You're using an outdated browser. Please upgrade to a modern browser for the best experience.
Hormonal Mechanisms of Fleshy Fruit
Edit
This entry is adapted from the peer-reviewed paper 10.3390/cells10051136

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.

ethylene fruit ripening softening plant hormone

1. Background

It is generally accepted that fleshy fruits can be divided into two classes, the climacteric fruits (i.e., apple, apricot, avocado, banana, tomato, etc.) and non-climacteric fruits (i.e., citrus, grape, orange, lemon, raspberry, strawberry, etc.). The main differences between these two groups are the characteristic burst of respiration and ethylene production that occurs at the onset of ripening in climacteric fruits [1][2][3]. Non-climacteric fruits respire and produce low levels of ethylene, and they can also sometimes respond to this hormone, which promotes, for example, de-greening of citrus. Non-climacteric fruits do not, however, show a burst of CO2 or ethylene production, which is the classic sign of ripening onset in climacteric fruit. This distinction between two types of fruits is somewhat arbitrary, however, and ripening of both types of fruits involves hormones and similar changes in gene expression, often regulated by structurally related transcription factors (TFs). Hormone signalling operates primarily by modulating expression or action of TFs plus genes involved in hormone biosynthesis, perception and signalling. TFs can also directly and indirectly affect expression of genes required for hormone synthesis, and expression of some ripening TFs is regulated developmentally or by environmental stimuli. Consequently, there is a balance between developmental, environmental, hormonal and genetic cues that govern the processes of fruit development and ripening.
The tomato (Solanum lycopersicum) was selected as a model for fruit ripening and the complete genome sequence was determined in 2012 [4]. The tomato genome contains 58 TF families, including a total of 1845 putative TFs [5]. For a complete understanding of the ripening process, it is necessary to know how these TFs and different hormones and environmental factors operate and interact at the molecular level to coordinate the myriad of ripening reactions. Although the genetic and biochemical changes that occur during ripening are important determinants of fruit quality, if some aspects of ripening, such as softening, proceed too far, the fruit become susceptible to infection, spoilage and rotting. Thus, understanding how the different facets of ripening are regulated can help improve fruit quality and quantity, prevent waste and contribute to improved nutrition and food security.
Although tomato has been an important ripening model [1][6][7][8][9][10], the fact that ripening has arisen several times during the course of evolution, and the differences between climacteric and non-climacteric fruits, caution against a “one type fits all” model [11]. Furthermore, initial conclusions about the function of key tomato ripening “master regulator” TFs (NAC-NOR, MADS-RIN, SPL-CNR), which strongly influenced ripening models, have turned out to be misleading and their roles in ripening have been revised [12][13][14][15][16][17][18].

2. Main Physiological and Biochemical Changes Are Regulated by Ripening Genes

Massive technological progress has accelerated the accumulation and analysis of data in the last 15 years. Complete genomic sequences of hundreds of angiosperms are now available, including over 90 fruit species of economic importance (https://simple.wikipedia.org/wiki/List_of_fruits, accessed on May 6 2021) and other horticultural crops [19][20], and the number is rapidly increasing. With the advent of RNA-seq technology, transcriptomic sequences for many developmental processes, including ripening, are rapidly becoming available. Where it once took 2–3 years to identify and characterise the structure and expression of a single gene, it is now possible to acquire this information for 25,000 genes in a few weeks, and, unlike the early years, clues to gene function can often be gained from DNA sequence homology searches against previously characterised genes. Many ripening genes affecting different aspects of fruit physiology and biochemistry have been identified by this approach [21]. Although this impressive progress has contributed large amounts of data (Sol Genomics Network, https://solgenomics.net/; Tomato Expression Atlas, http://tea.sgn.cornell.edu/, accessed on 6 May 2021), there is still a need to consider it in a physiological and biochemical context, in order to understand its significance and unravel the hormonal, genetic and biochemical regulatory mechanisms involved in ripening.

2.1. Colour Changes during Ripening

Visual clues are extremely important for signalling at a distance to frugivores the availability of ripe fruit. A wide range of animals, including seed-dispersers such as bats, rodents, primates and many different types of birds, with different vision systems use visible (380 to 700 nm) or UV light (mainly UVA, 315 to 400 nm) to detect them. Different organisms can have between 1 and 4 functioning colour receptors. Many mammals, including bats and rodents, are dichromats (i.e., have only two types of colour receptor), yet are capable of distinguishing ripe fruits from leaves. Most new world monkeys are also dichromats, whereas most other primates have three types of colour receptors (i.e., they are trichromats), which confer improved colour discrimination.
There are four main mechanisms involved in colour change in fruits:
  • (1) Loss of chlorophyll from chloroplasts, which is accompanied by the disassembly and recycling of some thylakoid membranes and photosynthetic proteins.
  • (2) Accumulation of coloured carotenoids such as β-carotene and lycopene in lipid globules or other characteristic membrane-bound structures in the developing chromoplasts, which arise either by conversion of chloroplasts or develop from other types of plastids [22][23][24][25].
  • (3) The accumulation of flavonoids or anthocyanins pigments in the cell vacuoles.
  • (4) The production of UV-reflecting components such as surface waxy layers, fatty deposits within cells or from parallel sheets of membranes that generate iridescence due to thin film interferences of light [26].
The synthesis of anthocyanins and carotenoids during ripening has been the most intensively studied at the molecular level and involves the selective expression of genes encoding specific enzymes in their respective metabolic pathways.
Much of the knowledge on the regulation of carotenoid biosynthesis has been obtained from tomato and can be inferred to apply to other fleshly fruits (Figure 1), although it should be emphasised that structurally different carotenoids can occur in different types of fruits. Fruits rich in carotenoids provide a rich source of dietary pro-vitamin A [1][27]. The precursor of carotenoid biosynthesis, geranylgeranyl pyrophosphate (GGPP), is synthesised via the methylerythritol-4-phosphate (MEP) pathway. Two GGPP molecules produce phytoene, catalysed by phytoene synthase (PSY). Phytoene is converted into lycopene by undergoing a sequential series of desaturation and isomerisation reactions by phytoene desaturase (PDS), ζ-carotene isomerase (ZISO), ζ-carotene desaturase (ZDS) and carotene isomerase (CRTISO). Lycopene can be cyclised by lycopene cyclase (LCY) to form α-carotene, generating lutein, catalysed by carotene hydroxylase (CHX). Alternatively, lycopene can be cyclised by LCY or chromoplast-specific lycopene β-cyclase (CYCB) to form β-carotene, which is converted into β-cryptoxanthin and then into zeaxanthin by CHX [28]. Tomato PSY1 was the first carotenoid biosynthetic enzyme to be identified [29] and the pathways and enzymic steps for carotenoid production are now well-established [28]. In tomato, the PSY1 isoform is involved in synthesis of carotenoids in ripening fruit, whereas PSY2 performs this function in green tissues. Several other key genes are also upregulated during ripening [30][31] and there is also substantial variation between fruits. A recent review of mutations underlying colour differences between different fruits and varieties highlighted mutations affecting coding sequences and promoters of a number of carotenoid biosynthetic enzymes, including CRTISO, ZISO, CHX, CYCB, etc. [28][32].
Cells 10 01136 g001 550
Figure 1. The carotenoid biosynthesis pathway and variations in different fruits (redrawn and modified from Lado et al. [31] and Luan et al. [28]). Each fruit labelled with a number in blue is positioned in the pathway at the level of the predominant carotenoid responsible for its coloration: 1, Lemon (Citrus limon); 2, Sweet orange Pinalate mutant; 3, Tomato tangerine mutant; 4, Grape (Vitis vinifera); Immature green pepper (Capsicum annuum); Kiwifruit (Actinidia chinensis); Peel of immature mandarin (Citrus reticulata, Citrus clementina, Citrus unshiu); Avocado (Persea americana); 5, Tomato (Solanum lycopersicum); Red watermelon (Citrullus lanatus); Pulp of red grapefruit (Citrus paradisi); Red papaya (Carica papaya); Gac (Momordica cochinchinensis); 6, Orange-flesh melon (Cucumis melo); Orange-flesh apricot (Prunus armeniaca); Orange-flesh pumpkin (Cucurbita maxima); 7, Yellow papaya (Carica papaya); Loquat (Eriobotyra japonica); Pulp of mandarin (Citrus reticulata, Citrus clementina, Citrus unshiu); 8, Yellow-flesh peach (Prunus persica); Orange pepper (Capsicum annuum); 9, Mango. PSY, phytoene synthase; PDS, phytoene desaturase; ZISO, ζ-carotene isomerase; ZDS, ζ-carotene desaturase; CRTISO, lycopene isomerase; LCY, lycopene cyclase; CYCB, chromoplast specific lycopene β-cyclase; CHX, carotene hydroxylase; ZEP, zeaxanthin epoxidase; VDE, violaxanthin de-epoxidase; NSY, neoxanthin synthase; NCED, 9-cis-epoxycarotenoid dioxygenase. Note that the hormone ABA, which is discussed in Section 3.3, is produced from this pathway. Some of these metabolites are also utilised in the biosynthesis of hormones, such as GA, strigolactones and β-cyclocital, but these pathways are omitted from this figure because they are not discussed in this review.
Anthocyanins are water-soluble, purple and red pigments (cyanidin, pelargonidin and delphinidin derivatives) that accumulate in the vacuoles of epidermal and/or flesh cells of fruits, as they ripen. They are synthesised from precursors generated from the upper part of the phenylpropanoid pathway (not shown). Many fruits are enriched with anthocyanins, such as cyanindin-3-glucoside (C3G), which is the predominant anthocyanin in Chinese bayberry [33], mulberry, apple peel [34][35][36] and peach skin [37], and other predominant anthocyanins such as pelargonidin in strawberry [38], cyanidin and delphinidin in grape skin [39] and cyanidin-3-rutinoside in cherry [40].
Transcriptional regulation of the downstream structural genes (such as chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonoid 3′-hydroxylase (F3′H), flavonol synthase (FLS), dihydroflavonol 4-reductase (DFR), flavone 3′-O-methyltransferase 1 (OMT1) and anthocyanidin synthase (ANS)) governs the three main branches that lead to the production of the different flavonoid pigments in many plant species [41] (Figure 2).
Cells 10 01136 g002 550
Figure 2. The anthocyanins biosynthetic pathway and variations in different fruits. This figure is redrawn and modified from Gayomba et al. [42]. The flavonol biosynthetic pathway is illustrated, showing enzymatic steps, and the responsible enzyme is indicated in red. CHI, chalcone isomerase; CHS, chalcone synthase; F3H, flavanone 3-hydroxylase; F3′H, flavonoid 3′-hydroxylase; F3′5′H, flavonoid 3′,5′-hydroxylase; FLS, flavonol synthase; DFR, dihydroflavonol reductase; OMT1, flavone 3′-O-methyltransferase 1.
Expression of many of the anthocyanin biosynthetic genes is regulated by a conserved mechanism involving a complex comprised of three types of TFs: MYB + bHLH (basic helix–loop–helix) + WD40 (WD40 repeat protein) (MBW) [43][44]. There are many different types of MYBs, including transcriptional activators, and some, such as the R3-MYB protein MYBL2 or the R2R3-MYB protein MYB27, possess a C-terminal EAR motif and act as repressors [45].
External colour change mechanisms are not universal, however, and ripe ‘Hayward’ kiwifruit remain green, or greenish brown externally and light green internally, whereas ‘Hort16A’ kiwifruit turn gold internally [46]. Fruit inner pericarp of Actinidia chinensis cv. Hort22D has red flesh, because AcMYBF110 is thought to activate the transcription of DFR, ANS and F3GT1 [47]. In addition, upregulation of MYBA1-1 and MYB5-1 by low temperature enhances anthocyanin accumulation in ‘Hongyang’ kiwifruit by transcriptional activation of ANS1, ANS2, DFR1, DFR2 and UFGT2 [48]. Also, different mechanisms are not mutually exclusive, and several can operate in the same fruit. For example, during ripening of some apples, the chloroplasts in the peel cells lose chlorophyll and accumulate carotenoids, and sometimes also anthocyanins, although some varieties remain green [36][49]. Tomatoes normally lose chlorophyll and accumulate carotenoids, but “greenflesh” mutant fruit retain some thylakoids and chlorophylls, and at the same time, they accumulate carotenoids, and consequently, the fruit appear a dirty-brown colour [50]. Furthermore, tomatoes can also accumulate anthocyanins as well as carotenoids if they are manipulated to express the necessary genes [51]. Strawberries, black grapes and Chinese bayberry are examples of fruits that lose chlorophyll and normally only accumulate anthocyanins [38][52][53].

