Skip to main content
SpringerLink
Log in

Genome-wide identification of Aux/IAA and ARF gene families in bread wheat (Triticum aestivum L.)

  • Original Article
  • Published:
Protoplasma Aims and scope Submit manuscript

Abstract

Wheat (Triticum aestivum L.) is one of the most important food crops in the world. Somatic embryogenesis is an event that is triggered by the presence of auxin hormone for the induction of somatic cells to get converted to embryonic cells. Somatic embryogenesis represents the most important process of totipotency of plants. The role of auxins is widely understood during various stages of embryogenesis including polarity establishment, de-differentiation, re-differentiations, and morphogenesis. Many of the Aux/IAAs and ARFs which are part of auxin signaling components have been identified to play various roles during embryogenesis. In this analysis, the Aux/IAAs and ARFs of T. aestivum have been analyzed at the genome-scale; their structure, function, and evolutionary relatedness were determined. Several Aux/IAAs and ARFs components of T. aestivum have been found to exclusively regulate axis formation, meristem commitment, and other re-differentiation processes by differential expression studies.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

References

  • Bailey TL, Boden M, Buske FA et al (2009) MEME Suite: tools for motif discovery and searching. Nucleic Acids Res 37:202–208

    Article  Google Scholar 

  • Bassuner BM, Lam R, Lukowitz W, Yeung EC (2006) Auxin and root initiation in somatic embryos of Arabidopsis. Plant Cell Rep 26:1–11

    Article  Google Scholar 

  • Bjellqvist B, Basse B, Olsen E, Celis JE (1994) Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 15(1):529–539

    Article  CAS  Google Scholar 

  • Boer DR, Freire-Rios A, Van den Berg WA, Saaki T, Manfield IW, Kepinski S, Lopez-Vidrieo I, Franco-Zorrilla JM, De Vries SC, Solano R et al (2014) Structural basis for DNA binding specificity by the auxin-dependent ARF transcription factors. Cell 156:577–589

    Article  CAS  Google Scholar 

  • Dinesh DC, Kovermann M, Gopalswamy M, Hellmuth A, Calderon Villalobos LI, Lilie H, Balbach J, Abel S (2015) Solution structure of the PsIAA4 oligomerization domain reveals interaction modes for transcription factors in early auxin response. Proc Natl Acad Sci 112:6230–6235

    Article  CAS  Google Scholar 

  • Gliwicka M, Nowak K, Balazadeh S, Mueller-Roeber B, Gaj MD (2013) Extensive modulation of the transcription factor transcriptome during somatic embryogenesis in Arabidopsis thaliana. PLoS ONE 8:69261

    Article  Google Scholar 

  • Grones P, Friml J (2015) Auxin transporters and binding proteins at a glance. J Cell Sci 128:1–7

    Article  CAS  Google Scholar 

  • Hagen G, Guilfoyle T (2002) Auxin-responsive gene expression: genes, promoters, and regulatory factors. Plant Mol Biol 49:373–385

    Article  CAS  Google Scholar 

  • Hu B, Jin J, Guo A-Y et al (2015) GSDS 2.0: an upgraded gene features visualization server. Bioinformatics 31:1296–1297

    Article  Google Scholar 

  • International Wheat Genome Sequencing Consortium (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361

  • Jarosova J, Kundu JK (2010) Validation of reference genes as internal control for studying viral infections in cereals by quantitative real-time RT-PCR. BMC Plant Biol 10:146

    Article  Google Scholar 

  • Jing H, Yang X, Zhang J, Liu X, Zheng H, Dong G, Nian J, Feng J, Xia B, Qian Q et al (2015) Peptidyl-prolyl isomerization targets rice Aux/IAAs for proteasomal degradation during auxin signalling. Nat Commun 6:7395

    Article  CAS  Google Scholar 

  • Kang H, Lee CB, Kwon SH (2021) Comparative transcriptome analysis during developmental stages of direct somatic embryogenesis in Tilia amurensis Rupr. Sci Rep 11:6359

    Article  CAS  Google Scholar 

  • Kazan K (2013) Auxin and the integration of environmental signals into plant root development. Ann Bot 112:1655–1665

    Article  Google Scholar 

  • Kazan K, Lyons R (2014) Intervention of phytohormone pathways by pathogen effectors. Plant Cell 26:2285–2309

    Article  CAS  Google Scholar 

  • Kepinski S, Leyser O (2004) Auxin-induced SCF/TIR1-Aux/IAA interaction involves stable modification of the SCF/TIR1 complex. Proc Natl Acad Sci 101:12381–12386

    Article  CAS  Google Scholar 

  • Kepinski S, Leyser O (2005) The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature 435:446–451

    Article  CAS  Google Scholar 

  • Kieffer M, Neve J, Kepinski S (2010) Defining auxin response contexts in plant development. Curr Opin Plant Biol 13:12–20

    Article  CAS  Google Scholar 

  • Lin Y, Lai Z, Tian Q, Lin L, Lai R, Yang M et al (2015) Endogenous target mimics down-regulate miR160 mediation of ARF10, -16 and -17 cleavage during somatic embryogenesis in Dimocarpus longan Lour. Front Plant Sci 6:956

    Article  Google Scholar 

  • Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21:3448–3449

    Article  CAS  Google Scholar 

  • Mahalakshmi A, Khurana P, Khurana JP (2003) Rapid induction of somatic embryogenesis by 2,4-D in leaf base cultures of wheat (Triticum aestivum L.). Plant Biotechnol 20:267–273

    Article  CAS  Google Scholar 

  • Mahalakshmi A, Singla B, Khurana JP, Khurana P (2007) Role of calcium–calmodulin in auxin-induced somatic embryogenesis in leaf base cultures of wheat (Triticum aestivum var. HD 2329). Plant Cell Tissue Organ Cult 88:167–174

