EjNAC3 transcriptionally regulates chilling-induced lignification of loquat fruit via physical interaction with an atypical CAD-like gene

The MADS-box gene EjAGL15 positively regulates lignin deposition in the flesh of loquat fruit during its storage

Introduction

Lignification of fruit flesh is a common physiological disorder that occurs during post-harvest storage, resulting in the deterioration of fruit quality. Lignin deposition in loquat fruit flesh occurs due to chilling injury or senescence, at temperatures around 0°C or 20°C, respectively. Despite extensive research on the molecular mechanisms underlying chilling-induced lignification, the key genes responsible for the lignification process during senescence in loquat fruit remain unknown. MADS-box genes, an evolutionarily conserved transcription factor family, have been suggested to play a role in regulating senescence. However, it is still unclear whether MADS-box genes can regulate the lignin deposition that arises from fruit senescence.

Methods

Both senescence- and chilling-induced flesh lignification were simulated by applying temperature treatments on loquat fruits. The flesh lignin content during the storage was measured. Transcriptomic, quantitative reverse transcription PCR and correlation analysis were employed to identify key MADS-box genes that may be involved in flesh lignification. The Dual-luciferase assay was utilized to identify the potential interactions between MADS-box members and genes in phenylpropanoid pathway.

Results and Discussion

The lignin content of the flesh samples treated at 20°C or 0°C increased during storage, but at different rates. Results from transcriptome analysis, quantitative reverse transcription PCR, and correlation analysis led us to identify a senescence-specific MADS-box gene, EjAGL15, which correlated positively with the variation in lignin content of loquat fruit. Luciferase assay results confirmed that EjAGL15 activated multiple lignin biosynthesis-related genes. Our findings suggest that EjAGL15 functions as a positive regulator of senescence-induced flesh lignification in loquat fruit.

Transcriptomic and Metabolomic Analysis Reveals a Protein Module Involved in Pre-harvest Apple Peel Browning

Peel browning is a natural phenomenon that adversely affects the appearance of fruits. Research on the regulation of browning in apples (Malus × domestica Borkh.) has mainly focused on post-harvest storage, while studies at the pre-harvest stage are relatively rare. Apple is an economically important horticultural crop prone to peel browning during growth, especially when the fruits are bagged (dark conditions). The present study's integrated transcriptomics and metabolomics analysis revealed that pre-harvest apple peel browning was primarily due to changes in phenolics and flavonoids. The detailed analysis identified MdLAC7's (laccase 7) role in the pre-harvest apple peel browning process. Transient injection, overexpression, and CRISPR/Cas9 knockout of the MdLAC7 gene in apple fruit and calli identified vallinic acid, anthocyanidin, tannic acid, sinapic acid, and catechinic acid as its catalytic substrates. In addition, yeast one-hybrid (Y1H) assay, electrophoretic mobility shift assay (EMSA), luciferase (LUC) reporter assay, and ChIP-PCR analysis revealed that MdWRKY31 binds to the promoter of MdLAC7 and positively regulates its activity to promote peel browning of bagged fruits (dark conditions). Interestingly, upon light exposure, the light-responsive transcription factor MdHY5 (ELONGATED HYPOCOTYL 5) bound to the promoter of MdWRKY31 and inhibited the gene's expression, thereby indirectly inhibiting the function of MdLAC7. Subsequent analysis showed that MdHY5 binds to the MdLAC7 promoter at the G-box1/2 site and directly inhibits its expression in vivo. Thus, the study revealed the MdLAC7-mediated mechanism regulating pre-harvest apple peel browning and demonstrated the role of light in inhibiting MdLAC7 activity and subsequently reducing peel browning. These results provide theoretical guidance for producing high-quality apple fruits.

The Regulatory Mechanisms and Control Technologies of Chilling Injury and Fungal Diseases of Postharvest Loquat Fruit

Loquat is a popular fruit widely cultivated all over the world. It is rich in minerals and carotenoids and has high commercial value. At room temperature, loquat fruit is impressionable to water and nutritional losses, physical damage, and microbial decay, resulting in a short postharvest life. Low-temperature storage is routinely used to prolong the shelf life of loquat fruit; however, cold storage can also lead to lignification of flesh tissue, which is one of the major symptoms of chilling injury (CI), reducing the quality and economic value of the fruit. In addition, fruit decay caused by microbial infection is another important reason for postharvest losses of loquat. To reduce quality deterioration and optimize the postharvest storage strategies of loquat fruit, considerable progress has been made in the physiological and molecular biological studies of CI, microbial decay, and preservation technologies of loquat fruit during the postharvest phase in recent decades. This review summarizes the current research progress and provides a reference for the improvement of loquat fruit quality.

Transcriptional regulation of fleshy fruit texture

Fleshy fruit texture is a critically important quality characteristic of ripe fruit. Softening is an irreversible process which operates in most fleshy fruits during ripening which, together with changes in color and taste, contributes to improvements in mouthfeel and general attractiveness. Softening results mainly from the expression of genes encoding enzymes responsible for cell wall modifications but starch degradation and high levels of flavonoids can also contribute to texture change. Some fleshy fruit undergo lignification during development and post-harvest, which negatively affects eating quality. Excessive softening can also lead to physical damage and infection, particularly during transport and storage which causes severe supply chain losses. Many transcription factors (TFs) that regulate fruit texture by controlling the expression of genes involved in cell wall and starch metabolism have been characterized. Some TFs directly regulate cell wall targets, while others act as part of a broader regulatory program governing several aspects of the ripening process. In this review, we focus on advances in our understanding of the transcriptional regulatory mechanisms governing fruit textural change during fruit development, ripening and post-harvest. Potential targets for breeding and future research directions for the control of texture and quality improvement are discussed.

