Skip to main content

Thank you for visiting nature.com. 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.

  • Article
  • Published:

A stigmatic gene confers interspecies incompatibility in the Brassicaceae

Nature Plants volume 5, pages 731–741 (2019)Cite this article

Subjects

Abstract

Pre-zygotic interspecies incompatibility in angiosperms is a male–female relationship that inhibits the formation of hybrids between two species. Here, we report on the identification of STIGMATIC PRIVACY 1 (SPRI1), an interspecies barrier gene in Arabidopsis thaliana. We show that the rejection activity of this stigma-specific plasma membrane protein is effective against distantly related Brassicaceae pollen tubes and is independent of self-incompatibility. Point-mutation experiments and functional tests of synthesized hypothetical ancestral forms of SPRI1 suggest evolutionary decay of SPRI1-controlled interspecies incompatibility in self-compatible A. thaliana. Hetero-pollination experiments indicate that SPRI1 ensures intraspecific fertilization in the pistil when pollen from other species are present. Our study supports the idea that SPRI1 functions as a barrier mechanism that permits entrance of pollen with an intrinsic signal from self species.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Fig. 1: Identification of an interspecific incompatibility-related gene locus via GWAS.
Fig. 2: SPRI1 function has been lost multiple times in the self-compatible A. thaliana.
Fig. 3: SPRI1 is functionally independent of SI.
Fig. 4: Col-0 pollen can mentor the penetration of M. littorea pollen tubes into A. thaliana stigma.
Fig. 5: SPRI1 rejects pollen from distantly related species.
Fig. 6: SPRI1 ensures efficient fertilization under heterologous pollination conditions.

Similar content being viewed by others

Data availability

Sequence data can be found at The Arabidopsis Information Resource database (https://www.arabidopsis.org/) or in the 1001 genomes website (1001genomes.org). Raw phenotype data used for the GWAS has been deposited in the GWA-Portal (https://gwas.gmi.oeaw.ac.at/#/study/4205/overview) and Arapheno (https://doi.org/10.21958/study:37). Raw data for pollen tube count was deposited to Mendeley (https://doi.org/10.17632/yzy85dtwk3.1). All other data are available in the article or in the Supplementary information.

References

  1. de Nettancourt, D. Incompatibility and Incongruity in Wild and Cultivated Plants (Springer, 2001).

  2. Hogenboom, N. G. & Mather, K. Incompatibility and incongruity: two different mechanisms for the non-functioning of intimate partner relationships. Proc. Roy. Soc. B 188, 361–375 (1975).

    Article  Google Scholar 

  3. Okuda, S. et al. Defensin-like polypeptide LUREs are pollen tube attractants secreted from synergid cells. Nature 458, 357–361 (2009).

    Article  CAS  Google Scholar 

  4. Takeuchi, H. & Higashiyama, T. Tip-localized receptors control pollen tube growth and LURE sensing in Arabidopsis. Nature 531, 245–248 (2016).

    Article  CAS  Google Scholar 

  5. Boehm, T. Quality control in self/nonself discrimination. Cell 125, 845–858 (2006).

    Article  CAS  Google Scholar 

  6. Igic, B., Lande, R. & Kohn, J. R. Loss of self-incompatibility and its evolutionary consequences. Int. J. Plant Sci. 169, 93–104 (2008).

    Article  Google Scholar 

  7. Fujii, S., Kubo, K. & Takayama, S. Non-self- and self-recognition models in plant self-incompatibility. Nat. Plants 2, 16130 (2016).

    Article  CAS  Google Scholar 

  8. Harada, Y. et al. Mechanism of self-sterility in a hermaphroditic chordate. Science 320, 548–550 (2008).

    Article  CAS  Google Scholar 

  9. Kubo, K. et al. Collaborative non-self recognition system in S-RNase-based self-incompatibility. Science 330, 796–799 (2010).

    Article  CAS  Google Scholar 

  10. Takayama, S. et al. Direct ligand-receptor complex interaction controls Brassica self-incompatibility. Nature 413, 534–538 (2001).

    Article  CAS  Google Scholar 

  11. Wheeler, M. J. et al. Identification of the pollen self-incompatibility determinant in Papaver rhoeas. Nature 459, 992–995 (2009).

    Article  CAS  Google Scholar 

  12. Wilkins, K. A. et al. Self-incompatibility-induced programmed cell death in field poppy pollen involves dramatic acidification of the incompatible pollen tube cytosol. Plant Physiol. 167, 766–779 (2015).

