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Functional & Integrative Genomics

, Volume 10, Issue 2, pp 207–214 | Cite as

The water-deficit stress- and red-rot-related genes in sugarcane

  • Vikrant Gupta
  • Saurabh Raghuvanshi
  • Ambika Gupta
  • Navin Saini
  • Anupama Gaur
  • M. S. Khan
  • R. S. Gupta
  • J. Singh
  • S. K. Duttamajumder
  • S. Srivastava
  • A. Suman
  • Jitendra P. Khurana
  • Raman Kapur
  • Akhilesh K. TyagiEmail author
Short Communication

Abstract

Sugarcane is an important international commodity as a valuable agricultural crop especially in developing countries. Sequencing was carried out to generate >35,000 expressed sequence tags (ESTs) from healthy as well as red-rot-infected tissue of Indian subtropical variety of sugarcane. Subsequent clustering with existing sugarcane ESTs in public databases identified 4,087 clusters, including 85 clusters that preferentially express upon Colletotrichum falcatum (red-rot) infection, which were previously unreported. Real-time reverse transcription–PCR profiling of selected EST clusters identified several sugarcane clusters that show differential expression in response to biotic and abiotic stress conditions. Twenty-five stress-related clusters showed >2-fold relative expression during water-deficit stress in sugarcane. Similarly, EST clusters could be identified, which exhibit association with red-rot disease when assessed in red-rot-susceptible and red-rot-resistant varieties of sugarcane. Such EST clusters are good candidates for in-depth analysis to elucidate stress-responsive pathways in sugarcane and facilitate genetic manipulation to tailor this crop for tolerance to various stresses.

Keywords

cDNA library Disease-related genes EST Quantitative real-time PCR Red-rot Water-deficit stress-related genes Sugarcane 

Abbreviations

EST

Expressed sequence tag

NBS-LRR

Nucleotide binding site leucine-rich repeat

qRT-PCR

Quantitative reverse transcription polymerase chain reaction

Notes

Acknowledgment

We gratefully acknowledge the financial support of Department of Biotechnology and University Grants Commission, Government of India.

Supplementary material

10142_2009_144_MOESM1_ESM.txt (40 kb)
Supplementary File 1 Sequences of the stress clusters discussed in the study. (TXT 39 kb)
10142_2009_144_MOESM2_ESM.txt (5 kb)
Supplementary File 2 Primer sequences for real-time RT-PCR analysis of the selected sugarcane stress clusters. (TXT 5 kb)
10142_2009_144_MOESM3_ESM.txt (9 kb)
Supplementary Table 1 Functional annotation of sugarcane EST clusters preferentially expressed upon Colletotrichum falcatum (red rot) infection on the basis of similarity to the UniprotKB protein entries. (TXT 9 kb)
10142_2009_144_MOESM4_ESM.txt (39 kb)
Supplementary Figure 1 Expression profiles of various red-rot-related genes in response to Colletotrichum falcatum Cf 01 (red-rot) challenge. Expressions of sugarcane genes that were down-regulated in tolerant variety are shown. Stress cluster 41–47 are derived from the subtractive cDNA library from red-rot-infected sugarcane stem. (TXT 39 kb)

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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Vikrant Gupta
    • 1
  • Saurabh Raghuvanshi
    • 1
  • Ambika Gupta
    • 1
  • Navin Saini
    • 1
  • Anupama Gaur
    • 1
  • M. S. Khan
    • 2
  • R. S. Gupta
    • 2
  • J. Singh
    • 2
  • S. K. Duttamajumder
    • 2
  • S. Srivastava
    • 2
  • A. Suman
    • 2
  • Jitendra P. Khurana
    • 1
  • Raman Kapur
    • 2
  • Akhilesh K. Tyagi
    • 1
    • 3
    • 1
    Email author
  1. 1.Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
  2. 2.Indian Institute of Sugarcane ResearchLucknowIndia
  3. 3.National Institute of Plant Genome ResearchNew DelhiIndia

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