Plant Cell Reports

, Volume 32, Issue 1, pp 61–75 | Cite as

Comprehensive analysis of NAC domain transcription factor gene family in Vitis vinifera

Original Paper


Key message

Genome-wide identification of grapevineNACdomain genes and investigation of their chromosome locations, gene structures, duplication, evolution, phylogeny and expression profiles.


Grapevine is a widely used fruit crop. NAC (NAM, ATAF1/2 and CUC2) domain genes are plant-specific transcription factors (TFs) that comprise a conserved NAM domain in the N-terminus. Members of this gene family have been reported to contribute to plant development. During this study, 74 NAC genes were identified from 12× assembled grapevine genomic sequences. The duplication patterns, genomic structures and phylogeny of these 74 grapevine NAC genes were investigated. To understand the roles of VvNAC during grapevine development, their expression profiles in different tissues including leaf, tendril, inflorescence, stem, root and veraison berry skin were tested using quantitative real-time PCR. Analysis revealed expression diversity of various VvNAC genes among different grapevine tissues. To identify candidate grapevine NAC genes with a role in response to stress, publicly available microarray data were obtained to calculate their expression change under abiotic and biotic treatments, with a number of VvNAC genes displaying up-regulation after stress induction. Therefore, this study has uncovered more knowledge relating to the gene structures, chromosome organizations, evolution, expression profiles and functions of VvNAC genes.


Grapevine Vitis vinifera NAC domain Gene family 



Financial support for this work was provided by the National Natural Science Foundation of China (NSFC Accession No.: 31171931 and 31130047).

Supplementary material

299_2012_1340_MOESM1_ESM.xls (35 kb)
Supplementary material 1 (XLS 35 kb)
299_2012_1340_MOESM2_ESM.xls (30 kb)
Supplementary material 2 (XLS 29 kb)
299_2012_1340_MOESM3_ESM.xls (58 kb)
Supplementary material 3 (XLS 58 kb)


