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Identification of tomato root growth regulatory genes and transcription factors through comparative transcriptomic profiling of different tissues

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Abstract

Tomato is an economically important vegetable crop and a model for development and stress response studies. Although studied extensively for understanding fruit ripening and pathogen responses, its role as a model for root development remains less explored. In this study, an Illumina-based comparative differential transcriptomic analysis of tomato root with different aerial tissues was carried out to identify genes that are predominantly expressed during root growth. Sequential comparisons revealed ~ 15,000 commonly expressed genes and ~ 3000 genes of several classes that were mainly expressed or regulated in roots. These included 1069 transcription factors (TFs) of which 100 were differentially regulated. Prominent amongst these were members of families encoding Zn finger, MYB, ARM, bHLH, AP2/ERF, WRKY and NAC proteins. A large number of kinases, phosphatases and F-box proteins were also expressed in the root transcriptome. The major hormones regulating root growth were represented by the auxin, ethylene, JA, ABA and GA pathways with root-specific expression of certain components. Genes encoding carbon metabolism and photosynthetic components showed reduced expression while several protease inhibitors were amongst the most highly expressed. Overall, the study sheds light on genes governing root growth in tomato and provides a resource for manipulation of root growth for plant improvement.

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Data access

The raw data analyzed for this study have been deposited in the NCBI Sequence Read Archive (SRA) database under BioProject accession ID: PRJNA589155 (https://www.ncbi.nlm.nih.gov/bioproject).

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Acknowledgements

The work was supported by Council of Scientific and Industrial Research (CSIR), Delhi, India under the network project BSC0204 to VAS and APS. VK is grateful to CSIR, India for Senior Research Fellowship. AM is grateful to DST, Government of India for Senior Research Fellowship. DS is grateful to CSIR, India for project fellowship. We also thank Ram Awadh for taking care of tomato plants in glass house.

Funding

This study was funded by CSIR, India under the projects BSC0204.

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Authors and Affiliations

  1. Plant Gene Expression Lab, Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001, India

    Vinod Kumar, Deepika Singh, Adity Majee, Shikha Singh, Mehar Hasan Asif, Aniruddha P. Sane & Vidhu A. Sane

  2. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India

    Vinod Kumar, Adity Majee, Mehar Hasan Asif, Aniruddha P. Sane & Vidhu A. Sane

  3. Integral University, Lucknow, 226026, India

    Deepika Singh &  Roohi

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  1. Vinod Kumar
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Contributions

VAS and APS conceived the idea and designed the experiments. VK, AM and DS performed the experiments and data analysis. MHA, SS, VK and VAS carried out bioinformatic analysis. VK, MHA, APS and VAS prepared the manuscript. All authors have read and approved the manuscript.

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Correspondence to Vidhu A. Sane.

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NBRI MS Number is CSIR-NBRI_MS/2020/06/04.

Integral MS Number is IU/R&D/2020-MCN00817.

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Kumar, V., Singh, D., Majee, A. et al. Identification of tomato root growth regulatory genes and transcription factors through comparative transcriptomic profiling of different tissues. Physiol Mol Biol Plants 27, 1173–1189 (2021). https://doi.org/10.1007/s12298-021-01015-0

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  • DOI: https://doi.org/10.1007/s12298-021-01015-0

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