Four HD-ZIPs are involved in banana fruit ripening by activating the transcription of ethylene biosynthetic and cell wall-modifying genes

Exploring Genomic Regions Associated with Fruit Traits in Pepper: Insights from Multiple GWAS Models

This study utilized 303 pepper accessions from diverse Capsicum species to explore fruit traits, including length, width, wall thickness, and weight. Descriptive statistics revealed a mean fruit length of 66.19 mm, width of 23.48 mm, wall thickness of 1.89 mm, and weight of 15.29 g, with significant variability, particularly in fruit weight. Correlation analysis demonstrated strong positive relationships between fruit width, weight, and fruit wall thickness (r = 0.89 and r = 0.86, respectively), while fruit length showed weaker correlations with these traits. Analysis of fruit positions revealed that the majority of accessions had a pendent fruit position (156), followed by erect (85) and intermediate (8). In terms of fruit shape, triangular and narrow triangular shapes were the most common, observed in 102 and 98 accessions, respectively. Genome-wide association studies (GWAS) identified significant single nucleotide polymorphisms (SNPs) associated with fruit traits across four models (Blink, FarmCPU, MLM, MLMM). The number of significantly associated SNPs were as follows: fruit length (89), fruit width (55), fruit weight (63), fruit wall thickness (48), fruit shape (151), and fruit position (51). Several genes were also identified where the SNPs are located or adjacent to, providing candidate genes for further exploration of the genetic basis of fruit morphology. Notably, genes such as E3 ubiquitin-protein ligase RGLG1 (associated with fruit width), Homeobox-leucine zipper protein HDG11 (involved in fruit width), Auxin response factor 23 (linked to fruit shape), and ATP-dependent zinc metalloprotease FtsH (related to fruit weight) were identified. These findings enhance our understanding of the genetic basis of fruit morphology in Capsicum, offering valuable insights for breeding and agricultural practices.

Transcriptome analysis reveals regulatory mechanism of postharvest softening in kiwiberry

BACKGROUND

Kiwiberry is an emerging edible fruit with market potential owing to its advantages of small size, thin and hairless skin, and sweet taste. However, kiwiberry is highly susceptible to softening after harvest, which poses a challenge for storage and transport. To reveal the underlying cause of kiwiberry softening, it is essential to investigate the characteristics of postharvest fruit and the molecular mechanisms that affect changes in fruit firmness.

RESULTS

Morphological observations and analysis of physical parameters showed that the skin of kiwiberry did not change markedly from the 1st to the 7th day after harvest, while the colour of the inner pericarp gradually turned yellow. By the 9th day of room temperature storage, the kiwiberries began to rot. The hardness decreased rapidly from the 1st to the 5th day postharvest, reaching the low level on the 5th day. The starch and pectin contents of kiwiberry showed a downward trend with increasing storage time. Transcriptome sequencing and weighted gene co-expression network analysis identified 29 key genes associated with the changes in the hardness of kiwiberry after harvest. Gene Ontology enrichment analysis indicated that these 29 genes are mainly involved in pectin metabolism, starch synthesis, starch decomposition, and starch metabolism. In addition, three transcription factors, AGL31, HAT14, and ALC, were identified to be strongly positively correlated with the 29 genes that affect the hardness changes of kiwiberry after harvest, and 28 of the 29 key genes were predicted to be regulated by HAT14.

CONCLUSIONS

These results reveal the changes in morphological characteristics and physiological indicators during the postharvest ripening and softening of kiwiberry stored under room temperature conditions. Transcriptome analysis identified 29 key genes and three transcription factors that affect the firmness changes of postharvest kiwiberry. The results of this study thus provide insight into the transcriptional regulatory mechanism of kiwiberry softening during storage to improve the postharvest quality.

