Molecular Biology Reports

, Volume 41, Issue 4, pp 2229–2241 | Cite as

Differentially expressed genes in response to gamma-irradiation during the vegetative stage in Arabidopsis thaliana

  • Jin-Baek Kim
  • Sang Hoon Kim
  • Bo-Keun Ha
  • Si-Yong Kang
  • Cheol Seong Jang
  • Yong Weon Seo
  • Dong Sub Kim


Biochemical and physiological processes in plants are affected by gamma-irradiation, which causes significant changes in gene transcripts and expression. To identify the differentially expressed Arabidopsis genes in response to gamma-irradiation, we performed a microarray analysis with rosette leaves during the vegetative stage. Arabidopsis plants were exposed to a wide spectrum doses of gamma ray (100, 200, 300, 400, 800, 1200, 1600 or 2000 Gy) for 24 h. At the dose range from 100 to 400 Gy, irradiated plants were found to be shorter than controls after 8 days of irradiation, while doses over 800 Gy caused severe growth retardation. Therefore, 100 and 800 Gy were selected as adequate doses for microarray analysis to identify differentially expressed genes. Among the 20,993 genes used as microarray probes, a total number of 496 and 1,042 genes were up-regulated and down-regulated by gamma-irradiation, respectively (P < 0.05). We identified the characteristics of the genes that were up-and down-regulated fourfold higher genes by gamma irradiation according to The arabidopsis information resource gene ontology. To confirm the microarray results, we performed a northern blot and quantitative real-time PCR with several selected genes that had a large difference in expression after irradiation. In particular, genes associated with lipid transfer proteins, histones and transposons were down-regulated by 100 and/or 800 Gy of gamma irradiation. The expression patterns of selected genes were generally in agreement with the microarray results, although there were quantitative differences in the expression levels.


Arabidopsis thaliana Gamma-irradiation Microarray analysis Northern blot Quantitative real-time PCR 



The Arabidopsis Information Resource


Gene Ontology


Quantitative real-time PCR


Reactive oxygen species


Single-strand breakage


Double-strand breakage




Days after seeding


Days after irradiation


Lipid transfer protein



This work was supported by grants from the Korea Science and Engineering foundation (KOSEF) in the Ministry of Science, ICT and Future Planning (MSIP) and the Korea Atomic Energy Research Institute (KAERI).

Supplementary material

11033_2014_3074_MOESM1_ESM.pdf (281 kb)
Supplementary material 1 (PDF 281 kb)
11033_2014_3074_MOESM2_ESM.pdf (86 kb)
Supplementary material 2 (PDF 85 kb)
11033_2014_3074_MOESM3_ESM.pdf (29 kb)
Supplementary material 3 (PDF 29 kb)
11033_2014_3074_MOESM4_ESM.pdf (288 kb)
Supplementary material 4 (PDF 287 kb)