    Article  CAS  Google Scholar 

  13. Thomas, S. G. & Franklin-Tong, V. E. Self-incompatibility triggers programmed cell death in Papaver pollen. Nature 429, 305–309 (2004).

    Article  CAS  Google Scholar 

  14. Lewis, D. & Crowe, L. K. Unilateral interspecific incompatibility in flowering plants. Heredity 12, 233–256 (1958).

    Article  Google Scholar 

  15. Lewis, D. Incompatibility in flowering plants. Biol. Rev. 24, 472–496 (1949).

    Article  CAS  Google Scholar 

  16. Hiscock, S. J. & Dickinson, H. G. Unilateral incompatibility within the Brassicaceae: further evidence for the involvement of the self-incompatibility (S)-locus. Theor. Appl. Genet. 86, 744–753 (1993).

    Article  CAS  Google Scholar 

  17. Li, W. & Chetelat, R. T. A pollen factor linking inter- and intraspecific pollen rejection in tomato. Science 330, 1827–1830 (2010).

    Article  CAS  Google Scholar 

  18. Murfett, J. et al. S RNase and interspecific pollen rejection in the genus Nicotiana: multiple pollen-rejection pathways contribute to unilateral incompatibility between self-incompatible and self-compatible species. Plant Cell 8, 943–958 (1996).

    Article  CAS  Google Scholar 

  19. Li, W. & Chetelat, R. T. Unilateral incompatibility gene ui1.1 encodes an S-locus F-box protein expressed in pollen of Solanum species. Proc. Natl Acad. Sci. USA 112, 4417–4422 (2015).

    Article  CAS  Google Scholar 

  20. Tovar-Méndez, A. et al. Restoring pistil-side self-incompatibility factors recapitulates an interspecific reproductive barrier between tomato species. Plant J. 77, 727–736 (2014).

    Article  Google Scholar 

  21. Burdfield-Steel, E. R. & Shuker, D. M. Reproductive interference. Curr. Biol. 21, R450–R451 (2011).

    Article  CAS  Google Scholar 

  22. Tsuchimatsu, T. et al. Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene. Nature 464, 1342–1346 (2010).

    Article  CAS  Google Scholar 

  23. Seren, U. et al. GWAPP: A web application for genome-wide association mapping in Arabidopsis. Plant Cell 24, 4793–4805 (2012).

    Article  CAS  Google Scholar 

  24. Hooper, C. M. et al. SUBAcon: a consensus algorithm for unifying the subcellular localization data of the Arabidopsis proteome. Bioinformatics 30, 3356–3364 (2014).

    Article  CAS  Google Scholar 

  25. Iwano, M. et al. Calcium signalling mediates self-incompatibility response in the Brassicaceae. Nat. Plants 1, 15128 (2015).

    Article  CAS  Google Scholar 

  26. Klepikova, A. V., Kasianov, A. S., Gerasimov, E. S., Logacheva, M. D. & Penin, A. A. A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling. Plant J. 88, 1058–1070 (2016).

    Article  CAS  Google Scholar 

  27. Novikova, P. Y. et al. Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nat. Genet. 48, 1077–1082 (2016).

    Article  CAS  Google Scholar 

  28. Murat, F. et al. Understanding Brassicaceae evolution through ancestral genome reconstruction. Genome Biol. 16, 1–17 (2015).

    Article  Google Scholar 

  29. Mizukami, A. G. et al. The AMOR arabinogalactan sugar chain induces pollen-tube competency to respond to ovular guidance. Curr. Biol. 26, 1091–1097 (2016).

    Article  CAS  Google Scholar 

  30. Hemler, M. E. Tetraspanin functions and associated microdomains. Nat. Rev. Mol. Cell Biol. 6, 801–811 (2005).

    Article  CAS  Google Scholar 

  31. Miyado, K. et al. Requirement of CD9 on the egg plasma membrane for fertilization. Science 287, 321–324 (2000).

    Article  CAS  Google Scholar 

  32. Boavida, L. C., Qin, P., Broz, M., Becker, J. D. & McCormick, S. Arabidopsis tetraspanins are confined to discrete expression domains and cell types in reproductive tissues and form homo- and heterodimers when expressed in yeast. Plant Physiol. 163, 696–712 (2013).

    Article  CAS  Google Scholar 

  33. Tsuchiya, T. in Sexual Reproduction in Animals and Plants (eds Sawada, H. et al.) 305–325 (Springer, 2014).

  34. Vanacker, H., Lu, H., Rate, D. N. & Greenberg, J. T. A role for salicylic acid and NPR1 in regulating cell growth in Arabidopsis. Plant J. 28, 209–216 (2001).