2.2. Fruit Softening

It is generally accepted that fruit softening during ripening is, at least partly, due to cell wall changes catalysed by wall-modifying enzymes. Investigations with many fruits have shown that there are at least 10 different types of cell wall-modifying enzymes that are expressed during ripening [54], and these are believed to collectively contribute to the change in texture, leading to alterations in the structure and hydration of cell wall polymers, leading to softening. These include the pectin-modifying enzymes: pectinesterase (PE), pectate lyase (PL), polygalacturonase (PG) and β-galactosidase (β-GAL), and the hemicellulose/cellulose-modifying enzymes: 1,4-β-glucanase, xyloglucan transglycosylase/hydrolase (XTH) and expansin (EXP). It is clear that several of these enzymes have specific actions affecting cell wall structure that contribute to texture changes, although there is no single enzyme that makes a major contribution to softening [54][55]. Expansins allow cellulose microfibrils to slide over one another without covalent modification, and PG reduces the chain length of pectins, which does have some effect because it decreases the viscosity of tomato extracts [56]. Softening of intact fruit is largely unaffected, although some small increase in firmness has been detected in antisense-PG tomatoes [57]. Furthermore, an analysis of PG/EXP1 knockdown tomato fruit showed that they were firmer, had higher total soluble solids, denser cell walls and thicker cuticles than fruit of other genotypes [58], and also showed reduced skin cracking [58]. More recently, RNAi knockdown and CRISPR/Cas9 knockout experiments showed that eliminating PL produced firmer tomatoes, although softening was not abolished [59].
The question of the regulation of cell wall metabolising enzymes was addressed early on and there are differences between fruits. PG transcripts in tomato are very sensitive to low levels of ethylene [60]. The situation varies in different fruits, however, and in melon, which expresses three PG genes, accumulation of CmPG1 transcripts is dependent on ethylene, whereas regulation of CmPG2 is ethylene-independent and expression of CmPG3 is regulated by both ethylene-dependent and ethylene-independent factors [61][62].
Attempts to delay fruit softening and improve fruit quality by manipulating stress responses during storage have provided new insights into the role of a group of cell wall-modifying enzymes in causing texture change. Deterioration of peaches is delayed if they are stored at 0 °C. Upon removal from storage, however, they fail to undergo normal softening, and consequently, the texture is disliked by consumers due to the failure to produce the normal levels of a group of cell wall-modifying enzymes. A low-temperature conditioning (LTC) treatment at 8 °C, however, prior to 0 °C storage, results in much improved softening upon return to room temperature after 0 °C storage. The explanation for this is that after transfer to room temperature, transcripts for PG, PL, PE, β-1,4-endoglucanase, xylosidase (XYL), EXP1, GAL and XTH are all substantially increased, provided the peaches were acclimated at 8 °C prior to 0 °C storage [63]. Similarly, in persimmon fruit, many cultivars are astringent, due to the high soluble tannins content, which consumers find unacceptable. There are several postharvest treatment methods for removing these soluble tannins. One successful approach is to store the fruits in a 95% CO2 + 1% O2 atmosphere. This postharvest high CO2/anaerobic storage leads to acetaldehyde production, which precipitates the soluble tannins, reducing or eliminating the astringency. Unfortunately, however, persimmon treated in this way tend to soften too much. It was found that adding the ethylene perception inhibitor 1-MCP to the 95% CO2 + 1% O2 storage atmosphere greatly reduced the appearance of ethylene response factor TFs (ERFs) 8, 18 and 19, that upregulate a similar group of genes as those in peach, which together are responsible for modifying cell walls in persimmon fruit [64]. This indicates that ethylene is responsible for stimulating persimmon softening. Significantly, the promoters of the cell wall genes in peach also have ERF binding sites [63], suggesting that in both of these cases, ethylene may be involved in regulating several different genes that modify cell wall structure and softening [54]. The situation in non-climacteric fruits is less clear. Villarreal et al. [65] provided evidence that ethephon (which produces ethylene in treated plants) and 1-MCP treatment (which inhibits ethylene perception and action) influenced the expression of both PG and β-Gal, although Nardi et al. [66] showed that accumulation of FaEXP2 in strawberry fruit, whilst appearing to be influenced by both ABA and auxin, was unaffected by either ethylene or 1-MCP.

2.3. Synthesis and Accumulation of Organic Acids, Sugars and Volatiles Contribute to Taste and Aroma

The main taste characteristics of fruit are derived from the relative concentrations of organic acids and sugars [67]. The most common sugars are sucrose, glucose and fructose, which are ultimately derived from photosynthate imported during development. This soluble carbohydrate is often converted to starch and stored in the plastids of unripe fruit. During ripening, the starch is initially metabolised to maltose and glucose, by a network of starch-degrading and sugar-metabolising enzymes. During development, bananas accumulate 20–25% fresh weight of starch, which is converted to sugars during ripening. In some other fruits, photosynthesis by fruit chloroplasts can also contribute to the accumulation of stored starch prior to ripening. Eighteen starch degradation-associated enzymes from banana have been identified bound to the surface of starch granules, and ten showed increased activity during fruit ripening. The accumulation of transcripts and enzyme activities of some of these genes are ethylene inducible. A transcriptional activator MabHLH6 (a basic helix–loop–helix TF) preferentially binds to the promoters of 11 genes encoding starch degradation enzymes and transactivates their promoters [68]. Other types of TFs are also involved in regulating expression of starch degradation genes, since a zinc finger TF, DNA BINDING WITH ONE FINGER (AdDof3), physically interacts with the promoter and transactivates the AdBAM3L (β-amylase) gene in ripening kiwifruit [69]. The metabolism of the large amount of starch in banana not only generates sugars during ripening but also contributes directly to a reduction in firmness, in addition to cell wall changes outlined in Section 2.2. Sugar accumulation often involves the activities of sucrose synthase and sucrose phosphate synthase [70], and appropriate transporters [71] and increases in acid and neutral invertases during ripening of tomato convert sucrose to glucose and fructose, which enhances sweetness [72]. In watermelon, four genes involved in the metabolism of sugars have been identified as being expressed in different watermelon genotypes, including three sugar transporters, SWEET, EDR6 and STP, two sucrose phosphate synthases and sucrose synthase genes [73].
Unlike sugars, which are imported to the fruit as photosynthate, organic acids are generally synthesised in situ, mostly from sugars, metabolised starch and products of cell wall metabolism [61]. Malate and citrate are the most common fruit organic acids that accumulate in both climacteric and non-climacteric fruits during fruit development, although other acids are found in some fruits. In watermelon, three genes involved in the TCA cycle and pH regulation have been identified that are believed to play a role in organic acid accumulation [73].
During ripening, organic acids can slowly decrease in concentration in some fruits, as the malate, and sometimes citrate, are utilised as respiratory substrates, whereas sugar contents generally continue to increase. It is possible that these sugars and organic acid may have another role, since sugars are known to be signalling molecules as well as being a form of soluble carbohydrate [74]. Furthermore, when malate metabolism in tomato was modified by antisense inhibition of the activities of mitochondrial malate dehydrogenase (MDH), it was found that lines with low malate showed an increased accumulation of starch. Fruit softening and the content of chlorophylls, carotenoids and other pigments were also affected, and the low-MDH tomatoes showed increased susceptibility to Botrytis cinerea infection. It is possible that some of these effects are due to the altered redox state due to lowered malate, leading to several biochemical changes [75].
The characteristic flavour and aroma notes of different fruits are conferred by a range of different volatile components that are synthesised from several different biochemical pathways. Lipoxygenase (LOX) and alcohol dehydrogenase (ADH) in tomato [76][77] and alcohol acyl-transferase (AAT) in melon [78] were among the first enzymes to be identified that were associated with production of flavour and aroma volatiles during ripening. Identifying the correct LOX in tomato turned out to be complicated because there were at least five different isoforms involved in different biochemical pathways, including the production of jasmonic acid (JA), which will be discussed later. Antisense technology, using targeting sequences specific for each gene, identified the plastid-located TOMLOX C as playing a critical role in production of lipid-derived C6, and later, C5 volatiles [11]. Alcohol acetyltransferase (AAT1) is important in volatile ester synthesis [78][79] and the final step in the pathway, conversion of aldehydes to alcohols, requires ADH2 activity [77]. Recently, an increase in FaLOX5 transcripts has been correlated with volatile esters’ production in ripening strawberry, and FaMYB11 promoted volatile accumulation partly through the transcriptional activation of FaLOX5 [80]. Many other genes are now known that contribute to the production of flavour volatiles, and it is important to recognise that they are derived from several different biochemical pathways, including fatty acids, amino acids and carotenoids (Figure 3). Key genes that contribute to aroma and flavour in ripe tomato fruits include branched-chain amino acid aminotransferases (BCAT1), which is important in the production of branched-chain amino acids [81][82][83]. A major group of amino acid-derived flavour and aroma compounds, benzenoids (C6–C1), are synthesised from L-phenylalanine, including benzaldehyde and benzyl alcohol. The first step in this biosynthetic pathway is catalysed by L-phenylalanine ammonia lyase (PAL), encoded by the PAL3 gene, which converts phenylalanine to trans-cinnamic acid [84]. Aromatic amino acid decarboxylase (AADC1A) mediates the first step in the production of phenylalanine-derived volatiles in tomato fruits [85], and the transcripts of the carotenoid cleavage dioxygenase 1 (CCD1B) gene also participate in aroma volatiles from the amino acid pathway.
Cells 10 01136 g003 550
Figure 3. Biochemical origin of volatile compounds in fruits (redrawn from Aragüez and Valpuesta [84]; Klee and Tieman [86]). Key aspects of primary metabolism, which provides the substrates for secondary metabolism, are shown on the left. Solid lines indicate a validated step in a pathway, with the responsible enzyme indicated in red. Volatiles are indicated in blue. Broadly, volatiles are derived from the fatty acid (for example, Z-3-hexenol), carotenoid cleavage (for example, geranylacetone) or phenylpropanoid (the C6–C3 compounds) pathways. In addition, volatile alcohols can be reversibly converted to esters by the action of an alcohol acetyltransferase (AAT1) and a carboxymethylesterase (carboxylesterase 1 (CXE1)). LoxC, lipoxygenase C; HPL, fatty acid hydroperoxide lyase; ADH2, alcohol dehydrogenase 2; BCAT, branched-chain amino acid aminotransferases; AADC, aromatic amino acid decarboxylase; CCD1, carotenoid cleavage deoxygenase 1.
Terpenoids constitute the largest group of plant volatile secondary metabolites [87][88] and function in attraction and defence during vegetative and reproductive growth. They are synthesised from isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) via two pathways: the cytosol-located mevalonate (MVA) pathway and the methyl-erythritol phosphate (MEP) pathway in the plastid [89]. Terpene synthases (TPS) catalyse the terminal steps in the pathways and use geranyl diphosphate (GPP), trans-trans-farnesyl diphosphate (trans-trans-FPP, usually referred to as FPP) and geranylgeranyl diphosphate (GGPP) to form monoterpenes (C10), sesquiterpenes (C15) and diterpenes (C20), respectively. There are many different TPSs, and differences in their catalytic mechanisms generate a wide range of different terpenoids [90][91]. TPS families have been identified in many plants, including Arabidopsis, tomato, grapevine, apple, orange and kiwifruit [92][93][94][95]. Monoterpenes and sesquiterpenes are volatile and contribute to the characteristic aroma of fruits, including citrus [96]. CitAP2.10 [97] and CitERF71 [98] have been reported to regulate the synthesis of the sesquiterpenes valencene and E-geraniol respectively, in citrus. Nieuwenhuizen et al. [99] showed that mutation in the NAC binding region of TPS promoters in two kiwifruit species influences their monoterpene contents.

