Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Two genetic changes in cis-regulatory elements caused evolution of petal spot position in Clarkia

A Retraction to this article was published on 26 June 2020

This article has been updated


A major premise in evolutionary developmental biology is that regulatory changes, often involving cis-regulatory elements, are responsible for much morphological evolution. This premise is supported by recent investigations of animal development, but information is just beginning to accumulate regarding whether it also applies to the evolution of plant morphology1,2,3,4. Here, we identify the genetic differences between species in the genus Clarkia that are responsible for evolutionary change in an ecologically important element of floral colour patterns: spot position. The evolutionary shift in spot position was due to two simple genetic changes that resulted in the appearance of a transcription factor binding site mutation in the R2R3 Myb gene that changes spot formation. These genetic changes caused R2R3 Myb to be activated by a different transcription factor that is expressed in a different position in the petal. These results suggest that the regulatory rewiring paradigm is as applicable to plants as it is to animals, and support the hypothesis that cis-regulatory changes may often play a role in plant morphological evolution.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Photographs of Clarkia flowers.
Fig. 2: Hypothesized molecular mechanism of shift in petal spot position.
Fig. 3
Fig. 4: Function of CgbHLH1 and CgCPC1 in C. gracilis petals.

Similar content being viewed by others

Change history

  • 26 June 2020

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.


  1. Wray, G. A. The evolutionary significance of cis-regulatory mutations. Nat. Rev. Genet. 8, 206–216 (2007).

    Article  CAS  PubMed  Google Scholar 

  2. Carroll, S. B. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134, 25–36 (2008).

    Article  CAS  PubMed  Google Scholar 

  3. Wittkopp, P. J. & Kalay, G. Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat. Rev. Genet. 13, 59–69 (2011).

    Article  PubMed  Google Scholar 

  4. Martik, M. L., Lyons, D. C. & McClay, D. R. Developmental gene regulatory networks in sea urchins and what we can learn from them. F1000Research 5, 203 (2016).

    Article  Google Scholar 

  5. Della Pina, S., Souer, E. & Koes, R. Arguments in the evo-devo debate: say it with flowers!. J. Exp. Botany 65, 2231–2242 (2014).

    Article  Google Scholar 

  6. Specht, C. D. & Howarth, D. G. Adaptation in flower form: a comparative evodevo approach. New Phytol. 206, 74–90 (2015).

    Article  PubMed  Google Scholar 

  7. Arnaud, N. et al. The same regulatory point mutation changed seed-dispersal structures in evolution and domestication. Curr. Biol. 21, 1215–1219 (2011).

    Article  CAS  PubMed  Google Scholar 

  8. Doebley, J. & Lukens, L. transcriptional regulators and the evolution of plant form. Plant Cell. 10, 1075–1082 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Sobel, J. M. & Streisfeld, M. A. Flower color as a model system for studies in plant evo-devo. Front. Plant Sci. 4, 321 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  10. Sicard, A. et al. Standing genetic variation in a tissue-specific enhancer underlies selfing-syndrome evolution in Capsella. Proc. Natl. Acad. Sci. USA 113, 13911–13916 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Kusters, E. et al. Changes in cis-regulatory elements of a key floral regulator are associated with divergence of inflorescence architectures. Development 142, 2822–2831 (2015).

    Article  CAS  PubMed  Google Scholar 

  12. Jones, K. N. Pollinator behavior and postpollination reproductive success in alternative floral phenotypes of Clarkia gracilis (Onagraceae). Int. J. Plant Sci. 157, 733–738 (1996).

    Article  Google Scholar 

  13. Eckhart, V. M. et al. Frequency-dependent pollinator foraging in polymorphic Clarkia xantiana ssp. xantiana populations: Implications for flower-colour evolution and pollinator interactions. Oikos 112, 412–421 (2006).

    Article  Google Scholar 

  14. Ellis, A. G. & Johnson, S. D. Floral mimicry enhances pollen export: the evolution of pollination by sexual deceit outside of the Orchidaceae. Am. Nat. 176, E143–E151 (2010).

    Article  PubMed  Google Scholar 

  15. Lewis, H. & Lewis, M. E. The genus Clarkia. Univ. Calif. Publ. Bot. 20, 241–392 (1955).

    Google Scholar 

  16. Gottlieb, L. D. & Ford, V. S. Genetic studies of the pattern of floral pigmentation in Clarkia gracilis. Heredity 60, 237–246 (1988).

    Article  Google Scholar 

  17. Abdel-Hameed, F. & Snow, R. The origin of the allotetraploid Clarkia gracilis. Evolution 26, 74–83 (1972).

    Article  PubMed  Google Scholar 

  18. Martins, T. R., Jiang, P. & Rausher, M. How petals change their spots: cis-regulatory re-wiring in Clarkia (Onagraceae). New Phytol. 216, 510–518 (2017).

    Article  CAS  PubMed  Google Scholar 

  19. Martins, T. R. et al. Precise spatiotemporal regulation of the anthocyanin biosynthetic pathway leads to petal spot formation in Clarkia gracilis (Onagraceae). New Phytol. 197, 958–969 (2013).

