Skip to main content
SpringerLink
Log in

Identification and characterization of a new dwarf locus DS-4 encoding an Aux/IAA7 protein in Brassica napus

  • Original Article
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Key message

A dominant dwarfing gene, ds - 4 , encodes an Aux/IAA protein that negatively regulates plant stature through an auxin signaling pathway.

Abstract

Dwarfism is an important agronomic trait affecting yield in many crop species. The molecular mechanisms underlying dwarfism in oilseed rape (Brassica napus) are poorly understood, restricting the progress of breeding dwarf varieties in this species. Here, we identified and characterized a new dwarf locus, DS-4, in B. napus. Next-generation sequencing-assisted genetic mapping and candidate gene analysis found that DS-4 encodes a nucleus-targeted auxin/indole-3-acetic acid (Aux/IAA) protein. A substitution (P87L) was found in the highly conserved degron motif of the Aux/IAA7 protein in the ds-4 mutant. This mutation co-segregated with the phenotype of individuals in the BC1F2 population. The P87L substitution was confirmed as the cause of the extreme dwarf phenotype by ectopic expression of the mutant allele BnaC05.iaa7 (equivalent to ds-4) in Arabidopsis. The P87L substitution blocked the interaction of BnaC05.iaa7 with TRANSPORT INHIBITOR RESPONSE 1 in the presence of auxin. The BnaC05.IAA7 gene is highly expressed in the cotyledons, hypocotyls, stems and leaves, but weakly in the roots and seeds of B. napus. Our findings provide new insights into the molecular mechanisms underlying dominant (gain-of-function) dwarfism in B. napus. Our identification of a distinct gene locus controlling plant height may help to improve lodging resistance in oilseed rape.

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

Similar content being viewed by others

References

  • Calderon-Villalobos LI, Tan X, Zheng N et al (2010) Auxin perception–structural insights. Cold Spring Harbor Perspect Biol 2:a005546

    Article  CAS  Google Scholar 

  • Campbell NR, Harmon SA, Narum SR (2015) Genotyping-in-thousands by sequencing (GT-seq): a cost effective SNP genotyping method based on custom amplicon sequencing. Mol Ecol Resour 15:855–867

    Article  CAS  PubMed  Google Scholar 

  • Cassani E, Bertolini E, Cerino Badone F et al (2009) Characterization of the first dominant dwarf maize mutant carrying a single amino acid insertion in the VHYNP domain of the dwarf8 gene. Mol Breed 24:375–385

    Article  CAS  Google Scholar 

  • Chalhoub B, Denoeud F, Liu S et al (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345:950–953

    Article  CAS  PubMed  Google Scholar 

  • Chen R, Rosen E, Masson PH (1999) Gravitropism in higher plants. Plant Physiol 120:343–350

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen Y, Hou MM, Liu LJ et al (2014) The maize DWARF1 encodes a gibberellin 3-oxidase and is dual localized to the nucleus and cytosol. Plant Physiol 166:2028–2039

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16:735–743

    Article  CAS  PubMed  Google Scholar 

  • Davière J-M, Achard P (2016) A pivotal role of DELLAs in regulating multiple hormone signals. Mol Plant 9:10–20

    Article  CAS  PubMed  Google Scholar 

  • Dinesh DC, Villalobos LIAC, Abel S (2016) Structural biology of nuclear auxin action. Trends Plant Sci 21:302–316

    Article  CAS  PubMed  Google Scholar 

  • Doyle JJ (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    Google Scholar 

  • Foisset N, Delourme R, Barret P et al (1995) Molecular tagging of the dwarf BREIZH (Bzh) gene in Brassica napus. Theor Appl Genet 91:756–761

    Article  CAS  PubMed  Google Scholar 

  • Foisset N, Delourme R, Barret P et al (1996) Molecular-mapping analysis in Brassica napus using isozyme, RAPD and RFLP markers on a doubled-haploid progeny. Theor Appl Genet 93:1017–1025

