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Dehydrin gene expression provides an indicator of low temperature and drought stress: transcriptome-based analysis of Barley (Hordeum vulgare L.)

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Abstract

Low temperature and drought have major influences on plant growth and productivity. To identify barley genes involved in responses to these stresses and to specifically test the hypothesis that the dehydrin (Dhn) multigene family can serve as an indicator of the entire transcriptome response, we investigated the response of barley cv. Morex to: (1) gradual drought over 21 days and (2) low temperature including chilling, freeze–thaw cycles, and deacclimation over 33 days. We found 4,153 genes that responded to at least one component of these two stress regimes, about one fourth of all genes called “present” under any condition. About 44% (1,822 of 4,153) responded specifically to drought, whereas only 3.8% (158 of 4,153) were chilling specific and 2.8% (119 of 4,153) freeze–thaw specific, with 34.1% responsive to freeze–thaw and drought. The intersection between chilling and drought (31.9%) was somewhat smaller than the intersection between freeze–thaw and drought, implying an element of osmotic stress response to freeze–thaw. About 82.4% of the responsive genes were similar to Arabidopsis genes. The expression of 13 barley Dhn genes mirrored the global clustering of all transcripts, with specific combinations of Dhn genes providing an excellent indicator of each stress response. Data from these studies provide a robust reference data set for abiotic stress.

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Acknowledgments

This work was supported by USDA-IFAFS 01-52100-11346, “An integrated physical and expression map of barley for Triticeae improvement”; NSF DBI-0321756, “Coupling expressed sequences and bacterial artificial chromosome resources to access the barley genome”; and USDA-NRI 02-35300-12548, “HarvEST: a portable EST database viewer.”

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Authors and Affiliations

  1. Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA

    Livia Tommasini, Jan T. Svensson, Edmundo M. Rodriguez, Abdul Wahid, Marina Malatrasi, Kenji Kato, Steve Wanamaker, Josh Resnik & Timothy J. Close

  2. Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA

    Livia Tommasini

  3. Department of Plant Biology, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark

    Jan T. Svensson

  4. Basic Sciences Department, Universidad Autónoma Agraria Antonio Narro, Buenavista, Saltillo, Coahuila, 25315, México

    Edmundo M. Rodriguez

  5. Department of Botany, University of Agriculture, Faisalabad, 38040, Pakistan

    Abdul Wahid

  6. Sez. Genetica e Biotecnologie Ambientali, Dip Scienze Ambientali, Universitá di Parma, Parma, Italy

    Marina Malatrasi

  7. Faculty of Agriculture, Okayama University, Okayama, Okayama, 700-8530, Japan

    Kenji Kato

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Electronic supplementary material

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Supplementary Fig. 1

PCA plot of gene expression under low temperature and drought stress in replicate samples. Each dot represents the transcriptome response to a particular condition (PDF 35.1 KB)

Supplementary Fig. 2

Functional classification of all drought- and low-temperature-regulated genes categorized based on MIPS using homologous sequences of Arabidopsis (E value cutoff = e −10). Only the main functional categories are listed, and overrepresented categories are indicated with an asterisk. Complete functional classification is listed in Supplemental Tables 16i–ii (PDF 6.75 KB)

Supplementary Fig. 3

QT clustering of drought- and low-temperature-responsive genes. The y-axis is the normalized signal intensity (log10), and in the x-axis, samples are ordered according to increasing drought stress levels (91% SWC to 9% SWC) and time progression in the low-temperature experiment (n.a. nonacclimated, c chilling; f/t freeze/thaw; d.a. deacclimated) (PDF 15.3 KB)

Supplementary Table S1

qPCR primer sequences (PDF 3.30 KB)

Supplementary Table S2

Developmentally regulated genes in the low-temperature experiment (PDF 29 KB)

Supplementary Table S3

Developmentally regulated genes in the drought experiment (PDF 407 KB)

Supplementary Table S4

Genes responsive to low-temperature stress release (PDF 84 KB)

Supplementary Table S5

“Present” genes in the drought experiment (PDF 1.58 MB)

Supplementary Table S6

“Present” genes in the low-temperature experiment. (PDF 1.26 MB)

Supplementary Table S7

. Genes present in the low-temperature and drought experiments including developmentally regulated and stress release responsive genes (PDF 1.67 MB)

Supplementary Table S8

Genes present in the low-temperature and drought experiments, without developmentally regulated and stress release responsive genes (PDF 1.16 MB)

Supplementary Table S9

Differentially expressed genes in the drought experiment (PDF 381 KB)

Supplementary Table S10

Differentially expressed genes in the low-temperature experiment (PDF 445 KB)

Supplementary Table S11i

Annotation of genes upregulated at 69% SWC (PDF 19.6 KB)

Supplementary Table S11ii

Annotation of genes upregulated at 38% SWC (PDF 77.9 KB)

Supplementary Table S11iii

Annotation of genes upregulated at 20% SWC (PDF 167 KB)

Supplementary Table S11iv

Annotation of genes upregulated at 11% SWC (PDF 247 KB)

Supplementary Table S11v

Annotation of genes upregulated at 9% SWC (PDF 164 KB)

Supplementary Table S11vi

Annotation of genes downregulated at 69% SWC (PDF 16.7 KB)

Supplementary Table S11vii

Annotation of genes downregulated at 38% SWC (PDF 56 KB)

