Journal of Genetics

, 98:46 | Cite as

Transcriptome analysis of finger millet (Eleusine coracana (L.) Gaertn.) reveals unique drought responsive genes

  • M. S. Parvathi
  • Karaba N. NatarajaEmail author
  • Y. A. Nanja Reddy
  • Mahantesha B. N. Naika
  • M. V. Channabyre Gowda
Research Article


Finger millet (Eleusine coracana (L.) Gaertn.), an important \(\hbox {C}_{4}\) species is known for its stress hardiness and nutritional significance. To identify novel drought responsive mechanisms, we generated transcriptome data from leaf tissue of finger millet, variety GPU-28, exposed to gravimetrically imposed drought stress so as to simulate field stress conditions. De novo assembly-based approach yielded 80,777 and 90,830 transcripts from well-irrigated (control) and drought-stressed samples, respectively. A total of 1790 transcripts were differentially expressed between the control and drought-stress treatments. Functional annotation and pathway analysis indicated activation of diverse drought-stress signalling cascade genes such as serine threonine protein phosphatase 2A (PP2A), calcineurin B-like interacting protein kinase31 (CIPK31), farnesyl pyrophosphate synthase (FPS), signal recognition particle receptor \(\upalpha \) (SRPR \(\alpha \)) etc. The basal regulatory genes such as TATA-binding protein (TBP)-associated factors (TAFs) were found to be drought responsive, indicating that genes associated with housekeeping or basal regulatory processes are activated under drought in finger millet. A significant portion of the expressed genes was uncharacterized, belonging to the category of proteins of unknown functions (PUFs). Among the differentially expressed PUFs, we attempted to assign putative function for a few, using a novel annotation tool, Proteins of Unknown Function Annotation Server. Analysis of PUFs led to the discovery of novel drought responsive genes such as pentatricopeptide repeat proteins and tetratricopeptide repeat proteins that serve as interaction modules in multiprotein interactions. The transcriptome data generated can be utilized for comparative analysis, and functional validation of the genes identified would be useful to understand the drought adaptive mechanisms operating under field conditions in finger millet, as has been already attempted for a few candidates such as CIPK31 and TAF6. Such an attempt is needed to enhance the productivity of finger millet under water-limited conditions, and/or to adopt the implicated mechanisms in other related crops.


finger millet drought transcriptome ontology differentially expressed genes Eleusine coracana 



We acknowledge the Department of Biotechnology, Government of India, New Delhi for funding the adhoc project Phenomics and Genomics of Ragi (file no. BT/PR5791/AGR/2/852/2012; D.O. no. BT/AB/Climate/2007 (Part II)). This project is also partially funded by the Indian Council of Agricultural Research (AICRP-Small Millets), New Delhi, India. We also thank the Department of  Science and Technology, Government of India, for infrastructure support under DST-FIST programme. MS Parvathi would like to thank University Grants Commission, New Delhi, India for awarding Junior Research Fellowship (F. 17-3/2002 (SA-I)) during the course of the study.

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Copyright information

© Indian Academy of Sciences 2019

Authors and Affiliations

  • M. S. Parvathi
    • 1
  • Karaba N. Nataraja
    • 1
    Email author
  • Y. A. Nanja Reddy
    • 1
    • 2
  • Mahantesha B. N. Naika
    • 1
    • 3
  • M. V. Channabyre Gowda
    • 2
  1. 1.Department of Crop PhysiologyUniversity of Agricultural SciencesBengaluru India
  2. 2.AICRP (Small Millets)ICAR-UASBengaluru India
  3. 3.Department of Biotechnology and Crop Improvement, K.R.C. College of HorticultureUniversity of Horticultural SciencesBagalkot India

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