Polyamines Regulate Strawberry Fruit Ripening by Abscisic Acid, Auxin, and Ethylene

Polyamines: pleiotropic molecules regulating plant development and enhancing crop yield and quality

Polyamines (PAs) are pleiotropic bioorganic molecules. Cellular PA contents are determined by a balance between PA synthesis and degradation. PAs have been extensively demonstrated to play vital roles in the modulation of plant developmental processes and adaptation to various environmental stresses. In this review, the latest advances on the diverse roles of PAs in a range of developmental processes, such as morphogenesis, organogenesis, growth and development, and fruit ripening, are summarized and discussed. Besides, the crosstalk between PAs and phytohormones or other signalling molecules, including H2O2 and NO, involved in these processes is dwelled on. In addition, the attempts made to improve the yield and quality of grain and vegetable crops through altering the PA catabolism are enumerated. Finally, several other vital questions that remain unanswered are proposed and discussed. These include the mechanisms underlying the cooperative regulation of developmental processes by PAs and their interplaying partners like phytohormones, H2O2 and NO; PA transport for maintaining homeostasis; and utilization of PA anabolism/catabolism for generating high-yield and good-quality crops. This review aims to gain new insights into the pleiotropic role of PAs in the modulation of plant growth and development, which provides an alternative approach for manipulating and engineering valuable crop varieties that can be used in the future.

PbARF19-mediated auxin signaling regulates lignification in pear fruit stone cells

The stone cells in pear fruits cause rough flesh and low juice, seriously affecting the taste. Lignin has been demonstrated as the main component of stone cells. Auxin, one of the most important plant hormone, regulates most physiological processes in plants including lignification. However, the concentration effect and regulators of auxin on pear fruits stone cell formation remains unclear. Here, endogenous indole-3-acetic acid (IAA) and stone cells were found to be co-localized in lignified cells by immunofluorescence localization analysis. The exogenous treatment of different concentrations of IAA demonstrated that the application of 200 µM IAA significantly reduced stone cell content, while concentrations greater than 500 µM significantly increased stone cell content. Besides, 31 auxin response factors (ARFs) were identified in pear genome. Putative ARFs were predicted as critical regulators involved in the lignification of pear flesh cells by phylogenetic relationship and expression analysis. Furthermore, the negative regulation of PbARF19 on stone cell formation in pear fruit was demonstrated by overexpression in pear fruitlets and Arabidopsis. These results illustrated that the PbARF19-mediated auxin signal plays a critical role in the lignification of pear stone cell by regulating lignin biosynthetic genes. This study provides theoretical and practical guidance for improving fruit quality in pear production.

Metabolomic and transcriptomic analysis of flavonoids biosynthesis mechanisms in mulberry fruit (Hongguo 2) under exogenous hormone treatments

The mulberry fruit is prized for its superior nutrition value and abundant color due to its high flavone content. To enhance comprehension of flavone biogenesis induced by external hormones, we sprayed exogenous ethylene (ETH), indoleacetic acid (IAA) and spermine (SPM) on mulberry fruit (Hongguo 2) during its color-changed period. The levels of anthocyanin, titratable acid, soluble sugar and endogenous hormones were determined after hormone treatment, integrated transcriptome and metabolome analysis were performed for mechanism exploration. Our results indicated that exogenous ETH, SPM, and IAA play important roles in mulberry ripening, including acid reduction, sugar increase and flavonoid synthesis.

Chromosome-level genome assembly of navel orange cv. Gannanzao (Citrus sinensis Osbeck cv. Gannanzao)

Navel orange cv. Gannanzao is a variant of the navel orange cv. Newhall (Citrus sinensis Osbeck cv. Newhall) that exhibits an earlier maturation, making it commercially valuable. However, the mechanisms underlying its early maturation remain obscure. To address this question, we conducted genome sequencing and de novo assembly of navel orange cv. Gannanzao. The assembled genome sequence is 334.57 Mb in length with a GC content of 31.48%. It comprises 318 contigs (N50 = 3.23 Mb) and 187 scaffolds (N50 = 31.86 Mb). The Benchmarking Universal Single-Copy Orthologs test demonstrates 94.6% completeness. The annotation revealed 23,037 gene models, 164.95 Mb of repetitive sequences, and 2,554 noncoding RNAs. A comparative analysis identified 323 fruit ripening-related genes in navel orange cv. Gannanzao genome, while navel orange cv. Newhall genome contained 345 such genes. These genes were organized into 320 orthologous gene families, with 30.3% of them exhibiting differences in gene copy numbers between the 2 genomes. Additionally, we identified 15 fruit ripening-related genes that have undergone adaptive evolution, suggesting their potential role in advancing fruit maturation in navel orange cv. Gannanzao. Whole-genome sequencing and annotation of navel orange cv. Gannanzao provides a valuable resource to unravel the early maturation mechanism of citrus and enriches the genomic resources for citrus research.