Passion fruit HD-ZIP genes: Characterization, expression variance, and overexpression PeHB31 enhanced drought tolerance via lignin pathway

The HD-ZIP (homeodomain-leucine zipper) genes hold significant importance in transcriptional regulation, especially in plant development and responses to abiotic stresses. However, a comprehensive study targeting HD-ZIP family members in passion fruit has been absent. In our current research, 34 HD-ZIP family members (PeHBs) were identified by bioinformatics analysis. Transcriptome analysis revealed that PeHBs exhibited distinct expression patterns when subjected to the four different abiotic stresses, and significant differential expression of PeHBs was also found among the three developmental stages of the fruit and between the purple and yellow genotype passion fruit leaves. An integrated metabolome and transcriptome analysis further revealed that the HD-ZIP III class gene PeHB31 (homologous to ATHB8), was co-upexpressed with lignans in yellow fruit P. edulis (commonly used as a resistance rootstock) when compared to purple fruit P. edulis. The transformation of Arabidopsis and yeast with the PeHB31 gene showed an enhancement in their capacity to withstand drought conditions. Notably, the transgenic Arabidopsis plants exhibited an increase in lignin content within the vascular tissues of their stems. This research lays the groundwork for future studies on the control mechanisms of lignin biosynthesis by HD-ZIP genes (especially HD-ZIP classes III and I) involved in drought tolerance.

Genome-wide characterization and expression analysis of the HD-Zip II gene family in response to drought and GA3 stresses in Nicotiana tabacum

BACKGROUND

Homeodomain-leucine ZIPper (HD-ZIP) transcription factors play crucial roles in plant growth, development, and stress responses. The HD-ZIP family is categorised into four groups (HD-ZIP I-IV). While extensive genome-wide studies have been conducted on the HD-ZIP I, III, and IV subfamily in Nicotiana tabacum (tobacco), comprehensive reports on the HD-ZIP II subfamily genes are limited.

METHODS

Bioinformatics resources and tools were utilised to analyse molecular characteristics, phylogenetic homology, and protein interactions. Expression pattern analyses in various tissues and the relative expression of NtHD-ZIP II genes under drought and GA3 treatment were assessed by qRT-PCR.

RESULTS

In this study, 24 HD-ZIP II members were systematically identified and categorised into seven independent clades through phylogenetic analysis involving tobacco and other plant species. We found that 19 NtHD-ZIP II genes exhibited tissue-specific expression. The transcripts of NtHD-ZIPII3, 4, 14, 23, 24 were notably induced under the drought treatments, while those of NtHD-ZIPII7, 11, 12, 20 were suppressed. Furthermore, NtHD-ZIPII15 transcripts decreased following GA3 treatment, whereas the transcripts of NtHD-ZIPII7, 8, 11, 12 were induced after GA3 treatment. Notably, an increase in trichomes was observed in tobacco leaves treated with GA3 and subjected to drought.

CONCLUSIONS

The expression levels of some HD-ZIP II genes were altered, and an increase in glandular trichomes was induced under GA3 and drought treatments in tobacco. Overall, our findings provide insights into the expression patterns of NtHD-ZIP II genes and will facilitate their functional characterisation in future studies.

MaBEL1 regulates banana fruit ripening by activating cell wall and starch degradation-related genes

Banana is a typical subtropical fruit, sensitive to chilling injuries and prone to softening disorder. However, the underlying regulatory mechanisms of the softening disorder caused by cold stress remain obscure. Herein, we found that BEL1-LIKE HOMEODOMAIN transcription factor 1 (MaBEL1) and its associated proteins regulate the fruit softening and ripening process. The transcript and protein levels of MaBEL1 were up-regulated with fruit ripening but severely repressed by the chilling stress. Moreover, the MaBEL1 protein interacted directly with the promoters of the cell wall and starch degradation-related genes, such as MaAMY3, MaXYL32, and MaEXP-A8. The transient overexpression of MaBEL1 alleviated fruit chilling injury and ripening disorder caused by cold stress and promoted fruit softening and ripening of "Fenjiao" banana by inducing ethylene production and starch and cell wall degradation. The accelerated ripening was also validated by the ectopic overexpression in tomatoes. Conversely, MaBEL1-silencing aggravated the chilling injury and ripening disorder and repressed fruit softening and ripening by inhibiting ethylene production and starch and cell wall degradation. MaABI5-like and MaEBF1, the two positive regulators of the fruit softening process, interacted with MaBEL1 to enhance the promoter activity of the starch and cell wall degradation-related genes. Moreover, the F-box protein MaEBF1 does not modulate the degradation of MaBEL1, which regulates the transcription of MaABI5-like protein. Overall, we report a novel MaBEL1-MaEBF1-MaABI5-like complex system that mediates the fruit softening and ripening disorder in "Fenjiao" bananas caused by cold stress.