Transcriptome Analysis Reveals Candidate Lignin-Related Genes and Transcription Factors during Fruit Development in Pomelo (Citrus maxima)

Juice sac granulation (a physiological disorder) leads to large postharvest losses of pomelo (Citrus maxima). Previous studies have shown that juice sac granulation is closely related to lignin accumulation, while the molecular mechanisms underlying this disorder remain elusive in pomelo. Our results showed that the lignin content in NC (near the core) and FC (far away from the core) juice sacs overall increased from 157 DPA (days post anthesis) to 212 DPA and reached a maximum at 212 DPA. Additionally, the lignin content of NC juice sacs was higher than that of FC juice sacs. In this study, we used transcriptome-based weighted gene co-expression network analysis (WGCNA) to address how lignin formation in NC and FC juice sacs is generated during the development of pomelo. After data assembly and bioinformatic analysis, we found a most correlated module (black module) to the lignin content, then we used the 11 DEGs in this module as hub genes for lignin biosynthesis. Among these DEGs, PAL (phenylalanine ammonia lyase), HCT (hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase), 4CL2 (4-coumarate: CoA ligase), C4H (cinnamate 4-hydroxylase), C3'H (p-coumarate 3-hydroxylase), and CCoAOMT1 (caffeoyl CoA 3-Omethyltransferase) were the most distinct DEGs in granulated juice sacs. Co-expression analysis revealed that the expression patterns of several transcription factors such as MYB, NAC, OFP6, and bHLH130 are highly correlated with lignin formation. In addition, the expression patterns of the DEGs related to lignin biosynthesis and transcription factors were validated by qRT-PCR, and the results were highly concordant with the RNA-seq results. These results would be beneficial for further studies on the molecular mechanism of lignin accumulation in pomelo juice sacs and would help with citrus breeding.

Impact of melatonin application on lignification in water bamboo shoot during storage

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Melatonin (MT) delayed water bamboo shoot lignification and hardness.

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MT treatment decreased the lignin biosynthesis through reducing enzyme activity.

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MT treatment inhibited the expression of lignin biosynthesis related genes.

Melatonin, a crucial bioactive molecule, involved in several physiological processes in plants. This study investigated the effects of melatonin (MT) treatment on lignification, including firmness, lignin, lignified-enzyme activities, the expression patterns of genes encoding corresponding enzymes and transcription factors in water bamboo shoot during storage for 8 days. MT treatment decreased the firmness and content of lignin. It inhibited the degradation of total phenols and ascorbic acid and delayed the lignin biosynthesis, via reducing the activities of phenylalanine ammonia-lyse cinnamyl alcohol dehydrogenase and peroxidase, as well as lignin biosynthesis-related genes expression levels. Transcription factors of ZlNAC1, ZlNAC2, ZlNAC3 and ZlNAC4 from NAC family and ZlMYB1 and ZlMYB2 from MYB family were increased in water bamboo shoot after harvest and MT-treated markedly reduced their expression. Therefore, our findings supply a fundamental understanding of MT treatment suppression of lignification and establish a foundation for further research on transcriptional regulation.

An EjbHLH14-EjHB1-EjPRX12 module is involved in methyl jasmonate alleviation of chilling-induced lignin deposition in loquat fruit

Loquat fruit are susceptible to chilling injuries induced by postharvest storage at low temperature. The major symptoms are increased lignin content and flesh firmness, which cause a leathery texture. Pretreatment with methyl jasmonate (MeJA) can alleviate this low-temperature-induced lignification, but the mechanism is not understood. In this study, we characterized a novel class III peroxidase, EjPRX12, and studied its relationship to lignification. Transcript levels of EjPRX12 were attenuated following MeJA pretreatment, consistent with the reduced lignin content in fruit. In vitro enzyme activity assay indicated that EjPRX12 polymerized sinapyl alcohol, and overexpression of EjPRX12 in Arabidopsis promoted lignin accumulation, indicating that it plays a functional role in lignin polymerization. We also identified an HD-ZIP transcription factor, EjHB1, repressed by MeJA pretreatment, which directly bound to and significantly activated the EjPRX12 promoter. Overexpression of EjHB1 in Arabidopsis promoted lignin accumulation with induced expression of lignin-related genes, especially AtPRX64. Furthermore, a JAZ-interacting repressor, EjbHLH14, was characterized, and it is proposed that MeJA pretreatment caused EjbHLH14 to be released to repress the expression of EjHB1. These results identified a novel regulatory pathway involving EjbHLH14-EjHB1-EjPRX12 and revealed the molecular mechanism whereby MeJA alleviated lignification of loquat fruit at low temperature.

NAC Transcription Factor Family Regulation of Fruit Ripening and Quality: A Review

The NAC transcription factor (TF) family is one of the largest plant-specific TF families and its members are involved in the regulation of many vital biological processes during plant growth and development. Recent studies have found that NAC TFs play important roles during the ripening of fleshy fruits and the development of quality attributes. This review focuses on the advances in our understanding of the function of NAC TFs in different fruits and their involvement in the biosynthesis and signal transduction of plant hormones, fruit textural changes, color transformation, accumulation of flavor compounds, seed development and fruit senescence. We discuss the theoretical basis and potential regulatory models for NAC TFs action and provide a comprehensive view of their multiple roles in modulating different aspects of fruit ripening and quality.

Integrative transcriptomic and metabolomic data provide insights into gene networks associated with lignification in postharvest Lei bamboo shoots under low temperature

Lei bamboo (Phyllostachys violascens) shoots are delicious food in Asia. Here, the molecular basis of lignification in postharvest Lei bamboo shoots under low temperature (LT) is revealed by transcriptomic and metabolomics analyses for the first time. We identified substantial accumulations of jasmonates (JAs) and major lignin biosynthesis precursors (coumarin, trans-4-coumaric acid, trans-ferulic acid and L-phenylalanine). Transcriptome analysis indicated that some regulatory genes were significantly differentially expressed, and the expression patterns of them were highly consistent with the changes in the key lignin precursors or JA profiles. Co-expression analysis showed that the LT responsive genes PvCRPK-4/-5, PvICE2-1/2, PvDREB2B might form a network module with the lignin (PvC3H-2/3, PvC4H-2/4, PvCAD-1/2/3/4, etc.) or JA biosynthesis genes (PvOPR2, PvJAZ-4 and PvPEX5, etc.), indicating a LT-lignification or LT-JA-lignification regulatory pathway in Lei bamboo shoots. Above all, our findings provide new an insight into the LT-associated lignification in postharvest bamboo shoots.

