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Identified trans-splicing of YELLOW-FRUITED TOMATO 2 encoding the PHYTOENE SYNTHASE 1 protein alters fruit color by map-based cloning, functional complementation and RACE

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Found a trans-splicing of PHYTOENE SYNTHASE 1 alters tomato fruit color by map-based cloning, functional complementation and RACE providing an insight into fruit color development.

Abstract

Color is an important fruit quality trait and a major determinant of the economic value of tomato (Solanum lycopersicum). Fruit color inheritance in a yellow-fruited cherry tomato (cv. No. 22), named yellow-fruited tomato 2 (yft2), was shown to be controlled by a single recessive gene, YFT2. The YFT2 gene was mapped in a 95.7 kb region on chromosome 3, and the candidate gene, PHYTOENE SYNTHASE 1 (PSY1), was confirmed by functional complementation analysis. Constitutive over expression of PSY1 in yft2 increased the accumulation of carotenoids and resulted in a red fruit color, while no causal mutation was detected in the YFT2 allele of yft2, compared with red-fruited SL1995 cherry tomato or cultivated variety (cv. M82). Expression of YFT2 3′ region in yft2 was significantly lower than in SL1995, and further studies revealed a difference in YFT2 post-transcriptional processing in yft2 compared with SL1995 and cv. M82, resulting in a longer YFT2 transcript. The alternatively trans-spliced allele of YFT2 in yft2 is predicted to encode a novel LT-YFT2 protein of 432 amino acid (AA) residues, compared to the 412 AA YFT2 protein of SL1995. The trans-spliced event also resulted in significantly down regulated expression of YFT2 in yft2 tomato, and the YFT2 allele suppressed expression of the downstream genes involved in the carotenoid biosynthesis pathway and carotenoids synthesis by a mechanism of the feed-forward regulation. In conclusion, we found that trans-splicing of YFT2 alters tomato fruit color, providing new insights into fruit color development.

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Acknowledgements

The authors are grateful to Dr. Dani Zamir and the TGRC (Tomato Genetic Resource Center, UC, Davis) for providing tomato seeds. We thank Dr. Pin Liu (Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University) for help with the carotenoid analysis. We thank PlantScribe (www.plantscribe.com) for editing this manuscript. This work was supported by a National Key Research and Development Project [2016YFD0100204-28]; the National Natural Science Foundation of China [31672158, 31872112]; the Key Technology Research and the Development Program of Shanghai Technology Committee [16391900900] and the Shanghai Jiao Tong University Agri-X Fund (2015).

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Authors and Affiliations

  1. Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China

    Lulu Chen, Wenzhen Li, Yongpeng Li, Keyu Du & Lingxia Zhao

  2. Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China

    Lulu Chen, Wenzhen Li, Xuechao Feng & Lingxia Zhao

  3. Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, 200240, China

    Ge Wang

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  1. Lulu Chen
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  2. Wenzhen Li
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Contributions

LXZ conceived and designed the research, and wrote the manuscript. LLC performed the main experimental work and wrote the manuscript; WZL and YPL participated in the mapping; XCF and KYD conducted HPLC analysis; GW participated in the ultrastructural analysis.

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Correspondence to Lingxia Zhao.

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Chen, L., Li, W., Li, Y. et al. Identified trans-splicing of YELLOW-FRUITED TOMATO 2 encoding the PHYTOENE SYNTHASE 1 protein alters fruit color by map-based cloning, functional complementation and RACE. Plant Mol Biol 100, 647–658 (2019). https://doi.org/10.1007/s11103-019-00886-y

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