A 21-bp InDel in the promoter of STP1 selected during tomato improvement accounts for soluble solid content in fruits

Abstract

Domestication and improvement are important processes that generate the variation in genome and phonotypes underlying crop improvement. Unfortunately, during selection for certain attributes, other valuable traits may be inadvertently discarded. One example is the decline in fruit soluble solids content (SSC) during tomato breeding. Several genetic loci for SSC have been identified, but few reports on the underlying mechanisms are available. In this study we performed a genome-wide association study (GWAS) for SSC of the red-ripe fruits in a population consisting of 481 tomato accessions with large natural variations and found a new quantitative trait locus, STP1, encoding a sugar transporter protein. The causal variation of STP1, a 21-bp InDel located in the promoter region 1124 bp upstream of the start codon, alters its expression. STP1 Insertion accessions with an 21-bp insertion have higher SSC than STP1 Deletion accessions with the 21-bp deletion. Knockout of STP1 in TS-23 with high SSC using CRISPR/Cas9 greatly decreased SSC in fruits. In vivo and in vitro assays demonstrated that ZAT10-LIKE, a zinc finger protein transcription factor (ZFP TF), can specifically bind to the promoter of STP1 Insertion to enhance STP1 expression, but not to the promoter of STP1 Deletion , leading to lower fruit SSC in modern tomatoes. Diversity analysis revealed that STP1 was selected during tomato improvement. Taking these results together, we identified a naturally occurring causal variation underlying SSC in tomato, and a new role for ZFP TFs in regulating sugar transporters. The findings enrich our understanding of tomato evolution and domestication, and provide a genetic basis for genome design for improving fruit taste.

Acknowledgements

This work was supported by grants from the National Key Research & Development Plan (2021YFD1200201; 2022YFD1200502), the National Natural Science Foundation of China (31972426; 31991182; 32060685), the Wuhan Biological Breeding Major Project (2022021302024852), the International Cooperation Promotion Plan of Shihezi University (GJHZ202104), the Key Project of Hubei Hongshan Laboratory (2021hszd007), the Hubei Key Research & Development Plan (2022BBA0062; 2022BBA0066), and the Fundamental Research Funds for the Central Universities (2662022YLPY001).

Author contributions

Y.Z. designed and supervised the project. Y.W. did most of the experiments and wrote the manuscript. C.S. performed the GWAS data analysis. P.G., F.L., L.Z., Y.W., J.T., X.Z., H.D., W.G., and F.W. performed some of the experiments. W.X., D.G., Y.Z., and Z.Y. advised on experiments and revised the manuscript.

Conflict of interest statement

All authors declare no conflicts of interest.

Data availability

All data supporting the results of this study can be obtained in this article or in the supplementary materials.

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