    Article  CAS  Google Scholar 

  35. Doughty, J., Wong, H. Y. & Dickinson, H. G. Cysteine-rich pollen coat proteins (PCPs) and their Interactions with stigmatic S (incompatibility) and S-related proteins in Brassica: putative roles in SI and pollination. Ann. Bot. 85, 161–169 (2000).

    Article  CAS  Google Scholar 

  36. Takada, Y. et al. Duplicated pollen–pistil recognition loci control intraspecific unilateral incompatibility in Brassica rapa. Nat. Plants 3, 17096 (2017).

    Article  CAS  Google Scholar 

  37. Zhang, Z. et al. A pectin methylesterase gene at the maize Ga1 locus confers male function in unilateral cross-incompatibility. Nat. Commun. 9, 3678 (2018).

    Article  Google Scholar 

  38. Tsuchimatsu, T. et al. Patterns of polymorphism at the self-incompatibility Locus in 1,083 Arabidopsis thaliana genomes. Mol. Biol. Evol. 34, 1878–1889 (2017).

    Article  CAS  Google Scholar 

  39. Platt, A. et al. The scale of population structure in Arabidopsis thaliana. PLoS Genet. 6, e1000843 (2010).

    Article  Google Scholar 

  40. Shimizu, K. K., Kudoh, H. & Kobayashi, M. J. Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology. Ann. Bot. 108, 777–787 (2011).

    Article  CAS  Google Scholar 

  41. Saito, K. et al. Luminescent proteins for high-speed single-cell and whole-body imaging. Nat. Commun. 3, 1262 (2012).

    Article  Google Scholar 

  42. Rawat, V. et al. Improving the annotation of Arabidopsis lyrata using RNA-seq data. PLoS ONE 10, e0137391 (2015).

    Article  Google Scholar 

  43. Wang, Z.-P. et al. Egg cell-specific promoter-controlled CRISPR/Cas9 efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation. Genome Biol. 16, 144 (2015).

    Article  Google Scholar 

  44. Iwano, M. et al. Fine-tuning of the cytoplasmic Ca2+ concentration is essential for pollen tube growth. Plant Physiol. 150, 1322–1334 (2009).

    Article  CAS  Google Scholar 

  45. Shiba, H. et al. Alteration of the self-incompatibility phenotype in Brassica by transformation of the antisense SLG gene. Biosci. Biotechnol. Biochem. 64, 1016–1024 (2000).

    Article  CAS  Google Scholar 

  46. Hasegawa, J. et al. Three-dimensional imaging of plant organs using a simple and rapid transparency technique. Plant Cell Physiol. 57, 462–472 (2016).

    Article  CAS  Google Scholar 

  47. Seren, Ü. GWA-Portal: Genome-wide association studies made easy. Methods Mol. Biol. 1761, 303–319 (2018).

    Article  CAS  Google Scholar 

  48. The 1001 Genomes Consortium 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166, 481–491 (2016).

    Article  Google Scholar 

  49. Bandelt, H.-J., Forster, P. & Röhl, A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16, 37–48 (1999).

    Article  CAS  Google Scholar 

  50. South, A. rworldmap: A new R package for mapping global data. R Journal 3, 35–43 (2011).

    Article  Google Scholar 

  51. Durvasula, A. et al. African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA 114, 5213–5218 (2017).

    Article  CAS  Google Scholar 

  52. Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567–580 (2001).

    Article  CAS  Google Scholar 

  53. Hofmann, K. & Stoffel, W. TMBASE-A database of membrane spanning protein segments. Biol. Chem. 374, 166 (1993).

    Google Scholar 

  54. Käll, L., Krogh, A. & Sonnhammer, E. L. L. Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server. Nucleic Acids Res. 35, W429–W432 (2007).

    Article  Google Scholar 

  55. Tsirigos, K. D., Peters, C., Shu, N., Käll, L. & Elofsson, A. The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. Nucleic Acids Res. 43, W401–W407 (2015).

    Article  CAS  Google Scholar 

  56. Hirokawa, T., Boon-Chieng, S. & Mitaku, S. SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 14, 378–379 (1998).

    Article  CAS  Google Scholar 

  57. Juretić, D., Zoranić, L. & Zucić, D. Basic charge clusters and predictions of membrane protein topology. J. Chem. Inf. Comput. Sci. 42, 620–632 (2002).

    Article  Google Scholar 

  58. Haudry, A. et al. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat. Genet. 45, 891–898 (2013).

    Article  CAS  Google Scholar 

  59. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

    Article  CAS  Google Scholar 

  60. Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10 (2011).