3. Ripening Is Influenced by Multiple Hormones and Light

The initiation and coordination of fruit development and ripening is complex and still not completely understood. Ethylene production is initiated at the onset of ripening and mature fruits have the ability to both synthesise their own ethylene and to respond to external ethylene by initiating ripening [2]. There is considerable evidence that hormones other than ethylene are also involved in fruit development and ripening (discussed in [100]). Auxin has been known for many decades to be required for fruit growth in strawberry [101], and gibberellins and auxins cause parthenocarpic fruit development in tomato [102]. Auxins and cytokinins can circumvent the requirement for fertilisation and stimulate development of parthenocarpic fruits [103]. It is possible that signals such as abscisic acid (ABA) from mature seeds could trigger the onset of ripening, but the fact that parthenocarpic tomatoes, bananas and grapes ripen without seeds indicates that such signalling is not an absolute requirement for ripening to occur [104]. There are now many reports showing that auxin, ABA and jasmonic acid (JA) also influence expression of genes involved in the biosynthesis of ethylene and other aspects of the ripening control network, as discussed later.

3.1. Ethylene Initiates and Promotes Ripening

Ethylene production occurs at a low level throughout plant growth and development but increases during biotic and abiotic stresses, abscission, ripening and senescence. During ripening onset and progression, there is a massive burst of ethylene production, which occurs in two stages, called system-1 and system-2 ethylene synthesis [10][105][106][107], and when system-2 is activated, ethylene synthesis becomes autocatalytic. In tomato, 14 ACC synthase (ACS) genes (ACS1A/B-13) and 7 ACC oxidase (ACO) genes (ACO1-7) have been identified [108][109]. ACS1A and ACS6 are mainly involved in system-1 ethylene production, and ACS2 and ACS4 in system-2 [108][109]. ACO1 participates in system-1 ethylene synthesis and ACO1 and ACO4 are involved in system-2 ethylene in tomato, but the ACO gene family has not been as well-studied as the ACS family [10][108]. ACO1 expression increases strongly and correlates well with the autocatalytic rise in ethylene production. ACO2 expression drops to a basal level during further fruit development and ripening. At the onset of ripening, ACO3 expression strongly increases. There is a temporal increase in ACO4 expression during the breaker stage, mainly in the columella and placenta tissue. ACO5 expression increases slightly after anthesis and remains at a similar level during further fruit development and ripening. ACO6 has a low expression during fruit development but a temporary high expression during the breaker stage, followed by a gradual decline during further ripening. ACO7 is only basally expressed during fruit development and ripening [108]. Antisense gene silencing was used to test the function of ACS and ACO genes expressed during tomato ripening, and this resulted in the inhibition of ethylene synthesis and slowed or prevented both fruit ripening and leaf senescence [105][106][107], which validated the conclusions drawn about the role of ethylene from experiments with Ag+ (plant ethylene responses inhibitor [110]) and confirmed using 1-MCP (a specific inhibitor of ethylene perception and action [111]). Theologis [112] also showed that the respiratory climacteric was abolished in tomatoes in which ACS genes were inhibited. They did not produce ethylene, but ripening was restored by supplying ethylene externally. The roles of ethylene biosynthesis genes have been functionally verified in other fruits as well, such as melon [113], pear [114], kiwifruit [115] and apple [116].
Several TFs have been shown to influence ethylene synthesis, including MADS-RIN [5][117], HB-1 [118], NAC1/4 [119][120] and NAC4/9 [121][122] in tomato, and also apple MdERF2 [123], kiwifruit AdNAC6/7 [18][124] and banana MaERF9/11 [125]. The relationship between MADS-RIN and ethylene in controlling ripening has recently been clarified Figure 4 and Figure 5). Treatment of RIN-deficient fruit (engineered using CRISPR/Cas9) with propylene (an ethylene analogue used to study system-1 and system-2 ethylene [126]) showed that they were unable to initiate system-2 ethylene production [13]. RIN-deficient fruit undergo partial ripening, however, and if ethylene is added externally, they ripen slightly more, but not fully, whereas if 1-MCP is added just before the onset of ripening, ripening initiation and progression are almost completely inhibited for at least 20 days. This demonstrates that ethylene is sufficient to initiate ripening (Figure 4). This fits with the previous demonstration that RIN activates transcription of ACS2 and ACS4 [127], for system-2 ethylene synthesis. Li et al. [13] proposed a model (Figure 6) in which ethylene signalling initiates ripening, where RIN is required to upregulate system-2 ethylene synthesis and also many other ripening-related genes are required for the progression of full ripening. Several other plant hormones (discussed later in Section 3) also upregulate specific ACS and ACO genes and stimulate ripening by promoting ethylene production.
Cells 10 01136 g004 550
Figure 4. Ethylene response of WT and RIN-deficient tomato fruits (reproduced with the permission from Li et al. [13]). Effect of exogenous ethylene and ethylene perception inhibitor 1-MCP treatment on ripening progression of RIN-CRISPR tomato fruit. WT and RIN-CRISPR tomato fruits were picked at MG stages and treated and replenished daily with ethylene (100 ppm) and 1-MCP (10 ppm) or air continually for up to 15 days. Fruits in horizontal rows are biological replicates. Enlarged photos of representative samples are shown compared to WT fruits on the right. The red scale bar represents 2 cm.
At the genetic level, ethylene effects are brought about by ERFs. Tomato has 77 ERFs, which can be divided into nine subclades (A–J), and some are activators, while others are repressors. Members of the ERF F subclade possess the transcriptional repression EAR-motif [128]. A number of different ERFs have been shown to regulate individual genes or processes, contributing to changes in colour, flavour, texture and aroma in different fruits [129]. During ripening, transcripts for 27 ERFs accumulate, while mRNA levels for another 28 decrease [130], which suggests that different ERFs have contrasting roles in fruit development and ripening. Differences between ERF expression in the tomato ripening mutants ripening inhibitor (rin), non-ripening (nor), Never-ripe (Nr) and wild-type (WT) identified ERFs that were both strongly up- and down-regulated during normal ripening. Three ERFs, members of sub-class E, were dramatically downregulated in the mutants, indicating that they probably had important roles in controlling ripening events [130]. Several tomato ERFs have been shown to be involved in fruit softening, probably by mediating ethylene production [131], and ERFs have been identified in ripening apple, banana, citrus, grape, kiwifruit, persimmon and tomato [54][132][133][134]. AP2a, which belongs to the AP2/ERF family, appears to be involved in repressing ethylene production, since reducing AP2a expression results in enhanced ethylene production and softer fruits [131]. One problem associated with the designation of TFs as ERFs is that the attribution is most often made on the basis of computer sequence analysis and homology rather than functional assay. This overlooks the possibility that some so-called ‘ERFs’ are actually regulated by hormones other than ethylene, such as auxin, ABA, JA, etc., and similar arguments can be advanced for other TF families, such as the auxin response factors (ARFs), discussed in Section 3.2. This could explain why some ERF-type genes are expressed in non-climacteric fruits, where hormones other than ethylene are important in ripening regulation. Future challenges will involve unravelling the molecular mechanisms underlying the specificity of ethylene responses during plant development and fruit ripening. Deciphering the function of ERF genes in both ethylene-dependent and ethylene-independent processes during ripening and identifying the target genes of individual ERFs will be instrumental in clarifying their specific contribution to fruit ripening [109].

3.2. Auxin Delays Ripening and Antagonises the Effects of Ethylene

Physiological studies suggested that auxin plays an inhibitory role in fruit ripening [135][136], and reverse genetics experiments support this idea [137][138][139][140][141]. Low internal auxin concentration or reduced auxin signalling activity are believed to increase the sensitivity of fruit tissue to ethylene, promoting the transition from system-1 to system-2 autocatalytic ethylene production.
Auxin can be synthesised in the chloroplasts from tryptophan and then via either indole-3-acetamide or indole-3-pyruvic acid, to generate IAA [142]. There is also an important tryptophan-independent auxin biosynthesis pathway in the cytosol, involving TAA and a multigene family of YUCCA genes, which encode flavin-containing monooxygenases [143][144]. There are three types of auxin transcriptional regulators, ARFs, Aux/IAA and TOPLESS (TPS) proteins. ARFs play a key role in regulating the expression of auxin response genes and act in concert with Aux/IAAs to control auxin-dependent transcriptional activity of target genes. There are 47 ARF genes in banana [145], 22 in tomato [146] and 19 in sweet orange [147]. Most have an N-terminal DNA-binding domain, a variable central transcriptional regulatory region, which can function as an activator or repressor domain, and a carboxy-terminal dimerization domain, that allows formation of either ARF/ARF homodimers or ARF/Aux/IAA hetero-dimers.
Experiments with several ARFs have indicated that they play a role in tomato fruit development and ripening. The over-expression of tomato ARF2A resulted in a blotchy ripening pattern, with some parts of the fruit ripening faster than others [138]. The downregulation of tomato ARF4 also altered ripening-associated phenotypes, such as firmness, sugar and chlorophyll content, leading to dark green fruit and blotchy ripening [141][148], and Yuan et al. [149] found a similar phenotype with tomato ARF10, which is involved in regulating chlorophyll and sugar accumulation during tomato fruit development [149]. ARF2A expression is reduced in the nor, rin and Nr ripening mutants and responds to exogenous application of ethylene, auxin and ABA [138]. ARF2A homodimerizes and also interacts with the ABA STRESS RIPENING (ASR1) protein, suggesting that ASR1 could link ABA and ethylene-dependent ripening [138]. Both auxin and ethylene cis-regulatory elements are present in the promoter regions of a number of ARFs, suggesting that they may be regulated by both hormones [146][150]. Furthermore, AtARF7 and AtARF19 are believed to be involved in the ethylene response in Arabidopsis [151] and several ERF genes are also induced by auxin [152][153]. The two ARF2 paralogs in the tomato genome, SlARF2A and SlARF2B, are nuclear localised where they repress auxin-responsive genes. In fruit tissues, SlARF2A is ethylene-regulated, while SlARF2B is auxin-induced [139]. Taken together, these results indicate substantial interactions between ethylene and auxin in the regulation of ARFs and ERFs. SAURs (small auxin-upregulated RNAs) are believed to be involved in various auxin-related actions [154], and Sl-SAUR69, which shows reduced expression in the rin mutant, is involved in changing auxin signalling or transport. Overexpression of Sl-SAUR69 in tomato causes premature initiation of ripening, whereas its downregulation delays ripening initiation [137][140].

3.3. Abscisic Acid (ABA), Jasmonic Acid (JA) and Brassinosteroids (BR) Promote Ethylene Synthesis and Fruit Ripening, while Salicylic Acid (SA) Inhibits Ripening

3.3.1. ABA

There are many reports of the effects of ABA on ripening, as discussed by Zhu et al. [155] and reviewed recently by Kou et al. [156][157][158]. ABA is synthesised from carotenoids via the action of 9-cis-epoxycarotenoid dehydrogenase (NCED) [159][160]. Treating fruits of tomato, apple, grape, kiwifruit, peach and strawberry with ABA or ABA inhibitors, either enhanced or retarded the production of carotenoids, anthocyanins, volatiles, pectolytic enzymes and softening [156][161][162][163][164][165].
ABA can increase the levels of ACS and ACO activity and their transcripts [166][167], which would be expected to promote various aspects of ripening by increasing ethylene production. Several TFs have already been identified that activate transcription of ACS and ACO genes, such as RIN, HB-1 and ERFs [109][118][127], and it is important to establish which TFs respond to ABA in order to upregulate ethylene biosynthesis genes. It has been shown that NAC19/48 in tomato can directly induce the expression of ACO1 and ACS2, and virus-induced gene silencing (VIGS) of tomato NAC4 and NAC9 reduced ACS2, ACS4 and ACO1 expression. Interestingly, there are binding sites for ABF (ABA responsive element-binding factor) TFs in the promoter regions of NOR and RIN genes [168], so the question arises: does ABA promote ethylene synthesis and ripening through an effect on these genes, as well as having an effect on ethylene synthesis?