  1. 1.
    Ahloowalia BS, Maluszynski M (2001) Induced mutations:a new paradigm in plant breeding. Euphytica 118:167–173CrossRefGoogle Scholar
  2. 2.
    Shi J-M, Guo J-G, Li W-J, Zhang M, Huang L, Sun Y-Q (2010) Cytogenetic effects of low doses of energetic carbon ions on rice after exposures of dry seeds, wet seeds and seedlings. J Radiat Res 51:235–242PubMedCrossRefGoogle Scholar
  3. 3.
    Kobayashi Y, Funayama T, Hamada N, Sakashita T, Konishi T, Imasake H, Yasuda K, Hatashita M, Takagi K, Hatori S, Suzuki K, Yamauchi M, Yamashita S, Tomita M, Kobayashi K, Usami N, Wu L (2009) Microbeam irradiation facilities for radiobiology in Japan and China. J Radiat Res 50(Suppl.):A29–A47PubMedCrossRefGoogle Scholar
  4. 4.
    Tanaka A, Shikazono N, Hase Y (2010) Studies on biological effects of ion beams on lethality, molecular nature of mutation, mutation rate, and spectrum of mutation phenotype for mutation breeding in higher plants. J Radiat Res 51:223–233PubMedCrossRefGoogle Scholar
  5. 5.
    Ohnishi T, Takahashi A, Ohnishi K (2002) Studies about space radiation promote new fields in radiation biology. J Radiat Res 43(Suppl.):S7–S12PubMedCrossRefGoogle Scholar
  6. 6.
    Ahloowalia BS, Maluszynski M, Nichterlein K (2004) Global impact of mutation-derived varieties. Euphytica 135:187–204CrossRefGoogle Scholar
  7. 7.
    Naito K, Kusaba M, Shikazono N, Takano T, Tanaka A, Tanisaka T, Nishimura M (2005) Transmissible and nontransmissible mutations induced by irradiating Arabidopsis thaliana pollen with γ-rays and carbon ions. Genetics 169:881–889PubMedCentralPubMedCrossRefGoogle Scholar
  8. 8.
    Vizir IY, Mulligan BJ (1999) Genetics of gamma-irradiation induced mutations in Arabidopsis thaliana: large chromosomal deletions can be rescued through the fertilization of diploid eggs. J Hered 90:412–417PubMedCrossRefGoogle Scholar
  9. 9.
    Rakwal R, Agrawal GK, Shibato J, Imanaka T, Fukutani S, Tamogami S, Endo S, Sahoo SK, Masuo Y, Kimura S (2009) Ultra low-dose radiation: stress responses and impacts using rice as a grass model. Int J Mol Sci 10:1215–1225PubMedCentralPubMedCrossRefGoogle Scholar
  10. 10.
    Ricaud L, Proux C, Renou J-P, Pichon O, Fochesato S, Ortet P, Montané M-H (2007) ATM-mediated transcriptional and developmental response to γ-rays in Arabidopsis. PLoS One 2(5):e430PubMedCentralPubMedCrossRefGoogle Scholar
  11. 11.
    Nagata T, Yamada H, Du Z, Todoriki S, Kikuchi S (2005) Microarray analysis of genes that respond to gamma-irradiation in Arabidopsis. J Agric Food Chem 53:1022–1030PubMedCrossRefGoogle Scholar
  12. 12.
    Kovalchuk I, Molinier J, Yao Y, Arkhipov A, Kovalchuk O (2007) Transcriptome analysis reveals fundamental differences in plant response to acute and chronic exposure to ionizing radiation. Mutat Res 624:101–113PubMedCrossRefGoogle Scholar
  13. 13.
    Kim J-H, Moon YR, Kim J-S, Oh M-H, Lee J-W, Chung BY (2007) Transcriptome profile of Arabidopsis rosette leaves during the reproductive stage after exposure to ionizing radiation. Radiat Res 168:267–280PubMedCrossRefGoogle Scholar
  14. 14.
    Wright EG, Coates PJ (2006) Untargeted effects of ionizing radiation: implications for radiation pathology. Mutat Res 597:119–132PubMedCrossRefGoogle Scholar
  15. 15.
    Sachs RK, Hlatky LR, Trask BJ (2000) Radiation-produced chromosome aberrations. Trends Genet 16:143–146PubMedCrossRefGoogle Scholar
  16. 16.