    Article  CAS  Google Scholar 

  • Maraschin FS, Memelink J, Offringa R (2009) Auxin-induced, SCF(TIR1)-mediated poly-ubiquitination marks Aux/IAA proteins for degradation. Plant J 59:100–109

    Article  CAS  Google Scholar 

  • Ooi SE, Choo CN, Ishak Z, Ong-Abdullah M (2012) A candidate auxin-responsive expression marker gene, e.g., IAA9, for somatic embryogenesis in oil palm (Elaeis guineensis Jacq.). Plant Cell Tissue Organ Cult 110:201–212

    Article  CAS  Google Scholar 

  • Piya S, Shrestha SK, Binder B, Stewart CN Jr, Hewezi T (2014) Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis. Front Plant Sci 5:744

    Article  Google Scholar 

  • Qiao L, Zhang X, Han X, Zhang L, Li X, Zhan H, Ma J, Luo P, Zhang W, Cui L et al (2015) A genome-wide analysis of the auxin/indole-3-acetic acid gene family in hexaploid bread wheat (Triticum aestivum L.). Front Plant Sci 6:770

  • Qiao L et al (2018) Characterization and expression patterns of auxin response factors in Wheat. Front Plant Sci 9:1395

    Article  Google Scholar 

  • Reed JW (2001) Roles and activities of Aux/IAA proteins in Arabidopsis. Trends Plant Sci 6:420–425

    Article  CAS  Google Scholar 

  • Sato A, Yamamoto KT (2008) What’s the physiological role of domain II-less Aux/IAA proteins? Plant Signal Behav 3:496–497

    Article  Google Scholar 

  • Schaller GE, Bishopp A, Kieber JJ (2015) The yin-yang of hormones: cytokinin and auxin interactions in plant development. Plant Cell 27:44–63

    Article  CAS  Google Scholar 

  • Shannon P, Markiel A, Ozier O et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504

    Article  CAS  Google Scholar 

  • Shi Qi, Zhang Y, To V-T, Shi J, Zhang D, Cai W (2020) Genome-wide characterization and expression analyses of the auxin/indole-3-acetic acid (Aux/IAA) gene family in barley (Hordeum vulgare L.) Sci Rep 10:10242

  • Singla B, Tyagi AK, Khurana JP, Khurana P (2007) Analysis of expression profile of selected genes expressed during auxin-induced somatic embryogenesis in leaf base system of wheat (Triticum aestivum) and their possible interactions. Plant Mol Biol 65:677–692

    Article  CAS  Google Scholar 

  • Smet ID, Jurgens G (2007) Patterning the axis in plants–auxin in control. Curr Opin Genet Dev 17:337–343

    Article  Google Scholar 

  • Tiwari SB, Hagen G, Guilfoyle T (2003) The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell 15:533–543

    Article  CAS  Google Scholar 

  • Wang Y, Deng D, Bian Y, Lv Y, Qin X (2010) Genome-wide analysis of primary auxin-responsive Aux/IAA gene family in maize (Zea mays L.). Mol Biol Rep 37:3991–4001

    Article  CAS  Google Scholar 

  • Winkler M, Niemeyer M, Hellmuth A, Janitza P, Christ G, Samodelov SL, Wilde V, Majovsky P, Trujillo M, Zurbriggen MD et al (2017) Variation in auxin sensing guides Aux/IAA transcriptional repressor ubiquitylation and destruction. Nat Commun 8:15706

    Article  CAS  Google Scholar 

  • Woodward AW, Bartel B (2005) Auxin: regulation, action, and interaction. Annu Rev Plant Biol 95:707–735

    CAS  Google Scholar 

  • Yang JH, Han SJ, Yoon EK, Lee WS (2006) Evidence of an auxin signal pathway, microRNA167-ARF8-GH3, and its response to exogenous auxin in cultured rice cells. Nucleic Acids Res 34:1892–1899

    Article  CAS  Google Scholar 

Download references

Acknowledgements

Authors are thankful to Department of Biotechnology and Department of Science &Technology-Fund for Improvement of S&T Infrastructure (DST-FIST) and JC Bose National Fellowship to PK of the Science and Engineering Research Board (SERB) for the financial support.

Author information

Authors and Affiliations

  1. Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India

    Chanderkant Chaudhary, Nikita Sharma & Paramjit Khurana

Authors
  1. Chanderkant Chaudhary
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nikita Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Paramjit Khurana
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

CC and NS performed the experiments. CC and PK wrote and formatted the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Paramjit Khurana.

Ethics declarations

Conflicts of interest

The authors declare that they do not have any conflict of interest.

Additional information

Handling Editor: Pengguo Xia

Publisher's note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

709_2022_1773_MOESM1_ESM.tiff

Supplementary Table 1 Summary of structural features such as locus id, gene name, gene length, protein length, intron number, isoelectric point (PI) and molecular weight (MW) identified for the Triticum Aux/IAA gene family (TIFF 2197 KB)

709_2022_1773_MOESM2_ESM.tiff

Supplementary Table 2 Summary of structural features such as locus id, gene name, gene length, protein length, intron number, isoelectric point (PI) and molecular weight (MW) identified for the Triticum ARF gene family (TIFF 2197 KB)

Supplementary Table 3 List of primers used for qPCR of TaIAAs and TaARFs (TIFF 2197 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chaudhary, C., Sharma, N. & Khurana, P. Genome-wide identification of Aux/IAA and ARF gene families in bread wheat (Triticum aestivum L.). Protoplasma 260, 257–270 (2023). https://doi.org/10.1007/s00709-022-01773-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00709-022-01773-y

Keywords

Search

Navigation