Heterologous Overexpression of Apple MdKING1 Promotes Fruit Ripening in Tomato

Fruit ripening is governed by a complex regulatory network, and ethylene plays an important role in this process. MdKING1 is a γ subunit of SNF1-related protein kinases (SnRKs), but the function was unclear. Here, we characterized the role of MdKING1 during fruit ripening, which can promote fruit ripening through the ethylene pathway. Our findings reveal that MdKING1 has higher expression in early-ripening cultivars than late-ripening during the early stage of apple fruit development, and its transcription level significantly increased during apple fruit ripening. Overexpression of MdKING1 (MdKING1 OE) in tomatoes could promote early ripening of fruits, with the increase in ethylene content and the loss of fruit firmness. Ethylene inhibitor treatment could delay the fruit ripening of both MdKING1 OE and WT fruits. However, MdKING1 OE fruits turned fruit ripe faster, with an increase in carotenoid content compared with WT. In addition, the expression of genes involved in ethylene biosynthesis (SlACO1, SlACS2, and SlACS4), carotenoid biosynthesis (SlPSY1 and SlGgpps2a), and fruit firmness regulation (SlPG2a, SlPL, and SlCEL2) was also increased in the fruits of MdKING1 OE plants. In conclusion, our results suggest that MdKING1 plays a key role in promoting tomato fruit ripening, thus providing a theoretical basis for apple fruit quality improvement by genetic engineering in the future.

Comprehensive analysis of OpHD-ZIP transcription factors related to the regulation of camptothecin biosynthesis in Ophiorrhiza pumila

Ophiorrhiza pumila, as a folk herb belonging to the Rubiaceae family, has become a potential source of camptothecin (CPT), which is a monoterpenoid indole alkaloid with good antitumor property. However, the camptothecin content in this herb is low, and is far from meeting the increasing clinical demand. Understanding the transcriptional regulation of camptothecin biosynthesis provides an effective strategy for improvement of camptothecin yield. Previous studies have demonstrated several transcription factors that are related to camptothecin biosynthesis, while the functions of HD-ZIP members in O. pumila have not been investigated yet. In this study, 32 OpHD-ZIP transcription factor members were genome-wide identified. Phylogenetic tree showed that these OpHD-ZIP proteins are divided into four subfamilies. Based on the transcriptome data, nine OpHD-ZIP genes were shown to be predominantly expressed in O. pumila roots, which were in line with the camptothecin biosynthetic genes. Co-expression analysis showed that OpHD-ZIP7 and OpHD-ZIP20 were potentially related to the modulation of camptothecin biosynthesis. Dual-luciferase reporter assays (Dual-LUC) showed that both OpHD-ZIP7 and OpHD-ZIP20 could activate the expression of camptothecin biosynthetic genes OpIO and OpTDC. In conclusion, this study offered the promising data for exploring the roles of OpHD-ZIP transcription factors in regulating camptothecin biosynthesis.

Ethylene Response Factor MaERF012 Modulates Fruit Ripening by Regulating Chlorophyll Degradation and Softening in Banana

Ethylene response factors (ERFs) are one of largest plant-specific transcription factor families involved in fruit ripening. However, the regulatory mechanism by which ERFs modulate fruit yellowing and softening remains unknown in banana. We previously found that the transcription of MaERF012 was closely related to 'Fenjiao' banana fruit ripening. Herein, we found that MaERF012 was differentially expressed in the fruit pulp and peel and was closely related to fruit ripening. MaERF012 activated the promoter activity of one chlorophyll degradation gene (MaSGR1), two starch degradation genes (MaGWD1 and MaAMY3), and three cell wall degradation genes (MaPL8, MaEXP-A8, and MaXYL23-like), which were tested by EMSA, Y1H, and DLR. Transient overexpression of MaERF012 accelerates fruit ripening by promoting fruit yellowing and softening by up-regulating the transcription of chlorophyll, starch, and cell wall degradation genes. Over-expression of MaERF012 alters the transcriptome profiles of the fruit peel and pulp, and the differentially expressed genes were mainly enriched in starch and sucrose metabolism, plant hormone signal transduction, biosynthesis of secondary metabolism, and fructose and mannose metabolism. Overall, the data showed that MaERF012 acts as a transcriptional activator by regulating fruit ripening by activating the transcription of chlorophyll, starch, and cell wall degradation genes.

