Acta Physiologiae Plantarum

, Volume 35, Issue 6, pp 1915–1924

Analysis of the barley leaf transcriptome under salinity stress using mRNA-Seq

  • Mark Ziemann
  • Atul Kamboj
  • Runyararo M. Hove
  • Shanon Loveridge
  • Assam El-Osta
  • Mrinal Bhave
Original Paper

DOI: 10.1007/s11738-013-1230-0

Cite this article as:
Ziemann, M., Kamboj, A., Hove, R.M. et al. Acta Physiol Plant (2013) 35: 1915. doi:10.1007/s11738-013-1230-0

Abstract

Salinity is a threat to crops in many parts of the world, and together with drought, it is predicted to be a serious constraint to food security. However, understanding the impact of this stressor on plants is a major challenge due to the involvement of numerous genes and regulatory pathways. While transcriptomic analyses of barley (Hordeum vulgare L.) under salt stress have been reported with microarrays, there are no reports as yet of the use of mRNA-Seq. We demonstrate the utility of mRNA-Seq by analysing cDNA libraries derived from acutely salt-stressed and unstressed leaf material of H. vulgare cv. Hindmarsh. The data yielded >50 million sequence tags which aligned to 26,944 sequences in the Unigene reference database. To gain maximum information, we performed de novo assembly of unaligned reads and discovered >3,800 contigs, termed novel tentative consensus sequences, which are either new, or significant improvements on current databases. Differential gene expression screening found 48 significantly up-regulated and 62 significantly down-regulated transcripts. The work provides comprehensive insights into genome-wide effects of salinity and is a new resource for the study of gene regulation in barley and wheat. Further, the bioinformatics workflow may be applicable to other non-model plants to establish their transcriptomes and identify unique sequences.

Keywords

Salinity Barley Gene expression mRNA-Seq 

Supplementary material

11738_2013_1230_MOESM1_ESM.xls (19 mb)
Supplementary material 1 (XLS 19447 kb)
11738_2013_1230_MOESM2_ESM.docx (4.5 mb)
Supplementary material 2 (DOCX 4575 kb)
11738_2013_1230_MOESM3_ESM.docx (22 kb)
Supplementary material 3 (DOCX 22 kb)

Copyright information

© Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków 2013

Authors and Affiliations

  • Mark Ziemann
    • 1
  • Atul Kamboj
    • 2
  • Runyararo M. Hove
    • 2
  • Shanon Loveridge
    • 1
  • Assam El-Osta
    • 1
  • Mrinal Bhave
    • 2
  1. 1.Baker IDI Heart and Diabetes InstituteMelbourneAustralia
  2. 2.Environment and Biotechnology Centre, Faculty of Life and Social SciencesSwinburne University of TechnologyHawthornAustralia