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The Soybean Transcriptogram Allows a Wide Genome-to-Single-Gene Analysis That Evinces Time-Dependent Drought Response

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Abstract

The drought response is a genome-wide phenomenon that, due to its complexity, is hard to achieve a “universal” response requiring an analysis method that takes this characteristic into account. Here, the Transcriptogramer tool was used to (i) produce a Glycine max ordering list based on protein–protein associations and (ii) analyze transcriptome data from soybean roots submitted to dehydration for 1, 6, and 12 h in a genome-wide scale. Sixteen, five, and six gene ontology (GO) categories were differentially expressed at 1, 6, and 12 h of drought stress, respectively. The most enriched GO categories are cell division, cell cycle, cell wall organization, stress responses, hormone signaling pathways, phosphorelay signal transduction, and regulation of gene expression. In total, 274 genes were differentially expressed (DE). The list includes 15 calcium-binding proteins, 17 TIFY, 3 ABA receptors, 5 E2 ubiquitin-conjugatin enzymes, 2 E3 ligases, 4 proteasome regulatory subunits, 1 chloroplastic superoxide dismutase, 1 peroxidase, and 10 thioredoxin-encoding genes already known to be related to drought response. The Transcriptogramer has evinced a global reprogrammed transcriptome and revealed that the most observable effects of water deficit occur during the first hour.

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Acknowledgements

We would like to thank Dr. Steven B. Cannon (US Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit) for granting permission to use the RNA-Seq data published by his group.

Funding

This work was supported by MCTI/CNPq/CAPES/FAPs no. 16/2014-National Institute of Science and Technology (INCT) in Biotech Assets Applied to Drought and Pests of Relevant Crops to Agrobusiness [88887.136360/2017–00-465480/2014-4]

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Authors and Affiliations

  1. Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto Nacional de Ciência e Tecnologia: Biotec Seca-Pragas, Instituto de Biociências Universidade Federal do Rio Grande do Sul (UFRGS, Porto Alegre, RS, 91501-970, Brazil

    Luisa Abruzzi de Oliveira-Busatto, Ricardo Luís Mayer Weber & Maria Helena Bodanese-Zanettini

  2. Instituto de Física, Instituto Nacional de Ciência e Tecnologia: Sistemas Complexos Universidade Federal do Rio Grande do Sul (UFRGS, Porto Alegre, RS, 91501-970, Brazil

    Rita Maria Cunha de Almeida

  3. Programa de Pós-Graduação em Fitotecnia, Departamento de Plantas de Lavoura, Faculdade de Agronomia, Universidade Federal do Rio Grande Do Sul (UFRGS, Porto Alegre, RS, 91501-970, Brazil

    Débora Favero, Christian Bredemeier & Cecília Paz da Silva Giordano

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  1. Luisa Abruzzi de Oliveira-Busatto
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  2. Rita Maria Cunha de Almeida
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  3. Ricardo Luís Mayer Weber
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  5. Christian Bredemeier
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  6. Cecília Paz da Silva Giordano
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  7. Maria Helena Bodanese-Zanettini
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Contributions

LAOB, RMCA, and MHBZ conceived the study; LAOB, RMCA, RLMW, and CPSG conducted the experiments; LAOB and RMCA analyzed the data, and LAOB, DF, RMCA, CB, and MHBZ wrote the manuscript. All authors read and approved the final version.

Corresponding author

Correspondence to Maria Helena Bodanese-Zanettini.

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Key Message

• The soybean root transcriptome undertakes an important reprogramming specially during the first hour of drought stress. The Transcriptogramer has evinced a global reprogramed transcriptome and biological processes not detected by conventional tools

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de Oliveira-Busatto, L.A., de Almeida, R.M.C., Weber, R.L.M. et al. The Soybean Transcriptogram Allows a Wide Genome-to-Single-Gene Analysis That Evinces Time-Dependent Drought Response. Plant Mol Biol Rep 40, 1–27 (2022). https://doi.org/10.1007/s11105-021-01297-4

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