Tropical Plant Biology

, Volume 9, Issue 4, pp 215–228

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 Mangrauthia
  • Surekha Agarwal
  • B. Sailaja
  • N. Sarla
  • S. R. Voleti
Article

DOI: 10.1007/s12042-016-9170-7

Cite this article as:
Mangrauthia, S.K., Agarwal, S., Sailaja, B. et al. Tropical Plant Biol. (2016) 9: 215. doi:10.1007/s12042-016-9170-7

Abstract

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.

Keywords

Gene expression Heat stress qPCR RNA sequencing 

Abbreviations

ABA

Abscisic acid

cDNA

Complementary DNA

CDP-DAG

CDP-diacylglycerol

DREB

Dehydration responsive element binding

GA

Gibberellic acid

GO

Gene ontologies

GST

Glutathione S-transferase

HCL

Hierachical clustering

HSP

Heat shock proteins

HTG

High temperature germinated

JA

Jasmonic acid

JAR

Jasmonic acid-amino synthetase

JAZ

Jasmonate ZIM domain-containing protein

KEGG

Kyoto encyclopedia of genes and genomes

LEA-3

Late embryogenesis abundant protein, group 3

LOX

Lipoxygenase

LTP

Lipid transfer protein

N22

Nagina 22

NAS

Nicotianamine synthase

PCR

Polymerase chain reaction

qRT-PCR

Quantitative reverse transcriptional PCR

RAB

Responsive to ABA

ROS

Reactive oxygen species

SAM

S-adenosyl-L-methionine

TFs

Transcription factors

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)

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

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