    Datta K, Neumann RD, Winters TA (2005) Characterization of complex apurinic/apyrimidinic-site clustering associated with an authentic site-specific radiation-induced DNA double-strand break. Proc Natl Acad Sci U SA 102:10569–10574CrossRefGoogle Scholar
  17. 17.
    Britt AB (1999) Molecular genetics of DNA repair in higher plants. Trends Plant Sci 4:20–25PubMedCrossRefGoogle Scholar
  18. 18.
    Kobayashi J, Iwabuchi K, Miyagawa K, Sonoda E, Suzuki K, Takana M, Tauchi H (2008) Current topics in DNA double-strand break repair. J Radiat Res 49:93–103PubMedCrossRefGoogle Scholar
  19. 19.
    Hefner E, Preuss SB, Britt AB (2003) Arabidopsis mutants sensitive to gamma radiation include the homologue of the human repair gene ERCC1. J Exp Bot 54:669–680PubMedCrossRefGoogle Scholar
  20. 20.
    Jackson SP (2001) Detecting, signaling and repairing DNA double-strands breaks. Biochem Soc Trans 29:655–661Google Scholar
  21. 21.
    Hayashi T, Aoki S (1985) Effect of irradiation on the carbohydrate metabolism responsible for sucrose accumulation in potatoes. J Agric Food Chem 33:13–17Google Scholar
  22. 22.
    Nagata T, Todoriki S, Hayasi T, Shibata Y, Mori M, Kanagae H, Kikuchi S (1999) Gamma-radiation induces leaf trichome formation in Arabidopsis. Plant Physiol 120:113–120PubMedCentralPubMedCrossRefGoogle Scholar
  23. 23.
    Nagata T, Todoriki S, Masumizu T, Suda I, Furuta S, Du Z, Kikuchi S (2003) Levels of active oxygen species are controlled by ascorbic acid and anthocyanin in Arabidopsis. J Agric Food Chem 51:2992–2999PubMedCrossRefGoogle Scholar
  24. 24.
    Nagata T, Todoriki S, Kikuchi S (2004) Radical expansion of root cells and elongation of root hairs of Arabidopsis thaliana induced by massive doses of gamma irradiation. Plant Cell Physiol 45:1557–1565PubMedCrossRefGoogle Scholar
  25. 25.
    Hays JB (2001) Arabidopsis thaliana, a versatile model system for study of eukaryotic genome-maintenance functions. DNA Repair 1:579–600CrossRefGoogle Scholar
  26. 26.
    Zhu T, Wang X (2000) Large-scale profiling of the Arabidopsis transcriptome. Plant Physiol 124:1472–1476PubMedCentralPubMedCrossRefGoogle Scholar
  27. 27.
    Kehoe DM, Villand P, Somerville S (1999) DNA microarrays for studies of higher plants and other photosynthetic organism. Trends Plant Sci 4:38–41PubMedCrossRefGoogle Scholar
  28. 28.
    Yuan Y, Gilmore J, Conner T (1998) Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarray. Plant J 15:821–833CrossRefGoogle Scholar
  29. 29.
    Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA (2004) Transcriptional code of a eukaryotic genome. Nature 431:99–104PubMedCentralPubMedCrossRefGoogle Scholar
  30. 30.
    Barrett MT, Scheffer A, Ben-Dor A, Sampas N, Lipson D, Kincaid R, Tsang P, Curry B, Baird K, Meltzer PS, Yakhini Z, Bruhn L, Laderman S (2004) Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci U S A 101:17765–17770PubMedCentralPubMedCrossRefGoogle Scholar
  31. 31.
    Mockler TC, Ecker JR (2005) Application of DNA tilling arrays for whole-genome analysis. Genomics 85:1–15PubMedCrossRefGoogle Scholar
  32. 32.
    Shida T (2004) Application DNA microarray to toxicological research. J Env Pathol Toxicol Oncol 23:13–31CrossRefGoogle Scholar
  33. 33.
    Yoshiyama K, Conklin PA, Huefner ND, Britt AB (2009) Suppressor of gamma response 1(SOG1) encodes a putative transcription factor governing multiple responses to DNA damage. Proc Natl Acad Sci USA 106:12843–12848PubMedCentralPubMedCrossRefGoogle Scholar