    Article  CAS  PubMed  Google Scholar 

  • Fu J, Ren F, Lu X et al (2016) A tandem array of ent-kaurene synthases in maize with roles in gibberellin and more specialized metabolism. Plant Physiol 170:742–751

    Article  CAS  PubMed  Google Scholar 

  • Gray WM, Kepinski S, Rouse D et al (2001) Auxin regulates SCFTIR1-dependent degradation of AUX/IAA proteins. Nature 414:271–276

    Article  CAS  PubMed  Google Scholar 

  • Griffiths J, Murase K, Rieu I et al (2006) Genetic characterization and functional analysis of the GID1 gibberellin receptors in Arabidopsis. Plant Cell 18:3399–3414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guilfoyle T (2016) The PB1 domain in auxin response factor and Aux/IAA proteins: a versatile protein interaction module in the auxin response. Plant Cell 27:33–43

    Article  CAS  Google Scholar 

  • Hedden P (2003) The genes of the green revolution. Trends Genet 19:5–9

    Article  CAS  PubMed  Google Scholar 

  • Helliwell CA, Poole A, Peacock WJ et al (1999) Arabidopsis ent-kaurene oxidase catalyzes three steps of gibberellin biosynthesis. Plant Physiol 119:507–510

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hobbie L, McGovern M, Hurwitz LR et al (2000) The axr6 mutants of Arabidopsis thaliana define a gene involved in auxin response and early development. Development 127:23–32

    CAS  PubMed  Google Scholar 

  • Itoh H, Ueguchi-Tanaka M, Sakamoto T et al (2002) Modification of rice plant height by suppressing the height-controlling gene, D18, in rice. Breed Sci 52:215–218

    Article  CAS  Google Scholar 

  • Itoh H, Tatsumi T, Sakamoto T et al (2004) A rice semi-dwarf gene, Tan-Ginbozu (D35), encodes the gibberellin biosynthesis enzyme, ent-kaurene oxidase. Plant Mol Biol 54:533–547

    Article  CAS  PubMed  Google Scholar 

  • Jefferson RA, Kavanagh TA, Bevan MW (1987) GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J 6:3901–3907

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Khush GS (2001) Green revolution: the way forward. Nat Rev Genet 2:815–822

    Article  CAS  PubMed  Google Scholar 

  • Li H, Wang Y, Li X et al (2011) A GA-insensitive dwarf mutant of Brassica napus L. correlated with mutation in pyrimidine box in the promoter of GID1. Mol Biol Rep 38:191–197

    Article  CAS  PubMed  Google Scholar 

  • Liscum E, Reed J (2002) Genetics of Aux/IAA and ARF action in plant growth and development. Plant Mol Biol 49:387–400

    Article  CAS  PubMed  Google Scholar 

  • Liu C, Wang J, Huang T et al (2010) A missense mutation in the VHYNP motif of a DELLA protein causes a semi-dwarf mutant phenotype in Brassica napus. Theor Appl Genet 121:249–258

    Article  CAS  PubMed  Google Scholar 

  • Luo J, Zhou J, Zhang J (2018) Aux/IAA gene family in plants: molecular structure, regulation, and function. Int J Mol Sci 19:259

    Article  CAS  PubMed Central  Google Scholar 

  • Mahmood S, Li Z, Yue X et al (2016) Development of INDELs markers in oilseed rape (Brassica napus L.) using re-sequencing data. Mol Breed 36:79

    Article  CAS  Google Scholar 

  • Michelmore RW, Paran I, Kesseli R (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832

    Article  CAS  PubMed  Google Scholar 

  • Miersch S, Gertz A, Breuer F et al (2016) Influence of the semi-dwarf growth type on seed yield and agronomic parameters at low and high nitrogen fertilization in winter oilseed rape. Crop Sci 56:1573–1585

