3 Biotech

, 8:195 | Cite as

Differential gene expression profiling through transcriptome approach of Saccharum spontaneum L. under low temperature stress reveals genes potentially involved in cold acclimation

  • Dharshini Selvarajan
  • Chakravarthi Mohan
  • Vignesh Dhandapani
  • Gauri Nerkar
  • Ashwin Narayan Jayanarayanan
  • Manoj Vadakkancherry Mohanan
  • Naveenarani Murugan
  • Lovejot Kaur
  • Mahadevaiah Chennappa
  • Ravinder Kumar
  • Minturam Meena
  • Bakshi Ram
  • Appunu Chinnaswamy
Original Article


Sugarcane (Saccharum sp.) is predominantly grown in both tropics and subtropics in India, and the subtropics alone contribute more than half of sugarcane production. Sugarcane active growth period in subtropics is restricted to 8–9 months mainly due to winter’s low temperature stress prevailing during November to February every year. Being a commercial crop, tolerance to low temperature is important in sugarcane improvement programs. Development of cold tolerant sugarcane varieties require a deep knowledge on molecular mechanism naturally adapted by cold tolerant genotypes during low temperature stress. To understand gene regulation under low temperature stress, control and stressed (10 °C, 24 h) leaf samples of cold tolerant S. spontaneum IND 00-1037 collected from high altitude region in Arunachal Pradesh were used for transcriptome analysis using the Illumina NextSeq 500 platform with paired-end sequencing method. Raw reads of 5.1 GB (control) and 5.3 GB (stressed) obtained were assembled using trinity and annotated with UNIPROT, KEGG, GO, COG and SUCEST databases, and transcriptome was validated using qRT-PCR. The differential gene expression (DGE) analysis showed that 2583 genes were upregulated and 3302 genes were down-regulated upon low temperature stress. A total of 170 cold responsive transcriptional factors belonging to 30 families were differentially regulated. CBF6 (C-binding factor), a DNA binding transcriptional activation protein associated with cold acclimation and freezing tolerance was differentially upregulated. Many low temperature responsive genes involved in various metabolic pathways, viz. cold sensing through membrane fluidity, calcium and lipid signaling genes, MAP kinases, phytohormone signaling and biosynthetic genes, antioxidative enzymes, membrane and cellular stabilizing genes, genes involved in biosynthesis of polyunsaturated fatty acids, chaperones, LEA proteins, soluble sugars, osmoprotectants, lignin and pectin biosynthetic genes were also differentially upregulated. Potential cold responsive genes and transcriptional factors involved in cold tolerance mechanism in cold tolerant S. spontaneum IND 00-1037 were identified. Together, this study provides insights into the cold tolerance to low temperature stress in S. spontaneum, thus opening applications in the genetic improvement of cold stress tolerance in sugarcane.


Low temperature stress S. spontaneum Transcriptome Cold sensor Signaling qRT-PCR Cold responsive genes 



The authors thank ICAR-Sugarcane Breeding Institute, Coimbatore for providing the necessary infrastructure. We would like to thank Dr. G. Hemaprabha, Head, Division of Crop Improvement and Dr. N. Subramonian, Emeritus Scientist, ICAR-SBI for their critical comments on the content. Thanks to Mr. K. Selvamuthu for his technical assistance to carry out the work.

Author contributions

DS and AC designed and performed the experiments. DS, CM, ANJ, MVM, NM CM, RK and MM wrote the manuscript. VD did the MapMan analysis of the data. GN did the artwork for figures. AC and BR revised the manuscript. All authors read and approved the final manuscript.


The authors thank the Science and Engineering Research Board (SERB), Department of Science and Technology for financial support (Grant No.SB/YS/LS-165/2013). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Compliance with ethical standards

Conflict of interest

The authors have declared that no competing interests exist.

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Dharshini Selvarajan
    • 1
  • Chakravarthi Mohan
    • 1
  • Vignesh Dhandapani
    • 3
  • Gauri Nerkar
    • 1
  • Ashwin Narayan Jayanarayanan
    • 1
  • Manoj Vadakkancherry Mohanan
    • 1
  • Naveenarani Murugan
    • 1
  • Lovejot Kaur
    • 1
  • Mahadevaiah Chennappa
    • 1
  • Ravinder Kumar
    • 2
  • Minturam Meena
    • 2
  • Bakshi Ram
    • 1
  • Appunu Chinnaswamy
    • 1
  1. 1.Division of Crop ImprovementICAR-Sugarcane Breeding InstituteCoimbatoreIndia
  2. 2.Division of Crop ImprovementICAR-Sugarcane Breeding Institute Regional CentreKarnalIndia
  3. 3.Molecular Genetics and Genomics Laboratory, Department of HorticultureChungnam National UniversityDaejeonSouth Korea

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