Transcription Factor CitERF16 Is Involved in Citrus Fruit Sucrose Accumulation by Activating CitSWEET11d

Sugars are the primary products of photosynthesis and play an important role in plant growth and development. They contribute to sweetness and flavor of fleshy fruits and are pivotal to fruit quality, and their translocation and allocation are mainly dependent on sugar transporters. Genome-wide characterization of Satsuma mandarin identified eighteen SWEET family members that encode transporters which facilitate diffusion of sugar across cell membranes. Analysis of the expression profiles in tissues of mandarin fruit at different developmental stages showed that CitSWEET11d transcripts were significantly correlated with sucrose accumulation. Further studies indicated that overexpression of CitSWEET11d in citrus callus and tomato fruit showed a higher sucrose level compared to wild-type, suggesting that CitSWEET11d could enhance sucrose accumulation. In addition, we identified an ERF transcription factor CitERF16 by yeast one-hybrid screening assay which could directly bind to the DRE cis-element on the promoter of CitSWEET11d. Overexpression of CitERF16 in citrus callus significantly induced CitSWEET11d expression and elevated sucrose content, suggesting that CitERF16 acts as a positive regulator to promote sucrose accumulation via trans-activation of CitSWEET11d expression.

Genome-Wide Identification of NAC Transcription Factor Family in Juglans mandshurica and Their Expression Analysis during the Fruit Development and Ripening

The NAC (NAM, ATAF and CUC) gene family plays a crucial role in the transcriptional regulation of various biological processes and has been identified and characterized in multiple plant species. However, genome-wide identification of this gene family has not been implemented in Juglans mandshurica, and specific functions of these genes in the development of fruits remain unknown. In this study, we performed genome-wide identification and functional analysis of the NAC gene family during fruit development and identified a total of 114 JmNAC genes in the J. mandshurica genome. Chromosomal location analysis revealed that JmNAC genes were unevenly distributed in 16 chromosomes; the highest numbers were found in chromosomes 2 and 4. Furthermore, according to the homologues of JmNAC genes in Arabidopsis thaliana, a phylogenetic tree was constructed, and the results demonstrated 114 JmNAC genes, which were divided into eight subgroups. Four JmNAC gene pairs were identified as the result of tandem duplicates. Tissue-specific analysis of JmNAC genes during different developmental stages revealed that 39 and 25 JmNAC genes exhibited upregulation during the mature stage in walnut exocarp and embryos, indicating that they may serve key functions in fruit development. Furthermore, 12 upregulated JmNAC genes were common in fruit ripening stage in walnut exocarp and embryos, which demonstrated that these genes were positively correlated with fruit development in J. mandshurica. This study provides new insights into the regulatory functions of JmNAC genes during fruit development in J. mandshurica, thereby improving the understanding of characteristics and evolution of the JmNAC gene family.

The NAM/ATAF1/2/CUC2 transcription factor PpNAC.A59 enhances PpERF.A16 expression to promote ethylene biosynthesis during peach fruit ripening

Peach is a typical climacteric fruit that releases ethylene during fruit ripening. Several studies have been conducted on the transcriptional regulation of ethylene biosynthesis in peach fruit. Herein, an ethylene response factor, PpERF.A16, which was induced by exogenous ethylene, could enhance ethylene biosynthesis by directly inducing the expression of 1-aminocyclopropane-1-carboxylic acid synthase (PpACS1) and 1-aminocyclopropane-1-carboxylic acid oxidase (PpACO1) genes. Moreover, the NAM/ATAF1/2/CUC2 (NAC) transcription factor (TF) PpNAC.A59 was coexpressed with PpERF.A16 in all tested peach cultivars. Interestingly, PpNAC.A59 can directly interact with the promoter of PpERF.A16 to induce its expression but not enhance LUC activity driven by any promoter of PpACS1 or PpACO1. Thus, PpNAC.A59 can indirectly mediate ethylene biosynthesis via the NAC-ERF signaling cascade to induce the expression of both PpACS1 and PpACO1. These results enrich the genetic network of fruit ripening in peach and provide new insight into the ripening mechanism of other perennial fruits.

The MdMYB16/MdMYB1-miR7125-MdCCR module regulates the homeostasis between anthocyanin and lignin biosynthesis during light induction in apple

Light induces anthocyanin accumulation and hence decides the coloration of apple fruit. It also plays a key role in regulating the biosynthesis of other secondary metabolites. However, the crosstalk between anthocyanin and lignin metabolism during light induction, which affects the edible quality and visual quality of apple fruit, respectively, have rarely been characterized. In this study, we identified and functionally elucidated the roles of miR7125 and its target, cinnamoyl-coenzyme A reductase gene (CCR), in regulating the homeostasis between anthocyanin and lignin biosynthesis during light induction. Overexpressing miR7125 or inhibiting CCR transiently in apple fruit promoted anthocyanin biosynthesis but reduced lignin production under light-induced conditions. Consistently, opposite results were observed under the background of repressed miR7125 or overexpressed CCR. We found that the repressor MdMYB16 and the activator MdMYB1 bound to the miR7125 promoter. Transient repression of MdMYB16 upregulated miR7125 expression significantly, accompanied by decreased levels of MdCCR transcript, resulting in a reduction in the lignin biosynthesis and an increase in anthocyanin accumulation. However, transient overexpression of MdMYB16 produced the opposite effects to MdMYB16-RNAi. The results reveal a novel mechanism by which the MdMYB16/MdMYB1-miR7125-MdCCR module collaboratively regulates homeostasis between anthocyanin and lignin biosynthesis under light induction in apple.

