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Four class A AUXIN RESPONSE FACTORs promote tomato fruit growth despite suppressing fruit set

Abstract

In flowering plants, auxin produced in seeds after fertilization promotes fruit initiation. The application of auxin to unpollinated ovaries can also induce parthenocarpy (seedless fruit production). Previous studies have shown that auxin signalling components SlIAA9 and SlARF7 (a class A AUXIN RESPONSE FACTOR (ARF)) are key repressors of fruit initiation in tomato (Solanum lycopersicum). A similar repressive role of class A ARFs in fruit set has also been observed in other plant species. However, evidence is lacking for a role of any class A ARF in promoting fruit development as predicted in the current auxin signalling model. Here we generated higher-order tomato mutants of four class A SlARFs (SlARF5, SlARF7, SlARF8A and SlARF8B) and uncovered their precise combinatorial roles that lead to suppressing and promoting fruit development. All four class A SlARFs together with SlIAA9 inhibited fruit initiation but promoted subsequent fruit growth. Transgenic tomato lines expressing truncated SlARF8A/8B lacking the IAA9-interacting PB1 domain displayed strong parthenocarpy, further confirming the promoting role of SlARF8A/8B in fruit growth. Altering the doses of these four SlARFs led to biphasic fruit growth responses, showing their versatile dual roles as both negative and positive regulators. RNA-seq and chromatin immunoprecipitation–quantitative PCR analyses further identified SlARF8A/8B target genes, including those encoding MADS-BOX transcription factors (AG1, MADS2 and AGL6) that are key repressors of fruit set. These results support the idea that SlIAA9/SlARFs directly regulate the transcription of these MADS-BOX genes to inhibit fruit set. Our study reveals the previously unknown dual function of four class A SlARFs in tomato fruit development and illuminates the complex combinatorial effects of multiple ARFs in controlling auxin-mediated fruit set and fruit growth.

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Fig. 1: arf8aarf8bcrispr mutants displayed strong parthenocarpy.
Fig. 2: ARF5, ARF7, ARF8A and ARF8B all contribute to fruit initiation and growth.
Fig. 3: Parthenocarpy phenotypes of 3F2H–ARF8A-OE, 3F2H–ARF8A-NT and 3F2H–ARF8B-NT transgenic lines.
Fig. 4: ARFs and IAA9 showed distinctive spatial localization in ovaries.
Fig. 5: Identification of 8a8b-responsive and auxin-responsive genes in ovaries by RNA-seq analysis.
Fig. 6: Spatial expression patterns of auxin-responsive ARF8A/8B target genes.
Fig. 7: Confirmation of ARF8A/8B target genes by ChIP–qPCR and RT–qPCR.
Fig. 8: Model of class A ARFs and IAA9 in controlling fruit initiation and growth in tomato.

Data availability

The RNA-seq data have been deposited in the NCBI Sequence Read Archive under BioProject PRJNA929538. Source data are provided with this paper.

References

  1. Gillaspy, G., Ben-David, H. & Gruissem, W. Fruits: a developmental perspective. Plant Cell 5, 1439–1451 (1993).

    Article  PubMed  PubMed Central  Google Scholar 

  2. Seymour, G. B., Ostergaard, L., Chapman, N. H., Knapp, S. & Martin, C. Fruit development and ripening. Annu. Rev. Plant Biol. 64, 219–241 (2013).

    Article  CAS  PubMed  Google Scholar 

  3. Fenn, M. A. & Giovannoni, J. J. Phytohormones in fruit development and maturation. Plant J. 105, 446–458 (2021).

    Article  CAS  PubMed  Google Scholar 

  4. Srivastava, A. & Handa, A. K. Hormonal regulation of tomato fruit development: a molecular perspective. J. Plant Growth Regul. 24, 67–82 (2005).

    Article  CAS  Google Scholar 

  5. Dorcey, E., Urbez, C., Blazquez, M. A., Carbonell, J. & Perez-Amador, M. A. Fertilization-dependent auxin response in ovules triggers fruit development through the modulation of gibberellin metabolism in Arabidopsis. Plant J. 58, 318–332 (2009).

