Plant Molecular Biology

, Volume 99, Issue 6, pp 603–620 | Cite as

Genome-wide analysis of the Chinese cabbage IQD gene family and the response of BrIQD5 in drought resistance

  • Jingping Yuan
  • Tongkun Liu
  • Zhanghong Yu
  • Yan Li
  • Haibo Ren
  • Xilin Hou
  • Ying LiEmail author


Key message

Thirty-five IQD genes were identified and analysed in Chinese cabbage and BrIQD5 transgenic plants enhanced the drought resistance of plants.


The IQD (IQ67-domain) family plays an important role in various abiotic stress responses in plant species. However, the roles of IQD genes in the Chinese cabbage response to abiotic stress remain unclear. Here, 35 IQD genes, from BrIQD1 to BrIQD35, were identified in Chinese cabbage (Brassica rapa ssp. pekinensis). Based on the phylogenetic analysis, these genes were clustered into three subfamilies (I-III), and members within the same subfamilies shared conserved exon–intron distribution and motif composition. The 35 BrIQD genes were unevenly distributed on 9 of the 10 chromosomes with 4 segmental duplication events. Ka/Ks ratios showed that the duplicated BrIQDs had mainly experienced strong purifying selection. Quantitative real-time polymerase chain reaction of 35 BrIQDs under PEG6000 indicated that BrIQD5 was significantly induced by PEG6000. To verify BrIQD5 function, BrIQD5 was heterologously overexpressed in tobacco and was silenced in Chinese cabbage. BrIQD5-overexpressed plants showed more tolerance to drought stress than wild-type plants, while BrIQD5-silenced plants in Chinese cabbage showed decreased drought tolerance. Additionally, six BrIQD5 potential interactive proteins were isolated by the yeast two-hybrid assay, including BrCaMa, BrCaMb and four other stress-related proteins. Motif IQ1 of BrIQD5 is important for the interaction with BrCaMa and BrCaMb, and the isoleucine in motif IQ1 is an essential amino acid for calmodulin binding to BrIQD5. The identification and cloning of the new Chinese cabbage drought tolerance genes will promote the drought-resistant breeding of Chinese cabbage and help to better understand the mechanism of IQD involved in the drought tolerance of plants.


BrIQD5 Chinese cabbage Drought stress IQD genes Overexpression Virus-induced gene silencing 



This work was supported by the National Natural Science Foundation of China (Nos. 31471886 and 31872106) and National Vegetable Industry Technology System (CARS-23-A-06), Jiangsu Modern Agriculture (vegetable) Industrial Technology System (SXGC [2017] 273), and a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions.

Author contributions

YL (Ying Li) and XLH conceived and designed the experiments. JPY, TKL and ZHY performed the experiments. YL (Yan Li) and HBR performed the qRTPCR. JPY wrote the manuscript. All authors read and approved the final manuscript.

Supplementary material

11103_2019_839_MOESM1_ESM.docx (4 mb)
Supplementary material 1 (DOCX 4146 KB)


