Molecular Breeding

, Volume 34, Issue 2, pp 761–768 | Cite as

Transcriptome analysis of barley identifies heat shock and HD-Zip I transcription factors up-regulated in response to multiple abiotic stresses

  • Takashi Matsumoto
  • Hiromi Morishige
  • Tsuyoshi Tanaka
  • Hiroyuki Kanamori
  • Takao Komatsuda
  • Kazuhiro Sato
  • Takeshi Itoh
  • Jianzhong Wu
  • Shingo Nakamura
Short communication


Analyzing barley gene expression profiles in response to abiotic stress is critical to understanding how barley manages stress, and provides vital information to improve environmental stress tolerance for stable crop production. We developed an Agilent 60-mer oligo DNA microarray with 42,491 probe sets based on the sequences of 36,632 barley (Hordeum vulgare L.) full-length cDNA clones and conducted global expression profiling on barley seedlings subjected to desiccation, salt, cold and abscisic acid (ABA). We identified 281 genes that were differentially expressed in response to desiccation, salt, and cold stresses and ABA treatment. Among them, a class C heat shock transcription factor (HvHsfC1) and a homeodomain leucine zipper (HD-Zip) family I transcription factor (HvHox22) showed more than tenfold and fourfold higher expression, respectively, in response to the stimuli. Heat shock and HD-Zip transcription factors function as important regulators in stress responses in rice (Oryza sativa) and Arabidopsis thaliana; our results suggest these two transcription factors also play important roles in abiotic stress responses in barley. We mapped HvHox22 to the long arm of chromosome 2H and HvHsfC1 to the long arm of 4H, where drought resistance quantitative trait loci were previously detected. Our microarray data and identification of these stress response genes provide key information for dissection of the mechanism of abiotic stress tolerance in barley.


Barley Full-length cDNA Transcriptome Stress response Drought tolerance Transcription factors 



We thank Dr. Y. Nagamura and Dr. R. Motoyama (National Institute of Agrobiological Sciences) for technical help with microarray analysis. This research was supported by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Integrated research project for plant, insect and animal using genome technology GD-1001, and Genomics for Agricultural Innovation, TRC and TRG-1008).

Supplementary material

11032_2014_48_MOESM1_ESM.doc (43 kb)
Supplementary material 1 (DOC 43 kb)
11032_2014_48_MOESM2_ESM.xls (28 kb)
Supplementary material 2 (XLS 28 kb)
11032_2014_48_MOESM3_ESM.xls (24 kb)
Supplementary material 3 (XLS 25 kb)
11032_2014_48_MOESM4_ESM.xls (29 kb)
Supplementary material 4 (XLS 29 kb)
11032_2014_48_MOESM5_ESM.xls (28 kb)
Supplementary material 5 (XLS 28 kb)
11032_2014_48_MOESM6_ESM.doc (36 kb)
Supplementary material 6 (DOC 37 kb)
11032_2014_48_MOESM7_ESM.doc (34 kb)
Supplementary material 7 (DOC 34 kb)
11032_2014_48_MOESM8_ESM.doc (640 kb)
Supplementary material 8 (DOC 642 kb)


