Toward a tastier tomato: Recovering the lost STP1 variant in modern tomato to improve soluble solid in fruit

In a study recently published in the journal Horticulture Research, researchers 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.

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.