Phenolic compounds, widely recognized as polyphenols, are prevalent chemical constituents in a variety of fruits and vegetables and play a pivotal role in enzymatic browning by acting as substrates for the enzymes that catalyze this reaction (Singh et al., 2016). These compounds belong to a class of secondary metabolites synthesized via complex and irreversible pathways, notably the shikimate and phenylpropanoid pathways, which are exclusive to plants. Such pathways contribute to plant defense mechanisms against herbivores, microbial pathogens, invertebrate pests, and environmental stressors (Sun et al., 2022).

The structure of phenolic compounds is characterized by an aromatic ring bearing one or more hydroxyl groups, and their biosynthesis is primarily routed through the shikimate pathway, which leverages intermediates from carbohydrate metabolism (Singh et al., 2017). The oxidation potential of monocyclic phenolics is greatest for compounds with 2,4,5-trihydroxy substituents and lowest in monophenols. Typically, a wide range of 1,2-dihydroxyarenes, also referred to as ortho-dihydroxyphenols, are particularly prone to oxidation by polyphenol oxidase (PPO) due to the ortho positioning of the hydroxyl groups, which facilitates oxidation (Parveen et al., 2010).

The oxidation process mediated by PPOs is significantly influenced by the characteristics of the phenolic side chain, including the nature and number of hydroxyl groups and their placement on the aromatic ring (Winters et al., 2008). These structural attributes also determine the extent to which these compounds can undergo indirect oxidation through interactions with PPO reaction products. The substrate specificity of PPOs varies depending on the plant species and isoform, with a generally higher affinity for diphenols over monophenols. Consequently, polyphenols are recognized as the principal contributors to enzymatic browning in postharvest storage and processing of crops.

Enzymatic browning is a biochemical process in which specific enzymes oxidize phenolic compounds to form quinones, which then non-enzymatically polymerize to produce brown pigments (Zhu et al., 2023). The chief enzyme implicated in this browning reaction is polyphenol oxidase (PPO), which is categorized into two main types: EC 1.10.3.1 (including o-diphenol oxygen oxidoreductase, diphenol oxidase, and catechol oxidase) and EC 1.14.18.1 (encompassing tyrosinase, cresolase, and monophenol monooxygenase) (Moon et al., 2020). PPO enzymes are located within the cytoplasm, while their phenolic substrates are typically housed within plastids. Tissue damage in plants triggers the migration of PPO enzymes from the cytoplasm to the plastids, facilitating their interaction with the substrates.

Ortho-quinones, the products of PPO activity, display electrophilic characteristics, making them prone to nucleophilic attacks from a variety of biomolecules, such as proteins, peptides, amino acids, water, and other polyphenols. These interactions lead to the formation of Michael-type adducts, contributing to the complexity of the browning pigments (Loizzo et al., 2012; Schieber, 2018). Additionally, peroxidase (POD, EC 1.11.1.7) is another thermostable enzyme that significantly contributes to oxidative browning reactions (Shrestha et al., 2020). Utilizing hydrogen peroxide (H2O2) as a cofactor, POD catalyzes the single-electron oxidation of a wide array of substrates, further promoting enzymatic browning. It simultaneously reduces hydrogen peroxide to water, thus participating actively in the browning process (Nokthai et al., 2010).

Therefore, both PPO and POD are instrumental in the enzymatic browning process. They not only share common substrates but also their concerted action on diphenolic substrates can lead to melanin formation, which is a key component of the browning phenotype in plants.

Reactive oxygen species (ROS) are byproducts of cellular processes such as photosynthesis, respiration, and other metabolic activities. These include singlet oxygen (1O₂), hydrogen peroxide (H₂O₂), superoxide anions (O₂−), hydroxyl radicals (OH·), lipid peroxide (ROOR′), and alkyl radicals (R) (Li et al., 2019a). At low concentrations, ROS act as signaling molecules within plant cells, playing a pivotal role in various physiological functions. It can induce both reversible and irreversible oxidative post-translational modifications to proteins involved in many signaling cascades (Waszczak et al., 2015). However, when produced in excess, ROS can cause oxidative stress, which is detrimental to the organism.

High levels of ROS can induce senescence, compromising the integrity and functionality of cellular membranes. This interaction between ROS and cellular biomolecules can lead to their modification or inactivation, resulting in organelle dysfunction and structural cellular changes (Rezayian et al., 2019). During postharvest storage and processing, the accumulation of ROS and free radicals can trigger browning reactions. Specifically, peel browning is often attributed to the release of cellular contents following the loss of membrane permeability caused by ROS surges (Lin et al., 2020).

