Tropical Plant Biology

, Volume 9, Issue 4, pp 215–228 | Cite as

Transcriptome Analysis of Oryza sativa (Rice) Seed Germination at High Temperature Shows Dynamics of Genome Expression Associated with Hormones Signalling and Abiotic Stress Pathways

  • Satendra Kumar MangrauthiaEmail author
  • Surekha Agarwal
  • B. Sailaja
  • N. Sarla
  • S. R. Voleti


Seed germination directly affects growth and yield of rice. Germination process is highly dependent on temperature which regulates expression of several genes and proteins in germinating tissue. Whole genome mRNA sequencing of rice germinated at optimum (30 °C) and high temperature (42 °C) was performed using Ion Torrent Sequencing. Bioinformatics analysis of sequence data was done to survey the expressed genes, gene ontology, and pathway analysis. High temperature altered the expression of genes involved in fatty acid, amino acid, carbohydrate, and energy metabolism. Genes involved in reserve degradation, protein folding and stress responses were also significantly affected. Induced expression of genes like dehydration responsive element binding (DREB), RAB (responsive to ABA), and late embryogenesis abundant (LEA) proteins suggested important role of these proteins in high temperature germinated (HTG) rice. The pathway analysis of differentially expressed genes at high temperature suggested the altered expression of transcripts associated with ABA and jasmonate signalling, antioxidants (peroxidase and ascorbate peroxidase), heat shock proteins (HSP 20 and HSP70 family), heat shock protein binding protein1 (HSPBP1, HSP70-interacting protein) and other stress associated pathways. In present scenario where very limited information is available on genome wide transcripts expression during germination process, the transcriptome study done in rice provides an opportunity to better understand the genes expression and regulation of seed germination, which is highly influenced by temperature.


Gene expression Heat stress qPCR RNA sequencing 



Abscisic acid


Complementary DNA




Dehydration responsive element binding


Gibberellic acid


Gene ontologies


Glutathione S-transferase


Hierachical clustering


Heat shock proteins


High temperature germinated


Jasmonic acid


Jasmonic acid-amino synthetase


Jasmonate ZIM domain-containing protein


Kyoto encyclopedia of genes and genomes


Late embryogenesis abundant protein, group 3




Lipid transfer protein


Nagina 22


Nicotianamine synthase


Polymerase chain reaction


Quantitative reverse transcriptional PCR


Responsive to ABA


Reactive oxygen species




Transcription factors



Authors are highly thankful to the Director, ICAR- Indian Institute of Rice Research (formerly Directorate of Rice Research), for his kind support. Financial support received from NICRA (National Initiative on Climate Resilient Agriculture) project is acknowledged. Authors are thankful to Genotypic Pvt. Ltd. for sequencing services.

Authors Contribution

SKM, NS, SRV- designed the experiment; SKM, SA, and BS- performed the experiments; SA and SKM- analysed the data and wrote the manuscript.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

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Supplementary Figure 2

Double standard curves of qRT-PCR. (JPG 1014 kb)

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Supplementary Figure 3

Melting temperature curves of qRT-PCR. (JPG 988 kb)


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Satendra Kumar Mangrauthia
    • 1
    Email author
  • Surekha Agarwal
    • 1
  • B. Sailaja
    • 1
  • N. Sarla
    • 1
  • S. R. Voleti
    • 1
  1. 1.ICAR-Indian Institute of Rice research (IIRR)HyderabadIndia

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