Abscisic acid-responsive transcription factors PavDof2/6/15 mediate fruit softening in sweet cherry

Softening is a key step during fruit ripening that is modulated by the interplay between multiple phytohormones. The antagonistic action of abscisic acid (ABA) and auxin determines the rate of fruit ripening and softening. However, the transcription factors that integrate ABA and auxin signals to regulate fruit softening remain to be determined. In this study, we identified several DNA-binding with One Finger (Dof) transcription factors essential for ABA-promoted fruit softening, based on transcriptome analysis of two sweet cherry (Prunus avium L.) varieties with different fruit firmness. We show that PavDof6 directly binds to the promoters of genes encoding cell wall-modifying enzymes to activate their transcription, while PavDof2/15 directly repress their transcription. Transient overexpression of PavDof6 and PavDof2/15 in sweet cherry fruits resulted in precocious and delayed softening, respectively. In addition, we show that the auxin response factor PavARF8, the expression of whose encoding gene is repressed by ABA, activates PavDof2/15 transcription. Furthermore, PavDof2/6/15 and PavARF8 directly bind to the 9-cis-epoxycarotenoid dioxygenase 1 (PavNCED1) promoter and regulate its expression, forming a feedback mechanism for ABA-mediated fruit softening. These findings unveil the physiological framework of fruit softening and establish a direct functional link between the ABA-PavARF8-PavDofs module and cell-wall-modifying genes in mediating fruit softening.

A tomato HD-zip I transcription factor, VAHOX1, acts as a negative regulator of fruit ripening

Homeodomain-leucine zipper (HD-Zip) transcription factors are only present in higher plants and are involved in plant development and stress responses. However, our understanding of their participation in the fruit ripening of economical plants, such as tomato (Solanum lycopersicum), remains largely unclear. Here, we report that VAHOX1, a member of the tomato HD-Zip I subfamily, was expressed in all tissues, was highly expressed in breaker+4 fruits, and could be induced by ethylene. RNAi repression of VAHOX1 (VAHOX1-RNAi) resulted in accelerated fruit ripening, enhanced sensitivity to ethylene, and increased total carotenoid content and ethylene production. Conversely, VAHOX1 overexpression (VAHOX1-OE) in tomato had the opposite effect. RNA-Seq results showed that altering VAHOX1 expression affected the transcript accumulation of a series of genes involved in ethylene biosynthesis and signal transduction and cell wall modification. Additionally, a dual-luciferase reporter assay, histochemical analysis of GUS activity and a yeast one-hybrid (Y1H) assay revealed that VAHOX1 could activate the expression of AP2a. Our findings may expand our knowledge about the physiological functions of HD-Zip transcription factors in tomato and highlight the diversities of transcriptional regulation during the fruit ripening process.

The roles of HD-ZIP proteins in plant abiotic stress tolerance

Homeodomain leucine zipper (HD-ZIP) proteins are plant-specific transcription factors that contain a homeodomain (HD) and a leucine zipper (LZ) domain. The highly conserved HD binds specifically to DNA and the LZ mediates homodimer or heterodimer formation. HD-ZIP transcription factors control plant growth, development, and responses to abiotic stress by regulating downstream target genes and hormone regulatory pathways. HD-ZIP proteins are divided into four subclasses (I-IV) according to their sequence conservation and function. The genome-wide identification and expression profile analysis of HD-ZIP proteins in model plants such as Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) have improved our understanding of the functions of the different subclasses. In this review, we mainly summarize and discuss the roles of HD-ZIP proteins in plant response to abiotic stresses such as drought, salinity, low temperature, and harmful metals. HD-ZIP proteins mainly mediate plant stress tolerance by regulating the expression of downstream stress-related genes through abscisic acid (ABA) mediated signaling pathways, and also by regulating plant growth and development. This review provides a basis for understanding the roles of HD-ZIP proteins and potential targets for breeding abiotic stress tolerance in plants.