Controlling the ROS pathway is essential for reducing browning and maintaining the quality of fruits and vegetables after harvest. Plants can mitigate browning by enhancing the activity of antioxidative enzymes and increasing the antioxidant content within the fruit, thus counteracting the accumulation of ROS (Ali et al., 2019; Li et al., 2019a; Liu et al., 2021b). The ROS metabolic pathway is regulated by three primary antioxidant enzymes: superoxide dismutase (SOD), ascorbate peroxidase (APX), and catalase (CAT). These enzymes play a critical role in maintaining ROS balance and protecting plants against oxidative stress (Li et al., 2019b). SOD catalyzes the dismutation of O₂ ⁻ into H₂O₂ and O₂, while APX and CAT efficiently detoxify H₂O₂. By reducing ROS levels, these enzymatic ROS scavengers not only prevent oxidative damage but also inhibit enzymatic browning processes (Li et al., 2019c).

The integrity of the plasma membrane plays a pivotal role in preventing browning in postharvest produce. Compromised cell membrane integrity facilitates the contact between phenolic compounds and oxidative enzymes, catalyzing the enzymatic browning process (Ma et al., 2022). This degradation is often indicated by a shift from unsaturated to saturated fatty acids in the membrane, coupled with an increase in lipid peroxidation products and enhanced membrane permeability (Lin et al., 2016).

Phospholipids are essential components of cellular membranes, and enzymes such as Phospholipase D (PLD) and lipoxygenase (LOX) are critical in the breakdown of membrane phospholipids, an early sign of senescence and browning in harvested tissues (Li et al., 2009; Sun et al., 2020). PLD catalyzes the hydrolysis of phosphatidylcholine (PC) or phosphatidylethanolamine (PE) to produce phosphatidic acid (PA), whereas LOX initiates the peroxidation of membrane lipids. This peroxidation can lead to the deterioration of the cell membrane’s structural integrity, resulting in the disruption of the phospholipid bilayer and loss of cellular compartmentalization, which are critical events preceding browning (Trabelsi et al., 2012).

Transcriptomics is the study of RNA expression profiles, including both coding and regulatory non-coding RNA sequences, within a given temporal context (Pandit et al., 2018; Luo et al., 2022). This analysis can be conducted through hybridization-based methods, such as microarrays, or sequence-based approaches, like direct cDNA sequencing. The browning process in postharvest produce involves significant changes in gene expression.

Early genetic studies focused on identifying key factors in the browning of postharvest fruits and vegetables, providing foundational insights into the underlying regulatory mechanisms (Coetzer et al., 2001). However, as whole-genome transcriptomic studies advanced, genes related to the browning process, including those involved in downstream signaling and anti-browning responses, have been somewhat neglected. Our current study employs transcriptome analysis of fresh-cut potato tubers to pinpoint critical genes implicated in browning, highlighting the roles of plant hormone biosynthesis, signaling molecules, and respiratory burst oxidase in this process (Wang et al., 2023a).

Senescence, a crucial stage in plant development, is intimately connected with browning. Zhou et al. (2020b) utilized long-read sequencing technology to identify a two-phase browning pattern in postharvest litchi, distinguishing the onset of senescence from the browning stage. Their findings underscored significant stage-specific biological pathway activations, such as cell wall degradation, oxidative processes, and disease responses during browning. Comparative transcriptomic analyses between browning-resistant and susceptible cultivars have revealed candidate genes and mechanisms involved in postharvest browning. A recent time-course study on fresh-cut eggplant employed transcriptome analysis to unravel the transcriptional regulation of browning, proposing two key regulatory networks related to tyrosine metabolism and phenylpropanoid biosynthesis (Liu et al., 2021c).

Transcriptomics has also been applied to understand how postharvest crops respond to anti-browning treatments. Zhao et al. (2021) explored how γ-aminobutyric acid (GABA) prevents browning in fresh-cut apples, finding that GABA modified the expression of genes related to the synthesis of browning enzymes and phenolic compounds. Similarly, the application of melatonin, an effective anti-browning agent, was shown to enhance the antioxidant system by regulating ROS-metabolism-related genes in a comparative transcriptome study (Min et al., 2023). Plant hormones, which play a critical role in regulating postharvest browning, have been studied as well; for instance, Liu et al. (2022b) demonstrated that 6-Benzylaminopurine (6-BA) effectively delayed browning in fresh-cut lettuce, with transcriptome analysis indicating a significant impact on phenolic-related metabolic pathways.

