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Comparative analysis of drought-responsive transcriptomes of sugarcane genotypes with differential tolerance to drought

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Abstract

Water stress causes considerable yield losses in sugarcane. To investigate differentially expressed genes under water stress, two sugarcane genotypes were subjected to three water-deficit levels (mild, moderate, and severe) and subsequent recovery and leaf transcriptome was generated using Illumina NextSeq sequencing. Among the differentially expressed genes, the tolerant genotype Co 06022 generated 2970 unigenes (p ≤ 0.05, functionally known, non-redundant DEGs) at 2-day stress, and there was a progressive decrease in the expressed genes as the stress period increased with 2109 unigenes at 6-day stress and 2307 unigenes at 10-day stress. There was considerable reduction at recovery with 1334 unigenes expressed at 10 days after recovery. However, in the susceptible genotype Co 8021, the number of unigenes expressed at 2 days was lower (2025) than the tolerant genotype and a further reduction was seen at 6-day stress (1552). During recovery, more differentially expressed genes were observed in the susceptible cultivar indicating that the cultivar has to activate more functions/processes to recover from the damage caused by stress. Comparison of DEGs between all stages of stress and recovery in both genotypes revealed that, the commonly up- and down-regulated genes across different stages were approximately double in the tolerant genotype. The most enriched gene ontology classes were heme binding, peroxidase activity and metal ion binding in the biological process and response to oxidative stress, hydrogen peroxide catabolic process and response to stress in the molecular function category. The cellular component was enriched with DEGs involved in extracellular region followed by integral component of membrane. The KEGG pathway analysis revealed important metabolic activities and functionally important genes involved in mitigating water-deficit stress in both the varieties. In addition, several unannotated genes in important pathways were detected and together may provide novel insights into water-deficit tolerance mechanisms in sugarcane. The reliability of the observed expression patterns was confirmed by qRT-PCR. The results of this study will help to identify useful genes for improving drought tolerance in sugarcane.

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Data availability

All the clean reads have been submitted as sequence read archive (SRA) in NCBI with the BioProject ID- PRJNA590595.

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Acknowledgements

The authors gratefully acknowledge for financial support and facilities provided by the Director, Sugarcane Breeding Institute, Coimbatore and also thank Genotypic Technology Pvt. Ltd., Bangalore for the transcriptome sequencing analysis.

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  1. Biotechnology Section, Division of Crop Improvement, Indian Council of Agricultural Research- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641 007, India

    A. Selvi, K. Devi, R. Manimekalai & P. T. Prathima

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  1. A. Selvi
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  2. K. Devi
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  3. R. Manimekalai
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AS: conceptualization, project administration, data analysis and interpretation of the data, supervision, writing, review and editing. KD: laboratory experiments, methodology, data analysis, validation, writing, review and editing. RM: methodology for RNA Seq, analysis and interpretation of the data. PTP: data analysis, interpretation of the data, methodology for validation, review and editing.

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Correspondence to A. Selvi.

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Selvi, A., Devi, K., Manimekalai, R. et al. Comparative analysis of drought-responsive transcriptomes of sugarcane genotypes with differential tolerance to drought. 3 Biotech 10, 236 (2020). https://doi.org/10.1007/s13205-020-02226-0

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