Genome-wide identification and characterization of NAC transcription factor family members in Trifolium pratense and expression analysis under lead stress

BACKGROUND

The NAC TF family is widely involved in plant responses to various types of stress. Red clover (Trifolium pratense) is a high-quality legume, and the study of NAC genes in red clover has not been comprehensive. The aim of this study was to analyze the NAC gene family of red clover at the whole-genome level and explore its potential role in the Pb stress response.

RESULTS

In this study, 72 TpNAC genes were identified from red clover; collinearity analysis showed that there were 5 pairs of large fragment replicators of TpNAC genes, and red clover was found to be closely related to Medicago truncatula. Interestingly, the TpNAC genes have more homologs in Arabidopsis thaliana than in soybean (Glycine max). There are many elements in the TpNAC genes promoters that respond to stress. Gene expression analysis showed that all the TpNAC genes responded to Pb stress. qRT-PCR showed that the expression levels of TpNAC29 and TpNAC42 were significantly decreased after Pb stress. Protein interaction network analysis showed that 21 TpNACs and 23 other genes participated in the interaction. In addition, the TpNAC proteins had three possible 3D structures, and the secondary structure of these proteins were mainly of other types. These results indicated that most TpNAC members were involved in the regulation of Pb stress in red clover.

CONCLUSION

These results suggest that most TpNAC members are involved in the regulation of Pb stress in red clover. TpNAC members play an important role in the response of red clover to Pb stress.

LC-MS and GC-MS Metabolomics Analyses Revealed That Different Exogenous Substances Improved the Quality of Blueberry Fruits under Soil Cadmium Toxicity

Exogenous substances (ESs) can regulate plant growth and respond to environmental stress, but the effects of different ESs on blueberry fruit quality under soil cadmium (Cd) toxicity and related metabolic mechanisms are still unclear. In this study, four ES treatments [salicylic acid (SA), spermidine (Spd), 2,4-epibrassinolide (EBR), and melatonin (MT)] significantly increased blueberry fruit size, single-fruit weight, sweetness, and anthocyanin content under soil Cd toxicity and effectively reduced fruit Cd content to safe consumption levels by promoting mineral uptake (Ca, Mg, Mn, Cu and Zn). Furthermore, a total of 445, 360, 429, and 554 differentially abundant metabolites (DAMs) (LC-MS) and 63, 48, 79, and 73 DAMs (GC-MS) were identified from four comparison groups (SA/CK, Spd/CK, EBR/CK and MT/CK), respectively. The analyses revealed that ESs improved blueberry fruit quality and tolerance to Cd toxicity mainly by regulating the changes in metabolites related to ABC transporters, the TCA cycle, flavonoid biosynthesis, and phenylpropanoid biosynthesis.

Integrating the multiple functions of CHLH into chloroplast-derived signaling fundamental to plant development and adaptation as well as fruit ripening

Chlorophyll (Chl)-mediated oxygenic photosynthesis sustains life on Earth. Greening leaves play fundamental roles in plant growth and crop yield, correlating with the idea that more Chls lead to better adaptation. However, they face significant challenges from various unfavorable environments. Chl biosynthesis hinges on the first committed step, which involves inserting Mg2+ into protoporphyrin. This step is facilitated by the H subunit of magnesium chelatase (CHLH) and features a conserved mechanism from cyanobacteria to plants. For better adaptation to fluctuating land environments, especially drought, CHLH evolves multiple biological functions, including Chl biosynthesis, retrograde signaling, and abscisic acid (ABA) responses. Additionally, it integrates into various chloroplast-derived signaling pathways, encompassing both retrograde signaling and hormonal signaling. The former comprises ROS (reactive oxygen species), heme, GUN (genomes uncoupled), MEcPP (methylerythritol cyclodiphosphate), β-CC (β-cyclocitral), and PAP (3'-phosphoadenosine-5'-phosphate). The latter involves phytohormones like ABA, ethylene, auxin, cytokinin, gibberellin, strigolactone, brassinolide, salicylic acid, and jasmonic acid. Together, these elements create a coordinated regulatory network tailored to plant development and adaptation. An intriguing example is how drought-mediated improvement of fruit quality provides insights into chloroplast-derived signaling, aiding the shift from vegetative to reproductive growth. In this context, we explore the integration of CHLH's multifaceted roles into chloroplast-derived signaling, which lays the foundation for plant development and adaptation, as well as fruit ripening and quality. In the future, manipulating chloroplast-derived signaling may offer a promising avenue to enhance crop yield and quality through the homeostasis, function, and regulation of Chls.