  34. 34.
    Abe K, Osakabe K, Ishikawa Y, Tagiri A, Yamanouchi H, Takyuu T, Yoshioka T, Ito T, Kobayashi M, Shinozaki K, Ichikawa H, Toki S (2009) Inefficient double-strand DNA break repair is associated with increased fasciation in Arabidopsis BRCA2 mutants. J Exp Bot 60:2751–2761PubMedCentralPubMedCrossRefGoogle Scholar
  35. 35.
    Lafarge S, Montane M-H (2003) Characterization of Arabidopsis thaliana ortholog of the human breast cancer susceptibility gene 1: AtBRCA1, strongly induced by gamma rays. Nucleic Acids Res 31:1148–1155PubMedCentralPubMedCrossRefGoogle Scholar
  36. 36.
    Chomczynski P, Mackey K (1995) Modification of the TRI reagent procedure for isolation of RNA from polysaccharide- and proteoglycan-rich sources. Biotechniques 19:942–945PubMedGoogle Scholar
  37. 37.
    Kim DS, Kim J-B, Goh EJ, Kim W-J, Lim SH, Seo YW, Jang CS, Kang SY (2011) Antioxidant response of Arabidopsis plants to gamma irradiation: genome-wide expression profiling of the ROS scavenging and signal transduction pathways. J Plant Physiol 168:1960–1971PubMedCrossRefGoogle Scholar
  38. 38.
    Kovalchuka O, Arkhipovb A, Barylyakc I, Karachovc I, Titovd V, Hohna B, Kovalchuka I (2000) Plants experiencing chronic internal exposure to ionizing radiation exhibit higher frequency of homologous recombination than acutely irradiated plants. Mutat Res 449:47–56CrossRefGoogle Scholar
  39. 39.
    Vandenhove H, Vanhoudt N, Cuypers A, van Hees M, Wannijn J, Horemans N (2010) Life-cycle chronic gamma exposure of Arabidopsis thaliana induces growth effects but no discernable effects on oxidative stress pathways. Plant Physiol Biochem 48:778–786PubMedCrossRefGoogle Scholar
  40. 40.
    Wi SG, Chung BY, Kim J-S, Kim J-H, Baek M-H, Lee J-W, Kim YS (2007) Effects of gamma-irradiation on morphological changes and biological responses in plants. Micron 38:553–564PubMedCrossRefGoogle Scholar
  41. 41.
    Wolff S (1992) Failla Memorial Lecture. Is radiation all bad? The search for adaptation. Radiat Res 131:117–123PubMedCrossRefGoogle Scholar
  42. 42.
    Casarett AP (1968) Radiation chemistry and effects of gamma-radiation on the cell. In: Casarett AP (ed) Radiation Biology. Prentice-Hall, Englewood CliffsGoogle Scholar
  43. 43.
    Dong Z, Saikumar P, Weinberg JM, Venkatachalam (1997) Internucleosomal DNA cleavage triggered by plasma membrane damage during necrotic cell death. Am J Pathol 151(5):1205–121344PubMedCentralPubMedGoogle Scholar
  44. 44.
    Arikawa E, Sun Y, Wang J, Zhou Q, Ning B, Dial SL, Guo L, Yang J (2008) Cross-platform comparison of SYBR green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study. BMC Genom. doi: 10.1186/1471-2164-9-328
  45. 45.
    Kim J-H, Kim JE, Lee MH, Lee SW, Cho EJ, Chung BY (2013) Integrated analysis of diverse transcriptomic data from Arabidopsis reveals genetic markers that reliably and reproducibly respond to ionizing radiation. Gene 518:273–279PubMedCrossRefGoogle Scholar
  46. 46.
    Guénin S, Mauriat M, Pelloux J, Wuytswinkel OV, Bellini C, Gutierrez L (2009) Normalization of qRT-PCR data: the necessity of adopting a systematic, experimental conditions-specific, validation of references. J Exp Bot 60:487–493PubMedCrossRefGoogle Scholar
  47. 47.