Proteomics investigates the abundance, expression, and interactions of proteins within organisms or cells. Unlike transcriptomic or genomic data, proteomic information provides a more direct understanding of the actual functional molecules in biological processes, as protein levels and activities cannot be fully predicted from RNA or DNA data alone (Mathabe et al., 2020). Proteins are central to the regulation and execution of nearly all biological functions, making proteomics essential for uncovering the molecular mechanisms that govern the development and browning of postharvest crops.

Recent proteomic studies have focused on gene expression and the accumulation of proteins during the storage and processing of crops (Feng et al., 2016). These studies have the potential to reduce postharvest losses due to browning by identifying and selecting crop varieties with enhanced tolerance to browning and other desirable quality traits. For instance, Qu et al. (2022) analyzed the proteome of postharvest mushroom fruiting bodies during storage, identifying 168 significantly regulated proteins involved in processes such as translation, carbohydrate metabolism, signal transduction, and amino acid metabolism. Their research also highlighted the role of AMPK and FOXO signaling pathways in the browning of mushrooms during storage. Ban et al. (2018) applied proteomics to study the effect of chitosan and carboxymethyl cellulose coatings on strawberries packaged in polyethylene terephthalate containers and stored at low temperatures. Their findings included the identification of a set of proteins related to browning, primarily associated with primary and secondary metabolism (Wang et al., 2017).

Beyond the linear sequence and three-dimensional structure of proteins, post-translational modifications (PTMs) greatly influence protein function and activity. For example, quantitative phosphoproteome analysis has shown that SN2 can reduce browning in fresh-cut potatoes by altering the phosphorylation levels of kinases. A network involving serine/arginine-rich proteins and mitogen-activated protein kinases has been proposed as a potential kinase-substrate interaction system that influences browning (Li et al., 2023).

Metabolomics is the holistic study of metabolites within a biological system under defined conditions, providing a snapshot of the physiological state of an organism. These metabolites reflect the final products of gene expression and regulatory interactions, often showing a more direct correlation with observed phenotypes than mRNA or protein levels. As a branch of omics science, metabolomics is particularly effective for its comprehensive coverage of biological processes and its ability to link genotype to phenotype. Current metabolomics research employs targeted, widely targeted, and untargeted strategies, requiring the use of sensitive and precise techniques like mass spectrometry (MS) coupled with gas chromatography (GC), liquid chromatography (LC), or nuclear magnetic resonance (NMR) spectroscopy (Meng et al., 2022).

The role of metabolomics in understanding the browning of postharvest crops has gained significant momentum. It is instrumental in identifying and characterizing bioactive compounds and chemical markers that may influence the quality and shelf-life of produce (Qiu et al., 2021; Gao et al., 2022). For instance, a study on pomegranate storage identified key secondary metabolites involved in aril browning, particularly those related to the biosynthesis pathways of flavonoids, flavonols, and isoflavonoids, with a focus on phenylpropanoid biosynthesis (Shi et al., 2022). Metabolomics has also revealed that the metabolic profile of morel mushrooms changes substantially during storage, with increases in amino acids and fatty acids and decreases in soluble sugars, organic acids, and certain phenolic compounds (Gao et al., 2022). Comparative metabolomics between lettuce cultivars with varying browning rates has pinpointed metabolites implicated in the browning process, such as differences in lysophospholipid levels, phospholipase and lipoxygenase activity, and the presence of caffeoylquinic acid derivatives (García et al., 2017).

The integration of various omics datasets is pivotal for unraveling the complex molecular mechanisms of enzymatic browning in postharvest crops. By combining multi-omics data, such as genomics, transcriptomics, proteomics, and metabolomics, researchers can gain a comprehensive understanding of the molecular events that affect postharvest crop quality (Aiese Cigliano et al., 2022; Xie et al., 2023). Data integration is a sophisticated process that requires advanced computational methods to merge and analyze diverse omics datasets effectively. Current research often utilizes functional and statistical networks to facilitate the visualization and interpretation of these complex data relationships, aiming to identify key metabolic hubs associated with the browning process.

Recent studies have demonstrated the power of multi-omics approaches in pinpointing the primary factors contributing to browning during postharvest treatments and storage (Qiao et al., 2022; Romero et al., 2022). For example, a combined transcriptomic and metabolomic investigation into the browning of fresh-cut eggplant identified fluctuations in membrane phospholipid and unsaturated fatty acid metabolites, as well as changes in the expression of genes related to membrane lipid metabolism (Liu et al., 2022a). Similarly, the analysis of harvested litchi using both transcriptomic and proteomic techniques has provided insights into the regulation of the anthocyanin biosynthesis pathway during the browning process (Qu et al., 2021).