  1. Abel S, Savchenko T, Levy M (2005) Genome-wide comparative analysis of the IQD gene families in Arabidopsis thaliana and Oryza sativa. BMC Evol Biol 5:72–84Google Scholar
  2. Bähler M, Rhoads A (2002) Calmodulin signaling via the IQ motif. FEBS Lett 513(1):107–113Google Scholar
  3. Bailey TL, Elkan C (1995) The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Sys Mol Biol 3:21–29Google Scholar
  4. Bao F, Du DL, An Y, Yang WR, Wang J, Cheng TR, Zhang QX (2017) Overexpression of prunus mume dehydrin genes in tobacco enhances tolerance to cold and drought. Front Plant Sci 8:151Google Scholar
  5. Bhattacharya S, Bunick CG, Chazin WJ (2004) Target selectivity in EF-hand calcium binding proteins. BBA-Mol Cell Res 1742(1):69–79Google Scholar
  6. Blanc G, Wolfe KH (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667–1678Google Scholar
  7. Bouché N, Yellin A, Snedden WA, Fromm H (2005) Plant-specific calmodulin-binding proteins. Annu Rev Plant Biol 56:435–466Google Scholar
  8. Bürstenbinder K, Savchenko T, Müller J, Adamson AW, Stamm G, Kwong R, Zipp BJ, Dinesh DC, Abel S (2013) Arabidopsis calmodulin-binding protein IQ67-domain 1 localizes to microtubules and interacts with kinesin light chain-related protein-1. J Biol Chem 288:1871–1882Google Scholar
  9. Cai R, Zhang C, Zhao Y, Zhu K, Wang Y, Jiang H, Xiang Y, Cheng B (2016) Genome-wide analysis of the IQD gene family in maize. Mol Genet Genomic 291:543–558Google Scholar
  10. Chen CN, Chu CC, Zentella R, Pan SM, Ho THD (2002) Athva22 gene family in Arabidopsis: phylogenetic relationship, ABA and stress regulation, and tissue-specific expression. Plant Mol Biol 49:631–642Google Scholar
  11. Choi JY et al (2002) Identification of calmodulin isoform-specific binding peptides from a phage-displayed random 22-mer peptide library. J Biol Chem 277(24):21630–21638Google Scholar
  12. Clapperton JA, Martin SR, Smerdon SJ, Gamblin SJ, Bayley PM (2002) Structure of the complex of calmodulin with the target sequence of calmodulin-dependent protein kinase I: studies of the kinase activation mechanism. Biochemistry 41(50):14669–14679Google Scholar
  13. Day IS, Reddy VS, Ali GS, Reddy A (2002) Analysis of EF-hand-containing proteins in Arabidopsis. Genome Bio 3(10):RESEARCH0056Google Scholar
  14. Dodd AN, Kudla J, Sanders D (2010) The language of calcium signaling. Annu Rev Plant Bio 61:593–620Google Scholar
  15. Emanuelsson O, Nielsen H, Brunak S, Heijne GV (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300:1005–1016Google Scholar
  16. Filiz E, Tombuloglu H, Ozyi̇gi̇t II (2013) Genome-wide analysis of IQ67 domain (IQD) gene families in Brachypodium distachyon. Plant Omics 6:425–432Google Scholar
  17. Fischer C, Kugler A, Hoth S, Dietrich P (2013) An IQ domain mediates the interaction with calmodulin in a plant cyclic nucleotide-gated channel. Plant Cell Physiol 54:573–584Google Scholar
  18. Gornall J, Betts R, Burke E, Clark R, Camp J, Willett K, Wiltshire A (2010) Implications of climate change for agricultural productivity in the early twenty-first century. PhilosT R Soc B 365:2973–2989Google Scholar
  19. Hoeflich KP, Ikura M (2002) Calmodulin in action: diversity in target recognition and activation mechanisms. Cell 108:739–742Google Scholar
  20. Huang GB, Zhang XH, Yang SL, Li JY, Xu CH, Rong ZY, Yang LY, Gong M (2012) Involvement of osmotic regulation in enhancement of drought resistance in tobacco (Nicotiana tabacum L.) plants through circular drought-hardening. J Plant Physiol 48:465–471Google Scholar
  21. Huang ZJ, Houten JV, Gonzalez G, Xiao H, Knaap EV (2013) Genome-wide identification, phylogeny and expression analysis of SUN, OFP and YABBY gene family in tomato. Mol Genet Genomics 288:111–129Google Scholar