3.3.2. Jasmonates

Jasmonates (jasmonic acid (JA) and methyl jasmonate (MeJA)) are important plant hormones derived from linolenic acid [169]. Work on several fruits has supported a role for JA in modulating ethylene synthesis and ripening, and in apple, JA induces ethylene synthesis by enhancing expression of MdMYC2, which is known to be involved in JA signalling. MdMYC2 promotes ethylene biosynthesis by binding to the promoters of MdACO1 and MdACS1 and by regulating apple ERFs [170]. However, if the expression of MdACS1 was blocked by 1-MCP, the MeJA treatment was ineffective in enhancing ethylene production. More recently, Wu et al. [171] showed that external ethylene and MeJA increased ethylene production, and this was correlated with higher transcripts of ACS genes AdACS1 and AdACS2, and ACS enzyme activity in kiwifruit.

3.3.3. Brassinosteroids

The brassinosteroids (BRs) are steroid hormones that play key roles in plant development and defence, and they also have a strong influence on aspects of fruit ripening in several fruits, including tomato, strawberry and persimmon. Application of brassinolide (BL, the most active brassinosteroid) to tomato fruit enhanced the accumulation of transcripts encoding the ethylene biosynthesis genes ACS2, ACS4, ACO1, ACO4 and the key carotenoid biosynthesis gene PSY1, and there was a concomitant acceleration of tomato fruit ripening [172]. Application of the BR biosynthesis inhibitor brassinazole (BZ) to persimmon fruit delayed aspects of ripening, and when the brassinosteroid 24-epibrassinolide (EBR) was applied externally, transcripts of DkACO2, DkACS1 and DkACS2, plus several genes encoding cell wall-modifying enzymes (DkPG1, DkPL1, DkPE2, DkEGase1), were upregulated. Furthermore, application of BR to large green strawberries promoted ripening, whereas the inhibitor BZ inhibited ripening. Furthermore, downregulation of brassinosteroid receptor FaBRI1 expression by VIGS also retarded the development of red colour in green strawberry fruit [173].

3.3.4. Salicylic Acid (SA)

Plants synthesise salicylic acid (SA) from chorismite in the plastids, via either the isochorismate synthase (ICS) and/or the phenylalanine ammonia-lyase (PAL) pathways [169][174]. The volatile derivative methyl salicylate (MeSA) is generated by methylation of SA by a specific form of O-methyltransferase [175]. Application of SA delays ripening of banana and kiwifruit [176][177] and there are several reports of the retardation of ripening by MeSA in mangos, papayas and sweet peppers [178][179]. The effect of MeSA, however, may depend on dose and time of application. Ding and Wang [180] showed in tomato that low concentrations (0.1 mM) of MeSA applied at the mature green stage and 0.01 mM of MeSA at the breaker stage enhanced the production of colour, ethylene and respiration. At a higher concentration (0.5 mM), however, MeSA prevented ethylene production, respiration and colour development, and this was associated with suppression of accumulation of ACS2 and ACS4 transcripts and delayed accumulation of ACO1. MeSA also delays processes such as softening, in addition to ethylene synthesis and colour change, but it is not clear whether the delay in ripening is due exclusively to the inhibition of ethylene biosynthesis transcripts or whether other ripening genes are also directly affected.

3.4. Influence of Light of Different Wavelengths on Ripening

Plants have several photoreceptor proteins containing chromophores that sense different regions of the visible and UV spectrum, including the phytochromes (PHYs) that perceive red (R) and far-red light (FR) and measure the R/FR ratio, the cryptochromes (CRYs), phototropins and ‘Zeitlupes’ that sense blue/UV-A light and the UV-B receptor UVR8, which senses UV-B light via a cluster of tryptophan residues [181].
The characterisation of the high-pigment (hp1 and hp2) tomato mutants contributed to understand the role of light signalling during plant development and ripening. Ripe fruits of these mutants have higher levels of ascorbic acid (vitamin C), carotenoids, flavonoids and tocopherol (vitamin E) [182][183][184], and there is a general stimulatory effect of light on isoprenoid metabolism in fruit and vegetative tissues [185][186]. These effects result from mutations in negative regulators of light signalling: hp1 is mutated in the nuclear protein UV-DAMAGED DNA BINDING PROTEIN1 (DDB1) and hp2 is mutated in a second nuclear protein, DEETIOLATED1 (DET1). The WT versions of these proteins are negative regulators of light signal transduction [183][187][188], and RNAi silencing of Sl-DDB1/HP1 or Sl-DET1/HP2 increased plastid biogenesis and carotenoid accumulation in tomato fruit [189][190]. Silencing of three other tomato light signalling regulators (CUL4, COP1, PIF1a) also increased fruit carotenoid levels [183][190][191], and suppressing the light signalling hub gene HY5 produced an opposite phenotype. Recent work has shown that tomato HY5 (ELONGATED HYPOCOTYL5) regulates fruit ripening by targeting genes involved in carotenoid biosynthesis and ethylene signalling, and may also affect the translation efficiency of a set of ripening-related genes by targeting ribosomal protein genes [192].
Cruz et al. [193] showed that the high carotenoid content in ripening hp2 fruits was associated with disturbed ethylene production, increased ethylene sensitivity and altered expression of several ripening TFs, including the downregulation of ERF.E4, a repressor of carotenoid synthesis, and altered auxin signalling. This was accompanied by severe downregulation of AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) genes and altered accumulation of ARFs transcripts, with ARF2 proteins (ARF2a and ARF2b), which are involved in tomato fruit ripening.
Thus, it is clear that there are strong interactions between light signalling, auxin and ethylene in tomato fruit, and that each make significant regulatory contributions to carotenoid biosynthesis and tomato fruit ripening [193]. Further work is required, however, before we can fully understand the molecular basis for the interactions between light, auxin and ethylene in the control of ripening.