  1. Agalou A, Purwantomo S, Ővernäs E, Johannesson H, Zhu X, Estiati A, Kam RJD, Engström P, Slamet-Loedin IH, Zhu Z, Wang M, Xiong L, Meijer AH, Ouwerkerk PBF (2008) A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members. Plant Mol Biol 66:87–103PubMedCrossRefGoogle Scholar
  2. Cattivelli L, Ceccarelli S, Romagosa I, Stanca M (2011) Abiotic stresses in barely: problems and solutions. In: Ullrich SE (ed) Barley: production, improvement, and uses. Wiley, Colorado, pp 282–306CrossRefGoogle Scholar
  3. Diab AA, Teulat-Merah B, This D, Ozturk NZ, Benscher D, Sorrells ME (2004) Identification of drought-inducible genes and differentially expressed sequence tags in barley. Theor Appl Genet 109:1417–1425PubMedCrossRefGoogle Scholar
  4. Dubouzet JG, Sakuma Y, Ito Y, Kasuga M, Dubouzet EG, Miura S, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression. Plant J 33:751–763PubMedCrossRefGoogle Scholar
  5. Jin GH, Gho HJ, Jung KH (2012) A systematic view of rice heat shock transcription factor family using phylogenomic analysis. J Plant Physiol 170:321–329PubMedCrossRefGoogle Scholar
  6. Jogaiah S, Govind SR, Tran LSP (2013) Systems biology-based approaches toward understanding drought tolerance in food crops. Crit Rev Biotechnol 33:23–29PubMedCrossRefGoogle Scholar
  7. Kant P, Gordon M, Kant S, Zolla G, Davydov O, Heimer YM, Chalifa-Caspi V, Shaged R, Barak S (2008) Functional-genomics-based identification of genes that regulate Arabidopsis responses to multiple abiotic stresses. Plant Cell Environ 31:697–714PubMedCrossRefGoogle Scholar
  8. Killian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D’Angelo C, Bornberg-Bauer E, Kudla J, Harter K (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J 50:347–363CrossRefGoogle Scholar
  9. Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175CrossRefGoogle Scholar
  10. Krishnan A, Ambavaram MMR, Harb A, Batlang U, Wittich PE, Pereira A (2009) Genetic networks underlying plant abiotic stress responses. In: Jenks MA, Wood AJ (eds) Genes for plant abiotic stress. Blackwell Publishing, Oxford, pp 263–279Google Scholar
  11. Mano Y, Kawasaki S, Takaiwa F, Komatsuda T (2001) Construction of a genetic map of barley (Hordeum vulgare L.) cross ‘Azumamugi’ × ‘Kanto Nakate Gold’ using a simple and efficient amplified fragment-length polymorphism system. Genome 44:284–292PubMedCrossRefGoogle Scholar
  12. Matsui A, Ishida J, Morosawa T, Mochizuki Y, Kaminuma E, Endo TA, Okamoto M, Nambara E, Nakajima M, Kwashima M, Satou M, Kim JM, Kabayashi N, Toyoda T, Shinozaki K, Seki M (2008) Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant Cell Physiol 49:1135–1149PubMedCrossRefGoogle Scholar
  13. Matsumoto T, Tanaka T, Sakai H, Amano N, Kanamori H, Kurita K, Kikuta A, Kamiya K, Yamamoto M, Ikawa H, Fujii N, Hori K, Itoh T, Sato K (2011) Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. Plant Physiol 156:20–28PubMedCentralPubMedCrossRefGoogle Scholar
  14. NDong C, Danyluk J, Wilson KE, Pocock T, Huner NPA, Sarthan F (2002) Cold-regulated cereal chloroplast late embryogenesis abundant-like proteins. Molecular characterization and functional analyses. Plant Physiol 129:1368–1381PubMedCentralPubMedCrossRefGoogle Scholar
  15. Nover L, Hharti K, Döring P, Mishra SK, Ganguli A, Scharf KD (2001) Arabidopsis and the heat stress transcription factor world: how many heat stress transcription factors do we need? Cell Stress Chaperon 6:177–189CrossRefGoogle Scholar
  16. Sato K, Shin-I T, Seki M, Shinozaki K, Yoshida H, Takeda K, Yamazaki Y, Conte M, Kohara Y (2009) Development of 5006 full-length cDNA in barley: a tool for accessing cereal genomics resources. DNA Res 16:81–89PubMedCentralPubMedCrossRefGoogle Scholar
  17. Scharf KD, Berberich T, Ebersberger I, Nover L (2012) The plant heat stress transcription factor (Hsf) family: structure, function and evolution. Biochim Biophys Acta 1819:104–119PubMedCrossRefGoogle Scholar
  18. Sessa G, Carabelli M, Ruberti I (1994) Identification of distinct families of HD-Zip proteins in Arabidopsis thaliana. In: Coruzzi GP (ed) Plant molecular biology. Springer, Berlin, pp 412–426Google Scholar
  19. Shinozaki K, Yamaguchi-Shinozaki K (1996) Molecular responses to drought and cold stress. Curr Opin Biotechnol 7:161–167PubMedCrossRefGoogle Scholar
  20. Swindell WR, Huebner M, Weber AP (2007) Transcriptional profiling of Arabidopsis heat shock proteins and transcription factors reveals extensive overlap between heat and non-heat stress response pathways. BMC Genom 8:125–139CrossRefGoogle Scholar
  21. Tondelli A, Francia E, Barabashi D, Aprile A, Skinner JS, Stockinger EJ, Stanca AM, Pecchioni N (2006) Mapping regulatory genes as candidates for cold and drought stress tolerance in barley. Theor Appl Genet 112:445–454PubMedCrossRefGoogle Scholar
  22. Tsuda K, Tsvetanov S, Takumi S, Mori N, Atanoassov A, Nakamura C (2000) New members of a cold-responsive group-3 Lea/Rab-related Cor gene family from common wheat (Triticum aestivum L.). Genes Genet Syst 75:179–188PubMedCrossRefGoogle Scholar
  23. Ymaguchi-Shinozaki K, Shinozaki K (2006) Transcription regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu Rev Plant Biol 57:781–803CrossRefGoogle Scholar
  24. Zhang S, Haider I, Kohlen W, Jiang L, Bouwmeester H, Meijer AH, Schluepmann H, Liu CM, Ouwerkerk PBF (2012) Function of the HD-Zip I gene Oshox22 in ABA-mediated drought and salt tolerances in rice. Plant Mol Biol 80:571–585PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Takashi Matsumoto
    • 1
  • Hiromi Morishige
    • 2
  • Tsuyoshi Tanaka
    • 1
  • Hiroyuki Kanamori
    • 1
  • Takao Komatsuda
    • 1
  • Kazuhiro Sato
    • 3
  • Takeshi Itoh
    • 1
  • Jianzhong Wu
    • 1
  • Shingo Nakamura
    • 2
  1. 1.National Institute of Agrobiological SciencesTsukubaJapan
  2. 2.National Institute of Crop ScienceTsukubaJapan
  3. 3.Institute of Plant Science and ResourcesOkayama UniversityKurashikiJapan

Personalised recommendations