Acta Physiologiae Plantarum

, Volume 35, Issue 6, pp 1915–1924 | Cite as

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

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

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Supplementary material 1 (XLS 19447 kb)
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Supplementary material 2 (DOCX 4575 kb)
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Supplementary material 3 (DOCX 22 kb)

References

  1. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11:R106PubMedCrossRefGoogle Scholar
  2. Ando K, Grumet R (2010) Transcriptional profiling of rapidly growing cucumber fruit by 454-pyrosequencing analysis. J Amer Soc Hort Sci 135:291–302Google Scholar
  3. Bartels D, Sunkar R (2005) Drought and salt tolerance in plants. Crit Rev Plant Sci 24:23–58CrossRefGoogle Scholar
  4. Close TJ (1996) Dehydrins: emergence of a biochemical role of a family of plant dehydration proteins. Physiol Plant 97:795–803CrossRefGoogle Scholar
  5. Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman A, Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R (2006) An atlas of gene expression from seed to seed through barley development. Funct Integr Genom 6:202–211CrossRefGoogle Scholar
  6. Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38(Suppl 2):w64–w70PubMedCrossRefGoogle Scholar
  7. Food and Agriculture Organisation of the United Nations (2005) Management of irrigation-induced salt-affected soils ftp://ftp.fao.org/agl/agll/docs/salinity_brochure_eng.pdf
  8. Forrest KL, Bhave M (2007) Major intrinsic proteins (MIPs) in plants: a complex gene family with major impacts on plant phenotype. Funct Integr Genom 7:263–289CrossRefGoogle Scholar
  9. Garg R, Patel RK, Tyagi AK, Jain M (2011) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res 18:53–63PubMedCrossRefGoogle Scholar
  10. Grains Research & Development Corporation (2008) GRDC impact assessment report series: an economic analysis of GRDC’s investment in barley breeding http://www.grdc.com.au/uploads/documents/GRDC_ImpAss_BarleyBreeding1.pdf
  11. Hoagland DR, Arnon DI (1950) The water culture method for growing plants without soil. University of California Agric, Exp station, Berkley Circular 347Google Scholar
  12. Hou X, Tong H, Selby J, Dewitt J, Peng X, He ZH (2005) Involvement of a cell wall-associated kinase, WAKL4, in Arabidopsis mineral responses. Plant Physiol 139:1704–1716PubMedCrossRefGoogle Scholar
  13. International Barley Genome Sequencing Consortium, Mayer KF, Waugh R, Brown JW, Schulman A, Langridge P, Platzer M, Fincher GB, Muehlbauer GJ, Sato K, Close TJ, Wise RP, Stein N (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 29:711–716Google Scholar
  14. Kawaura K, Mochida K, Ogihara Y (2008) Genome-wide analysis for identification of salt-responsive genes in common wheat. Funct Integr Genom 8:277–286CrossRefGoogle Scholar
  15. Langridge P, Paltridge N, Fincher G (2006) Functional genomics of abiotic stress tolerance in cereals. Briefings Funct Genom Proteom 4:343–354CrossRefGoogle Scholar
  16. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinforma 25:1754–1760CrossRefGoogle Scholar
  17. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAMtools. Bioinforma 25:2078–2079CrossRefGoogle Scholar
  18. Liu YH, Li HY, Shi YS, Song YC, Wang TY, Li Y (2009) A maize early responsive to dehydration gene, ZmERD4, provides enhanced drought and salt tolerance in Arabidopsis. Plant Mol Biol Rep 27:542–548CrossRefGoogle Scholar
  19. Ma Q, Dai X, Xu Y, Guo J, Liu Y, Chen N, Xiao J, Zhang D, Xu Z, Zhang X, Chong K (2009) Enhanced tolerance to chilling stress in OsMYB3R-2 transgenic rice is mediated by alteration in cell cycle and ectopic expression of stress genes. Plant Physiol 150:244–256PubMedCrossRefGoogle Scholar
  20. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNAseq: An assessment of technical reproducibility and comparison with gene expression arrays. Genom Res 18:1509–1517CrossRefGoogle Scholar
