/W-C represents W-D2/W-C and/or W-D10/W-C (W82-dehydrated-2 h and/or 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; DT-D/DT-C represents DT-D2/DT-C and/or DT-D10/DT-C (DT2008-dehydrated-2 h and/or 10 h vs. DT2008-well-watered control-0 h).

Mentions: In our experimental design, root transcriptomes of drought-sensitive W82 and drought-tolerant DT2008 were compared at 0 (unstressed), 2 (early stress), and 10 h (late stress) of dehydration (Figure 1A) by microarray analysis using the 66 K soybean GeneChip (Supplementary Table S1). The relative water content (RWC) of dehydrated plants was measured during dehydration treatment, and the values were 70.2 and 75.8% for W82 and DT2008, respectively, at 2 h, whereas the respective values at 10 h of dehydration were 18.1 and 40% (Figure 1B), indicating the mild and severe stress intensities. This experimental design thus allowed us to identify (i) dehydration-responsive genes in each cultivar in a time-course manner (W-D2/W-C and W-D10/W-C; DT-D2/DT-C and DT-D10/DT-C), as well as (ii) genes involved in regulatory network that regulates differential root trait (DT-C/W-C, DT-D2/W-D2, and DT-D10/W-D10), thereby potentially contributing to higher drought tolerance of DT2008 relative to W82.


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)

Experimental design and summary of the results of the microarray analysis. (A) Diagrams showing experimental design and comparisons. (B) Relative water content of W82 and DT2008 plants exposed to a dehydration treatment. Data represent the mean and SE (n = 5). Asterisks indicate significant differences as determined by a Student's t-test (*P < 0.05; **P < 0.01 and ***P < 0.001). (C) Upregulated and downregulated genes identified in each comparison from 34097 genes that were assigned with a putative function. Data were obtained from the results of three independent microarray experiments of three biological repeats. (D) Effect of stress intensity on gene expression in roots of W82 and DT2008 as indicated by Venn analysis of differentially expressed gene sets identified in (C). 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; W-D/W-C represents W-D2/W-C and/or W-D10/W-C (W82-dehydrated-2 h and/or 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; DT-D/DT-C represents DT-D2/DT-C and/or DT-D10/DT-C (DT2008-dehydrated-2 h and/or 10 h vs. DT2008-well-watered control-0 h).
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Figure 1: Experimental design and summary of the results of the microarray analysis. (A) Diagrams showing experimental design and comparisons. (B) Relative water content of W82 and DT2008 plants exposed to a dehydration treatment. Data represent the mean and SE (n = 5). Asterisks indicate significant differences as determined by a Student's t-test (*P < 0.05; **P < 0.01 and ***P < 0.001). (C) Upregulated and downregulated genes identified in each comparison from 34097 genes that were assigned with a putative function. Data were obtained from the results of three independent microarray experiments of three biological repeats. (D) Effect of stress intensity on gene expression in roots of W82 and DT2008 as indicated by Venn analysis of differentially expressed gene sets identified in (C). 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; W-D/W-C represents W-D2/W-C and/or W-D10/W-C (W82-dehydrated-2 h and/or 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; DT-D/DT-C represents DT-D2/DT-C and/or DT-D10/DT-C (DT2008-dehydrated-2 h and/or 10 h vs. DT2008-well-watered control-0 h).
Mentions: In our experimental design, root transcriptomes of drought-sensitive W82 and drought-tolerant DT2008 were compared at 0 (unstressed), 2 (early stress), and 10 h (late stress) of dehydration (Figure 1A) by microarray analysis using the 66 K soybean GeneChip (Supplementary Table S1). The relative water content (RWC) of dehydrated plants was measured during dehydration treatment, and the values were 70.2 and 75.8% for W82 and DT2008, respectively, at 2 h, whereas the respective values at 10 h of dehydration were 18.1 and 40% (Figure 1B), indicating the mild and severe stress intensities. This experimental design thus allowed us to identify (i) dehydration-responsive genes in each cultivar in a time-course manner (W-D2/W-C and W-D10/W-C; DT-D2/DT-C and DT-D10/DT-C), as well as (ii) genes involved in regulatory network that regulates differential root trait (DT-C/W-C, DT-D2/W-D2, and DT-D10/W-D10), thereby potentially contributing to higher drought tolerance of DT2008 relative to W82.

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