Supplementary Table S11viii

Annotation of genes downregulated at 20% SWC (PDF 87.9 KB)

Supplementary Table S11ix

Annotation of genes downregulated at 11% SWC (PDF 152 KB)

Supplementary Table S11x

Annotation of genes downregulated at 9% SWC (PDF 142 KB)

Supplementary Table S12i

Annotation of genes upregulated under drought stress (PDF 210 KB)

Supplementary Table S12ii

Annotation of genes downregulated under drought stress (PDF 168 KB)

Supplementary Table S12iii

Annotation of genes upregulated under chilling (PDF 112 KB)

Supplementary Table S12iv

Annotation of genes downregulated under chilling (PDF 96.7 KB)

Supplementary Table S12v

Annotation of genes upregulated under freeze–thaw (PDF 97 KB)

Supplementary Table S12vi

Annotation of genes downregulated under freeze–thaw (PDF 89.8 KB)

Supplementary Table S12vii

Annotation of genes upregulated under low temperature (PDF 159 KB)

Supplementary Table S12viii

Annotation of genes downregulated under low temperature (PDF 107 KB)

Supplementary Table S13

Annotation of 4,153 drought- and low-temperature-responsive genes (PDF 373 KB)

Supplementary Table S14i

Annotation of genes responsive exclusively to chilling (PDF 22.9 KB)

Supplementary Table S14ii

Annotation of genes responsive exclusively to chilling or freeze–thaw (PDF 21 KB)

Supplementary Table S14iii

Annotation of genes responsive exclusively to freeze–thaw (PDF 19.1 KB)

Supplementary Table S14iv

Annotation of genes responsive exclusively to chilling or drought (PDF 35.2 KB)

Supplementary Table S14v

Annotation of genes responsive to chilling, drought, or freeze–thaw (PDF 107 KB)

Supplementary Table S14vi

Annotation of genes responsive exclusively to drought or freeze–thaw (PDF 52.4 KB)

Supplementary Table S14vii

Annotation of genes responsive exclusively to drought (PDF 118 KB)

Supplementary Table S14viii

Annotation of genes upregulated exclusively by chilling (PDF 40.6 KB)

Supplementary Table S14ix

Annotation of genes upregulated exclusively by chilling or freeze–thaw (PDF 52 KB)

Supplementary Table S14x

Annotation of genes upregulated exclusively by freeze–thaw (PDF 40.8 KB)

Supplementary Table S14xi

Annotation of genes upregulated exclusively by chilling or drought (PDF 6.13 KB)

Supplementary Table S14xii

Annotation of genes up-regulated by chilling, drought or freeze–thaw (PDF 11.8 KB)

Supplementary Table S14xiii

Annotation of genes upregulated exclusively by drought and freeze–thaw (PDF 7.22 KB)

Supplementary Table S14xiv

Annotation of genes upregulated exclusively by drought (PDF 147 KB)

Supplementary Table S14xv

Annotation of genes downregulated exclusively by chilling (PDF 18.5 KB)

Supplementary Table S14xvi

Annotation of genes downregulated exclusively by chilling and freeze–thaw (PDF 67.1 KB)

Supplementary Table S14xvii

Annotation of genes downregulated exclusively by freeze–thaw (PDF 20.1 KB)

Supplementary Table S14xviii

Annotation of genes downregulated exclusively by chilling and drought (PDF 7.25 KB)

Supplementary Table S14xix

Annotation of genes downregulated exclusively by drought and freeze–thaw (PDF 5.64 KB)

Supplementary Table S14xx

Annotation of genes downregulated exclusively by drought (PDF 175 KB)

Supplementary Table S14xxi

Annotation of genes downregulated by chilling, drought, and freeze–thaw (PDF 9.13 KB)

Supplementary Table S15

Functional classification of 4,153 drought- and low-temperature-responsive genes (PDF 41.0 KB)

Supplementary Table S16

Functional classification of genes upregulated by drought (i), downregulated by drought (ii), upregulated by low temperature (iii), and downregulated by low temperature (iv) (PDF 182 KB)

Supplementary Table S17i

Functional classification of genes upregulated by drought only, included in QT group 1 (clusters 1, 14, and 35) (PDF 62.6 KB)

Supplementary Table S17ii

Functional classification of genes upregulated by both drought and low temperature, included in QT group 2 (clusters 3, 11, 22, 26, 39, and 40) (PDF 56.0 KB)

Supplementary Table S17iii

Functional classification of genes upregulated by low temperature only, included in QT cluster 20 (PDF 8.34 KB)

Supplementary Table S18

Functional classification of genes upregulated exclusively by drought (i), upregulated by low temperature and drought (ii), and upregulated exclusively by low temperature (iii) (PDF 64.9 KB)

Supplementary Table S19

Normalized expression values for Dhn genes in the drought, low-temperature, and reference experiments (PDF 5.13 KB)

Supplementary Table S20

Correlation between microarray and qPCR gene expression values (PDF 6.07 KB)

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Tommasini, L., Svensson, J.T., Rodriguez, E.M. et al. Dehydrin gene expression provides an indicator of low temperature and drought stress: transcriptome-based analysis of Barley (Hordeum vulgare L.). Funct Integr Genomics 8, 387–405 (2008). https://doi.org/10.1007/s10142-008-0081-z

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  • DOI: https://doi.org/10.1007/s10142-008-0081-z

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