  21. Meiri D, Breiman A (2009) Arabidopsis ROF1 (FKBP62) modulates thermotolerance by interacting with HSP90.1 and affecting the accumulation of HsfA2-regulated sHSPs. Plant J 59:387–399PubMedCrossRefGoogle Scholar
  22. Mizuno H, Kawahara Y, Sakai H, Kanamori H, Wakimoto H, Yamagata H, Oono Y, Wu J, Ikawa H, Itoh T, Matsumoto T (2010) Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L). BMC Genom 11:683–695CrossRefGoogle Scholar
  23. Mohammadi M, Kav NNV, Deyholos MK (2007) Transcriptional profiling of hexaploid wheat (Triticum aestivum L.) roots identifies novel, dehydration-responsive genes. Plant, Cell Environ 30:630–645CrossRefGoogle Scholar
  24. Munns R (2005) Genes and salt tolerance: bringing them together. New Phytol 167:645–663PubMedCrossRefGoogle Scholar
  25. Munns R, Tester M (2008) Mechanisms of salinity tolerance. Ann Rev Plant Biol 59:651–681CrossRefGoogle Scholar
  26. Rengasamy P (2006) World salinization with emphasis on Australia. J Expt Bot 57:1017–1023CrossRefGoogle Scholar
  27. Schreiber AW, Sutton T, Caldo RA, Kalashyan E, Lovell B, Mayo G, Muehlbauer GJ, Druka A, Waugh R, Wise RP, Langridge P, Baumann U (2009) Comparative transcriptomics in the Triticeae. BMC Genom 10:285–301CrossRefGoogle Scholar
  28. Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Taji T, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K (2002) Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 31:279–292PubMedCrossRefGoogle Scholar
  29. Selote DS, Khanna-Chopra R (2006) Drought-acclimation confers oxidative stress tolerance by inducing coordinated antioxidant defense at cellular and subcellular level in leaves of wheat seedlings. Physiol Plant 127:494–506CrossRefGoogle Scholar
  30. Severin AJ, Woody JL, Bolon YT, Joseph B, Diers BW, Farmer AD, Muehlbauer GJ, Nelson RT, Grant D, Specht JE, Graham MA, Cannon SB, May GD, Vance CP, Shoemaker RC (2010) RNA-Seq atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol 10:160–175PubMedCrossRefGoogle Scholar
  31. Shinozaki K, Yamaguchi-Shinozaki K (1997) Gene expression and signal transduction in water-stress response. Plant Physiol 115:327–334PubMedCrossRefGoogle Scholar
  32. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19:1117–1123PubMedCrossRefGoogle Scholar
  33. Suprunova T, Krugman T, Fahima T, Chen G, Shams I, Korol A, Nevo E (2004) Differential expression of dehydrin genes in wild barley, Hordeum spontaneum, associated with resistance to water deficit. Plant, Cell Environ 27:1297–1308CrossRefGoogle Scholar
  34. Tyerman SD, Niemietz CM, Bramley H (2002) Plant aquaporins: multifunctional water and solute channels with expanding roles. Plant, Cell Environ 25:173–194CrossRefGoogle Scholar
  35. Ueda A, Kathiresan A, Inada M, Narita Y, Nakamura T, Shi W, Takabe T, Bennett J (2004) Osmotic stress in barley regulates expression of a different set of genes than salt stress does. J Exp Bot 55:2213–2218PubMedCrossRefGoogle Scholar
  36. Urano K, Kurihara Y, Seki M, Shinozaki K (2010) ‘Omics’ analyses of regulatory networks in plant abiotic stress responses. Curr Opin Plant Biol 13:132–138PubMedCrossRefGoogle Scholar
  37. Walia H, Wilson C, Wahid A, Condamine P, Cui X, Close TJ (2006) Expression analysis of barley (Hordeum vulgare L.) during salinity stress. Funct Integr Genom 6:143–156CrossRefGoogle Scholar
  38. Walia H, Wilson C, Condamine P, Ismail AM, Xu J, Cui XP, Close TJ (2007) Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise. BMC Genom 8:87–100CrossRefGoogle Scholar
  39. Xu D, Duan X, Wang B, Hong B, Ho T, Wu R (1996) Expression of a late embryogenesis abundant protein gene, HVA1, from barley confers tolerance to water deficit and salt stress in transgenic rice. Plant Physiol 110:249–257PubMedGoogle Scholar
  40. Xu ZS, Xia LQ, Chen M, Cheng XG, Zhang RY, Li LC, Zhao YX, Lu Y, Ni ZY, Liu L, Qiu ZG, Ma YZ (2007) Isolation and molecular characterization of the Triticum aestivum L. ethylene-responsive factor1 (TaERF1) that increases multiple stress tolerance. Plant Mol Biol 65:719–732PubMedCrossRefGoogle Scholar

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

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