The MADS-Box Transcription Factor EjAGL65 Controls Loquat Flesh Lignification via Direct Transcriptional Inhibition of EjMYB8

Loquat fruit accumulates lignin in its flesh when undergoing chilling injury during postharvest storage, making it a suitable model for the study of flesh lignification. Transcriptional regulation of lignin biosynthesis is principally controlled by the NAC-MYB transcriptional cascade in model plants. Previous research has demonstrated that EjMYB8 activates lignin biosynthesis through direct interaction with the promoter of Ej4CL1. However, the classic NAC-MYB gene regulation network has not been established. Here, the MADS-box gene EjAGL65 was discovered by screening a cDNA library using the EjMYB8 promoter as bait in yeast. A phylogenetic analysis and structural comparisons revealed that EjAGL65 belongs to the Mδ subgroup of the MADS-box family, whose members have not been reported as being involved in the regulation of lignin deposition. EjAGL65 transcription was downregulated at 0°C compared to 5°C, indicating a negative correlation with the change of lignin content. A dual-luciferase assay indicated that EjAGL65 is capable of inhibiting the promoter activity of EjMYB8 in vivo. These results showed that the Mδ MADS-box gene EjAGL65 transcriptionally regulates EjMYB8 during postharvest chilling induced flesh lignification, which differs from the classical regulation model of lignin biosynthesis that has been illustrated for developmental lignin accumulation.

Biosynthetic labeling with 3-O-propargylcaffeyl alcohol reveals in vivo cell-specific patterned lignification in loquat fruits during development and postharvest storage

Lignification is a major cell wall modification that often results in the formation of sophisticated subcellular patterns during plant development or in response to environmental stresses. Precise localization of the spatiotemporal deposition of lignin is of great importance for revealing the lignification regulatory mechanism of individual cells. In loquat fruits, lignification typically increases the flesh lignin content and firmness, reducing their edibility and processing quality. However, the precise localization of the spatiotemporal active zones of lignification inside loquat fruit flesh remains poorly understood, and little is known about the contribution of patterned lignification to cell wall structure dynamics and the subsequent fruit-quality deterioration. Here, we performed an emerging bioorthogonal chemistry imaging technique to trace the in vivo patterned lignification dynamics in cells of loquat fruit flesh during development and storage. In developing fruits, lignified cells (LCs) and vascular bundles (VBs) were the zones of active lignification, and ring-like LCs deposited lignin at both the inner wall layer and the outer periphery sides. The domino effect of the generation of LCs was preliminarily visualized. In mature fruits, the newly formed lignin in the flesh of fruits during storage was specifically deposited in the corners and middle lamellae of parenchyma cells surrounding the VBs, resulting in the development of a reticular structure. Based on the findings, distinct spatiotemporal patterned lignification modes for different flesh cells in loquat fruits were proposed. These findings provide loquat lignification dynamics together with spatiotemporal data that can improve our understanding of the lignification process in planta.

Contribution of phenylpropanoid metabolism to plant development and plant-environment interactions

Phenylpropanoid metabolism is one of the most important metabolisms in plants, yielding more than 8,000 metabolites contributing to plant development and plant-environment interplay. Phenylpropanoid metabolism materialized during the evolution of early freshwater algae that were initiating terrestrialization and land plants have evolved multiple branches of this pathway, which give rise to metabolites including lignin, flavonoids, lignans, phenylpropanoid esters, hydroxycinnamic acid amides, and sporopollenin. Recent studies have revealed that many factors participate in the regulation of phenylpropanoid metabolism, and modulate phenylpropanoid homeostasis when plants undergo successive developmental processes and are subjected to stressful environments. In this review, we summarize recent progress on elucidating the contribution of phenylpropanoid metabolism to the coordination of plant development and plant-environment interaction, and metabolic flux redirection among diverse metabolic routes. In addition, our review focuses on the regulation of phenylpropanoid metabolism at the transcriptional, post-transcriptional, post-translational, and epigenetic levels, and in response to phytohormones and biotic and abiotic stresses.

The strawberry transcription factor FaRAV1 positively regulates anthocyanin accumulation by activation of FaMYB10 and anthocyanin pathway genes

The RAV (related to ABI3/viviparous 1) group of transcription factors (TFs) play multifaceted roles in plant development and stress responses. Here, we show that strawberry (Fragaria × ananassa) FaRAV1 positively regulates anthocyanin accumulation during fruit ripening via a hierarchy of activation processes. Dual-luciferase assay screening of all fruit-expressed AP2/ERFs showed FaRAV1 had the highest transcriptional activation of the promoter of FaMYB10, a key activator of anthocyanin biosynthesis. Yeast one-hybrid and electrophoretic mobility shift assays indicated that FaRAV1 could directly bind to the promoter of FaMYB10. Transient overexpression of FaRAV1 in strawberry fruit increased FaMYB10 expression and anthocyanin production significantly. Correspondingly, transient RNA interference-induced silencing of FaRAV1 led to decreases in FaMYB10 expression and anthocyanin content. Transcriptome analysis of FaRAV1-overexpressing strawberry fruit revealed that transcripts of phenylpropanoid and flavonoid biosynthesis pathway genes were up-regulated. Luciferase assays showed that FaRAV1 could also activate the promoters of strawberry anthocyanin biosynthetic genes directly, revealing a second level of FaRAV1 action in promoting anthocyanin accumulation. These results show that FaRAV1 stimulates anthocyanin accumulation in strawberry both by direct activation of anthocyanin pathway gene promoters and by up-regulation of FaMYB10, which also positively regulates these genes.

