This article focuses on the molecular and hormonal mechanisms underlying the control of fleshy fruit ripening and quality. Recent research on tomato shows that ethylene, acting through transcription factors, is responsible for the initiation of tomato ripening. Several other hormones, including abscisic acid (ABA), jasmonic acid (JA) and brassinosteroids (BR), promote ripening by upregulating ethylene biosynthesis genes in different fruits. Changes to histone marks and DNA methylation are associated with the activation of ripening genes and are necessary for ripening initiation. Light, detected by different photoreceptors and operating through ELONGATED HYPOCOTYL 5(HY5), also modulates ripening. Re-evaluation of the roles of ‘master regulators’ indicates that MADS-RIN, NAC-NOR, Nor-like1 and other MADS and NAC genes, together with ethylene, promote the full expression of genes required for further ethylene synthesis and change in colour, flavour, texture and progression of ripening. Several different types of non-coding RNAs are involved in regulating expression of ripening genes, but further clarification of their diverse mechanisms of action is required. We discuss a model that integrates the main hormonal and genetic regulatory interactions governing the ripening of tomato fruit and consider variations in ripening regulatory circuits that operate in other fruits.

Fruit development and ripening is regulated by genetic and environmental factors and is of critical importance for seed dispersal, reproduction and fruit quality. Tomato rin mutant fruit have a classic ripening-inhibited phenotype, which is attributed to a genomic DNA deletion resulting in the fusion of two truncated transcription factors, RIN and MC. In wild-type fruit, RIN, a MADS-box transcription factor, is a key regulator of the ripening gene expression network with hundreds of gene targets controlling changes in color, flavor, texture and taste during tomato fruit ripening; MC, on the other hand, has low expression in fruit, and the potential functions of the RIN-MC fusion gene in ripening remain unclear. Here, over-expression of RIN-MC in transgenic wild-type AC tomato fruits impaired several ripening processes, and down-regulating RIN-MC expression in the rin mutant was found to stimulate the normal yellow mutant fruit to produce a weak red color, suggesting a distinct negative role for RIN-MC in tomato fruit ripening. By comparative transcriptome analysis of rin and rin 35S::RIN-MC RNAi fruits, a total of 1168 and 1234 genes were identified as potential targets of RIN-MC activation and inhibition. Further, the RIN-MC fusion gene was shown to be translated into a chimeric transcription factor that was localized to the nucleus and was capable of protein interactions with other MADS-box factors. These results indicated that RIN-MC is functional and controls expression of many ripening genes, thereby contributing to the rin mutant phenotype.

Fleshy fruits become more susceptible to pathogen infection when they ripen; for example, changes in cell wall properties related to softening make it easier for pathogens to infect fruits. The need for high‐quality fruit has driven extensive research on improving pathogen resistance in important fruit crops such as tomato (Solanum lycopersicum). In this review, we summarize current progress in understanding how changes in fruit properties during ripening affect infection by pathogens. These changes affect physical barriers that limit pathogen entry, such as the fruit epidermis and its cuticle, along with other defenses that limit pathogen growth, such as preformed and induced defense compounds. The plant immune system also protects ripening fruit by recognizing pathogens and initiating defense responses involving reactive oxygen species production, mitogen‐activated protein kinase signaling cascades, and jasmonic acid, salicylic acid, ethylene, and abscisic acid signaling. These phytohormones regulate an intricate web of transcription factors (TFs) that activate resistance mechanisms, including the expression of pathogenesis‐related genes. In tomato, ripening regulators, such as RIPENING INHIBITOR and NON_RIPENING, not only regulate ripening but also influence fruit defenses against pathogens. Moreover, members of the ETHYLENE RESPONSE FACTOR (ERF) family play pivotal and distinct roles in ripening and defense, with different members being regulated by different phytohormones. We also discuss the interaction of ripening‐related and defense‐related TFs with the Mediator transcription complex. As the ripening processes in climacteric and non‐climacteric fruits share many similarities, these processes have broad applications across fruiting crops. Further research on the individual contributions of ERFs and other TFs will inform efforts to diminish disease susceptibility in ripe fruit, satisfy the growing demand for high‐quality fruit and decrease food waste and related economic losses.

