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

Nature Plants volume 9, pages 706–719 (2023)Cite this article

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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: arf8a arf8b crispr 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 8a 8b-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.

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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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Author notes

  1. Xiao Li

    Present address: School of Grassland Science, Beijing Forestry University, Beijing, P. R. China

  2. These authors contributed equally: Jianhong Hu, Xiao Li.

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  1. Department of Biology, Duke University, Durham, NC, USA

    Jianhong Hu, Xiao Li & Tai-ping Sun

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Contributions

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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Nature Plants thanks Mondher Bouzayen and Zhongchi Liu for their contribution to the peer review of this work.

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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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