  22. Irigoyen JJ, Einerich DW, Sánchez-Díaz M (1992) Water stress induced changes in concentrations of proline and total soluble sugars in nodulated alfalfa (Medicago sativd) plants. Physiol Plantarum 84:55–60Google Scholar
  23. Koch MA, Haubold B, Mitchell-Olds T (2000) Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol Biol Evol 17:1483–1498Google Scholar
  24. Letunic I, Doerks T, Bork P (2012) SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res 40:302–305Google Scholar
  25. Levy M, Wang Q, Kaspi R, Parrella MP, Abel S (2005) Arabidopsis IQD1, a novel calmodulin-binding nuclear protein, stimulates glucosinolate accumulation and plant defense. Plant J 43:79–96Google Scholar
  26. Li Z, Jiang HY, Zhou LY, Deng L, Lin YX, Peng XJ, Yan HW, Cheng BJ (2014) Molecular evolution of the HD-ZIP I gene family in legume genomes. Gene 533:218–228Google Scholar
  27. Li KQ, Xing CH, Yao ZH, Huang XS (2017) PbrMYB21, a novel MYB protein of Pyrus betulaefolia, functions in drought tolerance and modulates polyamine levels by regulating arginine decarboxylase gene. Plant Biotechnol J 15:1186–1203Google Scholar
  28. Lim YP, Plaha P, Choi SR, Uhm T, Hong CP, Bang J, Hur YK (2006) Toward unraveling the structure of Brassica rapa genome. Physiol Plantarum 126:585–591Google Scholar
  29. Lin F, Zhu C, Hui M, Xue C, Yuan L, Wang YY, Yan X (2014) The IQD gene family in soybean: structure, phylogeny, evolution and expression. PLoS ONE 9:e110896Google Scholar
  30. Liu X, Liu S, Wu JL, Zhang BY, Li XY, Yan YC, Li L (2013) Overexpression of Arachis hypogaea NAC3 in tobacco enhances dehydration and drought tolerance by increasing superoxide scavenging. Plant Physiol Biochem 70(1):354–359Google Scholar
  31. Liu DQ, Han Q, Shah T, Chen CY, Wang Q, Tang BF, Ge F (2018) A hybrid proline-rich cell-wall protein gene JsPRP1, from Juglans sigillata Dode confers both biotic and abiotic stresses in transgenic tobacco plants. Trees 32(5):1–11Google Scholar
  32. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2– ∆∆CT method. Methods 25:402–408Google Scholar
  33. Ma H, Feng L, Chen Z, Chen X, Zhao HL, Xiang Y (2014) Genome-wide identification and expression analysis of the IQD gene family in Populus trichocarpa. Plant Sci 229:96–110Google Scholar
  34. Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y (2005) Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci 102:5454–5459Google Scholar
  35. Mittler R (2002) Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci 7:405–410Google Scholar
  36. Moons A, Valcke R, Van Montagu M (2010) Low-oxygen stress and water deficit induce cytosolic pyruvate orthophosphate dikinase (PPDK) expression in roots of rice, a C3 plant. Plant J 15(1):89–98Google Scholar
  37. Park JS, Yu JG, Park YD (2017) Characterization of a drought tolerance-related gene of Brassica rapa in a transgenic tobacco plant. Hortic Environ Biot 58:48–55Google Scholar
  38. Park JS, Yu JG, Lee GH, Park YD (2018) Drought tolerance induction in transgenic tobacco through RNA interference of BrDST71, a drought-responsive gene from Chinese cabbage. Hortic Environ Biote 59(5):749–757Google Scholar
  39. Peng S, Huang ZC, Ou YLJ, Cheng J, Zeng FH (2011) Research progress of artificial promoter in plant genetic engineering. Plant Physiol J 47(2):141–146 (in chinese)Google Scholar
  40. Perochon A, Aldon D, Galaud JP, Ranty B (2011) Calmodulin and calmodulin-like proteins in plant calcium signaling. Biochimie 93:2048–2053Google Scholar
  41. Puhakainen T, Hess MW, Mäkelä P, Svensson J, Heino P, Palva ET (2004) Overexpression of multiple dehydrin genes enhances tolerance to freezing stress in Arabidopsis. Plant Mol Biol 54:743–753Google Scholar
  42. Rochfort SJ, Imsic M, Jones R, Trenerry VC, Tomkins B (2006) Characterization of flavonol conjugates in immature leaves of pakchoi [Brassica rapa L. ssp. chinensis L. (Hanelt.)] by HPLC-DAD and LC-MS / MS. J Agric Food Chem 54:4855–4860Google Scholar