ETHYLENE RESPONSE FACTOR39-MYB8 complex regulates low-temperature-induced lignification of loquat fruit

Flesh lignification is a specific chilling response that causes deterioration in the quality of stored red-fleshed loquat fruit (Eribotrya japonica) and is one aspect of wider chilling injury. APETALA2/ETHLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors are important regulators of plant low-temperature responses and lignin biosynthesis. In this study, the expression and action of 27 AP2/ERF genes from the red-fleshed loquat cultivar 'Luoyangqing' were investigated in order to identify transcription factors regulating low-temperature-induced lignification. EjERF27, EjERF30, EjERF36, and EjERF39 were significantly induced by storage at 0 °C but inhibited by a low-temperature conditioning treatment (pre-storage at 5 °C for 6 days before storage at 0 °C, which reduces low-temperature-induced lignification), and their transcript levels positively correlated with flesh lignification. A dual-luciferase assay indicated that EjERF39 could transactivate the promoter of the lignin biosynthetic gene Ej4CL1, and an electrophoretic mobility shift assay confirmed that EjERF39 recognizes the DRE element in the promoter region of Ej4CL1. Furthermore, the combination of EjERF39 and the previously characterized EjMYB8 synergistically transactivated the Ej4CL1 promoter, and both transcription factors showed expression patterns correlated with lignification in postharvest treatments and red-fleshed 'Luoyangqing' and white-fleshed 'Ninghaibai' cultivars with different lignification responses. Bimolecular fluorescence complementation and luciferase complementation imaging assays confirmed direct protein-protein interaction between EjERF39 and EjMYB8. These data indicate that EjERF39 is a novel cold-responsive transcriptional activator of Ej4CL1 that forms a synergistic activator complex with EjMYB8 and contributes to loquat fruit lignification at low temperatures.

Transcriptomic and Metabolic Analyses Provide New Insights into the Apple Fruit Quality Decline during Long-Term Cold Storage

Long-term low-temperature conditioning (LT-LTC) decreases apple fruit quality, but the underlying physiological and molecular basis is relatively uncharacterized. We identified 12 clusters of differentially expressed genes (DEGs) involved in multiple biological processes (i.e., sugar, malic acid, fatty acid, lipid, complex phytohormone, and stress-response pathways). The expression levels of genes in sugar pathways were correlated with decreasing starch levels during LT-LTC. Specifically, starch-synthesis-related genes (e.g., BE, SBE, and GBSS genes) exhibited downregulated expression, whereas sucrose-metabolism-related gene expression levels were up- or downregulated. The expression levels of genes in the malic acid pathway (ALMT9, AATP1, and AHA2) were upregulated, as well as the content of malic acid in apple fruit during LT-LTC. A total of 151 metabolites, mainly related to amino acids and their isoforms, amines, organic acids, fatty acids, sugars, and polyols, were identified during LT-LTC. Additionally, 35 organic-acid-related metabolites grouped into three clusters, I (3), II (22), and III (10), increased in abundance during LT-LTC. Multiple phytohormones regulated the apple fruit chilling injury response. The ethylene (ET) and abscisic acid (ABA) levels increased at CS2 and CS3, and jasmonate (JA) levels also increased during LT-LTC. Furthermore, the expression levels of genes involved in ET, ABA, and JA synthesis and response pathways were upregulated. Finally, some key transcription factor genes (MYB, bHLH, ERF, NAC, and bZIP genes) related to the apple fruit cold acclimation response were differentially expressed. Our results suggest that the multilayered mechanism underlying apple fruit deterioration during LT-LTC is a complex, transcriptionally regulated process involving cell structures, sugars, lipids, hormones, and transcription factors.

Effects of 1-Methylcyclopropene (1-MCP) and Ethylene on Postharvest Lignification of Common Beans (Phaseolus vulgaris L)

Postharvest 1-methylcyclopropene (1-MCP) treatment can inhibit the lignification of fruits and vegetables. The mode of action of 1-MCP is through inhibiting ethylene production, but the effect of 1-MCP and ethylene on lignification of common beans remains unknown. This work compared the effect of 0.5 μL L^-1 1-MCP and 100 μL L^-1 ethylene on the lignification of common beans during storage. Postharvest 1-MCP significantly inhibited the increase of the lignified cell group, sclerenchyma became thicker, vascular bundles thickened, and lignified cells grew during storage, while ethylene was the opposite. 1-MCP inhibited the increase in the respiration rate, sucrose phosphate synthase (SPS), sucrose synthase (SuSy), phenylalanine ammonialyase (PAL), cinnamyl alcohol dehydrogenase (CAD), and peroxidase (POD), whereas ethylene increased all of them. Ethylene treatment stimulated and 1-MCP inhibited the decline of reducing sugar and cellulose content. Expression of genes, including PvACO1, PvAOG1, PvSuSy2, PvPAL3, Pv4CL1, and PvCOMT1, with the lignin content being significantly increased in common beans during storage. 1-MCP treatment markedly inhibited the expression of PvACO1, PvSuSy2, PvPAL3, Pv4CL1, and PvCOMT1 genes, while strengthened the expression of PvETR1 and PvAOG1, while ethylene was the opposite. This work provides evidence that ethylene or abscisic acid (ABA) may play an important role in 1-MCP regulation of postharvest lignification in common beans and provides strategies for preserving the quality of fruits and vegetables during storage.

Soil fungal assemblage complexity is dependent on soil fertility and dominated by deterministic processes

In the processes controlling ecosystem fertility, fungi are increasingly acknowledged as key drivers. However, our understanding of the rules behind fungal community assembly regarding the effect of soil fertility level remains limited. Using soil samples from typical tea plantations spanning c. 2167 km north-east to south-west across China, we investigated the assemblage complexity and assembly processes of 140 fungal communities along a soil fertility gradient. The community dissimilarities of total fungi and fungal functional guilds increased with increasing soil fertility index dissimilarity. The symbiotrophs were more sensitive to variations in soil fertility compared with pathotrophs and saprotrophs. Fungal networks were larger and showed higher connectivity as well as greater potential for inter-module connection in more fertile soils. Environmental factors had a slightly greater influence on fungal community composition than spatial factors. Species abundance fitted the Zipf-Mandelbrot distribution (niche-based mechanisms), which provided evidence for deterministic-based processes. Overall, the soil fungal communities in tea plantations responded in a deterministic manner to soil fertility, with high fertility correlated with complex fungal community assemblages. This study provides new insights that might contribute to predictions of fungal community complexity.

