GREEN STRIPE, encoding methylated TOMATO AGAMOUS-LIKE 1, regulates chloroplast development and Chl synthesis in fruit

Fruit development involves chloroplast development, carotenoid accumulation and fruit coloration. Although genetic regulation of fruit development has been extensively investigated, epigenetic regulation of fruit coloration remains largely unexplored. Here, we report a naturally occurring epigenetic regulation ofTAGL1, and its impact on chloroplast development and fruit coloration. We used a genome-wide association study in combination with map-based cloning to identify theGREEN STRIPE(GS) locus, a methylated isoform ofTAGL1regulating diversified chloroplast development and carotenoid accumulation. Nonuniform pigmentation of fruit produced byGSwas highly associated with methylation of theTAGL1promoter, which is linked to a SNP at SL2.50ch07_63842838. High degrees of methylation of theTAGL1promoter downregulated its expression, leading to green stripes. By contrast, low degrees of methylation led to light green stripes ings. RNA-seq and ChIP collectively showed that the expression of genes involved with Chl synthesis and chloroplast development were significantly upregulated in green stripes relative to light green stripes. Quantitative PCR and dual luciferase assay confirmed that TAGL1 downregulates expression ofSlMPEC,SlPsbQ, andSlCAB, and upregulates expression ofPSY1- genes which are associated with chloroplast development and carotenoid accumulation. Altogether, our findings regarding theGSlocus demonstrate that naturally occurring methylation ofTAGL1has diverse effects on plastid development in fruit.