Summary: Fleshy fruits are commercially and nutritionally important but become more susceptible to pathogens as they ripen. Active defence mechanisms continue to function in ripe fruits but they are influenced by ripening regulators and ripening outcomes. Botrytis cinerea is one of the most important fruit fungal pathogens of tomato and jasmonic acid (JA) is the major defence phytohormone involved in response to B. cinerea infection. Pathogens induce the accumulation of bioactive jasmonoyl‐isoleucine (JA‐Ile), which transmits defence signals through a hub transcription factor (TF) MYC2 that regulates defence responses. This has been clarified in depth in leaves, but how ripening, and in particular the regulators NOR and RIN influence JA‐Ile‐mediated defence responses remains unclear. In this article, we demonstrate that knocking‐out NOR or RIN either singly (CR‐NOR, CR‐RIN) or together (CR‐NOR/RIN) weakens JA‐Ile accumulation in response to B. cinerea infection in tomato fruit. Both NOR and RIN physically interact with MYC2, and 110 of 569 differentially expressed genes (DEGs) in B. cinerea‐infected wild‐type (WT) fruits were identified as direct targets of MYC2. These included ethylene response factors (ERFs) such as ERF.A2, B12, C3, F4, G2/PTI6, whose transcripts accumulated in WT but were greatly reduced in either CR‐NOR or CR‐RIN infected fruits. Only MYC2 binding to ERF.F4 was severely impaired in CR‐NOR and CR‐RIN fruits. ERF.F4 transactivates PR‐STH2 and activates defence signalling in B. cinerea‐infected fruit. The increase in susceptibility to infection caused by promotion of ripening by RIN and NOR is thus partially compensated by their positive action in defence signalling.

Tomato MADS-RIN (RIN) transcription factor has been shown to be a master activator regulating fruit ripening. Recent studies have revealed that in addition to activating many other cell wall genes, it also represses expression of XTH5, XTH8, and MAN4a, which are positively related to excess flesh softening and cell wall degradation, which might indicate it has a potential role in pathogen resistance of ripening fruit. In this study, both wild-type (WT) and RIN-knockout (RIN-KO) mutant tomato fruit were infected with Botrytis cinerea to investigate the function of RIN in defense against pathogen infection during ripening. The results showed that RIN-KO fruit were much more sensitive to B. cinerea infection with larger lesion sizes. Transcriptome data and qRT-PCR assay indicate genes of phenylalanine ammonialyase (PAL) and chitinase (CHI) in RIN-KO fruit were reduced and their corresponding enzyme activities were decreased. Transcripts of genes encoding pathogenesis-related proteins (PRs), including PR1a, PRSTH2, and APETALA2/Ethylene Response Factor (AP2/ERF) including ERF.A1, Pti5, Pti6, ERF.A4, were reduced in RIN-KO fruit compared to WT fruit. Moreover, in the absence of RIN the expression of genes encoding cell wall-modifying enzymes XTH5, XTH8, MAN4a has been reported to be elevated, which is potentially correlated with cell wall properties. When present, RIN represses transcription of XTH5 by activating ERF.F4, a class II (repressor class) ERF gene family member, and ERF.F5. These results support the conclusion that RIN enhances ripening-related resistance to gray mold infection by upregulating pathogen-resistance genes and defense enzyme activities as well as reducing accumulation of transcripts encoding some cell wall enzymes.

The majority of genome-wide association study (GWAS) risk variants reside in non-coding DNA sequences. Understanding how these sequence modifications lead to transcriptional alterations and cell-to-cell variability can help unraveling genotype–phenotype relationships. Here, we describe a computational method, dubbed CAPE, which calculates the likelihood of a genetic variant deactivating enhancers by disrupting the binding of transcription factors (TFs) in a given cellular context. CAPE learns sequence signatures associated with putative enhancers originating from large-scale sequencing experiments (such as ChIP-seq or DNase-seq) and models the change in enhancer signature upon a single nucleotide substitution. CAPE accurately identifies causative cis-regulatory variation including expression quantitative trait loci (eQTLs) and DNase I sensitivity quantitative trait loci (dsQTLs) in a tissue-specific manner with precision superior to several currently available methods. The presented method can be trained on any tissue-specific dataset of enhancers and known functional variants and applied to prioritize disease-associated variants in the corresponding tissue.