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Transcriptome Profiling Through Next-Generation Sequencing in Sugarcane Under Moisture-Deficit Stress Condition

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Abstract

Sugarcane is an important industrial crop used for the production of sugar and biofuel. Moisture deficit is an important factor, leading to low productivity in sugarcane. Understanding the molecular changes under moisture-deficit stress helps in deciding the candidate genes to target while developing improved stress-tolerant sugarcane varieties. The changes in transcriptome profile were studied by sequencing total RNA isolated from roots of drought-resistant sugarcane variety, Co 94008, under moisture-deficit stress and unstressed conditions. The up-regulation of expression of genes dominated over down-regulation under moisture-deficit stress in sugarcane. More than 45,000 open reading frames (ORFs) were predicted in the transcripts observed under unstressed and stressed conditions. Highest numbers of ORFs were found to be involved in various metabolic processes, followed by cellular processes. Gene ontology analysis identified 27 genes which are related to the responses of water deprivation and stress. Of the identified ORFs, 1143 showed significant differential expression, of which 487 were up-regulated and 656 were down-regulated. Nine of the up-regulated genes showed more than 100-fold increased expression under stressed conditions than the unstressed conditions. Thirty-six differentially expressed genes were found to have microsatellites regions which can be used as potential sites for diversity analysis. Expression profile of transcription factors (TFs) was also altered in sugarcane under moisture-deficit stress. Of the TFs which showed differential expression, five TFs were quantified in real-time PCR and exhibited similar pattern of expression in both sequencing and real-time PCR. The present study provides insights into the changes in sugarcane transcriptome due to moisture-deficit stress which lead to a more comprehensive understanding of responses to moisture-deficit stress.

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Abbreviations

GAPDH:

Glyceraldehyde-3-phosphate dehydrogenase

ORFs:

Open reading frames

RDA:

Representational difference analysis

SAGE:

Serial analysis of gene expression

SSH:

Suppression subtractive hybridization

TFs:

Transcription factors

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Acknowledgements

We acknowledge the Indian Council for Cultural Relations, New Delhi, for the Financial Assistance in the form of Fellowship to the first author and the University of Agricultural Sciences, Dharwad, India, for the financial assistance to carry out this work. We Also thank Dr Sanjay B Patil, Senior Breeder Sugarcane, ARS—Sankeshwar, University of Agricultural Science, Dharwad, India, for providing the plant material.

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  1. Manel Dapanage

    Present address: Division of Crop Improvement, Sugarcane Research Institute, Uda Walawe, Sri Lanka

  2. Sumangala Bhat

    Present address: Department of Genetics and Plant Breeding, College of Agriculture, Dharwad, 580005, India

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  1. Department of Biotechnology, College of Agriculture, University of Agricultural Sciences, Dharwad, Dharwad, 580 005, Karnataka, India

    Manel Dapanage & Sumangala Bhat

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Dapanage, M., Bhat, S. Transcriptome Profiling Through Next-Generation Sequencing in Sugarcane Under Moisture-Deficit Stress Condition. Sugar Tech 22, 396–410 (2020). https://doi.org/10.1007/s12355-020-00806-1

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