CmMYB8 encodes an R2R3 MYB transcription factor which represses lignin and flavonoid synthesis in chrysanthemum

R2R3-MYB transcription factors are important regulators of the growth and development of plants. Here, CmMYB8 a chrysanthemum gene encoding an R2R3-MYB transcription factor, was isolated and functionally characterized. The gene was transcribed throughout the plant, but most strongly in the stem. When CmMYB8 was over-expressed, a number of genes encoding components of lignin synthesis were down-regulated, and the plants' lignin content was reduced. The composition of the lignin in the transgenic plants was also altered, and its S/G ratio was reduced. A further consequence of the over-expression of CmMYB8 was to lessen the transcript abundance of key genes involved in flavonoid synthesis, resulting in a reduced accumulation of flavonoids. The indication is that the CmMYB8 protein participates in the negative regulation of both lignin and flavonoid synthesis.

Auto- and mutual-regulation between two CitERFs contribute to ethylene-induced citrus fruit degreening

Citrus fruit postharvest degreening is a critical stage in marketing, carried out by exposure to ethylene or ethephon. Genome-wide screening of the AP2/ERF superfamily indicated that a novel ERF-II (CitERF6) was shown to trans-activate the CitPPH promoter. Expression of CitERF6 is associated with both developmental and postharvest degreening in citrus fruit. Transient and stable over-expression of CitERF6 in Nicotiana tabacum leaves and 'Ponkan' fruit also results in rapid chlorophyll degradation. Auto- and mutual-regulation was also found between CitERF6 and the previously characterized CitERF13 using the dual-luciferase and yeast one-hybrid assays. Moreover, substitution of the 35S promoter for endogenous promoters showed that both pCitERF6::CitERF6 and pCitERF13::CitERF13 were effective in trans-activating their promoters or triggering chlorophyll degradation. It is proposed that ethylene is one of the triggers activating promoters of CitERF6 and CitERF13, and subsequent auto- and mutual-regulation between CitERF6 and CitERF13 might facilitate the effect of ethylene, leading to fruit degreening.

PpNAC187 Enhances Lignin Synthesis in 'Whangkeumbae' Pear (Pyrus pyrifolia) 'Hard-End' Fruit

A disorder in pears that is known as 'hard-end' fruit affects the appearance, edible quality, and market value of pear fruit. RNA-Seq was carried out on the calyx end of 'Whangkeumbae' pear fruit with and without the hard-end symptom to explore the mechanism underlying the formation of hard-end. The results indicated that the genes in the phenylpropanoid pathway affecting lignification were up-regulated in hard-end fruit. An analysis of differentially expressed genes (DEGs) identified three NAC transcription factors, and RT-qPCR analysis of PpNAC138, PpNAC186, and PpNAC187 confirmed that PpNAC187 gene expression was correlated with the hard-end disorder in pear fruit. A transient increase in PpNAC187 was observed in the calyx end of 'Whangkeumbae' fruit when they began to exhibit hard-end symptom. Concomitantly, the higher level of PpCCR and PpCOMT transcripts was observed, which are the key genes in lignin biosynthesis. Notably, lignin content in the stem and leaf tissues of transgenic tobacco overexpressing PpNAC187 was significantly higher than in the control plants that were transformed with an empty vector. Furthermore, transgenic tobacco overexpressing PpNAC187 had a larger number of xylem vessel elements. The results of this study confirmed that PpNAC187 functions in inducing lignification in pear fruit during the development of the hard-end disorder.

Methyl Jasmonate Promotes Phospholipid Remodeling and Jasmonic Acid Signaling To Alleviate Chilling Injury in Peach Fruit

Chilling injury (CI) is a physiological disorder induced by cold, which heavily limit crop production and postharvest preservation worldwide. Methyl jasmonate (MeJA) can alleviate CI in various fruit species, including peach; however, the underlying molecular mechanism is poorly understood. Here, changes in contents of phenolics, lipids, and jasmonic acid (JA) and gene expressions are compared between MeJA and control fruit. Exogenous MeJA inhibited expressions of PpPAL1, PpPPO1, and PpPOD1/2 but did not affect the phenolic content. Furthermore, MeJA fruit showed lower relative electrolyte leakage, indicating less membrane damage. Meanwhile, the enrichment of linoleic acid in the potential lipid biomarkers, especially phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol, coincided with lower expressions of PpFAD8.1 but higher PpLOX3.1 and JA content. In the JA signaling pathway, MeJA significantly upregulated expressions of PpMYC2.2 and PpCBF3 but downregulated PpMYC2.1. In conclusion, adjustments of fatty acids in phospholipids contribute to MeJA-induced alleviation of CI in peach fruit via induction of the JA-mediated C-repeat-binding factor pathway.

Overexpression of Pear (Pyrus pyrifolia) CAD2 in Tomato Affects Lignin Content

PpCAD2 was originally isolated from the ‘Wangkumbae’ pear (Pyrus pyrifolia Nakai), and it encodes for cinnamyl alcohol dehydrogenase (CAD), which is a key enzyme in the lignin biosynthesis pathway. In order to verify the function of PpCAD2, transgenic tomato (Solanum lycopersicum) ‘Micro-Tom’ plants were generated using over-expression constructs via the agrobacterium-mediated transformation method. The results showed that the PpCAD2 over-expression transgenic tomato plant had a strong growth vigor. Furthermore, these PpCAD2 over-expression transgenic tomato plants contained a higher lignin content and CAD enzymatic activity in the stem, leaf and fruit pericarp tissues, and formed a greater number of vessel elements in the stem and leaf vein, compared to wild type tomato plants. This study clearly indicated that overexpressing PpCAD2 increased the lignin deposition of transgenic tomato plants, and thus validated the function of PpCAD2 in lignin biosynthesis.