  43. Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, Li J, Thiagarajan M, White JA, Quackenbush J (2006) TM4 microarray software suite. Method Enzymol 411(2):134–193Google Scholar
  44. Shen Q, Chen CN, Brands A, Pan SM, Ho TH (2001) The stress- and abscisic acid-induced barley gene hva22: developmental regulation and homologues in diverse organisms. Plant Mol Biol 45:327–340Google Scholar
  45. Snedden WA, Fromm H (1998) Calmodulin, calmodulin-related proteins and plant responses to the environment. Trends Plant Sci 3:299–304Google Scholar
  46. Snedden WA, Fromm H (2001) Calmodulin as a versatile calcium signal transducer in plants. New Phytol 151:35–66Google Scholar
  47. Stagge JH, Kohn I, Tallaksen LM, Stahl K (2015) Modeling drought impact occurrence based on meteorological drought indices in Europe. J Hydrol 530:37–50Google Scholar
  48. 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 28:2731–2739Google Scholar
  49. Tian CG, Zhou YP (2014) Research progress in plant IQ motif-containing calmodulin-binding proteins. Chin Bull Bot 48:447–460Google Scholar
  50. Wang LQ, Guo K, Li Y, Tu YY, Hu HZ, Wang BR, Cui XC, Peng LC (2010) Expression profiling and integrative analysis of the CESA/CSL superfamily in rice. BMC Plant Biol 10(1):282–297Google Scholar
  51. Wang X, Wang H, Wang J (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039Google Scholar
  52. Wu M, Li Y, Chen D, Liu H, Zhu D, Xiang Y (2016) Genome-wide identification and expression analysis of the IQD gene family in moso bamboo (Phyllostachys edulis). Sci Rep 6:24520Google Scholar
  53. Xia XJ, Gao CJ, Song LX, Zhou YH, Shi K, Yu JQ (2014) Role of H2O2 dynamics in brassinosteroid-induced stomatal closure and opening in Solanum lycopersicum. Plant Cell Environ 37:2036–2050Google Scholar
  54. Xiao BZ, Chen X, Xiang CB, Tang N, Zhang QF, Xiong LZ (2009) Evaluation of seven function known candidate genes for their effects on improving drought resistance of transgenic rice under field conditions. Mol Plant 2:73–83Google Scholar
  55. Xiong L, Schumaker KS, Zhu JK (2002) Cell signaling during cold, drought, and salt stress. Plant Cell 14:165–183Google Scholar
  56. Yu J, Yang XD, Wang Q, Gao LW, Yang Y, Xiao D, Liu TK, Li Y, Hou XL, Zhang CW (2018) Efficient virus-induced gene silencing in Brassica rapa, using a turnip yellow mosaic virus vector. Biol Plantarum 62(4):826–834Google Scholar
  57. Yue YS, Zhang MC, Zhang JC, Duan LS, Li ZH (2011) Arabidopsis LOS5/ABA3, overexpression in transgenic tobacco (Nicotiana tabacum, cv. Xanthi-nc) results in enhanced drought tolerance. Plant Sci 181(4):405–411Google Scholar
  58. Zentella R, Zhang ZL, Park M (2007) Global analysis of DELLA direct targets in early gibberellin signaling in Arabidopsis. Plant Cell 19:3037–3057Google Scholar
  59. Zhang Z, Li J, Zhao XQ, Wang J, Wong GK, Yu J (2006) KaKs calculating Ka and Ks through model selection and model averaging. Genom Proteom Bioinf 4:259–263Google Scholar
  60. Zhang L, Tian LH, Zhao JF, Song Y, Zhang CJ, Guo Y (2009) Identification of an apoplastic protein involved in the initial phase of salt stress response in rice root by two-dimensional electrophoresis. Plant Physiol 149:916–928Google Scholar
  61. Zhou YH, Lam HM, Zhang JH (2007) Inhibition of photosynthesis and energy dissipation induced by water and high light stresses in rice. J Exp Bot 58:1207–1217Google Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Jingping Yuan
    • 1
  • Tongkun Liu
    • 1
  • Zhanghong Yu
    • 1
  • Yan Li
    • 1
  • Haibo Ren
    • 1
  • Xilin Hou
    • 1
  • Ying Li
    • 1
    Email author
  1. 1.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of HorticultureNanjing Agricultural UniversityNanjingChina

Personalised recommendations