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Comparisons of the Effects of Elevated Vapor Pressure Deficit on Gene Expression in Leaves among Two Fast-Wilting and a Slow-Wilting Soybean.

Devi MJ, Sinclair TR, Taliercio E - PLoS ONE (2015)

Bottom Line: The effects of elevated VPD on the expression of genes in the leaves of three soybean accessions, Plant Introduction (PI) 416937, PI 471938 and Hutcheson (PI 518664) were investigated because these accessions have contrasting responses to VPD changes.TR of the slow-wilting PI 416937 is limited when VPD increases to greater than about 2 kPa.The inventory and analysis of differentially expressed genes in PI 416937 in response to VPD is a foundation for further investigation to extend the current understanding of plant hydraulic conductivity in drought environments.

View Article: PubMed Central - PubMed

Affiliation: Department of Crop Science, North Carolina State University, Raleigh, North Carolina, United States of America.

ABSTRACT
Limiting the transpiration rate (TR) of a plant under high vapor pressure deficit (VPD) has the potential to improve crop yield under drought conditions. The effects of elevated VPD on the expression of genes in the leaves of three soybean accessions, Plant Introduction (PI) 416937, PI 471938 and Hutcheson (PI 518664) were investigated because these accessions have contrasting responses to VPD changes. Hutcheson, a fast-wilting soybean, and PI 471938, a slow-wilting soybean, respond to increased VPD with a linear increase in TR. TR of the slow-wilting PI 416937 is limited when VPD increases to greater than about 2 kPa. The objective of this study was to identify the response of the transcriptome of these accessions to elevated VPD under well-watered conditions and identify responses that are unique to the slow-wilting accessions. Gene expression analysis in leaves of genotypes PI 471938 and Hutcheson showed that 22 and 1 genes, respectively, were differentially expressed under high VPD. In contrast, there were 944 genes differentially expressed in PI 416937 with the same increase in VPD. The increased alteration of the transcriptome of PI 416937 in response to elevated VPD clearly distinguished it from the other slow-wilting PI 471938 and the fast-wilting Hutcheson. The inventory and analysis of differentially expressed genes in PI 416937 in response to VPD is a foundation for further investigation to extend the current understanding of plant hydraulic conductivity in drought environments.

No MeSH data available.


Validation of transcriptome data with QRT-PCR.Genes for the validation were selected from significantly expressed categories of PI 416937 (A) and PI 471938 (B). The X-axis represents soybean genotype, and the Y-axis is log2 fold change of transcript levels at high VPD in comparison to low VPD (q<0.05). The first bars in 3A and 3B represent gene expression data from the transcriptome study in PI 416937 and PI 471938, and remaining bars indicate data from QRT-PCR study. Error bars represent the standard deviation.
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pone.0139134.g003: Validation of transcriptome data with QRT-PCR.Genes for the validation were selected from significantly expressed categories of PI 416937 (A) and PI 471938 (B). The X-axis represents soybean genotype, and the Y-axis is log2 fold change of transcript levels at high VPD in comparison to low VPD (q<0.05). The first bars in 3A and 3B represent gene expression data from the transcriptome study in PI 416937 and PI 471938, and remaining bars indicate data from QRT-PCR study. Error bars represent the standard deviation.

Mentions: The expression of ten genes using QRT-PCR provided validation of the transcriptome profiling data (Fig 3 and S2 Fig). The levels of expression of 8 candidate genes from PI 416937 and 2 candidate genes from PI 471938 were measured by QRT-PCR in replicates treated with high- or low-VPD not used for transcriptome analyses and compared with transcriptome profiling expression (Fig 3). Expression of 6 candidate genes was also validated in one of the replications used for transcriptome profiling (S2 Fig). Even though there was variation in the magnitude of the relative transcript abundance between the profiling data and QRT-PCR data in PI 416937 (Fig 3A), the patterns of accumulation were similar. QRT-PCR confirmed the differential regulation of the ankyrn repeat-containing gene (ANK) at high VPD in comparison with low VPD in PI 471938. However, differential expression of the heat shock protein (HSP) (Glyma18g52480) in PI471938 was not confirmed by QRT-PCR in the third replicate not used for transcriptome profiling (Fig 3B). The differential gene expression of the HSP reported in the transcriptome analysis was apparently a false positive as is expected in large data sets. Additionally, most of the analyses of the transcriptome data rely on the aggregate change of expressions in genes in a pathway and not just an individual gene, making the analysis robust against false positives. The general agreement of the QRT-PCR and transcriptome profiles for 9 out of 10 genes tested confirm the validity of the sequencing data in a third biological replication of the VPD treatments.