Label-free visualization of lignin deposition in loquats using complementary stimulated and spontaneous Raman microscopy

The lignification triggered by biotic or abiotic stresses hardens fruits and vegetables and eventually influences their consumer appeal. Extensive prior efforts have been made to unveil the underlying mechanism of flesh lignification, primarily focused on its physicochemical and molecular biological properties. Nevertheless, most of these studies used destroyed and homogenized bulk tissues as analytes; as a result, potentially valuable spatial information was lost. In this study, the deposition of lignin in loquat flesh during lignification was visualized from the tissue level to the single-cell level by combining the advantages of stimulated Raman scattering (SRS) and spontaneous Raman microscopy using label-free in situ molecular imaging. SRS has the advantages of being fast and providing large-area chemical imaging to reveal the spatial heterogeneity of lignin and cell wall polysaccharide distribution in loquat flesh. After 2 days of storage at 0 °C, increased lignins were observed by large-area SRS imaging. In addition, microscopic SRS images of the flesh cells indicated that the increased lignins were trapped in the cell corner (CC) and middle lamella (ML). Furthermore, the compositional and structural features of lignified cells (LCs), CC and ML of loquat flesh were investigated by spontaneous Raman microscopy, and the results showed that the LCs were a combination of lignin, cellulose, and hemicellulose, whereas CC and ML showed only deposited lignin and pectin without cross-linked cellulose and hemicellulose. This result further suggests that the lignins in the CC and ML regions of loquats were later synthesized alone during postharvest storage. This innovative combination of SRS and spontaneous Raman microscopy allows the label-free macroscale and fine chemical imaging of plant cell walls and will enhance our fundamental understanding of the structures and functions of the plant cell wall.

EjHAT1 Participates in Heat Alleviation of Loquat Fruit Lignification by Suppressing the Promoter Activity of Key Lignin Monomer Synthesis Gene EjCAD5

Texture attributes such as firmness and lignification are important for fruit quality. Lignification has been widely studied in model plants and energy crops, but fruit lignification has rarely been investigated, despite having an adverse effect on fruit quality and consumer preference. Chilling-induced loquat fruit lignification that occurs after harvest can be alleviated by heat treatment (HT) applied prior to low temperature storage. Enzyme activity assay showed that HT treatment could retard the low temperature-induced increase in cinnamyl alcohol dehydrogenase (CAD) activity. Transcript analysis and substrate activity assays of recombinant CAD proteins highlighted the key role of EjCAD5 in chilling-induced lignin biosynthesis. A novel homeobox-leucine zipper protein ( EjHAT1) was identified as a negative regulator of EjCAD5. Therefore, the effect of HT treatment on lignification may be partially due to the suppression of the EjCAD5 promoter activity by EjHAT1.

High-CO2/Hypoxia-Responsive Transcription Factors DkERF24 and DkWRKY1 Interact and Activate DkPDC2 Promoter

Identification and functional characterization of hypoxia-responsive transcription factors is important for understanding plant responses to natural anaerobic environments and during storage and transport of fresh horticultural products. In this study, yeast one-hybrid library screening using the persimmon (Diospyros kaki) pyruvate decarboxylase (DkPDC2) promoter identified three ethylene response factor (ERF) genes (DkERF23/DkERF24/DkERF25) and four WRKY transcription factor genes (DkWRKY/DdkWRKY5/DkWRKY6/DkWRKY7) that were differentially expressed in response to high CO2 (95%, with 4% N2 and 1% oxygen) and high N2 (99% N2 and 1% oxygen). Yeast one-hybrid assays and electrophoretic mobility shift assays indicated that DkERF23, DkERF24, DkERF25, DkWRKY6, and DkWRKY7 could directly bind to the DkPDC2 promoter. Dual-luciferase assays confirmed that these transcription factors were capable of transactivating the DkPDC2 promoter. DkERF24 and DkWRKY1 in combination synergistically transactivated the DkPDC2 promoter, and yeast two-hybrid and bimolecular fluorescence complementation assays confirmed protein-protein interaction between DkERF24 and DkWRKY1. Transient overexpression of DkERF24 and DkWRKY1 separately and in combination in persimmon fruit discs was effective in maintaining insolubilization of tannins, concomitantly with the accumulation of DkPDC2 transcripts. Studies with Arabidopsis (Arabidopsis thaliana) homologs AtERF1 and AtWRKY53 indicated that similar protein-protein interactions and synergistic regulatory effects also occur with the DkPDC2 promoter. We propose that an ERF and WRKY transcription factor complex contributes to responses to hypoxia in both persimmon fruit and Arabidopsis, and the possibility that this is a general plant response requires further investigation.

Transcriptome analysis provides insights into the regulation of metabolic processes during postharvest cold storage of loquat (Eriobotrya japonica) fruit

Loquat (Eriobotrya japonica) fruit accumulates lignin during postharvest storage under chilling conditions (0 °C), while low-temperature conditioning (LTC; 5 °C for 6 days followed by transfer to 0 °C) or heat treatment (HT; 40 °C for 4 h followed by transfer to 0 °C) can alleviate lignification. Here we compared transcriptome profiles of loquat fruit samples under LTC or HT to those stored at 0 °C at five time points from day 1 to day 8 after treatment. High-throughput transcriptome sequences were de novo assembled into 53,319 unique transcripts with an N50 length of 1306 bp. A total of 2235 differentially expressed genes were identified in LTC, and 1020 were identified in HT compared to 0 °C. Key genes in the lignin biosynthetic pathway, including EjPAL2, EjCAD1, EjCAD3, 4CL, COMT, and HCT, were responsive to LTC or HT treatment, but they showed different expression patterns during the treatments, indicating that different structural genes could regulate lignification at different treatment stages. Coexpression network analysis showed that these candidate biosynthetic genes were associated with a number of transcription factors, including those belonging to the AP2, MYB, and NAC families. Gene ontology (GO) enrichment analysis of differentially expressed genes indicated that biological processes such as stress responses, cell wall and lignin metabolism, hormone metabolism, and metal ion transport were significantly affected under LTC or HT treatment when compared to 0 °C. Our analyses provide insights into transcriptome responses to postharvest treatments in loquat fruit.