References

  1. Klee, H.J.; Giovannoni, J.J. Genetics and Control of Tomato Fruit Ripening and Quality Attributes. Annu. Rev. Genet. 2011, 45, 41–59.
  2. Karlova, R.; Chapman, N.; David, K.; Angenent, G.C.; Seymour, G.B.; De Maagd, R.A. Transcriptional control of fleshy fruit development and ripening. J. Exp. Bot. 2014, 65, 4527–4541.
  3. Cherian, S.; Figueroa, C.R.; Nair, H. ‘Movers and shakers’ in the regulation of fruit ripening: A cross-dissection of climacteric versus non-climacteric fruit. J. Exp. Bot. 2014, 65, 4705–4722.
  4. The Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 2012, 485, 635–641.
  5. Jin, J.; Tian, F.; Yang, D.-C.; Meng, Y.-Q.; Kong, L.; Luo, J.; Gao, G. PlantTFDB 4.0: Toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res. 2017, 45, D1040–D1045.
  6. Giovannoni, J.J. Genetic Regulation of Fruit Development and Ripening. Plant Cell 2004, 16, S170–S180.
  7. Giovannoni, J.J. Fruit ripening mutants yield insights into ripening control. Curr. Opin. Plant Biol. 2007, 10, 283–289.
  8. Gray, J.; Picton, S.; Shabbeer, J.; Schuch, W.; Grierson, D. Molecular biology of fruit ripening and its manipulation with antisense genes. Plant Mol. Biol. 1992, 19, 69–87.
  9. Grierson, D. Ethylene biosynthesis. In Fruit Ripening Physiology, Signalling and Genomics; Nath, P., Bouzayen, M., Mattoo, A.K., Pech, J.C., Eds.; CAB International: Oxfordshire, UK, 2014; pp. 178–192.
  10. Grierson, D. Ethylene and the control of fruit ripening. In The Molecular Biology and Biochemistry of Fruit Ripening; Seymour, G.B., Poole, M., Giovannoni, J.J., Tucker, G.A., Eds.; John Wiley and Sons: Hoboken, NJ, USA, 2013.
  11. Gao, L.; Gonda, I.; Sun, H.; Ma, Q.; Bao, K.; Tieman, D.M.; Burzynski-Chang, E.A.; Fish, T.L.; Stromberg, K.A.; Sacks, G.L.; et al. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nat. Genet. 2019, 51, 1044–1051.
  12. Gao, Y.; Wei, W.; Fan, Z.; Zhao, X.; Zhang, Y.; Jing, Y.; Zhu, B.; Zhu, H.; Shan, W.; Chen, J.; et al. Re-evaluation of the nor mutation and the role of the NAC-NOR transcription factor in tomato fruit ripening. J. Exp. Bot. 2020, 71, 3560–3574.
  13. Li, S.; Zhu, B.; Pirrello, J.; Xu, C.; Zhang, B.; Bouzayen, M.; Chen, K.; Grierson, D. Roles of RIN and ethylene in tomato fruit ripening and ripening-associated traits. New Phytol. 2020, 226, 460–475.
  14. Gao, Y.; Zhu, N.; Zhu, X.; Wu, M.; Jiang, C.-Z.; Grierson, D.; Luo, Y.; Shen, W.; Zhong, S.; Fu, D.-Q.; et al. Diversity and redundancy of the ripening regulatory networks revealed by the fruitENCODE and the new CRISPR/Cas9 CNR and NOR mutants. Hortic. Res. 2019, 6, 1–10.
  15. Li, S.; Chen, K.; Grierson, D. A critical evaluation of the role of ethylene and MADS transcription factors in the network controlling fleshy fruit ripening. New Phytol. 2019, 221, 1724–1741.
  16. Ito, Y.; Nishizawa-Yokoi, A.; Endo, M.; Mikami, M.; Shima, Y.; Nakamura, N.; Kotake-Nara, E.; Kawasaki, S.; Toki, S. Re-evaluation of the rin mutation and the role of RIN in the induction of tomato ripening. Nat. Plants 2017, 3, 866–874.
  17. Wang, R.; Tavano, E.C.D.R.; Lammers, M.; Martinelli, A.P.; Angenent, G.C.; De Maagd, R.A. Re-evaluation of transcription factor function in tomato fruit development and ripening with CRISPR/Cas9-mutagenesis. Sci. Rep. 2019, 9, 1–10.
  18. Wang, W.; Wang, J.; Wu, Y.; Li, D.; Allan, A.C.; Yin, X. Genome-wide analysis of coding and non-coding RNA reveals a conserved miR164-NAC regulatory pathway for fruit ripening. New Phytol. 2019, 225, 1618–1634.
  19. Chen, F.; Song, Y.; Li, X.; Chen, J.; Mo, L.; Zhang, X.; Lin, Z.; Zhang, L. Genome sequences of horticultural plants: Past, present, and future. Hortic. Res. 2019, 6, 1–23.
  20. Chen, F.; Dong, W.; Zhang, J.; Guo, X.; Chen, J.; Wang, Z.; Lin, Z.; Tang, H.; Zhang, L. The Sequenced Angiosperm Genomes and Genome Databases. Front. Plant Sci. 2018, 9, 418.
  21. Shinozaki, Y.; Nicolas, P.; Fernandez-Pozo, N.; Ma, Q.; Evanich, D.J.; Shi, Y.; Xu, Y.; Zheng, Y.; Snyder, S.I.; Martin, L.B.B.; et al. High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening. Nat. Commun. 2018, 9, 1–13.
  22. Egea, I.; Barsan, C.; Bian, W.; Purgatto, E.; Latche, A.; Chervin, C.; Bouzayen, M.; Pech, J.C. Chromoplast Differentiation: Current Status and Perspectives. Plant Cell Physiol. 2010, 51, 1601–1611.
  23. Kahlau, S.; Bock, R. Plastid Transcriptomics and Translatomics of Tomato Fruit Development and Chloro-plast-to-Chromoplast Differentiation: Chromoplast Gene Expression Largely Serves the Production of a Single Protein. Plant Cell 2008, 20, 856–874.
  24. Barsan, C.; Zouine, M.; Maza, E.; Bian, W.; Egea, I.; Rossignol, M.; Bouyssie, D.; Pichereaux, C.; Purgatto, E.; Bouzayen, M.; et al. Proteomic Analysis of Chloroplast-to-Chromoplast Transition in Tomato Reveals Metabolic Shifts Coupled with Disrupted Thylakoid Biogenesis Machinery and Elevated Energy-Production Components. Plant Physiol. 2012, 160, 708–725.
  25. Suzuki, M.; Takahashi, S.; Kondo, T.; Dohra, H.; Ito, Y.; Kiriiwa, Y.; Hayashi, M.; Kamiya, S.; Kato, M.; Fujiwara, M.; et al. Plastid Proteomic Analysis in Tomato Fruit Development. PLoS ONE 2015, 10, e0137266.
  26. Middleton, R.; Sinnott-Armstrong, M.; Ogawa, Y.; Jacucci, G.; Moyroud, E.; Rudall, P.J.; Prychid, C.; Conejero, M.; Glover, B.J.; Donoghue, M.J.; et al. Viburnum tinus Fruits Use Lipids to Produce Metallic Blue Structural Color. Curr. Biol. 2020, 30, 3804–3810.e2.
  27. Fraser, P.D.; Bramley, P.M. The biosynthesis and nutritional uses of carotenoids. Prog. Lipid Res. 2004, 43, 228–265.
  28. Luan, Y.; Fu, X.; Lu, P.; Grierson, D.; Xu, C. Molecular Mechanisms Determining the Differential Accumulation of Carotenoids in Plant Species and Varieties. Crit. Rev. Plant Sci. 2020, 39, 125–139.
  29. Fray, R.G.; Grierson, D. Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequencing, complementation and co-suppression. Plant Mol. Biol. 1993, 22, 589–602.
  30. Zhu, L.-S.; Liang, S.-M.; Chen, L.-L.; Wu, C.-J.; Wei, W.; Shan, W.; Chen, J.-Y.; Lu, W.-J.; Su, X.-G.; Kuang, J.-F. Banana MaSPL16 Modulates Carotenoid Biosynthesis during Fruit Ripening through Activating the Transcription of Lycopene β-Cyclase Genes. J. Agric. Food Chem. 2019, 68, 1286–1296.
  31. Lado, J.; Zacarías, L.; Rodrigo, M.J. Regulation of Carotenoid Biosynthesis During Fruit Development; Springer Science and Business Media LLC: Berlin/Heidelberg, Germany, 2016; Volume 79, pp. 161–198.
  32. Hermanns, A.S.; Zhou, X.; Xu, Q.; Tadmor, Y.; Li, L. Carotenoid Pigment Accumulation in Horticultural Plants. Hortic. Plant J. 2020, 6, 343–360.
  33. Zhang, W.; Li, X.; Zheng, J.; Wang, G.; Sun, C.; Ferguson, I.B.; Chen, K. Bioactive components and antioxidant capacity of Chinese bayberry (Myrica rubra Sieb. and Zucc.) fruit in relation to fruit maturity and postharvest storage. Eur. Food Res. Technol. 2008, 227, 1091–1097.
  34. Sánchez-Rabaneda, F.; Jáuregui, O.; Lamuela-Raventós, R.M.; Viladomat, F.; Bastida, J.; Codina, C. Qualitative analysis of phenolic compounds in apple pomace using liquid chromatography coupled to mass spectrometry in tandem mode. Rapid Commun. Mass Spectrom. 2004, 18, 553–563.
  35. Ceymann, M.; Arrigoni, E.; Schärer, H.; Nising, A.B.; Hurrell, R.F. Identification of apples rich in health-promoting flavan-3-ols and phenolic acids by measuring the polyphenol profile. J. Food Compos. Anal. 2012, 26, 128–135.
  36. Ma, C.; Liang, B.; Chang, B.; Yan, J.; Liu, L.; Wang, Y.; Yang, Y.; Zhao, Z. Transcriptome profiling of anthocyanin biosynthesis in the peel of ‘Granny Smith’ apples (Malus domestica) after bag removal. BMC Genom. 2019, 20, 353.
  37. Zhao, Y.; Dong, W.; Zhu, Y.; Allan, A.C.; Lin-Wang, K.; Xu, C. PpGST1, an anthocyanin-related glutathione S-transferase gene, is essential for fruit coloration in peach. Plant Biotechnol. J. 2019, 18, 1284–1295.
  38. Giampieri, F.; Tulipani, S.; Alvarez-Suarez, J.M.; Quiles, J.L.; Mezzetti, B.; Battino, M. The strawberry: Composition, nutritional quality, and impact on human health. Nutrition 2012, 28, 9–19.
  39. Jeong, S.T.; Goto-Yamamoto, N.; Hashizume, K.; Esaka, M. Expression of the flavonoid 3′-hydroxylase and fla-vonoid 3′,5′-hydroxylase genes and flavonoid composition in grape (Vitis vinifera). Plant Sci. 2006, 170, 61–69.
  40. Cao, J.; Jiang, Q.; Lin, J.; Li, X.; Sun, C.; Chen, K. Physicochemical characterisation of four cherry species (Prunus spp.) grown in China. Food Chem. 2015, 173, 855–863.
  41. Naing, A.H.; Kim, C.K. Roles of R2R3-MYB transcription factors in transcriptional regulation of anthocyanin biosynthesis in horticultural plants. Plant Mol. Biol. 2018, 98, 1–18.
  42. Gayomba, S.R.; Watkins, J.M.; Muday, G.K. Flavonols Regulate Plant Growth and Development through Regulation of Auxin Transport and Cellular Redox Status; Yoshida, K., Cheynier, V., Quideau, S., Eds.; John Wiley & Sons, Ltd.: Chichester, UK, 2017; pp. 143–170.
  43. Allan, A.C.; Espley, R.V. MYBs Drive Novel Consumer Traits in Fruits and Vegetables. Trends Plant Sci. 2018, 23, 693–705.
  44. Xu, W.; Dubos, C.; Lepiniec, L. Transcriptional control of flavonoid biosynthesis by MYB–bHLH–WDR complexes. Trends Plant Sci. 2015, 20, 176–185.
  45. Albert, N.W.; Davies, K.M.; Lewis, D.H.; Zhang, H.; Montefiori, M.; Brendolise, C.; Boase, M.R.; Ngo, H.; Jameson, P.E.; Schwinn, K.E. A Conserved Network of Transcriptional Activators and Repressors Regulates Anthocyanin Pigmentation in Eudicots. Plant Cell 2014, 26, 962–980.
  46. Sivakumaran, S.; Huffman, L.; Sivakumaran, S.; Drummond, L. The nutritional composition of Zespri® SunGold Kiwifruit and Zespri® Sweet Green Kiwifruit. Food Chem. 2018, 238, 195–202.
  47. Liu, Y.; Zhou, B.; Qi, Y.; Chen, X.; Liu, C.; Liu, Z.; Ren, X. Expression Differences of Pigment Structural Genes and Transcription Factors Explain Flesh Coloration in Three Contrasting Kiwifruit Cultivars. Front. Plant Sci. 2017, 8, 1507.
  48. Li, B.; Xia, Y.; Wang, Y.; Qin, G.; Tian, S. Characterization of Genes Encoding Key Enzymes Involved in Antho-cyanin Metabolism of Kiwifruit during Storage Period. Front. Plant Sci. 2017, 8, 341.
  49. Gross, J.; Zachariae, A.; Lenz, F.; Eckhardt, G. Carotenoid changes in the peel of the «Golden delicious» apple during ripening and storage. Z. Pflanzenphysiol. 1978, 89, 321–332.
  50. Ramirez, D.A.; Tomes, M.L. Relationship between Chlorophyll and Carotenoid Biosynthesis in Dirty-Red (Green-Flesh) Mutant in Tomato. Bot. Gaz. 1964, 125, 221–226.