    Article  CAS  PubMed  Google Scholar 

  6. Serrani, J. C., Fos, M., Atares, A. & Garcia-Martinez, J. L. Effect of gibberellin and auxin on parthenocarpic fruit growth induction in the cv Micro-Tom of tomato. J. Plant Growth Regul. 26, 211–221 (2007).

    Article  CAS  Google Scholar 

  7. Gorguet, B., van Heusden, A. W. & Lindhout, P. Parthenocarpic fruit development in tomato. Plant Biol. (Stuttg.) 7, 131–139 (2005).

    Article  CAS  PubMed  Google Scholar 

  8. Mutte, S. K. et al. Origin and evolution of the nuclear auxin response system. eLife 7, e33399 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  9. Israeli, A., Reed, J. W. & Ori, N. Genetic dissection of the auxin response network. Nat. Plants 6, 1082–1090 (2020).

    Article  CAS  PubMed  Google Scholar 

  10. Kato, H. et al. Design principles of a minimal auxin response system. Nat. Plants 6, 473–482 (2020).

    Article  CAS  PubMed  Google Scholar 

  11. Lavy, M. & Estelle, M. Mechanisms of auxin signaling. Development 143, 3226–3229 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Morffy, N. & Strader, L. C. Structural aspects of auxin signaling. Cold Spring Harb. Perspect. Biol. 14, a039883 (2022).

    Article  CAS  PubMed  Google Scholar 

  13. Leyser, O. Auxin signaling. Plant Physiol. 176, 465–479 (2018).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  15. Leydon, A. R. et al. Repression by the Arabidopsis TOPLESS corepressor requires association with the core mediator complex. eLife 10, e66739 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Guilfoyle, T. J. & Hagen, G. Auxin response factors. Curr. Opin. Plant Biol. 10, 453–460 (2007).

    Article  CAS  PubMed  Google Scholar 

  17. Audran-Delalande, C. et al. Genome-wide identification, functional analysis and expression profiling of the Aux/IAA gene family in tomato. Plant Cell Physiol. 53, 659–672 (2012).

    Article  CAS  PubMed  Google Scholar 

  18. Zhang, J. et al. A single-base deletion mutation in SlIAA9 gene causes tomato (Solanum lycopersicum) entire mutant. J. Plant Res. 120, 671–678 (2007).

    Article  CAS  PubMed  Google Scholar 

  19. Hu, J., Israeli, A., Ori, N. & Sun, T. P. The interaction between DELLA and ARF/IAA mediates crosstalk between gibberellin and auxin signaling to control fruit initiation in tomato. Plant Cell 30, 1710–1728 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Wang, H. et al. The tomato Aux/IAA transcription factor IAA9 is involved in fruit development and leaf morphogenesis. Plant Cell 17, 2676–2692 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Ueta, R. et al. Rapid breeding of parthenocarpic tomato plants using CRISPR/Cas9. Sci. Rep. 7, 507 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  22. Liu, S. et al. Tomato AUXIN RESPONSE FACTOR 5 regulates fruit set and development via the mediation of auxin and gibberellin signaling. Sci. Rep. 8, 2971 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  23. de Jong, M., Wolters-Arts, M., Feron, R., Mariani, C. & Vriezen, W. H. The Solanum lycopersicum auxin response factor 7 (SlARF7) regulates auxin signaling during tomato fruit set and development. Plant J. 57, 160–170 (2009).

    Article  PubMed  Google Scholar 

  24. Goetz, M., Vivian-Smith, A., Johnson, S. D. & Koltunow, A. M. AUXIN RESPONSE FACTOR8 is a negative regulator of fruit initiation in Arabidopsis. Plant Cell 18, 1873–1886 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Du, L. et al. SmARF8, a transcription factor involved in parthenocarpy in eggplant. Mol. Genet. Genomics 291, 93–105 (2016).

    Article  CAS  PubMed  Google Scholar 

  26. Zhou, J. et al. Gibberellin and auxin signaling genes RGA1 and ARF8 repress accessory fruit initiation in diploid strawberry. Plant Physiol. 185, 1059–1075 (2021).

