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

Jun 15, 2023

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

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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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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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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.).

Xiao Li

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

These authors contributed equally: Jianhong Hu, Xiao Li.

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

Jianhong Hu, Xiao Li & Tai-ping Sun

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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.

Correspondence to Tai-ping Sun.

The authors declare no competing interests.

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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Received: 30 March 2022

Accepted: 14 March 2023

Published: 10 April 2023

Issue Date: May 2023

DOI: https://doi.org/10.1038/s41477-023-01396-y

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