  51. Butelli, E.; Titta, L.; Giorgio, M.; Mock, H.-P.; Matros, A.; Peterek, S.; Schijlen, E.G.W.M.; Hall, R.D.; Bovy, A.G.; Luo, J.; et al. Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors. Nat. Biotechnol. 2008, 26, 1301–1308.
  52. Zhang, K.; Liu, Z.; Guan, L.; Zheng, T.; Jiu, S.; Zhu, X.; Jia, H.; Fang, J. Changes of Anthocyanin Component Biosynthesis in ‘Summer Black’ Grape Berries after the Red Flesh Mutation Occurred. J. Agric. Food Chem. 2018, 66, 9209–9218.
  53. Niu, S.-S.; Xu, C.-J.; Zhang, W.-S.; Zhang, B.; Li, X.; Lin-Wang, K.; Ferguson, I.B.; Allan, A.C.; Chen, K.-S. Coordinated regulation of anthocyanin biosynthesis in Chinese bayberry (Myrica rubra) fruit by a R2R3 MYB transcription factor. Planta 2010, 231, 887–899.
  54. Tucker, G.; Yin, X.; Zhang, A.; Wang, M.; Zhu, Q.; Liu, X.; Xie, X.; Chen, K.; Grierson, D. Ethylene and fruit softening. Food Qual. Saf. 2017, 1, 253–267.
  55. Wang, D.; Yeats, T.H.; Uluisik, S.; Rose, J.K.; Seymour, G.B. Fruit Softening: Revisiting the Role of Pectin. Trends Plant Sci. 2018, 23, 302–310.
  56. Smith, C.J.S.; Watson, C.F.; Morris, P.C.; Bird, C.R.; Seymour, G.B.; Gray, J.E.; Arnold, C.; Tucker, G.A.; Schuch, W.; Harding, S.; et al. Inheritance and effect on ripening of antisense polygalacturonase genes in transgenic tomatoes. Plant Mol. Biol. 1990, 14, 369–379.
  57. Langley, K.R.; Martin, A.; Stenning, R.; Murray, A.J.; Hobson, G.E.; Schuch, W.W.; Bird, C.R. Mechanical and optical assessment of the ripening of tomato fruit with reduced polygalacturonase activity. J. Sci. Food Agric. 1994, 66, 547–554.
  58. Jiang, F.; Lopez, A.; Jeon, S.; De Freitas, S.T.; Yu, Q.; Wu, Z.; Labavitch, J.M.; Tian, S.; Powell, A.L.T.; Mitcham, E. Disassembly of the fruit cell wall by the ripening-associated polygalacturonase and expansin influences tomato cracking. Hortic. Res. 2019, 6, 1–15.
  59. Uluisik, S.; Chapman, N.H.; Smith, R.; Poole, M.; Adams, G.; Gillis, R.B.; Besong, T.M.D.; Sheldon, J.; Stiegelmeyer, S.; Perez, L.; et al. Genetic improvement of tomato by targeted control of fruit softening. Nat. Biotechnol. 2016, 34, 950–952.
  60. Sitrit, Y.; Bennett, A.B. Regulation of Tomato Fruit Polygalacturonase mRNA Accumulation by Ethylene: A Re-Examination1. Plant Physiol. 1998, 116, 1145–1150.
  61. Pech, J.C.; Purgatto, E.; Bouzayen, M.; Latché, A. Ethylene and fruit ripening. In Annual Plant Reviews, Volume 44, The Plant Hormone Ethylene; McManus, M.T., Ed.; Wiley—Blackwell: Oxford, UK, 2012; pp. 275–304.
  62. Pech, J.C.; Bouzayen, M.; Latché, A. Climacteric fruit ripening: Ethylene-dependent and independent regulation of ripening pathways in melon fruit. Plant Sci. 2008, 175, 114–120.
  63. Wang, K.; Yin, X.-R.; Zhang, B.; Grierson, D.; Xu, C.-J.; Chen, K.-S. Transcriptomic and metabolic analyses provide new insights into chilling injury in peach fruit. Plant Cell Environ. 2017, 40, 1531–1551.
  64. Wang, M.; Zhu, Q.; Deng, C.; Luo, Z.; Sun, N.; Grierson, D.; Yin, X.; Chen, K. Hypoxia-responsive ERFs involved in postdeastringency softening of persimmon fruit. Plant Biotechnol. J. 2017, 15, 1409–1419.
  65. Villarreal, N.M.; Bustamante, C.A.; Civello, P.M.; Martínez, G.A. Effect of ethylene and 1-MCP treatments on strawberry fruit ripening. J. Sci. Food Agric. 2010, 90, 683–689.
  66. Nardi, C.; Villarreal, N.; Dotto, M.; Ariza, M.; Vallarino, J.; Martínez, G.; Valpuesta, V.; Civello, P. Influence of plant growth regulators on Expansin2 expression in strawberry fruit. Cloning and functional analysis of FaEXP2 promoter region. Postharvest Biol. Technol. 2016, 114, 17–28.
  67. Kader, A.A. Flavor quality of fruits and vegetables. J. Sci. Food Agric. 2008, 88, 1863–1868.
  68. Xiao, Y.-Y.; Kuang, J.-F.; Qi, X.-N.; Ye, Y.-J.; Wu, Z.-X.; Chen, J.-Y.; Lu, W.-J. A comprehensive investigation of starch degradation process and identification of a transcriptional activator MabHLH6 during banana fruit ripening. Plant Biotechnol. J. 2018, 16, 151–164.
  69. Zhang, A.-D.; Wang, W.-Q.; Tong, Y.; Li, M.-J.; Grierson, D.; Ferguson, I.; Chen, K.-S.; Yin, X.-R. Transcriptome Analysis Identifies a Zinc Finger Protein Regulating Starch Degradation in Kiwifruit. Plant Physiol. 2018, 178, 850–863.
  70. Winter, H.; Huber, S.C. Regulation of Sucrose Metabolism in Higher Plants: Localization and Regulation of Activity of Key Enzymes. Crit. Rev. Biochem. Mol. Biol. 2000, 35, 253–289.
  71. Giovannoni, J.; Nguyen, C.; Ampofo, B.; Zhong, S.; Fei, Z. The Epigenome and Transcriptional Dynamics of Fruit Ripening. Annu. Rev. Plant Biol. 2017, 68, 61–84.
  72. Schaffer, A.A.; Petreikov, M. Sucrose-to-starch metabolism in tomato fruit undergoing transient starch accumulation. Plant Physiol. 1997, 113, 739–746.
  73. Umer, M.J.; Safdar, L.; Gebremeskel, H.; Zhao, S.; Yuan, P.; Zhu, H.; Kaseb, M.O.; Anees, M.; Lu, X.; He, N.; et al. Identification of key gene networks controlling organic acid and sugar metabolism during watermelon fruit development by integrating metabolic phenotypes and gene expression profiles. Hortic. Res. 2020, 7, 1–13.
  74. Smeekens, S.; Hellmann, H.A. Sugar sensing and signaling in plants. Front. Plant Sci. 2014, 5, 113.
  75. Centeno, D.C.; Osorio, S.; Nunes-Nesi, A.; Bertolo, A.L.; Carneiro, R.T.; Araújo, W.L.; Steinhauser, M.-C.; Michalska, J.; Rohrmann, J.; Geigenberger, P.; et al. Malate Plays a Crucial Role in Starch Metabolism, Ripening, and Soluble Solid Content of Tomato Fruit and Affects Postharvest Softening. Plant Cell 2011, 23, 162–184.
  76. Chen, G.; Hackett, R.; Walker, D.; Taylor, A.; Lin, Z.; Grierson, D. Identification of a Specific Isoform of Tomato Lipoxygenase (TomloxC) Involved in the Generation of Fatty Acid-Derived Flavor Compounds. Plant Physiol. 2004, 136, 2641–2651.
  77. Speirs, J.; Lee, E.; Holt, K.; Yong-Duk, K.; Scott, N.S.; Loveys, B.; Schuch, W. Genetic Manipulation of Alcohol Dehydrogenase Levels in Ripening Tomato Fruit Affects the Balance of Some Flavor Aldehydes and Alcohols. Plant Physiol. 1998, 117, 1047–1058.
  78. Yahyaoui, F.E.L.; Wongs-Aree, C.; Latché, A.; Hackett, R.; Grierson, D.; Pech, J.-C. Molecular and biochemical characteristics of a gene encoding an alcohol acyl-transferase involved in the generation of aroma volatile esters during melon ripening. JBIC J. Biol. Inorg. Chem. 2002, 269, 2359–2366.
  79. Goulet, C.; Kamiyoshihara, Y.; Lam, N.; Richard, T.; Taylor, M.; Tieman, D.; Klee, H. Divergence in the enzymatic activities of a tomato and Solanum pennellii alcohol acyltransferase impacts fruit volatile ester composition. Mol. Plant 2015, 8, 153–162.
  80. Lu, H.; Luo, Z.; Li, D.; Jiang, Y.; Li, L. FaMYB11 promotes the accumulation of volatile esters by regulating FaLOX5 during strawberry (Fragaria × ananassa) ripening. Postharvest Biol. Technol. 2021, 178, 111560.
  81. Zhang, B.; Tieman, D.M.; Jiao, C.; Xu, Y.; Chen, K.; Fei, Z.; Giovannoni, J.J.; Klee, H.J. Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation. Proc. Natl. Acad. Sci. USA 2016, 113, 12580–12585.
  82. Kochevenko, A.; Klee, H.J.; Fernie, A.R.; Araújo, W.L. Molecular identification of a further branched-chain aminotransferase 7 (BCAT7) in tomato plants. J. Plant Physiol. 2012, 169, 437–443.
  83. Maloney, G.S.; Kochevenko, A.; Tieman, D.M.; Tohge, T.; Krieger, U.; Zamir, D.; Taylor, M.G.; Fernie, A.R.; Klee, H.J. Characterization of the Branched-Chain Amino Acid Aminotransferase Enzyme Family in Tomato. Plant Physiol. 2010, 153, 925–936.
  84. Aragüez, I.; Fernández, V.V. Metabolic engineering of aroma components in fruits. Biotechnol. J. 2013, 8, 1144–1158.
  85. Tieman, D.; Taylor, M.; Schauer, N.; Fernie, A.R.; Hanson, A.D.; Klee, H.J. Tomato Aromatic Amino Acid De-carboxylases Participate in Synthesis of the Flavor Volatiles 2-Phenylethanol and 2-Phenylacetaldehyde. Proc. Natl. Acad. Sci. USA 2006, 103, 8287–8292.
  86. Klee, H.J.; Tieman, D.M. The genetics of fruit flavour preferences. Nat. Rev. Genet. 2018, 19, 347–356.
  87. Gershenzon, J.; Dudareva, N. The function of terpene natural products in the natural world. Nat. Chem. Biol. 2007, 3, 408–414.
  88. Tholl, D. Biosynthesis and Biological Functions of Terpenoids in Plants. Blue Biotechnol. 2015, 148, 63–106.
  89. Vranová, E.; Coman, D.; Gruissem, W. Network Analysis of the MVA and MEP Pathways for Isoprenoid Synthesis. Annu. Rev. Plant Biol. 2013, 64, 665–700.
  90. Chen, F.; Tholl, D.; Bohlmann, J.; Pichersky, E. The family of terpene synthases in plants: A mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom. Plant J. 2011, 66, 212–229.
  91. Degenhardt, J.; Köllner, T.G.; Gershenzon, J. Monoterpene and sesquiterpene synthases and the origin of terpene skeletal diversity in plants. Phytochemistry 2009, 70, 1621–1637.
  92. Nieuwenhuizen, N.J.; Green, S.A.; Chen, X.; Bailleul, E.J.; Matich, A.J.; Wang, M.Y.; Atkinson, R.G. Functional Genomics Reveals That a Compact Terpene Synthase Gene Family Can Account for Terpene Volatile Production in Apple. Plant Physiol. 2013, 161, 787–804.
  93. Falara, V.; Akhtar, T.A.; Nguyen, T.T.; Spyropoulou, E.A.; Bleeker, P.M.; Schauvinhold, I.; Matsuba, Y.; Bonini, M.E.; Schilmiller, A.L.; Last, R.L.; et al. The Tomato Terpene Synthase Gene Family. Plant Physiol. 2011, 157, 770–789.
  94. Martin, D.M.; Aubourg, S.; Schouwey, M.B.; Daviet, L.; Schalk, M.; Toub, O.; Lund, S.T.; Bohlmann, J. Functional annotation, genome organization and phylogeny of the grapevine (Vitisvinifera) terpene synthase gene family based on genome assembly, FLcDNA cloning, and enzyme assays. BMC Plant Biol. 2010, 10, 226.
  95. Aubourg, S.; Lecharny, A.; Bohlmann, J. Genomic analysis of the terpenoid synthase (AtTPS) gene family of Arabidopsis thaliana. Mol. Genet. Genomics 2002, 267, 730–745.
  96. González-Mas, M.C.; Rambla, J.L.; López-Gresa, M.P.; Blázquez, M.A.; Granell, A. Volatile Compounds in Citrus Essential Oils: A Comprehensive Review. Front. Plant Sci. 2019, 10, 12.
  97. Shen, S.; Yin, X.; Zhang, B.; Xie, X.; Jiang, Q.; Grierson, D.; Chen, K. CitAP2.10activation of the terpene syn-thaseCsTPS1 is associated with the synthesis of (+)-valencene in ‘Newhall’ orange. J. Exp. Bot. 2016, 67, 4105–4115.
  98. Li, X.; Xu, Y.; Shen, S.; Yin, X.; Klee, H.; Zhang, B.; Chen, K. Transcription factor CitERF71 activates the terpene synthase gene CitTPS16 involved in the synthesis of E-geraniol in sweet orange fruit. J. Exp. Bot. 2017, 68, 4929–4938.
  99. Nieuwenhuizen, N.J.; Chen, X.; Wang, M.Y.; Matich, A.J.; Perez, R.L.; Allan, A.C.; Green, S.A.; Atkinson, R.G. Natural variation in monoterpene synthesis in kiwifruit: Transcriptional regulation of terpene synthases by NAC and ETH-YLENE-INSENSITIVE3-like transcription factors. Plant Physiol. 2015, 167, 1243–1258.