    Article  CAS  PubMed  Google Scholar 

  27. Kumar, R., Khurana, A. & Sharma, A. K. Role of plant hormones and their interplay in development and ripening of fleshy fruits. J. Exp. Bot. 65, 4561–4575 (2014).

    Article  CAS  PubMed  Google Scholar 

  28. Zouine, M. et al. Characterization of the tomato ARF gene family uncovers a multi-levels post-transcriptional regulation including alternative splicing. PLoS ONE 9, e84203 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  29. Liu, N. et al. Down-regulation of AUXIN RESPONSE FACTORS 6 and 8 by microRNA 167 leads to floral development defects and female sterility in tomato. J. Exp. Bot. 65, 2507–2520 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Israeli, A. et al. Multiple auxin-response regulators enable stability and variability in leaf development. Curr. Biol. 29, 1746–1759 e1745 (2019).

    Article  CAS  PubMed  Google Scholar 

  31. Pierre-Jerome, E., Jang, S. S., Havens, K. A., Nemhauser, J. L. & Klavins, E. Recapitulation of the forward nuclear auxin response pathway in yeast. Proc. Natl Acad. Sci. USA 111, 9407–9412 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Pierre-Jerome, E., Moss, B. L., Lanctot, A., Hageman, A. & Nemhauser, J. L. Functional analysis of molecular interactions in synthetic auxin response circuits. Proc. Natl Acad. Sci. USA 113, 11354–11359 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Wu, M. F., Tian, Q. & Reed, J. W. Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. Development 133, 4211–4218 (2006).

    Article  CAS  PubMed  Google Scholar 

  34. Pnueli, L., Hareven, D., Rounsley, S. D., Yanofsky, M. F. & Lifschitz, E. Isolation of the tomato AGAMOUS gene TAG1 and analysis of its homeotic role in transgenic plants. Plant Cell 6, 163–173 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Scharf, K. D., Berberich, T., Ebersberger, I. & Nover, L. The plant heat stress transcription factor (Hsf) family: structure, function and evolution. Biochim. Biophys. Acta 1819, 104–119 (2012).

    Article  CAS  PubMed  Google Scholar 

  36. Nakatsuka, A. et al. Differential expression and internal feedback regulation of 1-aminocyclopropane-1-carboxylate synthase, 1-aminocyclopropane-1-carboxylate oxidase, and ethylene receptor genes in tomato fruit during development and ripening. Plant Physiol. 118, 1295–1305 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Nitsch, L. M. et al. Abscisic acid levels in tomato ovaries are regulated by LeNCED1 and SlCYP707A1. Planta 229, 1335–1346 (2009).

    Article  CAS  PubMed  Google Scholar 

  38. Tournier, B. et al. New members of the tomato ERF family show specific expression pattern and diverse DNA-binding capacity to the GCC box element. FEBS Lett. 550, 149–154 (2003).

    Article  CAS  PubMed  Google Scholar 

  39. Olimpieri, I. et al. Tomato fruit set driven by pollination or by the parthenocarpic fruit allele are mediated by transcriptionally regulated gibberellin biosynthesis. Planta 226, 877–888 (2007).

    Article  CAS  PubMed  Google Scholar 

  40. Munoz-Bertomeu, J., Miedes, E. & Lorences, E. P. Expression of xyloglucan endotransglucosylase/hydrolase (XTH) genes and XET activity in ethylene treated apple and tomato fruits. J. Plant Physiol. 170, 1194–1201 (2013).

    Article  CAS  PubMed  Google Scholar 

  41. Quiroga, M. et al. A tomato peroxidase involved in the synthesis of lignin and suberin. Plant Physiol. 122, 1119–1127 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Allegre, A., Silvestre, J., Morard, P., Kallerhoff, J. & Pinelli, E. Nitrate reductase regulation in tomato roots by exogenous nitrate: a possible role in tolerance to long-term root anoxia. J. Exp. Bot. 55, 2625–2634 (2004).