    Article  CAS  PubMed  Google Scholar 

  20. Solovyev, V. V. & Salamov A. A. The Gene-Finder computer tools for analysis of human and model organisms genome sequences. In Proc. Fifth Int. Conf. Intelligent Systems for Molecular Biology (eds Rawling, C. et al.) 294-302 (AAAI Press, 1997).

  21. Lescot, M. et al. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 30, 325–327 (2002).

  22. Higo, K. et al. Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res. 27, 297–300 (1999).

  23. Massari, M. E. & Murre, C. Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms. Mol. Cell. Biol. 20, 429–440 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Bailey, P. C. et al. Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana. Plant Cell. 15, 2497–2501 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Heim, M. A. et al. The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol. Biol. Evol. 20, 735–747 (2003).

    Article  CAS  PubMed  Google Scholar 

  26. Ito, S. et al. Flowering bHLH transcriptional activators control expression of the photoperiodic flowering regulator CONSTANS. Arab. Proc. Natl. Acad. Sci. USA 109, 3582–3587 (2012).

    Article  CAS  Google Scholar 

  27. Takahashi, Y. et al. Reconstitution of abscisic acid signaling from the receptor to DNA via bHLH transcription factors. Plant Physiol. 174, 815–822 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Nakata, M. et al. A bhlh-type transcription factor, aba-inducible bhlh-type transcription factor/ja-associated myc2-like1, acts as a repressor to negatively regulate jasmonate signaling in Arabidopsis. Plant Cell. 25, 1641–1656 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Zhu, H. F. et al. CPC, a single-repeat R3 MYB, is a negative regulator of anthocyanin biosynthesis in Arabidopsis. Mol. Plant 2, 790–802 (2009).

    Article  CAS  PubMed  Google Scholar 

  30. Wada, T. et al. Epidermal cell differentiation in Arabidopsis determined by a Myb homolog, CPC. Science 277, 1113–1116 (1997).

    Article  CAS  PubMed  Google Scholar 

  31. Wada, T. et al. Role of a positive regulator of root hair development, CAPRICE, in Arabidopsis root epidermal cell differentiation. Development 129, 5409–5419 (2002).

    Article  CAS  PubMed  Google Scholar 

  32. Ogata, K. et al. Comparison of the free and DNA-complexed forms of the DMA-binding domain from c-Myb. Nat. Struct. Mol. Biol. 2, 309–320 (1995).

    Article  CAS  Google Scholar 

  33. Jin, H. & Cathie, M. Multifunctionality and diversity within the plant MYB-gene family. Plant Mol. Biol. 41.5, 577–585 (1999).

    Article  Google Scholar 

  34. Gould, S. J. Wonderful Life: The Burgess Shale and the Nature of History 163–165 (W. W. Norton & Company, New York, 1990).

  35. Blount, Z. D., Borland, C. Z. & Lenski, R. E. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc. Natl. Acad. Sci. USA 105, 7889–7906 (2008).

    Article  Google Scholar 

  36. Harms, M. J. & Thornton, J. W. Historical contingency and its biophysical basics in glucocorticoid receptor evolution. Nature 512, 203–207 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. De Smet, R. & Van de Peer, Y. Redundancy and rewiring of genetic networks following genome-wide duplication events. Curr. Opin. Plant Biol. 15.2, 168–176 (2012).

    Article  Google Scholar 

  38. Zhang, Z. L. et al. SCARECROW-LIKE3 promotes gibberellin signaling by antagonizing DELLA in Arabidopsis. Proc. Natl. Acad. Sci. USA 108, 2160–2165 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Wroblewski, T. et al. Optimization of Agrobacterium-mediated transient assays of gene expression in lettuce, tomato and Arabidopsis. Plant Biotechnol. J. 3, 259–273 (2005).

    Article  CAS  PubMed  Google Scholar 

  40. Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using realtime quantitative PCR and the 2-ΔΔCT method. Methods 25, 402–408 (2001).

    CAS  PubMed  Google Scholar 

  41. Javelle, M. et al. In situ hybridization for the precise localization of transcripts in plants. J. Vis. Exp. 57, 3328 (2011).

    Google Scholar 

Download references


We thank T. Martins, S. Zebell, C. Wilson and R. Zentella for technical advice. We thank X. Dong and F. Nijhout for comments on the manuscript. Photographs are by M. Below, K. Morse, V. Smith and B. Breckling. This work was supported by a National Science Foundation grant to M.D.R.

Author information

Authors and Affiliations



P.J. and M.D.R. designed the project; P.J. performed the experiments and the analyses; P.J. and M.D.R. wrote the paper.

Corresponding author

Correspondence to Peng Jiang.

Additional information

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figures 1–18, Supplementary Tables 1–3.

Life Sciences Reporting Summary

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jiang, P., Rausher, M. Two genetic changes in cis-regulatory elements caused evolution of petal spot position in Clarkia. Nature Plants 4, 14–22 (2018).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing