Ethephon induces coordinated ripening acceleration and divergent coloration responses in fig (Ficus carica L.) flowers and receptacles

ERF100 regulated by ERF28 and NOR controls pectate lyase 7, modulating fig (Ficus carica L.) fruit softening

The mechanism regulating fruit textural changes has not been fully elucidated. Transcription factor FcERF100 showed rapid transcription repression during drastic texture loss in fig (Ficus carica L.) fruit ripening. Transient overexpression of FcERF100 delayed fig fruit softening and significantly decreased the transcript abundance of a key cell wall-modifying pectate lyase gene, FcPL7. Yeast one-hybrid (Y1H) assay, chromatin immunoprecipitation-qPCR, electrophoretic mobility shift assay (EMSA), and dual-luciferase reporter assay revealed that FcERF100 represses FcPL7 transcription by direct promoter binding via GCC-box and DRE/CRT elements. Stable transgenic fig lines further verified FcERF100's inhibitory effect on FcPL7 expression. We detected FcERF28 as an upstream element of FcERF100 by Y1H and EMSA, revealing its binding to, and activation of FcERF100 by dual-luciferase assay. Taken together, the FcERF28-FcERF100 transcriptional cascade serves as a synergistic flow-limiting valve for FcPL7 abundance. We then identified a NAC transcription factor, FcNOR, using FcERF100 as the bait by yeast two-hybrid screening. FcNOR silencing retarded fig fruit softening, with decreased FcPL7 transcript and pectate lyase activity. FcNOR interacted with FcERF100 to form a protein complex, attenuating FcERF100's transcriptional repression of FcPL7. Moreover, FcNOR bound directly to the promoter of FcERF100 and inhibited its transcription. In addition, ethylene treatment upregulated FcNOR and FcPL7 expression and downregulated FcERF28 and FcERF100 expression. Our findings reveal a novel FcERF100-centered regulatory complex and resolve how the complex achieves the necessary cell wall modification during an early stage of fruit growth and implements drastic softening at fruit ripening by modulating component proportions.

The Effect of Ethephon on Ethylene and Chlorophyll in Zoysia japonica Leaves

Zoysia japonica (Zoysia japonica Steud.) is a kind of warm-season turfgrass with many excellent characteristics. However, the shorter green period and longer dormancy caused by cold stress in late autumn and winter are the most limiting factors affecting its application. A previous transcriptome analysis revealed that ethephon regulated genes in chlorophyll metabolism in Zoysia japonica under cold stress. Further experimental data are necessary to understand the effect and underlying mechanism of ethephon in regulating the cold tolerance of Zoysia japonica. The aim of this study was to evaluate the effects of ethephon by measuring the enzyme activity, intermediates content, and gene expression related to ethylene biosynthesis, signaling, and chlorophyll metabolism. In addition, the ethylene production rate, chlorophyll content, and chlorophyll a/b ratio were analyzed. The results showed that ethephon application in a proper concentration inhibited endogenous ethylene biosynthesis, but eventually promoted the ethylene production rate due to its ethylene-releasing nature. Ethephon could promote chlorophyll content and improve plant growth in Zoysia japonica under cold-stressed conditions. In conclusion, ethephon plays a positive role in releasing ethylene and maintaining the chlorophyll content in Zoysia japonica both under non-stressed and cold-stressed conditions.

Independent flavonoid and anthocyanin biosynthesis in the flesh of a red-fleshed table grape revealed by metabolome and transcriptome co-analysis

BACKGROUND

Red flesh is a desired fruit trait, but the regulation of red flesh formation in grape is not well understood. 'Mio Red' is a seedless table grape variety with light-red flesh and blue-purple skin. The skin color develops at veraison whereas the flesh color develops at a later stage of berry development. The flesh and skin flavonoid metabolomes and transcriptomes were analyzed.

RESULTS

A total of 161 flavonoids were identified, including 16 anthocyanins. A total of 66 flavonoids were found at significantly different levels in the flesh and skin (fold change ≥ 2 or ≤ 0.5, variable importance in projection (VIP) ≥ 1). The main anthocyanins in the flesh were pelargonidin and peonidin, and in the skin were peonidin, delphinidin, and petunidin. Transcriptome comparison revealed 57 differentially expressed structural genes of the flavonoid-metabolism pathway (log₂fold change ≥ 1, FDR < 0.05, FPKM ≥ 1). Two differentially expressed anthocyanin synthase (ANS) genes were annotated, ANS2 (Vitvi02g00435) with high expression in flesh and ANS1 (Vitvi11g00565) in skin, respectively. One dihydro flavonol 4-reductase (DFR, Vitvi18g00988) gene was differentially expressed although high in both skin and flesh. Screened and correlation analysis of 12 ERF, 9 MYB and 3 bHLH genes. The Y1H and dual luciferase assays showed that MYBA1 highly activates the ANS2 promoter in flesh and that ERFCBF6 was an inhibitory, EFR23 and bHLH93 may activate the DFR gene. These genes may be involved in the regulation of berry flesh color.

CONCLUSIONS

Our study revealed that anthocyanin biosynthesis in grape flesh is independent of that in the skin. Differentially expressed ANS, MYB and ERF transcription factors provide new clues for the future breeding of table grapes that will provide the health benefits as red wine.

Polygalacturonase gene family analysis identifies FcPG12 as a key player in fig (Ficus carica L.) fruit softening

BACKGROUND

The fig (Ficus carica L.) tree has high economic value. However, its fruit have a short shelf life due to rapid softening. Polygalacturonases (PGs) are essential hydrolases, responsible for the pectin degradation that plays a key role in fruit softening. However, fig PG genes and their regulators have not yet been characterized.

RESULTS

In this study, 43 FcPGs were identified in the fig genome. They were non-uniformly distributed on 13 chromosomes, and tandem repeat PG gene clusters were found on chromosomes 4 and 5. Ka/Ks calculation and collinear analysis indicated negative selection as the main driver of FcPG family expansion. Fourteen FcPGs were found expressed in fig fruit with FPKM values > 10, of which seven were positively correlated, and three, negatively correlated with fruit softening. Eleven FcPGs were upregulated and two downregulated in response to ethephon treatment. FcPG12, a member of the tandem repeat cluster on chromosome 4, was selected for further analyses due to its sharp increment in transcript abundance during fruit softening and its response to ethephon treatment. Transient overexpression of FcPG12 led to decreased fig fruit firmness and increased PG enzyme activity in the tissue. Two ethylene response factor (ERF)-binding GCC-box sites were found on the FcPG12 promoter. Yeast one-hybrid and dual luciferase assays showed that FcERF5 binds directly to the FcPG12 promoter and upregulates its expression. Transient overexpression of FcERF5 upregulated FcPG12 expression, thereby increasing PG activity and fruit softening.

CONCLUSIONS

Our study identified FcPG12 as a key PG gene in fig fruit softening, and its direct positive regulation by FcERF5. The results provide new information on the molecular regulation of fig fruit softening.

Genome-wide in silico identification of glutathione S-transferase (GST) gene family members in fig (Ficus carica L.) and expression characteristics during fruit color development

Glutathione S-transferase (GSTs), a large and diverse group of multi-functional enzymes (EC 2.5.1.18), are associated with cellular detoxification, various biotic and abiotic stress responses, as well as secondary metabolites transportation. Here, 53 members of the FcGST gene family were screened from the genome database of fig (Ficus carica), which were further classified into five subfamilies, and the tau and phi were the major subfamilies. These genes were unevenly distributed over all the 13 chromosomes, and 12 tandem and one segmental duplication may contribute to this family expansion. Syntenic analysis revealed that FcGST shared closer genetic evolutionary origin relationship with species from the Ficus genus of the Moraceae family, such as F. microcarpa and F. hispida. The FcGST members of the same subfamily shared similar gene structure and motif distribution. The α helices were the chief structure element in predicted secondary and tertiary structure of FcGSTs proteins. GO and KEGG indicated that FcGSTs play multiple roles in glutathione metabolism and stress reactions as well as flavonoid metabolism. Predictive promoter analysis indicated that FcGSTs gene may be responsive to light, hormone, stress stimulation, development signaling, and regulated by MYB or WRKY. RNA-seq analysis showed that several FcGSTs that mainly expressed in the female flower tissue and peel during 'Purple-Peel' fig fruit development. Compared with 'Green Peel', FcGSTF1, and FcGSTU5/6/7 exhibited high expression abundance in the mature fruit purple peel. Additionally, results of phylogenetic sequences analysis, multiple sequences alignment, and anthocyanin content together showed that the expression changes of FcGSTF1, and FcGSTU5/6/7 may play crucial roles in fruit peel color alteration during fruit ripening. Our study provides a comprehensive overview of the GST gene family in fig, thus facilitating the further clarification of the molecular function and breeding utilization.

AP2/ERF genes associated with superfast fig (Ficus carica L.) fruit ripening

Fig fruits have significant health value and are culturally important. Under suitable climatic conditions, fig fruits undergo a superfast ripening process, nearly doubling in size, weight, and sugar content over three days in parallel with a sharp decrease in firmness. In this study, 119 FcAP2/ERF genes were identified in the fig genome, namely 95 ERFs, 20 AP2s, three RAVs, and one soloist. Most of the ERF subfamily members (76) contained no introns, whereas the majority of the AP2 subfamily members had at least two introns each. Three previously published transcriptome datasets were mined to discover expression patterns, encompassing the fruit peel and flesh of the 'Purple Peel' cultivar at six developmental stages; the fruit receptacle and flesh of the 'Brown Turkey' cultivar after ethephon treatment; and the receptacle and flesh of parthenocarpic and pollinated fruits of the 'Brown Turkey' cultivar. Eighty-three FcAP2/ERFs (68 ERFs, 13 AP2s, one RAV, and one soloist) were expressed in the combined transcriptome dataset. Most FcAP2/ERFs were significantly downregulated (|log₂(fold change) | ≥ 1 and p-adjust < 0.05) during both normal fruit development and ethephon-induced accelerated ripening, suggesting a repressive role of these genes in fruit ripening. Five significantly downregulated ERFs also had repression domains in the C-terminal. Seven FcAP2/ERFs were identified as differentially expressed during ripening in all three transcriptome datasets. These genes were strong candidates for future functional genetic studies to elucidate the major FcAP2/ERF regulators of the superfast fig fruit ripening process.

Analysis of the Transcriptional Dynamics of Regulatory Genes During Peanut Pod Development Caused by Darkness and Mechanical Stress

Peanut is an oil crop with important economic value that is widely cultivated around the world. It blooms on the ground but bears fruit underground. When the peg penetrates the ground, it enters a dark environment, is subjected to mechanical stress from the soil, and develops into a normal pod. When a newly developed pod emerges from the soil, it turns green and stops growing. It has been reported that both darkness and mechanical stress are necessary for normal pod development. In this study, we investigated changes in gene expression during the reverse process of peg penetration: developmental arrest caused by pod (Pattee 3 pods) excavation. Bagging the aerial pods was used to simulate loss of mechanical pressure, while direct exposure of the aerial pods was used to simulate loss of both mechanical pressure and darkness. After the loss of mechanical stress and darkness, the DEGs were significantly enriched in photosynthesis, photosynthesis-antenna proteins, plant-pathogen interaction, DNA replication, and circadian rhythm pathways. The DNA replication pathway was enriched by down-regulated genes, and the other four pathways were enriched by upregulated genes. Upregulated genes were also significantly enriched in protein ubiquitination and calmodulin-related genes, highlighting the important role of ubiquitination and calcium signaling in pod development. Further analysis of DEGs showed that phytochrome A (Phy A), auxin response factor 9 (IAA9), and mechanosensitive ion channel protein played important roles in geocarpy. The expression of these two genes increased in subterranean pods but decreased in aerial pods. Based on a large number of chloroplast-related genes, calmodulin, kinases, and ubiquitin-related proteins identified in this study, we propose two possible signal transduction pathways involved in peanut geocarpy, namely, one begins in chloroplasts and signals down through phosphorylation, and the other begins during abiotic stress and signals down through calcium signaling, phosphorylation, and ubiquitination. Our study provides valuable information about putative regulatory genes for peanut pod development and contributes to a better understanding of the biological phenomenon of geocarpy.

Exogenous Ethylene Promotes Peel Color Transformation by Regulating the Degradation of Chlorophyll and Synthesis of Anthocyanin in Postharvest Mango Fruit

Due to geographical location and climatic factors, postharvest storage and preservation of tropical fruits and vegetables are still facing huge challenges. Ethephon (ETH) is widely used as an ethylene donor to achieve the commercial color and flavor of climacteric fruits. However, the effect of ETH on fruit coloration was affected by many factors, such as fruit species, plant hormones, and storage conditions. In this study, the main mango variety “Guifei” in Hainan, China, was used to study the effects of different concentrations of ETH on fruit ripening and coloration during storage at 25°C. Results showed that postharvest treatment with ETH (300, 500, and 900 mg·L⁻¹) enhanced the activities of ACS and ACO, stimulated the release of endogenous ethylene, and accelerated fruit softening and color transformation. Compared with control, ETH treatment not only accelerated the breakdown of chlorophyll with higher activities of Chlase and MDCase but also induced the synthesis of carotenoid and anthocyanin with higher activities of PAL, CHI, DFR, and UFGT. Moreover, the changes in DFR and UFGT activities coincided with the increase in ETH concentration. Further, correlation analysis showed that the production of endogenous ethylene induced by ETH was significantly negatively correlated with firmness and chlorophyll content, whereas positively correlated with MDA content and anthocyanin content. This study suggests that the positive effect of ETH on “Guifei” mango color transformation is concentration-dependent within a certain concentration range. Anthocyanin is the main pigment for the red formation of “Guifei” mango, and DFR and UFGT may play critical roles in anthocyanin synthesis. ETH promoted the red coloration by promoting the release of endogenous ethylene and enhancing the activities of anthocyanin synthesis enzymes.

Genome-wide analysis of JAZ family genes expression patterns during fig (Ficus carica L.) fruit development and in response to hormone treatment

BACKGROUND

Jasmonate-ZIM domain (JAZ) repressors negatively regulate signal transduction of jasmonates, which regulate plant development and immunity. However, no comprehensive analysis of the JAZ gene family members has been done in the common fig (Ficus carica L.) during fruit development and hormonal treatment.

RESULTS

In this study, 10 non-redundant fig JAZ family genes (FcJAZs) distributed on 7 chromosomes were identified in the fig genome. Phylogenetic and structural analysis showed that FcJAZ genes can be grouped into 5 classes. All the classes contained relatively complete TIFY and Jas domains. Yeast two hybrid (Y2H) results showed that all FcJAZs proteins may interact with the identified transcription factor, FcMYC2. Tissue-specific expression analysis showed that FcJAZs were highly expressed in the female flowers and roots. Expression patterns of FcJAZs during the fruit development were analyzed by RNA-Seq and qRT-PCR. The findings showed that, most FcJAZs were significantly downregulated from stage 3 to 5 in the female flower, whereas downregulation of these genes was observed in the fruit peel from stage 4 to 5. Weighted-gene co-expression network analysis (WGCNA) showed the expression pattern of FcJAZs was correlated with hormone signal transduction and plant-pathogen interaction. Putative cis-elements analysis of FcJAZs and expression patterns of FcJAZs which respond to hormone treatments revealed that FcJAZs may regulate fig fruit development by modulating the effect of ethylene or gibberellin.

CONCLUSIONS

This study provides a comprehensive analysis of the FcJAZ family members and provides information on FcJAZs contributions and their role in regulating the common fig fruit development.

APETALA2/ethylene responsive factor in fruit ripening: Roles, interactions and expression regulation

Insects and animals are attracted to, and feed on ripe fruit, thereby promoting seed dispersal. As a vital vitamin and nutrient source, fruit make up an indispensable and enjoyable component of the human diet. Fruit ripening involves a series of physiological and biochemical changes in, among others, pigmentation, chlorophyll (Chl) degradation, texture, sugar accumulation, and flavor. Growing evidence indicates that the coordinated and ordered trait changes during fruit ripening depend on a complex regulatory network consisting of transcription factors, co-regulators, hormonal signals, and epigenetic modifications. As one of the predominant transcription factor families in plants and a downstream component of ethylene signaling, more and more studies are showing that APETALA2/ethylene responsive factor (AP2/ERF) family transcription factors act as critical regulators in fruit ripening. In this review, we focus on the regulatory mechanisms of AP2/ERFs in fruit ripening, and in particular the recent results on their target genes and co-regulators. We summarize and discuss the role of AP2/ERFs in the formation of key fruit-ripening attributes, the enactment of their regulatory mechanisms by interaction with other proteins, their role in the orchestration of phytohormone-signaling networks, and the epigenetic modifications associated with their gene expression. Our aim is to provide a multidimensional perspective on the regulatory mechanisms of AP2/ERFs in fruit ripening, and a reference for understanding and furthering research on the roles of AP2/ERF in fruit ripening.

AGAMOUS Gene as a New Sex-Identification Marker in Fig (Ficus carica L.) Is More Efficient Than RAN1

Fig is an ancient gynodioecious fruit tree with females for commercial fruit production and hermaphrodites (males) sometimes used as pollen providers. An early sex-identification method would improve breeding efficiency. Three AGAMOUS (AG) genes were recruited from the Ficus carica genome using AG sequences from Ficus microcarpa and Ficus hispida. FcAG was 5230 bp in length, with 7 exons and 6 introns, and a 744-bp coding sequence. The gene was present in both female and male fig genomes, with a 15-bp deletion in the 7th exon. The other two AG genes (FcAG2-Gall_Stamen and FcAG3-Gall_Stamen) were male-specific, without the 15-bp deletion (759-bp coding sequence), and were only expressed in the gall and stamen of the male fig fruit. Using the deletion as the forward primer (AG-Marker), male plants were very efficiently identified by the presence of a 146-bp PCR product. The previously reported fig male and female polymorphism gene RESPONSIVE-TO-ANTAGONIST1 (RAN1) was also cloned and compared between male and female plants. Fifteen SNPs were found in the 3015-bp protein-coding sequence. Among them, 12 SNPs were identified as having sex-differentiating capacity by checking the sequences of 27 known male and 24 known female cultivars. A RAN1-Marker of 608 bp, including 6 SNPs, was designed, and a PCR and sequencing-based method was verified with 352 fig seedlings from two hybrid populations. Our results confirmed that the newly established AG-Marker is as accurate as the RAN1-Marker, and provide new clues to understanding Ficus sex determination.

Transcriptional and Hormonal Responses in Ethephon-Induced Promotion of Femaleness in Pumpkin

The number and proportion of female flowers per plant can directly influence the yield and economic benefits of cucurbit crops. Ethephon is often used to induce female flowers in cucurbits. However, the mechanism through which it affects floral sex differentiation in pumpkin is unknown. We found that the application of ethephon on shoot apical meristem of pumpkin at seedling stage significantly increased the number of female flowers and expedited the appearance of the first female flower. These effects were further investigated by transcriptome and hormone analyses of plants sprayed with ethephon. A total of 647 differentially expressed genes (DEGs) were identified, among which 522 were upregulated and 125 were downregulated. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analysis indicated that these genes were mainly enriched in plant hormone signal transduction and 1-aminocyclopropane-1-carboxylate oxidase (ACO). The results suggests that ethylene is a trigger for multiple hormone signaling, with approximately 4.2% of the identified DEGs involved in ethylene synthesis and multiple hormone signaling. Moreover, ethephon significantly reduced the levels of jasmonic acid (JA), jasmonoyl-L-isoleucine (JA-ILE), and para-topolin riboside (pTR) but increased the levels of 3-indoleacetamide (IAM). Although the level of 1-aminocyclopropanecarboxylic acid was not changed, the expression of ACO genes, which code for the enzyme catalyzing the key rate-limiting step in ethylene production, was significantly upregulated after ethephon treatment. The results indicate that the ethephon affects the transcription of ethylene synthesis and signaling genes, and other hormone signaling genes, especially auxin responsive genes, and modulates the levels of auxin, jasmonic acid, and cytokinin (CK), which may together contribute to femaleness.

Papain-Like Cysteine Protease Gene Family in Fig (Ficus carica L.): Genome-Wide Analysis and Expression Patterns

The papain-like cysteine proteases (PLCPs) are the most abundant family of cysteine proteases in plants, with essential roles in biotic/abiotic stress responses, growth and senescence. Papain, bromelain and ficin are widely used in food, medicine and other industries. In this study, 31 PLCP genes (FcPCLPs) were identified in the fig (Ficus carica L.) genome by HMM search and manual screening, and assigned to one of nine subfamilies based on gene structure and conserved motifs. SAG12 and RD21 were the largest subfamilies with 10 and 7 members, respectively. The FcPCLPs ranged from 1,128 to 5,075 bp in length, containing 1-10 introns, and the coding sequence ranged from 624 to 1,518 bp, encoding 207-505 amino acids. Subcellular localization analysis indicated that 24, 2, and 5 PLCP proteins were targeted to the lysosome/vacuole, cytoplasm and extracellular matrix, respectively. Promoter (2,000 bp upstream) analysis of FcPLCPs revealed a high number of plant hormone and low temperature response elements. RNA-seq revealed differential expression of 17 FcPLCPs in the inflorescence and receptacle, and RD21 subfamily members were the major PLCPs expressed in the fruit; 16 and 5 FcPLCPs responded significantly to ethylene and light, respectively. Proteome analyses revealed 18 and 5 PLCPs in the fruit cell soluble proteome and fruit latex, respectively. Ficins were the major PLCP in fig fruit, with decreased abundance in inflorescences, but increased abundance in receptacles of commercial-ripe fruit. FcRD21B/C and FcALP1 were aligned as the genes encoding the main ficin isoforms. Our study provides valuable multi-omics information on the FcPLCP family and lays the foundation for further functional studies.