Toward tasty tomato: recovering the lost STP1 variant in modern tomato to improve soluble solid in fruit

Core content: In this study, the authors 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 promoter region 1,124 bp upstream of the start codon, alters its expression. STP1^Insertion accessions with 21-bp insertion have higher SSC than STP1^Deletion accessions with 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 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.

Innovation: The authors identified a naturally occurring causal variation underlying SSC in tomato, and a new role for ZFP TFs in regulating sugar transporters. The findings enrich the understanding of tomato evolution and domestication, and provide a genetic basis for breeding tasty tomato.

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Reference

Authors

Ying Wang^{a, b}, Chunmei Shi^a, Pingfei Ge^a, Fangman Li^a Lihui Zhu^a, Yaru Wang^a, Jinbao Tao^a, Xingyu Zhang^a, Haiqiang Dong^a, Wenxian Gai^a, Fei Wang^a, Zhibiao Ye^a, Donald Grierson^c, Wei Xu^d*, Yuyang Zhang^{a, b*}

Affiliations

^a National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China

^b Hubei Hongshan Laboratory, Wuhan, 430070, China

^c Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK

^d Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization (Xinjiang Production and Construction Crops), College of Agriculture, Shihezi University, Shihezi, 832003, Xinjiang, China

About Professor Yuyang Zhang

Professor Yuyang Zhang from Huazhong Agricultural University has been focusing on tomato genetics and molecular breeding. Professor Wei Xu is from Shihezi University, China. Her research area includes germplasm evaluation and vegetable genetic breeding.