  1. Arvidsson S, Kwasniewski M, Riano-Pachon DM, Mueller-Roeber B (2008) QuantPrime—a flexible tool for reliable high-throughput primer design for quantitative PCR. BMC Bioinforma 9:465CrossRefGoogle Scholar
  2. Audran-Delalande C, Bassa C, Mila I, Regad F, Zouine M, Bouzayen M (2012) Genome-wide identification, functional analysis and expression profiling of the Aux/IAA gene family in tomato. Plant Cell Physiol 53(4):659–672PubMedCrossRefGoogle Scholar
  3. Carviel JL, Al-Daoud F, Neumann M, Mohammad A, Provart NJ, Moeder W, Yoshioka K, Cameron RK (2009) Forward and reverse genetics to identify genes involved in the age-related resistance response in Arabidopsis thaliana. Mol Plant Pathol 10(5):621–634PubMedCrossRefGoogle Scholar
  4. Chung PJ, Kim JK (2009) Epigenetic interaction of OsHDAC1 with the OsNAC6 gene promoter regulates rice root growth. Plant Signal Behav 4(7):675–677PubMedCrossRefGoogle Scholar
  5. Dash S, Van Hemert J, Hong L, Wise RP, Dickerson JA (2011) PLEXdb: gene expression resources for plants and plant pathogens. Nucleic Acids Res 40(Database issue):D1194–D1201PubMedGoogle Scholar
  6. Deluc L, Barrieu F, Marchive C, Lauvergeat V, Decendit A, Richard T, Carde JP, Merillon JM, Hamdi S (2006) Characterization of a grapevine R2R3-MYB transcription factor that regulates the phenylpropanoid pathway. Plant Physiol 140(2):499–511PubMedCrossRefGoogle Scholar
  7. Duval M, Hsieh TF, Kim SY, Thomas TL (2002) Molecular characterization of AtNAM: a member of the Arabidopsis NAC domain superfamily. Plant Mol Biol 50(2):237–248PubMedCrossRefGoogle Scholar
  8. Flagel LE, Wendel JF (2009) Gene duplication and evolutionary novelty in plants. New Phytol 183(3):557–564PubMedCrossRefGoogle Scholar
  9. Guo Y, Gan S (2006) AtNAP, a NAC family transcription factor, has an important role in leaf senescence. Plant J 46(4):601–612PubMedCrossRefGoogle Scholar
  10. Guo AY, Zhu QH, Chen X, Luo JC (2007) [GSDS: a gene structure display server]. Yi Chuan 29(8):1023–1026PubMedCrossRefGoogle Scholar
  11. Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J (2007) qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol 8:R19PubMedCrossRefGoogle Scholar
  12. Hu R, Qi G, Kong Y, Kong D, Gao Q, Zhou G (2010) Comprehensive analysis of NAC domain transcription factor gene family in Populus trichocarpa. BMC Plant Biol 10:145PubMedCrossRefGoogle Scholar
  13. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pe ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quetier F, Wincker P (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449(7161):463–467PubMedCrossRefGoogle Scholar
  14. Kim SG, Park CM (2007) Membrane-mediated salt stress signaling in flowering time control. Plant Signal Behav 2(6):517–518PubMedCrossRefGoogle Scholar
  15. Kim SY, Kim SG, Kim YS, Seo PJ, Bae M, Yoon HK, Park CM (2007) Exploring membrane-associated NAC transcription factors in Arabidopsis: implications for membrane biology in genome regulation. Nucleic Acids Res 35(1):203–213PubMedCrossRefGoogle Scholar
  16. Ko JH, Yang SH, Park AH, Lerouxel O, Han KH (2007) ANAC012, a member of the plant-specific NAC transcription factor family, negatively regulates xylary fiber development in Arabidopsis thaliana. Plant J 50(6):1035–1048PubMedCrossRefGoogle Scholar
  17. Le DT, Nishiyama R, Watanabe Y, Mochida K, Yamaguchi-Shinozaki K, Shinozaki K, Tran LS (2011) Genome-wide survey and expression analysis of the plant-specific NAC transcription factor family in soybean during development and dehydration stress. DNA Res 18(4):263–276PubMedCrossRefGoogle Scholar
  18. Matus JT, Poupin MJ, Canon P, Bordeu E, Alcalde JA, Arce-Johnson P (2010) Isolation of WDR and bHLH genes related to flavonoid synthesis in grapevine (Vitis vinifera L.). Plant Mol Biol 72(6):607–620Google Scholar
  19. Michelmore RW, Meyers BC (1998) Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res 8(11):1113–1130PubMedGoogle Scholar
  20. Nakashima K, Tran LS, Van Nguyen D, Fujita M, Maruyama K, Todaka D, Ito Y, Hayashi N, Shinozaki K, Yamaguchi-Shinozaki K (2007) Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J 51(4):617–630PubMedCrossRefGoogle Scholar
  21. Nuruzzaman M, Manimekalai R, Sharoni AM, Satoh K, Kondoh H, Ooka H, Kikuchi S (2010) Genome-wide analysis of NAC transcription factor family in rice. Gene 465(1–2):30–44PubMedCrossRefGoogle Scholar
  22. Ohnishi T, Sugahara S, Yamada T, Kikuchi K, Yoshiba Y, Hirano HY, Tsutsumi N (2005) OsNAC6, a member of the NAC gene family, is induced by various stresses in rice. Genes Genet Syst 80(2):135–139PubMedCrossRefGoogle Scholar
  23. Ooka H, Satoh K, Doi K, Nagata T, Otomo Y, Murakami K, Matsubara K, Osato N, Kawai J, Carninci P, Hayashizaki Y, Suzuki K, Kojima K, Takahara Y, Yamamoto K, Kikuchi S (2003) Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res 10(6):239–247PubMedCrossRefGoogle Scholar
  24. Riano-Pachon DM, Ruzicic S, Dreyer I, Mueller-Roeber B (2007) PlnTFDB: an integrative plant transcription factor database. BMC Bioinforma 8:42CrossRefGoogle Scholar
  25. Ruijter JM, Ramakers C, Hoogaars WMH, Karlen Y, Bakker O, van den Hoff MJB, Moorman AFM (2009) Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res 37:e45PubMedCrossRefGoogle Scholar
  26. Takada S, Hibara K, Ishida T, Tasaka M (2001) The CUP-SHAPED COTYLEDON1 gene of Arabidopsis regulates shoot apical meristem formation. Development 128(7):1127–1135PubMedGoogle Scholar
  27. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739PubMedCrossRefGoogle Scholar
  28. Tran LS, Quach TN, Guttikonda SK, Aldrich DL, Kumar R, Neelakandan A, Valliyodan B, Nguyen HT (2009) Molecular characterization of stress-inducible GmNAC genes in soybean. Mol Genet Genomics 281(6):647–664PubMedCrossRefGoogle Scholar
  29. Vroemen CW, Mordhorst AP, Albrecht C, Kwaaitaal MA, de Vries SC (2003) The CUP-SHAPED COTYLEDON3 gene is required for boundary and shoot meristem formation in Arabidopsis. Plant Cell 15(7):1563–1577PubMedCrossRefGoogle Scholar
  30. Wang X, Basnayake BM, Zhang H, Li G, Li W, Virk N, Mengiste T, Song F (2009) The Arabidopsis ATAF1, a NAC transcription factor, is a negative regulator of defense responses against necrotrophic fungal and bacterial pathogens. Mol Plant Microbe Interact 22(10):1227–1238PubMedCrossRefGoogle Scholar
  31. Wang Y, Wang X, Tang H, Tan X, Ficklin SP, Feltus FA, Paterson AH (2011) Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. PLoS ONE 6(12):e28150PubMedCrossRefGoogle Scholar
  32. Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H, Kissinger JC, Paterson AH (2012) MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids ResGoogle Scholar
  33. Zhao C, Avci U, Grant EH, Haigler CH, Beers EP (2008) XND1, a member of the NAC domain family in Arabidopsis thaliana, negatively regulates lignocellulose synthesis and programmed cell death in xylem. Plant J 53(3):425–436PubMedCrossRefGoogle Scholar
  34. Zhu T, Nevo E, Sun D, Peng J (2012a) Phylogenetic analyses unravel the evolutionary history of Nac proteins in plants. Evolution 66(6):1833–1848PubMedCrossRefGoogle Scholar
  35. Zhu Z, Shi J, He M, Cao J, Wang Y (2012b) Isolation and functional characterization of a transcription factor VpNAC1 from Chinese wild Vitis pseudoreticulata. Biotechnol Lett 34(7):1335–1342PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  1. 1.Key Laboratory of Plant Germplasm Enhancement and Speciality AgricultureWuhan Botanical Garden, Chinese Academy of SciencesWuhanChina
  2. 2.Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant ResourcesInstitute of Botany, Chinese Academy of SciencesBeijingPeople’s Republic of China
  3. 3.Graduate School of Chinese Academy of SciencesBeijingChina

Personalised recommendations