Elimination or Removal of Ethylene for Fruit and Vegetable Storage via Low-Temperature Catalytic Oxidation

Ethylene acts as an important hormone to trigger the ripening and senescence of fruits and vegetables (F&V). Thus, it is essential to eliminate trace ethylene and prevent F&V losses effectively. There are several technologies currently applying to control the ethylene concentration in the storage and transportation environment, including adsorption, gene modification, oxidation, etc. These protocols will be compared, and special attention will be paid to the low-temperature catalytic oxidation that has already been applied to practical production in this review. The active sites, supports, and reaction and deactivation mechanism of the catalysts for the low-temperature ethylene oxidation will be discussed and evaluated systematically to provide new insights for the development of effective catalysts, along with the suggestion of some perspectives for future research on this important catalytic system for F&V preservation.

Genome-Wide Characterization of R2R3-MYB Transcription Factors in Pitaya Reveals a R2R3-MYB Repressor HuMYB1 Involved in Fruit Ripening through Regulation of Betalain Biosynthesis by Repressing Betalain Biosynthesis-Related Genes

The MYB (myeloblastosis) superfamily constitutes one of the most abundant transcription factors (TFs) regulating various biological processes in plants. However, the molecular characteristics and functions of MYB TFs in pitaya remain unclear. To date, no genome-wide characterization analysis of this gene family has been conducted in the Cactaceae species. In this study, 105 R2R3-MYB members were identified from the genome data of Hylocereus undatus and their conserved motifs, physiological and biochemical characteristics, chromosome locations, synteny relationship, gene structure and phylogeny were further analyzed. Expression analyses suggested that three up-regulated HuMYBs and twenty-two down-regulated HuMYBs were probably involved in fruit ripening of pitaya. Phylogenetic analyses of R2R3-MYB repressors showed that seven HuMYBs (HuMYB1, HuMYB21, HuMYB48, HuMYB49, HuMYB72, HuMYB78 and HuMYB101) were in clades containing R2R3-MYB repressors. HuMYB1 and HuMYB21 were significantly down-regulated with the betalain accumulation during fruit ripening of ‘Guanhuahong’ pitaya (H. monacanthus). However, only HuMYB1 had R2 and R3 repeats with C1, C2, C3 and C4 motifs. HuMYB1 was localized exclusively to the nucleus and exhibited transcriptional inhibition capacities. Dual luciferase reporter assay demonstrated that HuMYB1 inhibited the expression of betalain-related genes: HuADH1, HuCYP76AD1-1 and HuDODA1. These results suggested that HuMYB1 is a potential repressor of betalain biosynthesis during pitaya fruit ripening. Our results provide the first genome-wide analyses of the R2R3-MYB subfamily involved in pitaya betalain biosynthesis and will facilitate functional analysis of this gene family in the future.

Genome-wide characterization and expression profiling of Eucalyptus grandis HD-Zip gene family in response to salt and temperature stress

BACKGROUND

The HD-Zip transcription factors are unique to plants and play an essential role in plant growth, development and stress responses. The HD-Zip transcription factor family consists of a highly conserved homeodomain (HD) and a leucine zipper domain (LZ) domain. Although the HD-Zip gene family has been extensively studied in many plant species, a systematic study of the Eucalyptus HD-Zip family has not been reported until today. Here, we systematically identified 40 HD-Zip genes in Eucalyptus (Eucalyptus grandis). Besides, we comprehensively analyzed the HD-Zips of Eucalyptus by studying the homology, conserved protein regions, gene structure, 3D structure of the protein, location of the genes on the chromosomes and the expression level of the genes in different tissues.

RESULTS

The HD-Zip family in Eucalyptus has four subfamilies, which is consistent with other plants such as Arabidopsis and rice. Moreover, genes that are in the same group tend to have similar exon-intron structures, motifs, and protein structures. Under salt stress and temperature stress, the Eucalyptus HD-Zip transcription factors show a differential expression pattern.

CONCLUSIONS

Our findings reveal the response of HD-Zip transcription factors under salt and temperature stresses, laying a foundation for future analysis of Eucalyptus HD-Zip transcription factors.