  100. Schaefer, H.M.; Schaefer, V.; Vorobyev, M. Are Fruit Colors Adapted to Consumer Vision and Birds Equally Efficient in Detecting Colorful Signals? Am. Nat. 2007, 169, S159–S169.
  101. Nitsch, J.P. Free Auxins and Free Tryptophane in the Strawberry. Plant Physiol. 1955, 30, 33–39.
  102. Serrani, J.C.; Carrera, E.; Ruiz-Rivero, O.; Gallego-Giraldo, L.; Peres, L.E.P.; García-Martínez, J.L. Inhibition of Auxin Transport from the Ovary or from the Apical Shoot Induces Parthenocarpic Fruit-Set in Tomato Mediated by Gibberellins. Plant Physiol. 2010, 153, 851–862.
  103. Ding, J.; Chen, B.; Xia, X.; Mao, W.; Shi, K.; Zhou, Y.; Yu, J. Cytokinin-Induced Parthenocarpic Fruit Development in Tomato Is Partly Dependent on Enhanced Gibberellin and Auxin Biosynthesis. PLoS ONE 2013, 8, e70080.
  104. Joldersma, D.; Liu, Z. The making of virgin fruit: The molecular and genetic basis of parthenocarpy. J. Exp. Bot. 2018, 69, 955–962.
  105. Picton, S.; Barton, S.L.; Bouzayen, M.; Hamilton, A.J.; Grierson, N. Altered fruit ripening and leaf senescence in tomatoes expressing an antisense ethylene-forming enzyme transgene. Plant J. 1993, 3, 469–481.
  106. Oeller, P.W.; Lu, M.W.; Taylor, L.P.; Pike, D.A.; Theologis, A. Reversible inhibition of tomato fruit senescence by antisense RNA. Science 1991, 254, 437–439.
  107. Hamilton, A.J.; Lycett, G.W.; Grierson, D.S. Antisense gene that inhibits synthesis of the hormone ethylene in transgenic plants. Nat. Cell Biol. 1990, 346, 284–287.
  108. Houben, M.; Van de Poel, B. 1-Aminocyclopropane-1-carboxylic acid oxidase (ACO): The enzyme that makes the plant hormone ethylene. Front. Plant Sci. 2019, 10, 695.
  109. Liu, M.; Pirrello, J.; Chervin, C.; Roustan, J.-P.; Bouzayen, M. Ethylene control of fruit ripening: Revisiting the complex network of transcriptional regulation. Plant Physiol. 2015, 169, 2380–2390.
  110. Beyer, E.M. A Potent Inhibitor of Ethylene Action in Plants. Plant Physiol. 1976, 58, 268–271.
  111. Reid, M.S.; Staby, G.L. A Brief History of 1-Methylcyclopropene. HortScience 2008, 43, 83–85.
  112. Theologis, A. One rotten apple spoils the whole bushel: The role of ethylene in fruit ripening. Cell 1992, 70, 181–184.
  113. Ayub, R.; Guis, M.; Ben Amor, M.; Gillot, L.; Roustan, J.-P.; Latché, A.; Bouzayen, M.; Pech, J.-C. Expression of ACC oxidase antisense gene inhibits ripening of cantaloupe melon fruits. Nat. Biotechnol. 1996, 14, 862–866.
  114. Gao, M.; Matsuta, N.; Murayama, H.; Toyomasu, T.; Mitsuhashi, W.; Dandekar, A.M.; Tao, R.; Nishimura, K. Gene expression and ethylene production in transgenic pear (Pyrus communis cv.‘La France’) with sense or antisense cDNA encoding ACC oxidase. Plant Sci. 2007, 173, 32–42.
  115. Atkinson, R.G.; Gunaseelan, K.; Wang, M.Y.; Luo, L.; Wang, T.; Norling, C.L.; Johnston, S.L.; Maddumage, R.; Schröder, R.; Schaffer, R.J. Dissecting the role of climacteric ethylene in kiwifruit (Actinidia chinensis) ripening using a 1-aminocyclopropane-1-carboxylic acid oxidase knockdown line. J. Exp. Bot. 2011, 62, 3821–3835.
  116. Dandekar, A.M.; Teo, G.; Defilippi, B.G.; Uratsu, S.L.; Passey, A.J.; Kader, A.A.; Stow, J.R.; Colgan, R.J.; James, D.J. Effect of Down-Regulation of Ethylene Biosynthesis on Fruit Flavor Complex in Apple Fruit. Transgenic Res. 2004, 13, 373–384.
  117. Fujisawa, M.; Nakano, T.; Shima, Y.; Ito, Y. A Large-Scale Identification of Direct Targets of the Tomato MADS Box Transcription Factor RIPENING INHIBITOR Reveals the Regulation of Fruit Ripening. Plant Cell 2013, 25, 371–386.
  118. Lin, Z.; Hong, Y.; Yin, M.; Li, C.; Zhang, K.; Grierson, D. A tomato HD-Zip homeobox protein, LeHB-1, plays an important role in floral organogenesis and ripening. Plant J. 2008, 55, 301–310.
  119. Meng, C.; Yang, D.; Ma, X.; Zhao, W.; Liang, X.; Ma, N.; Meng, Q. Suppression of tomato SlNAC1 transcription factor delays fruit ripening. J. Plant Physiol. 2016, 193, 88–96.
  120. Zhu, M.; Chen, G.; Zhou, S.; Tu, Y.; Wang, Y.; Dong, T.; Hu, Z. A New Tomato NAC (NAM/ATAF1/2/CUC2) Transcription Factor, SlNAC4, Functions as a Positive Regulator of Fruit Ripening and Carotenoid Accumulation. Plant Cell Physiol. 2013, 55, 119–135.
  121. Kou, X.; Liu, C.; Han, L.; Wang, S.; Xue, Z. NAC transcription factors play an important role in ethylene biosynthesis, reception and signaling of tomato fruit ripening. Mol. Genet. Genom. 2016, 291, 1205–1217.
  122. Ma, N.; Feng, H.; Meng, X.; Li, D.; Yang, D.; Wu, C.; Meng, Q. Overexpression of tomato SlNAC1transcription factor alters fruit pigmentation and softening. BMC Plant Biol. 2014, 14, 351.
  123. Li, T.; Tan, D.; Liu, Z.; Jiang, Z.; Wei, Y.; Zhang, L.; Li, X.; Yuan, H.; Wang, A. AppleMdACS6Regulates Ethylene Biosynthesis During Fruit Development Involving Ethylene-Responsive Factor. Plant Cell Physiol. 2015, 56, 1909–1917.
  124. Yin, X.-R.; Allan, A.C.; Chen, K.-S.; Ferguson, I.B. Kiwifruit EIL and ERF Genes Involved in Regulating Fruit Ripening. Plant Physiol. 2010, 153, 1280–1292.
  125. Xiao, Y.-Y.; Chen, J.-Y.; Kuang, J.-F.; Shan, W.; Xie, H.; Jiang, Y.-M.; Lu, W.-J. Banana ethylene response factors are involved in fruit ripening through their interactions with ethylene biosynthesis genes. J. Exp. Bot. 2013, 64, 2499–2510.
  126. McMurchie, E.J.; McGlasson, W.B.; Eaks, I.L. Treatment of Fruit with Propylene gives Information about the Biogenesis of Ethylene. Nat. Cell Biol. 1972, 237, 235–236.
  127. Fujisawa, M.; Nakano, T.; Ito, Y. Identification of potential target genes for the tomato fruit-ripening regulatorRIN by chromatin immunoprecipitation. BMC Plant Biol. 2011, 11, 26.
  128. Kagale, S.; Rozwadowski, K. EAR motif-mediated transcriptional repression in plants: An underlying mechanism for epigenetic regulation of gene expression. Epigenetics 2001, 6, 141–146.
  129. Gao, J.; Zhang, Y.; Li, Z.; Liu, M. Role of ethylene response factors (ERFs) in fruit ripening. Food Qual. Saf. 2020, 4, 15–20.
  130. Liu, M.; Gomes, B.L.; Mila, I.; Purgatto, E.; Peres, L.E.; Frasse, P.; Maza, E.; Zouine, M.; Roustan, J.-P.; Bouzayen, M.; et al. Comprehensive Profiling of Ethylene Response Factor Expression Identifies Ripening-Associated ERF Genes and Their Link to Key Regulators of Fruit Ripening in Tomato. Plant Physiol. 2016, 170, 1732–1744.
  131. Chung, M.-Y.; Vrebalov, J.; Alba, R.; Lee, J.; McQuinn, R.; Chung, J.-D.; Klein, P.; Giovannoni, J. A tomato (Solanum lycopersicum) APETALA2/ERF gene, SlAP2a, is a negative regulator of fruit ripening. Plant J. 2010, 64, 936–947.
  132. Fan, Z.-Q.; Kuang, J.-F.; Fu, C.-C.; Shan, W.; Han, Y.-C.; Xiao, Y.-Y.; Ye, Y.-J.; Lu, W.-J.; Lakshmanan, P.; Duan, X.-W.; et al. The Banana Transcriptional Repressor MaDEAR1 Negatively Regulates Cell Wall-Modifying Genes Involved in Fruit Ripening. Front. Plant Sci. 2016, 7, 1021.
  133. Fu, C.; Han, Y.; Qi, X.; Shan, W.; Chen, J.; Lu, W.; Kuang, J. Papaya CpERF9 acts as a transcriptional repressor of cell-wall-modifying genes CpPME1/2 and CpPG5 involved in fruit ripening. Plant Cell Rep. 2016, 35, 2341–2352.
  134. Han, Y.; Ban, Q.; Li, H.; Hou, Y.; Jin, M.; Han, S.; Rao, J. DkXTH8, a novel xyloglucan endotransglucosylase/hydrolase in persimmon, alters cell wall structure and promotes leaf senescence and fruit postharvest softening. Sci. Rep. 2016, 6, 39155.
  135. Fernandez-Pozo, N.; Zheng, Y.; Snyder, S.I.; Nicolas, P.; Shinozaki, Y.; Fei, Z.; Catala, C.; Giovannoni, J.J.; Rose, J.K.; Mueller, L.A. The Tomato Expression Atlas. Bioinformatics 2017, 33, 2397–2398.
  136. Lieberman, M.; Baker, J.E.; Sloger, M. Influence of Plant Hormones on Ethylene Production in Apple, Tomato, and Avocado Slices during Maturation and Senescence. Plant Physiol. 1977, 60, 214–217.
  137. Shin, J.-H.; Mila, I.; Liu, M.; Rodrigues, M.A.; Vernoux, T.; Pirrello, J.; Bouzayen, M. The RIN-regulated Small Auxin-Up RNA SAUR 69 is involved in the unripe-to-ripe phase transition of tomato fruit via enhancement of the sensitivity to ethylene. New Phytol. 2018, 222, 820–836.
  138. Breitel, D.A.; Chappell-Maor, L.; Meir, S.; Panizel, I.; Puig, C.P.; Hao, Y.; Yifhar, T.; Yasuor, H.; Zouine, M.; Bouzayen, M.; et al. AUXIN RESPONSE FACTOR 2 Intersects Hormonal Signals in the Regulation of Tomato Fruit Ripening. PLoS Genet. 2016, 12, e1005903.
  139. Hao, Y.; Hu, G.; Breitel, D.; Liu, M.; Mila, I.; Frasse, P.; Fu, Y.; Aharoni, A.; Bouzayen, M.; Zouine, M. Auxin Response Factor SlARF2 Is an Essential Component of the Regulatory Mechanism Controlling Fruit Ripening in Tomato. PLoS Genet. 2015, 11, e1005649.
  140. Su, L.; Diretto, G.; Purgatto, E.; Danoun, S.; Zouine, M.; Li, Z.; Roustan, J.-P.; Bouzayen, M.; Giuliano, G.; Chervin, C. Carotenoid accumulation during tomato fruit ripening is modulated by the auxin-ethylene balance. BMC Plant Biol. 2015, 15, 114.
  141. Jones, B.; Frasse, P.; Olmos, E.; Zegzouti, H.; Li, Z.G.; Latché, A.; Pech, J.C.; Bouzayen, M. Down-regulation of DR12, an auxin-response-factor homolog, in the tomato results in a pleiotropic phenotype including dark green and blotchy ripening fruit. Plant J. 2002, 32, 603–613.
  142. Mano, Y.; Nemoto, K. The pathway of auxin biosynthesis in plants. J. Exp. Bot. 2012, 63, 2853–2872.
  143. Cao, X.; Yang, H.; Shang, C.; Ma, S.; Liu, L.; Cheng, J. The Roles of Auxin Biosynthesis YUCCA Gene Family in Plants. Int. J. Mol. Sci. 2019, 20, 6343.
  144. Wang, B.; Chu, J.; Yu, T.; Xu, Q.; Sun, X.; Yuan, J.; Xiong, G.; Wang, G.; Wang, Y.; Li, J. Tryptophan-independent auxin biosynthesis contributes to early embryogenesis in Arabidopsis. Proc. Natl. Acad. Sci. USA 2015, 112, 4821–4826.
  145. Hu, W.; Zuo, J.; Hou, X.; Yan, Y.; Wei, Y.; Liu, J.; Li, M.; Xu, B.; Jin, Z. The auxin response factor gene family in banana: Genome-wide identification and expression analyses during development, ripening, and abiotic stress. Front. Plant Sci. 2015, 6, 742.
  146. Zouine, M.; Fu, Y.; Chateigner-Boutin, A.-L.; Mila, I.; Frasse, P.; Wang, H.; Audran-Delalande, C.; Roustan, J.-P.; Bouzayen, M. Characterization of the Tomato ARF Gene Family Uncovers a Multi-Levels Post-Transcriptional Regulation Including Alternative Splicing. PLoS ONE 2014, 9, e84203.
  147. Liang-Liang, X.; Ouyang, W.-Z.; Hou, X.-J.; Xie, L.-L.; Hu, C.-G.; Zhang, J.-Z. Genome-wide identification, isolation and expression analysis of auxin response factor (ARF) gene family in sweet orange (Citrus sinensis). Front. Plant Sci. 2015, 6, 119.
