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Yellow-Fruited Phenotype is Caused by an Insertion Event at 5’ UTR of YFT1 Allele in yft1 Mutant Tomato 1

The yft1 tomato mutant has a yellow-fruited phenotype controlled by a recessive gene (YFT1), which has been shown by map-based cloning to be a homolog of ETHYLENE INSENSITIVE 2 (EIN2). The genetic lesion of the YFT1 allele of yft1 is attributed to a 573 bp DNA fragment (IF573) insertion at 1,200 bp downstream of the transcription start site (TSS). Transcriptome analysis revealed that the mutation resulted in 5,053 differentially expressed genes (DEGs) in the fruit pericarp compared with the M82 wild type cultivar. These were annotated as being involved in ethylene synthesis, chromoplast development, and carotenoid synthesis. Genetic lesion in YFT1 caused a reduction in its own transcript levels in yft1 and impaired ethylene emission and signal transduction, delayed chromoplast development and decreased carotenoid accumulation. The molecular mechanism underlying the reduced expression of YFT1 in yft1 was examined at both the RNA and DNA levels. The IF573 event was shown to introduce two negative regulatory sequences located at -272 to -173 bp and -172 to -73 bp in the YFT1 allele promoter, causing alterative splicing due to aberrant splicing sites, and also altering the structure of the open reading frame in the 5’-UTR. This study contributes to the understanding of color formation in tomato fruit. One-sentence summary Lesion happened in regulatory region impairs expression of a key gene of ethylene signal pathway, and alters fruit color in tomato due to effect of carotenoids accumulation and ethylene synthesis.