Peach (Prunus persica) is a climacteric fruit with a relatively short shelf life due to its fast ripening or softening process. Here, we report the association of gene families encoding ethylene insensitive-3 like (EIL) and ethylene response factor (ERF) with fruit ripening in peach. In total, 3 PpEILs and 12 PpERFs were highly expressed in fruit, with the majority showing a peak of expression at different stages. All three EILs could activate ethylene biosynthesis genes PpACS1 and PpACO1. One out of the 12 PpERFs, termed PpERF.E2, is a homolog of ripening-associated ERFs in tomato, with a consistently high expression throughout fruit development and an ability to activate PpACS1 and PpACO1. Additionally, four subgroup F PpERFs harboring the EAR repressive motif were able to repress the PpACO1 promoter but could also activate the PpACS1 promoter. Promoter deletion assay revealed that PpEILs and PpERFs could participate in transcriptional regulation of PpACS1 through either direct or indirect interaction with various cis-elements. Taken together, these results suggested that all three PpEILs and PpERF.E2 are candidates involved in ethylene biosynthesis, and EAR motif-containing PpERFs may function as activator or repressor of ethylene biosynthesis genes in peach. Our study provides an insight into the roles of EILs and ERFs in the fruit ripening process.

Summary: Maturity date considerably influences fruit marketing period and commercial value and it is of particular importance in apple due to its association with fruit firmness that determines storage and shelf life, but the underlying mechanism remains unclear. In this study, we report a 61‐bp fragment duplication in the MdNAC18.1 promoter that underpins maturity date variation in apple. MdNAC18.1 is the crucial major gene for maturity date and was found to regulate fruit ripening by activating transcription of ethylene biosynthetic genes and ripening‐related transcription factors, including the MdNAC18.1 homologue MdNAC72 and the main regulator of JA signalling MdMYC2. Interestingly, MdNAC18.1 was capable of binding to the promoter itself containing an additional NAC recognition site that arose from the 61‐bp duplication to repress its own expression, but could not bind to its own promoter without the 61‐bp duplication. Thus, the MdNAC18.1 allele with autosuppression function produces a phenotype of delayed maturity date and slower softening of fruit compared to that without autoregulation function. Our results demonstrate an autosuppression module that regulates the overall tempo of fruit ripening through fine‐tuning ethylene biosynthesis.

Apple is one of the most economically important and popular temperate fruit trees. The domestication of apple has resulted in substantial phenotypic differences, particularly between wild and cultivated varieties. However, the relationship between gene expression and phenotypic variations in apple remains poorly understood. Here, we present a comprehensive dataset featuring five distinct apple varieties, including two wild varieties and three representative cultivated varieties. The dataset comprises of both phenomics data, encompassing twelve fruit quality-related traits continuously measured over two years, and transcriptomic data obtained at different developmental stages with three biological replicates. We performed basic quality control process, gene expression normalization and differential gene expression analysis to demonstrate the utility and reliability of the dataset. Our findings indicate that gene expression strongly related with phenotypic variations in apple. This dataset serves as a valuable resource, encompassing phenomics and transcriptomic data in multiple formats, thereby facilitating further exploration of the relationships between gene expression and phenotypic traits in apple.