    Pyee J, Yu H, Kolattukudy PE (1994) Identification of a lipid transfer protein as the major protein in the surface wax of broccoli (Brassica Oleracea) leaves. Arch Biochem Biophys 311:460–468PubMedCrossRefGoogle Scholar
  48. 48.
    Park C-J, Shin R, Park JM, Lee G-J, Yu J-S, Paek K-H (2002) Induction of pepper cDNA encoding a lipid transfer protein during the resistance response to tobacco mosaic virus. Plant Mol Biol 48:243–254PubMedCrossRefGoogle Scholar
  49. 49.
    Buhot N, Douliez J-P, Jacquemard A, Marion D, Tran V, Maume BF, Milat M-L, Ponchet M, Mikès V, Kadar J-C, Blein J-P (2001) A lipid transfer protein binds to a receptor involved in the control of plant defense responses. FEBS Lett 509:27–30PubMedCrossRefGoogle Scholar
  50. 50.
    Sterk P, Booij H, Schellekens GA, Van Kammen A, De Vries SG (1991) Cell-specific expression of the carrot EP2 lipid transfer protein gene. Plant cell 3:907–921PubMedCentralPubMedCrossRefGoogle Scholar
  51. 51.
    Yi S-I, Park M-Y, Kim J-K, Choi YD (2009) AlLTPs from Allium species represent a novel class of lipid transfer protein that are localized in endomembrane compartments. Plant Biotechnol Rep 3:213–223CrossRefGoogle Scholar
  52. 52.
    Carvalho AO, Gomes VM (2007) Role of plant lipid transfer proteins in plant cell physiology: a concise review. Peptides 28:1144–1153CrossRefGoogle Scholar
  53. 53.
    Torres-Schumann S, Godoy JA, Pintor-Toro JA (1992) A probable lipid transfer protein gene is induced by NaCl in stems of tomato plants. Plant Mol Biol 18:749–757PubMedCrossRefGoogle Scholar
  54. 54.
    Colmenero-Flores JM, Campos F, Garciarrubio A, Covarrubias AA (1997) Characterization of Phaselous vulgaris cDNA clones responsive to water-deficit: identification of a novel late embryogenesis abundant-like protein. Plant Mol Biol 35:393–405PubMedCrossRefGoogle Scholar
  55. 55.
    Jang CS, Lee HJ, Chang SJ, Seo YW (2004) Expression and promoter analysis of the TaLTP1 gene induced by drought and salt stress in wheat (Triticum aestivum L.). Plant Sci 167:995–1001CrossRefGoogle Scholar
  56. 56.
    Li W, Zhang P, Fellers JP, Friebe B, Gill BS (2004) Sequence composition, organization, and evolution of the core Triticeae genome. Plant J 40:500–511PubMedCrossRefGoogle Scholar
  57. 57.
    SanMiguel P, Bennetzen JL (1998) Evidence that a recent increase in maize genome size was caused by the massive amplificaition of intergene retrotransposon. Ann Bot 82(Suppl A):37–44CrossRefGoogle Scholar
  58. 58.
    Wessler SR (1996) Plant retrotransposons: turned on by stress. Curr Biol 6(8):959–961PubMedCrossRefGoogle Scholar
  59. 59.
    Grandbastien M-A (1998) Activation of plant retrotransposons under stress conditions. Trends in Plant Sci 3(5):181–187CrossRefGoogle Scholar
  60. 60.
    McClintock B (1984) The significance of responses of the genome to challenge. Science 226:792–801PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Jin-Baek Kim
    • 1
    • 3
  • Sang Hoon Kim
    • 1
  • Bo-Keun Ha
    • 1
  • Si-Yong Kang
    • 1
  • Cheol Seong Jang
    • 2
  • Yong Weon Seo
    • 3
  • Dong Sub Kim
    • 1
  1. 1.Advanced Radiation Technology InstituteKorea Atomic Energy Research InstituteJeongeupRepublic of Korea
  2. 2.Department of Applied Plant Sciences TechnologyKangwon National UniversityChuncheonRepublic of Korea
  3. 3.Division of BiotechnologyKorea UniversitySeoulRepublic of Korea

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