    Article  CAS  Google Scholar 

  • Mockaitis K, Estelle M (2008) Auxin receptors and plant development: a new signaling paradigm. Annu Rev Cell Dev Biol 24:55–80

    Article  CAS  PubMed  Google Scholar 

  • Muangprom A, Thomas SG, Sun TP et al (2005) A novel dwarfing mutation in a green revolution gene from Brassica rapa. Plant Physiol 137:931–938

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Murase K, Hirano Y, Sun TP et al (2008) Gibberellin-induced DELLA recognition by the gibberellin receptor GID1. Nature 456:459–463

    Article  CAS  PubMed  Google Scholar 

  • Nagpal P, Walker LM, Young JC et al (2000) AXR2 encodes a member of the Aux/IAA protein family. Plant Physiol 123:563–574

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ramos JA, Zenser N, Leyser O et al (2001) Rapid degradation of auxin/indoleacetic acid proteins requires conserved amino acids of domain II and is proteasome dependent. Plant Cell 13:2349–2360

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Rinaldi MA, Bartel B, Liu J et al (2012) A gain-of-function mutation in IAA16 confers reduced responses to auxin and abscisic acid and impedes plant growth and fertility. Plant Mol Biol 79:359–373

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sasaki A, Ashikari M, Ueguchi-Tanaka M et al (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416:701–702

    Article  CAS  PubMed  Google Scholar 

  • Schindelin J, Arganda-Carreras I, Frise E et al (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9:676–682

    Article  CAS  PubMed  Google Scholar 

  • Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci USA 99:9043–9048

    Article  CAS  PubMed  Google Scholar 

  • Stepanova AN, Robertson-Hoyt J, Yun J et al (2008) TAA1-mediated auxin biosynthesis is essential for hormone crosstalk and plant development. Cell 133:177–191

    Article  CAS  PubMed  Google Scholar 

  • Takagi H, Abe A, Yoshida K et al (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183

    Article  CAS  PubMed  Google Scholar 

  • Tan X, Calderon-Villalobos LI, Sharon M et al (2007) Mechanism of auxin perception by the TIR1 ubiquitin ligase. Nature 446:640–645

    Article  CAS  PubMed  Google Scholar 

  • Tanabe S, Ashikari M, Fujioka S et al (2005) A novel cytochrome P450 is implicated in brassinosteroid biosynthesis via the characterization of a rice dwarf mutant, dwarf11, with reduced seed length. Plant Cell 17:776–790

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thiel T, Kota R, Grosse I et al (2004) SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development. Nucleic Acids Res 32:e5

    Article  PubMed  PubMed Central  Google Scholar 

  • Timpte C, Wilson AK, Estelle M (1994) The axr2-1 mutation of Arabidopsis thaliana is a gain-of-function mutation that disrupts an early step in auxin response. Genetics 138:1239–1249

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ueguchi-Tanaka M, Nakajima M, Katoh E et al (2007) Molecular interactions of a soluble gibberellin receptor, GID1, with a rice DELLA protein, SLR1, and gibberellin. Plant Cell 19:2140–2155

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • USDA ERS (2017) Oil crops yearbook. https://www.ers.usda.gov/data-products/oil-crops-yearbook.aspx. Accessed 30 Mar 2018

  • Wang M, Zhao Y, Chen F et al (2004) Inheritance and potentials of a mutated dwarfing gene ndf1 in Brassica napus. Plant Breed 123:449–453

    Article  CAS  Google Scholar 

  • Wang B, Wu ZK, Li Z et al (2018) Dissection of the genetic architecture of three seed-quality traits and consequences for breeding in Brassica napus. Plant Biotechnol J 16:1336–1348

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Weijers D, Wagner D (2016) Transcriptional responses to the auxin hormone. Annu Rev Plant Biol 67:539–574