Citrus sinensis MYB Transcription Factor CsMYB85 Induce Fruit Juice Sac Lignification Through Interaction With Other CsMYB Transcription Factors

Varieties of Citrus are commercially important fruits that are cultivated worldwide and are valued for being highly nutritious and having an appealing flavor. Lignification of citrus fruit juice sacs is a serious physiological disorder that occurs during postharvest storage, for which the underlying transcriptional regulatory mechanisms remain unclear. In this study, we identified and isolated a candidate MYB transcription factor, CsMYB85, that is involved in the regulation of lignin biosynthesis in Citrus sinensis, which has homologs in Arabidopsis and other plants. We found that during juice sac lignification, CsMYB85 expression levels increase significantly, and therefore, suspected that this gene may control lignin biosynthesis during the lignification process. Our results indicated that CsMYB85 binds the CsMYB330 promoter, regulates its expression, and interacts with CsMYB308 in transgenic yeast and tobacco. A transient expression assay indicated that Cs4CL1 expression levels and lignin content significantly increased in fruit juice sacs overexpressing CsMYB85. At4CL1 expression levels and lignin content were also significantly increased in Arabidopsis overexpressing CsMYB85. We accordingly present convincing evidence for the participation of the CsMYB85 transcription factor in fruit juice sac lignification, and thereby provide new insights into the transcriptional regulation of this process in citrus fruits.

Comparative Transcriptome Profiling in a Segregating Peach Population with Contrasting Juiciness Phenotypes

Cold storage of fruit is one of the methods most commonly employed to extend the postharvest lifespan of peaches ( Prunus persica (L.) Batsch). However, fruit quality in this species is affected negatively by mealiness, a physiological disorder triggered by chilling injury after long periods of exposure to low temperatures during storage and manifested mainly as a lack of juiciness, which ultimately modifies the organoleptic properties of peach fruit. The aim of this study was to identify molecular components and metabolic processes underlying mealiness in susceptible and nonsusceptible segregants. Transcriptome and qRT-PCR profiling were applied to individuals with contrasting juiciness phenotypes in a segregating F₂ population. Our results suggest that mealiness is a multiscale phenomenon, because juicy and mealy fruit display distinctive reprogramming processes affecting translational machinery and lipid, sugar, and oxidative metabolism. The candidate genes identified may be useful tools for further crop improvement.

Metabolic Dynamics During Loquat Fruit Ripening and Postharvest Technologies

Loquat is an important fruit widely cultivated worldwide with high commercial value. During loquat fruit development, ripening, and storage, many important metabolites undergo dramatic changes, resulting in accumulation of a diverse mixture of nutrients. Given the value of loquat fruit, significant progresses have been achieved in understanding the metabolic changes during fruit ripening and storage, as well as postharvest technologies applied in loquat fruit in recent years. The objective of the present review is to summarize currently available knowledge and provide new references for improving loquat fruit quality.

De Novo Analysis Reveals Transcriptomic Responses in Eriobotrya japonica Fruits during Postharvest Cold Storage

Cold storage is the primary preservation method of postharvest loquat fruits. However, cold storage also results in many chilling injury physiological disorders called lignification, which decreases the quality and economic value of the fruits. Few studies to date have focused on the transcriptomic responses associated with lignification except lignin synthesis pathways. This study aimed to explore the changes of loquat transcriptome during long-term cold storage. Our results showed that the gene expression patterns were differed among the five stages. The differentially expressed genes (DEGs) in response to cold storage were more intense and complex in earlier stage. The membrane-related genes preferentially responded to low temperature and were followed by intracellular-located genes. The cold-induced pathways were mainly concerned with signal transduction and secondary metabolism (i.e., lignin, pectin, cellulose, terpenoid, carotenoid, steroid) in the first three stages and were chiefly related to primary metabolism in the later two stages, especially energy metabolism. Further investigation suggested that 503 protein kinases, 106 protein phosphatases, and 40 Ca2+ signal components were involved in the cold signal transduction of postharvest loquat fruits. We predicted a pathway including 649 encoding genes of 49 enzymes, which displayed the metabolisms of major sugars and polysaccharides in cold-stored loquat fruits. The coordinated expression patterns of these genes might contribute to the changes of saccharides in the pathway. These results provide new insight into the transcriptomic changes of postharvest loquat fruits in response to cold storage environment, which may be helpful for improving the postharvest life of loquat in the future.

An ETHYLENE RESPONSE FACTOR-MYB Transcription Complex Regulates Furaneol Biosynthesis by Activating QUINONE OXIDOREDUCTASE Expression in Strawberry

4-Hydroxy-2,5-dimethyl-3(2H)-furanone is a major contributor to the aroma of strawberry (Fragaria × ananassa) fruit, and the last step in its biosynthesis is catalyzed by strawberry quinone oxidoreductase (FaQR). Here, an ethylene response factor (FaERF#9) was characterized as a positive regulator of the FaQR promoter. Linear regression analysis indicated that FaERF#9 transcript levels were correlated significantly with both FaQR transcripts and furanone content in different strawberry cultivars. Transient overexpression of FaERF#9 in strawberry fruit significantly increased FaQR expression and furaneol production. Yeast one-hybrid assays, however, indicated that FaERF#9 by itself did not bind to the FaQR promoter. An MYB transcription factor (FaMYB98) identified in yeast one-hybrid screening of the strawberry cDNA library was capable of both binding to the promoter and activating the transcription of FaQR by ∼5.6-fold. Yeast two-hybrid assay and bimolecular fluorescence complementation confirmed a direct protein-protein interaction between FaERF#9 and FaMYB98, and in combination, they activated the FaQR promoter 14-fold in transactivation assays. These results indicate that an ERF-MYB complex containing FaERF#9 and FaMYB98 activates the FaQR promoter and up-regulates 4-hydroxy-2,5-dimethyl-3(2H)-furanone biosynthesis in strawberry.