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Identification of Differentially Expressed Genes in Sugarcane During Pathogenesis of Colletotrichum falcatum by Suppression Subtractive Hybridization (SSH)

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Abstract

A suppression subtractive hybridization technique was used to identify differentially expressed genes in sugarcane in response to Colletotrichum falcatum, the fungal pathogen causing red rot in sugarcane. Messenger RNA (mRNA) samples collected from red rot resistant cv. Co 93009 at 6, 12, 24 and 48 h after pathogen challenge were pooled together and used as tester population. mRNA samples collected from red rot susceptible cv. CoC 671 at 6, 12, 24 and 48 h after pathogen challenge and control of samples of cv. Co 93009 and cv. CoC 671 were pooled together and used as the driver population. A forward subtraction enriched for differentially expressed ESTs in the resistant cultivar was carried out. At the end of subtraction, cloning and sequencing, 136 EST sequences were assembled into ten clusters/contigs. Based on TIGR homology search, the clusters were found to be involved in reactive oxygen species signaling, defense and the secretory pathway of plant innate immunity associated with hypersensitive response—mediated programmed cell death. Temporal gene expression pattern of the EST clusters by quantitative real time PCR revealed that, resistant cultivar had a higher level of gene expression than the susceptible cultivar in all the clusters till 48 h after pathogen inoculation. In conclusion, this study identified for the first time a set of differentially expressed EST clusters in red rot resistant sugarcane cultivar in response to C. falcatum infection.

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Abbreviations

SSH:

Suppression subtractive hybridization

C. falcatum :

Colletotrichum falcatum

PAMP:

Pathogen associated molecular pattern

PRRs:

Pattern recognition receptors

qRT-PCR:

Quantitative real time polymerase chain reaction

ESTs:

Expressed sequence tags

HR:

Hypersensitive response

PCD:

Programmed cell death

NO:

Nitric oxide

H2O2 :

Hydrogen peroxide

ROS:

Reactive oxygen species

ATP:

Adenosine triphosphate

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Acknowledgments

The authors are grateful to Dr. N. Vijayan Nair, Director of the institute for providing facilities and encouragement. We are thankful to ICAR, New Delhi for the financial support through the outreach research Project ALCOCERA.

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Authors and Affiliations

  1. Plant Pathology Section, Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, 641007, India

    M. Sathyabhama, R. Viswanathan, P. Malathi & A. Ramesh Sundar

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  1. M. Sathyabhama
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  2. R. Viswanathan
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  3. P. Malathi
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  4. A. Ramesh Sundar
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Correspondence to R. Viswanathan.

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Sathyabhama, M., Viswanathan, R., Malathi, P. et al. Identification of Differentially Expressed Genes in Sugarcane During Pathogenesis of Colletotrichum falcatum by Suppression Subtractive Hybridization (SSH). Sugar Tech 18, 176–183 (2016). https://doi.org/10.1007/s12355-014-0364-8

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  • DOI: https://doi.org/10.1007/s12355-014-0364-8

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