    Article  CAS  PubMed  Google Scholar 

  • Wilson AK, Pickett FB, Turner JC et al (1990) A dominant mutation in Arabidopsis confers resistance to auxin, ethylene and abscisic acid. Mol Genet Genom 222:377–383

    Article  CAS  Google Scholar 

  • Wu J, Kong X, Wan J et al (2011) Dominant and pleiotropic effects of a GAI gene in wheat results from a lack of interaction between DELLA and GID1. Plant Physiol 157:2120–2130

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu Z, Tang D, Liu K et al (2018) Characterization of a new semi-dominant dwarf allele of SLR1 and its potential application in hybrid rice breeding. J Exp Bot 69:4703–4713

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xue W, Xing Y, Weng X et al (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761–767

    Article  CAS  PubMed  Google Scholar 

  • Yamamuro C, Ihara Y, Wu X et al (2000) Loss of function of a rice brassinosteroid insensitive1 homolog prevents internode elongation and bending of the lamina joint. Plant Cell 12:1591–1606

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang X, Lee S, So JH et al (2004) The IAA1 protein is encoded by AXR5 and is a substrate of SCFTIR1. Plant J 40:772–782

    Article  CAS  PubMed  Google Scholar 

  • Yang H, Liu J, Huang S et al (2014) Selection and evaluation of novel reference genes for quantitative reverse transcription PCR (qRT-PCR) based on genome and transcriptome data in Brassica napus L. Gene 538:113–122

    Article  CAS  PubMed  Google Scholar 

  • Yi L, Chen C, Yin S et al (2018) Sequence variation and functional analysis of a FRIGIDA orthologue (BnaA3.FRI) in Brassica napus. BMC Plant Biol 18:32

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zeng X, Zhu L, Chen Y et al (2011) Identification, fine mapping and characterisation of a dwarf mutant (bnaC. dwf) in Brassica napus. Theor Appl Genet 122:421–428

    Article  PubMed  Google Scholar 

  • Zhao B, Li H, Li J et al (2017) Brassica napus DS-3, encoding a DELLA protein, negatively regulates stem elongation through gibberellin signaling pathway. Theor Appl Genet 130:727–741

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgement

The research was supported by the National Key Research and Development Program of China (2016YFD0101007AA102602).

Author information

Authors and Affiliations

  1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China

    Bo Zhao, Bo Wang, Zhaohong Li, Tao Guo, Junwei Zhao, Zhilin Guan & Kede Liu

Authors
  1. Bo Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Bo Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zhaohong Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Tao Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Junwei Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Zhilin Guan
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Kede Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kede Liu.

Ethics declarations

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Ethical standards

The authors declare that the experiments comply with the current laws of the country in which they were performed.

Additional information

Communicated by Maria Laura Federico.

Publisher's Note

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

Electronic supplementary material

Below is the link to the electronic supplementary material.

a

, Polymorphisms of the six INDELs and b, four SNP2CAPS markers were visualized on a 6% denaturing polyacrylamide gel and 3% agarose gel, respectively (PPTX 552 kb)

122_2019_3290_MOESM2_ESM.pptx

Alignment of amino acid sequences of BnaC05.IAA7 from the mutant ds-4, wild-type ZY821 and its homologs Bo5g093110 in Brassica oleracea TO1000. The conserved regions are indicated below the sequences with a black line. The red arrow indicates the Pro to Leu (P87L) mutation at position 87. Nuclear localization signals (NLS) are indicated by unfilled boxes (PPTX 90 kb)

122_2019_3290_MOESM3_ESM.xlsx

Sequence information of oligonucleotide primers used for mapping and cloning of DS-4 and for functional analysis of BnaC05.IAA7 in this study (XLSX 13 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhao, B., Wang, B., Li, Z. et al. Identification and characterization of a new dwarf locus DS-4 encoding an Aux/IAA7 protein in Brassica napus. Theor Appl Genet 132, 1435–1449 (2019). https://doi.org/10.1007/s00122-019-03290-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-019-03290-8

Search

Navigation