    Article  Google Scholar 

  61. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    Article  CAS  Google Scholar 

  62. Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article  Google Scholar 

  63. Ashkenazy, H. et al. FastML: a web server for probabilistic reconstruction of ancestral sequences. Nucleic Acids Res. 40, W580–W584 (2012).

    Article  CAS  Google Scholar 

  64. Slotte, T. et al. The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat. Genet. 45, 831–835 (2013).

    Article  CAS  Google Scholar 

  65. Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16, 276–277 (2000).

    Article  CAS  Google Scholar 

  66. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

    Article  CAS  Google Scholar 

  67. Couvreur, T. L. P. et al. Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae). Mol. Biol. Evol. 27, 55–71 (2010).

    Article  CAS  Google Scholar 

  68. Talavera, G. & Castresana, J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564–577 (2007).

    Article  CAS  Google Scholar 

  69. Ronquist, F. et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542 (2012).

    Article  Google Scholar 

Download references

Acknowledgements

We thank M. Okamura, M. Nara, T. Manabe, Y. Yamamoto, M. Niidome and M. Ishii for their technical assistance and A. Kawabe and Y. Kato for helpful discussions. This work was supported in part by Grants-in-Aid for Scientific Research on Innovative Areas (23113002, 16H06467 and 16H06464 to S. Takayama; 16H01467 and 18H04776 to S. Fujii; 17H05833 and 18H04813 to T.T. and 16H06469 to K.K.S.), Grants-in-Aid for Scientific Research (25252021 and 16H06380 to S.Takayama and 18H02456 to S. Fujii), Grant-in-Aid for Challenging Exploratory Research (15K14626 to S. Fujii) from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT), Swiss National Science Foundation to K.K.S. and Japan Science and Technology Agency (JST) PRESTO programme (JPMJPR16Q8) to S. Fujii.

Author information

Author notes

  1. Megumi Iwano

    Present address: Graduate School of Biostudies, Kyoto University, Kyoto, Japan

Authors and Affiliations

  1. Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan

    Sota Fujii, Yuka Kimura, Shota Ishida, Surachat Tangpranomkorn & Seiji Takayama

  2. Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan

    Sota Fujii, Hiroko Shimosato-Asano, Megumi Iwano, Shoko Furukawa, Wakana Itoyama, Yuko Wada & Seiji Takayama

  3. Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Saitama, Japan

    Sota Fujii

  4. Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan

    Takashi Tsuchimatsu

  5. Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland

    Kentaro K. Shimizu

  6. Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan

    Kentaro K. Shimizu

Authors
  1. Sota Fujii
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Takashi Tsuchimatsu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yuka Kimura
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shota Ishida
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Surachat Tangpranomkorn
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Hiroko Shimosato-Asano
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Megumi Iwano
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Shoko Furukawa
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Wakana Itoyama
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Yuko Wada
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Kentaro K. Shimizu
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Seiji Takayama
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

S. Fujii, K.K.S. and S. Takayama conceived the study. S. Fujii, T.T., K.K.S. and S. Takayama wrote the manuscript. S. Fujii conducted most of the experiments and data analysis. T.T. conducted the GWAS and the geographical analysis. H.S.-A., S. Furukawa, W.I. and Y.W. contributed to phenotyping in the GWAS. Y.K. performed the fluorescent pollen experiment. S.I. contributed to the transgenic experiments. S. Tangpranomkorn contributed to the sequence analysis. M.I. performed the microarray analysis and W.I. performed the real-time PCR.

Corresponding authors

Correspondence to Sota Fujii or Seiji Takayama.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information: Nature Plants thanks Daphne Goring and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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

Supplementary information

Supplementary Information

Supplementary Figs. 1–8, Supplementary Tables 1–5, and titles and legends for Supplementary Videos 1 and 2.

Reporting Summary

Supplementary Video 1

Time-lapse imaging analysis of a M. littorea pollen grain attached on a Col-0 stigmatic papilla cell (left) and on a spri1-1 stigmatic papilla cell (right).

Supplementary Video 2

Time-lapse imaging analysis of Col-0 and M. littorea pollen grains adjacently attached on a spri1-2 + SPRI1A stigmatic papilla cell.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Fujii, S., Tsuchimatsu, T., Kimura, Y. et al. A stigmatic gene confers interspecies incompatibility in the Brassicaceae. Nat. Plants 5, 731–741 (2019). https://doi.org/10.1038/s41477-019-0444-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41477-019-0444-6

This article is cited by

Search

Advanced search

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