Comparisons of the Effects of Elevated Vapor Pressure Deficit on Gene Expression in Leaves among Two Fast-Wilting and a Slow-Wilting Soybean.

Devi MJ, Sinclair TR, Taliercio E - PLoS ONE (2015)

Validation of transcriptome data with QRT-PCR.Genes for the validation were selected from significantly expressed categories of PI 416937 (A) and PI 471938 (B). The X-axis represents soybean genotype, and the Y-axis is log2 fold change of transcript levels at high VPD in comparison to low VPD (q<0.05). The first bars in 3A and 3B represent gene expression data from the transcriptome study in PI 416937 and PI 471938, and remaining bars indicate data from QRT-PCR study. Error bars represent the standard deviation.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591296&req=5

pone.0139134.g003: Validation of transcriptome data with QRT-PCR.Genes for the validation were selected from significantly expressed categories of PI 416937 (A) and PI 471938 (B). The X-axis represents soybean genotype, and the Y-axis is log2 fold change of transcript levels at high VPD in comparison to low VPD (q<0.05). The first bars in 3A and 3B represent gene expression data from the transcriptome study in PI 416937 and PI 471938, and remaining bars indicate data from QRT-PCR study. Error bars represent the standard deviation.
Mentions: The expression of ten genes using QRT-PCR provided validation of the transcriptome profiling data (Fig 3 and S2 Fig). The levels of expression of 8 candidate genes from PI 416937 and 2 candidate genes from PI 471938 were measured by QRT-PCR in replicates treated with high- or low-VPD not used for transcriptome analyses and compared with transcriptome profiling expression (Fig 3). Expression of 6 candidate genes was also validated in one of the replications used for transcriptome profiling (S2 Fig). Even though there was variation in the magnitude of the relative transcript abundance between the profiling data and QRT-PCR data in PI 416937 (Fig 3A), the patterns of accumulation were similar. QRT-PCR confirmed the differential regulation of the ankyrn repeat-containing gene (ANK) at high VPD in comparison with low VPD in PI 471938. However, differential expression of the heat shock protein (HSP) (Glyma18g52480) in PI471938 was not confirmed by QRT-PCR in the third replicate not used for transcriptome profiling (Fig 3B). The differential gene expression of the HSP reported in the transcriptome analysis was apparently a false positive as is expected in large data sets. Additionally, most of the analyses of the transcriptome data rely on the aggregate change of expressions in genes in a pathway and not just an individual gene, making the analysis robust against false positives. The general agreement of the QRT-PCR and transcriptome profiles for 9 out of 10 genes tested confirm the validity of the sequencing data in a third biological replication of the VPD treatments.

Bottom Line: The effects of elevated VPD on the expression of genes in the leaves of three soybean accessions, Plant Introduction (PI) 416937, PI 471938 and Hutcheson (PI 518664) were investigated because these accessions have contrasting responses to VPD changes.TR of the slow-wilting PI 416937 is limited when VPD increases to greater than about 2 kPa.The inventory and analysis of differentially expressed genes in PI 416937 in response to VPD is a foundation for further investigation to extend the current understanding of plant hydraulic conductivity in drought environments.

View Article: PubMed Central - PubMed

Affiliation: Department of Crop Science, North Carolina State University, Raleigh, North Carolina, United States of America.

ABSTRACT
Limiting the transpiration rate (TR) of a plant under high vapor pressure deficit (VPD) has the potential to improve crop yield under drought conditions. The effects of elevated VPD on the expression of genes in the leaves of three soybean accessions, Plant Introduction (PI) 416937, PI 471938 and Hutcheson (PI 518664) were investigated because these accessions have contrasting responses to VPD changes. Hutcheson, a fast-wilting soybean, and PI 471938, a slow-wilting soybean, respond to increased VPD with a linear increase in TR. TR of the slow-wilting PI 416937 is limited when VPD increases to greater than about 2 kPa. The objective of this study was to identify the response of the transcriptome of these accessions to elevated VPD under well-watered conditions and identify responses that are unique to the slow-wilting accessions. Gene expression analysis in leaves of genotypes PI 471938 and Hutcheson showed that 22 and 1 genes, respectively, were differentially expressed under high VPD. In contrast, there were 944 genes differentially expressed in PI 416937 with the same increase in VPD. The increased alteration of the transcriptome of PI 416937 in response to elevated VPD clearly distinguished it from the other slow-wilting PI 471938 and the fast-wilting Hutcheson. The inventory and analysis of differentially expressed genes in PI 416937 in response to VPD is a foundation for further investigation to extend the current understanding of plant hydraulic conductivity in drought environments.

No MeSH data available.