    Article  CAS  PubMed  Google Scholar 

  43. Yang, Z., Tian, L., Latoszek-Green, M., Brown, D. & Wu, K. Arabidopsis ERF4 is a transcriptional repressor capable of modulating ethylene and abscisic acid responses. Plant Mol. Biol. 58, 585–596 (2005).

    Article  CAS  PubMed  Google Scholar 

  44. Shinozaki, Y. et al. Ethylene suppresses tomato (Solanum lycopersicum) fruit set through modification of gibberellin metabolism. Plant J. 83, 237–251 (2015).

    Article  CAS  PubMed  Google Scholar 

  45. Wang, H. et al. Regulatory features underlying pollination-dependent and -independent tomato fruit set revealed by transcript and primary metabolite profiling. Plant Cell 21, 1428–1452 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Tang, N., Deng, W., Hu, G., Hu, N. & Li, Z. Transcriptome profiling reveals the regulatory mechanism underlying pollination dependent and parthenocarpic fruit set mainly mediated by auxin and gibberellin. PLoS ONE 10, e0125355 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  47. Klap, C. et al. Tomato facultative parthenocarpy results from SlAGAMOUS-LIKE 6 loss of function. Plant Biotechnol. J. 15, 634–647 (2017).

    Article  CAS  PubMed  Google Scholar 

  48. Molesini, B., Dusi, V., Pennisi, F. & Pandolfini, T. How hormones and MADS-box transcription factors are involved in controlling fruit set and parthenocarpy in tomato. Genes (Basel) 11, 1441 (2020).

    Article  CAS  PubMed  Google Scholar 

  49. Hu, G. et al. Histone posttranslational modifications rather than DNA methylation underlie gene reprogramming in pollination-dependent and pollination-independent fruit set in tomato. N. Phytol. 229, 902–919 (2021).

    Article  CAS  Google Scholar 

  50. Lavy, M. et al. Constitutive auxin response in Physcomitrella reveals complex interactions between Aux/IAA and ARF proteins. eLife 5, e13325 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  51. Tao, S. & Estelle, M. Mutational studies of the Aux/IAA proteins in Physcomitrella reveal novel insights into their function. N. Phytol. 218, 1534–1542 (2018).

    Article  CAS  Google Scholar 

  52. Peterson, B. A. et al. Genome-wide assessment of efficiency and specificity in CRISPR/Cas9 mediated multiple site targeting in Arabidopsis. PLoS ONE 11, e0162169 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  53. Bajwa, V. S. et al. Identification and functional analysis of tomato BRI1 and BAK1 receptor kinase phosphorylation sites. Plant Physiol. 163, 30–42 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Heberle, H., Meirelles, G. V., da Silva, F. R., Telles, G. P. & Minghim, R. InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinf. 16, 169 (2015).

    Article  Google Scholar 

  55. Tian, T. et al. agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Res. 45, W122–W129 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank T. Nolan and L. Wang for helpful advice on QuantSeq analysis; Z. Nimchuk for providing the CRISPR–Cas9 vectors; J. Nemhauser and E. Pierre-Jerome for providing the ARC constructs, yeast strains and detailed protocols; and N. Ori and A. Israeli for sharing their unpublished results. We also thank A. Israeli, N. Ori, Z.-M. Pei, J. Reed and L. Strader for helpful comments on the manuscript and the China Scholarship Council (CSC) for scholarship support (CSC fellowship no. 201803250091 to X.L.). This work was supported by the US Department of Agriculture (grant no. 2018-67013-27395 to T.-P.S.) and the National Institutes of Health (grant no. R01 GM100051 to T.-P.S.).

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J.H. and T.-P.S. conceived and designed the research project. J.H. and X.L. performed the experiments. J.H., X.L. and T.-P.S. analysed the data. J.H. and T.-P.S. wrote the manuscript.

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Correspondence to Tai-ping Sun.

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Hu, J., Li, X. & Sun, Tp. Four class A AUXIN RESPONSE FACTORs promote tomato fruit growth despite suppressing fruit set. Nat. Plants 9, 706–719 (2023). https://doi.org/10.1038/s41477-023-01396-y

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