EIN3-Like family members fine-tune fruit coloration by divergently regulating flavonoid and carotenoid biosynthesis in tomato

Abstract Ethylene is a critical phytohormone controlling fruit ripening and quality traits. Ethylene insensitive 3 (EIN3) and its homologs EIN3-like (EILs) are central to the ethylene signaling pathway by directly regulating the expression of ethylene-responsive genes. Despite the established role of these factors in ethylene response and fruit ripening, the specific contributions and potential functional divergence among SlEIL family members in the regulation of different fruit quality traits in tomato (Solanum lycopersicum) remain largely unexplored. In this study, we obtained two types of SlEIL co-suppression lines with pink- or yellow-colored fruits due to different expression levels of the four SlEIL family genes. Through characterization of the pink- or yellow-colored fruits, we uncovered that SlEIL1–4 act redundantly in promoting fruit softening and flavor by activating target genes encoding proteins that function in cell wall remodeling and flavor metabolism. However, SlEILs are functionally divergent in flavonoid and carotenoid metabolism by differentially regulating the expression of SlMYB12, a key transcription factor regulating flavonoid biosynthesis, and SlZISO, an important structural gene in the carotenoid biosynthetic pathway. The outcomes of this study not only unveil the distinct regulatory mechanism of SlEILs in fruit ripening and quality traits but also provide insight into creating different fruit colors in tomato through molecular breeding by targeting SlEIL family genes.