  148. Sagar, M.; Chervin, C.; Mila, I.; Hao, Y.; Roustan, J.-P.; Benichou, M.; Gibon, Y.; Biais, B.; Maury, P.; Latché, A.; et al. SlARF4, an Auxin Response Factor Involved in the Control of Sugar Metabolism during Tomato Fruit Development. Plant Physiol. 2013, 161, 1362–1374.
  149. Yuan, Y.; Mei, L.; Wu, M.; Wei, W.; Shan, W.; Gong, Z.; Zhang, Q.; Yang, F.; Yan, F.; Zhang, Q.; et al. SlARF10, an auxin response factor, is involved in chlorophyll and sugar accu-mulation during tomato fruit development. J. Exp. Bot. 2018, 69, 5507–5518.
  150. Muday, G.K.; Rahman, A.; Binder, B.M. Auxin and ethylene: Collaborators or competitors? Trends Plant Sci. 2012, 17, 181–195.
  151. Li, J.; Dai, X.; Zhao, Y. A Role for Auxin Response Factor 19 in Auxin and Ethylene Signaling in Arabidopsis. Plant Physiol. 2006, 140, 899–908.
  152. Pirrello, J.; Prasad, B.C.; Zhang, W.; Chen, K.; Mila, I.; Zouine, M.; Latche, A.; Pech, J.C.; Ohme-Takagi, M.; Regad, F.; et al. Functional analysis and binding affinity of tomato ethylene response factors provide insight on the molecular bases of plant differential responses to ethylene. BMC Plant Biol. 2012, 12, 190.
  153. Trainotti, L.; Tadiello, A.; Casadoro, G. The involvement of auxin in the ripening of climacteric fruits comes of age: The hormone plays a role of its own and has an intense interplay with ethylene in ripening peaches. J. Exp. Bot. 2007, 58, 3299–3308.
  154. Ren, H.; Gray, W.M. SAUR Proteins as Effectors of Hormonal and Environmental Signals in Plant Growth. Mol. Plant 2015, 8, 1153–1164.
  155. Zhu, F.; Luo, T.; Liu, C.; Wang, Y.; Zheng, L.; Xiao, X.; Zhang, M.; Yang, H.; Yang, W.; Xu, R.; et al. A NAC transcription factor and its interaction protein hinder abscisic acid biosynthesis by synergistically repressing NCED5 in Citrus reticulata. J. Exp. Bot. 2020, 71, 3613–3625.
  156. Kou, X.; Yang, S.; Chai, L.; Wu, C.; Zhou, J.; Liu, Y.; Xue, Z. Abscisic acid and fruit ripening: Multifaceted analysis of the effect of abscisic acid on fleshy fruit ripening. Sci. Hortic. 2021, 281, 109999.
  157. Kou, X.; Zhou, J.; Wu, C.E.; Yang, S.; Liu, Y.; Chai, L.; Xue, Z. The interplay between ABA/ethylene and NAC TFs in tomato fruit ripening: A review. Plant Mol. Biol. 2021, 1–16.
  158. Yang, S.; Zhou, J.; Watkins, C.B.; Wu, C.; Feng, Y.; Zhao, X.; Xue, Z.; Kou, X. NAC transcription factors SNAC4 and SNAC9 synergistically regulate tomato fruit ripening by affecting expression of genes involved in ethylene and abscisic acid metabolism and signal transduction. Postharvest Biol. Technol. 2021, 178, 111555.
  159. Finkelstein, R.R.; Rock, C.D. Abscisic Acid Biosynthesis and Response. Arab. Book 2002, 1, e0058.
  160. Taylor, I.B.; Burbidge, A.; Thompson, A.J. Control of abscisic acid synthesis. J. Exp. Bot. 2000, 51, 1563–1574.
  161. Zhang, M.; Yuan, B.; Leng, P. The role of ABA in triggering ethylene biosynthesis and ripening of tomato fruit. J. Exp. Bot. 2009, 60, 1579–1588.
  162. Zhang, M.; Leng, P.; Zhang, G.; Li, X. Cloning and functional analysis of 9-cis-epoxycarotenoid dioxygenase (NCED) genes encoding a key enzyme during abscisic acid biosynthesis from peach and grape fruits. J. Plant Physiol. 2009, 166, 1241–1252.
  163. Jia, H.-F.; Chai, Y.-M.; Li, C.-L.; Lu, D.; Luo, J.-J.; Qin, L.; Shen, Y.-Y. Abscisic Acid Plays an Important Role in the Regulation of Strawberry Fruit Ripening. Plant Physiol. 2011, 157, 188–199.
  164. Sun, L.; Yuan, B.; Zhang, M.; Wang, L.; Cui, M.; Wang, Q.; Leng, P. Fruit-specific RNAi-mediated suppression of SlNCED1 increases both lycopene and β-carotene contents in tomato fruit. J. Exp. Bot. 2012, 63, 3097–3108.
  165. Leng, P.; Yuan, B.; Guo, Y. The role of abscisic acid in fruit ripening and responses to abiotic stress. J. Exp. Bot. 2013, 65, 4577–4588.
  166. Soto, A.; Ruiz, K.B.; Ravaglia, D.; Costa, G.; Torrigiani, P. ABA may promote or delay peach fruit ripening through modulation of ripening- and hormone-related gene expression depending on the developmental stage. Plant Physiol. Biochem. 2013, 64, 11–24.
  167. Mou, W.; Li, D.; Bu, J.; Jiang, Y.; Khan, Z.U.; Luo, Z.; Mao, L.; Ying, T. Comprehensive Analysis of ABA Effects on Ethylene Biosynthesis and Signaling during Tomato Fruit Ripening. PLoS ONE 2016, 11, e0154072.
  168. Diretto, G.; Frusciante, S.; Fabbri, C.; Schauer, N.; Busta, L.; Wang, Z.; Matas, A.; Fiore, A.; Rose, J.; Fernie, A.; et al. Manipulation of beta-carotene levels in tomato fruits results in increased ABA content and extended shelf life. Plant Biotechnol. J. 2020, 18, 1185–1199.
  169. Pérez-Llorca, M.; Muñoz, P.; Müller, M.; Munné-Bosch, S. Biosynthesis, Metabolism and Function of Auxin, Salicylic Acid and Melatonin in Climacteric and Non-climacteric Fruits. Front. Plant Sci. 2019, 10, 136.
  170. Li, T.; Xu, Y.; Zhang, L.; Ji, Y.; Tan, D.; Yuan, H.; Wang, A. The Jasmonate-Activated Transcription Factor MdMYC2 Regulates Ethylene Response Factor and Ethylene Biosynthetic Genes to Promote Ethylene Biosynthesis during Apple Fruit Ripening. Plant Cell 2017, 29, 1316–1334.
  171. Wu, Y.; Liu, X.; Fu, B.; Zhang, Q.; Tong, Y.; Wang, J.; Wang, W.; Grierson, D.; Yin, X. Methyl jasmonate enhances ethylene synthesis in kiwifruit by inducing NAC genes that activate ACSJ. Agric. Food Chem. 2020, 68, 3267–3276.
  172. Zhu, T.; Tan, W.-R.; Deng, X.-G.; Zheng, T.; Zhang, D.-W.; Lin, H.-H. Effects of brassinosteroids on quality attributes and ethylene synthesis in postharvest tomato fruit. Postharvest Biol. Technol. 2015, 100, 196–204.
  173. Chai, Y.; Zhang, Q.; Tian, L.; Li, C.; Xing, Y.; Qin, L.; Shen, Y. Brassinosteroid is involved in strawberry fruit ripening. Plant Growth Regul. 2013, 69, 63–69.
  174. Lefevere, H.; Bauters, L.; Gheysen, G. Salicylic Acid Biosynthesis in Plants. Front. Plant Sci. 2020, 11, 338.
  175. Tieman, D.; Zeigler, M.; Schmelz, E.; Taylor, M.G.; Rushing, S.; Jones, J.B.; Klee, H.J. Functional analysis of a tomato salicylic acid methyl transferase and its role in synthesis of the flavor volatile methyl salicylate. Plant J. 2010, 62, 113–123.
  176. Srivastava, M.K.; Dwivedi, U.N. Delayed ripening of banana fruit by salicylic acid. Plant Sci. 2000, 158, 87–96.
  177. Zhang, Y.; Chen, K.; Zhang, S.; Ferguson, I. The role of salicylic acid in postharvest ripening of kiwifruit. Postharvest Biol. Technol. 2003, 28, 67–74.
  178. González-Aguilar, G.; Buta, J.; Wang, C. Methyl jasmonate and modified atmosphere packaging (MAP) reduce decay and maintain postharvest quality of papaya ‘Sunrise’. Postharvest Biol. Technol. 2003, 28, 361–370.
  179. Han, J.; Tian, S.; Meng, X.; Ding, Z. Response of physiologic metabolism and cell structures in mango fruit to exogenous methyl salicylate under low-temperature stress. Physiol. Plant 2006, 128, 125–133.
  180. Ding, C.-K.; Wang, C.Y. The dual effects of methyl salicylate on ripening and expression of ethylene biosynthetic genes in tomato fruit. Plant Sci. 2003, 164, 589–596.
  181. Fiorucci, A.-S.; Fankhauser, C. Plant Strategies for Enhancing Access to Sunlight. Curr. Biol. 2017, 27, R931–R940.
  182. Yen, H.C.; Shelton, B.A.; Howard, L.R.; Lee, S.; Vrebalov, J.; Giovannoni, J.J. The tomato high-pigment (hp) locus maps to chromosome 2 and influences plastome copy number and fruit quality. Theor. Appl. Genet. 1997, 95, 1069–1079.
  183. Liu, Y.; Roof, S.; Ye, Z.; Barry, C.; Van Tuinen, A.; Vrebalov, J.; Bowler, C.; Giovannoni, J. Manipulation of light signal transduction as a means of modifying fruit nutritional quality in tomato. Proc. Natl. Acad. Sci. USA 2004, 101, 9897–9902.
  184. Kolotilin, I.; Koltai, H.; Tadmor, Y.; Bar-Or, C.; Reuveni, M.; Meir, A.; Nahon, S.; Shlomo, H.; Chen, L.; Levin, I. Transcriptional profiling of high pigment-2 tomato mutant links early fruit plastid biogenesis with its overproduction of phytonutrients. Plant Physiol. 2007, 145, 389–401.
  185. Alba, R.; Cordonnier-Pratt, M.; Pratt, L.H. Fruit-localized phytochromes regulate lycopene accumulation independently of ethylene production in tomato. Plant Physiol. 2000, 123, 363–370.
  186. Schofield, A.; Paliyath, G. Modulation of carotenoid biosynthesis during tomato fruit ripening through phytochrome regulation of phytoene synthase activity. Plant Physiol. Biochem. 2005, 43, 1052–1060.
  187. Mustilli, A.C.; Fenzi, F.; Ciliento, R.; Alfano, F.; Bowler, C. Phenotype of the tomato high pigment-2 mutant is caused by a mutation in the tomato homolog of DEETIOLATED1. Plant Cell 1999, 11, 145–157.
  188. Schroeder, D.F.; Gahrtz, M.; Maxwell, B.B.; Cook, R.; Kan, J.M.; Alonso, J.M.; Ecker, J.R.; Chory, J. De-Etiolated 1 and Damaged DNA Binding Protein 1 Interact to Regulate Arabidopsis Photomorphogenesis. Curr. Biol. 2002, 12, 1462–1472.
  189. Davuluri, G.R.; van Tuinen, A.; Fraser, P.D.; Manfredonia, A.; Newman, R.; Burgess, D.; Brummell, D.A.; King, S.R.; Palys, J.; Uhlig, J.; et al. Fruit-specific RNAi-mediated suppression of DET1 enhances carotenoid and flavonoid content in tomatoes. Nat. Biotechnol. 2005, 23, 890–895.
  190. Wang, S.; Liu, J.; Feng, Y.; Niu, X.; Giovannoni, J.; Liu, Y. Altered plastid levels and potential for improved fruit nutrient content by downregulation of the tomato DDB1-interacting protein CUL4. Plant J. 2008, 55, 89–103.
  191. Llorente, B.; Andrea, L.D.; Ruiz-Sola, M.A.; Botterweg, E.; Pulido, P.; Andilla, J.; Loza-Alvarez, P.; Rodriguez-Concepcion, M. Tomato fruit carotenoid biosynthesis is adjusted to actual ripening progression by a light-dependent mechanism. Plant J. 2016, 85, 107–119.
  192. Wang, W.; Wang, P.; Li, X.; Wang, Y.; Tian, S.; Qin, G. The transcription factor SlHY5 regulates the ripening of tomato fruit at both the transcriptional and translational levels. Hortic. Res. 2021, 8, 1–15.
  193. Cruz, A.B.; Bianchetti, R.E.; Alves, F.R.R.; Purgatto, E.; Peres, L.E.P.; Rossi, M.; Freschi, L. Light, Ethylene and Auxin Signaling Interaction Regulates Carotenoid Biosynthesis During Tomato Fruit Ripening. Front. Plant Sci. 2018, 9, 1370.
More
© Text is available under the terms and conditions of the Creative Commons Attribution (CC BY) license; additional terms may apply. By using this site, you agree to the Terms and Conditions and Privacy Policy.
Upload a video for this entry
Information
Subjects: Plant Sciences
Contributor MDPI registered users' name will be linked to their SciProfiles pages. To register with us, please refer to https://encyclopedia.pub/register :
Donald Grierson
View Times: 741
Revisions: 2 times (View History)
Update Date: 25 May 2021
Table of Contents
Academic Video Service
Feedback