Abscisic acid biosynthesis, metabolism and signaling in ripening fruit

Fruits are highly recommended nowadays in human diets because they are rich in vitamins, minerals, fibers and other necessary nutrients. The final stage of fruit production, known as ripening, plays a crucial role in determining the fruit's quality and commercial value. This is a complex physiological process, which involves many phytohormones and regulatory factors. Among the phytohormones involved in fruit ripening, abscisic acid (ABA) holds significant importance. ABA levels generally increase during the ripening process in most fruits, and applying ABA externally can enhance fruit flavor, hasten softening, and promote color development through complex signal regulation. Therefore, gaining a deeper understanding of ABA's mechanisms in fruit ripening is valuable for regulating various fruit characteristics, making them more suitable for consumption or storage. This, in turn, can generate greater economic benefits and reduce postharvest losses. This article provides an overview of the relationship between ABA and fruit ripening. It summarizes the effects of ABA on ripening related traits, covering the biochemical aspects and the underlying molecular mechanisms. Additionally, the article discusses the interactions of ABA with other phytohormones during fruit ripening, especially ethylene, and provides perspectives for future exploration in this field.

Alleviation role of exogenous cadaverine on cell cycle, endogenous polyamines amounts and biochemical enzyme changes in barley seedlings under drought stress

Cadaverine (Cad), which has an independent synthesis pathway compared to other polyamine (PA) types, contributes to the health of plants by regulating plant growth and development, abiotic stress tolerance and antioxidant defense mechanisms. In this work, experiments were carried out to understand the effects of exogenous Cad (10 µM) application under drought stress (%22 PEG 6000) and without stress on cell cycle, total protein content, endogenous PA levels, and biochemical enzyme activities in barley (Hordeum vulgare cv. Burakbey) considering the potential of Cad to stimulate the drought-related tolerance system. Cad application in a stress-free environment showed an effect almost like low-impact drought stress, causing changes in all parameters examined compared to samples grown in distilled water environment (Control). The results clearly show that Cad applied against the negative effects of drought stress on all parameters creates a drought resistance mechanism of the plant. Accordingly, Cad applied together with drought stress increased the density of cells in the cell cycle (G1-S and S-G2 phases) and the amount of endogenous (spermidine 10% and spermine 40%) PAs. In addition, while superoxide dismutase (SOD) (5%), (CAT) (55%) and ascorbate peroxidase (APX) (18%) enzyme levels increased, a stress response mechanism occurred due to the decrease in total protein content (20%) and malondialdehyde (MDA) (80%). As a result, exogenous application of 10 µM Cad showed that it reduced the negative effects of drought stress on endogenous PA amounts, cell division and biochemical activities in barley.

Molecular bases of strawberry fruit quality traits: Advances, challenges, and opportunities

The strawberry is one of the world's most popular fruits, providing humans with vitamins, fibers, and antioxidants. Cultivated strawberry (Fragaria × ananassa) is an allo-octoploid and highly heterozygous, making it a challenge for breeding, quantitative trait locus (QTL) mapping, and gene discovery. Some wild strawberry relatives, such as Fragaria vesca, have diploid genomes and are becoming laboratory models for the cultivated strawberry. Recent advances in genome sequencing and CRISPR-mediated genome editing have greatly improved the understanding of various aspects of strawberry growth and development in both cultivated and wild strawberries. This review focuses on fruit quality traits that are most relevant to the consumers, including fruit aroma, sweetness, color, firmness, and shape. Recently available phased-haplotype genomes, single nucleotide polymorphism (SNP) arrays, extensive fruit transcriptomes, and other big data have made it possible to locate key genomic regions or pinpoint specific genes that underlie volatile synthesis, anthocyanin accumulation for fruit color, and sweetness intensity or perception. These new advances will greatly facilitate marker-assisted breeding, the introgression of missing genes into modern varieties, and precise genome editing of selected genes and pathways. Strawberries are poised to benefit from these recent advances, providing consumers with fruit that is tastier, longer-lasting, healthier, and more beautiful.

Widely Targeted Metabolomic Profiling Combined with Transcriptome Analysis Provides New Insights into Lipid Biosynthesis in Seed Kernels of Pinus koraiensis

Lipid-rich Pinus koraiensis seed kernels are highly regarded for their nutritional and health benefits. To ascertain the molecular mechanism of lipid synthesis, we conducted widely targeted metabolomic profiling together with a transcriptome analysis of the kernels in P. koraiensis cones at various developmental stages. The findings reveal that 148 different types of lipid metabolites, or 29.6% of total metabolites, are present in kernels. Among those metabolites, the concentrations of linoleic acid, palmitic acid, and α-linolenic acid were higher, and they steadily rose as the kernels developed. An additional 10 hub genes implicated in kernel lipid synthesis were discovered using weighted gene co-expression network analysis (WGCNA), gene interaction network analysis, oil body biosynthesis, and transcriptome analysis. This study used lipid metabolome and transcriptome analyses to investigate the mechanisms of key regulatory genes and lipid synthesis molecules during kernel development, which served as a solid foundation for future research on lipid metabolism and the creation of P. koraiensis kernel food.

Genome-Wide Identification, Evolution and Expression Profile Analysis of NAC Transcription Factor in Simmondsia chinensis

NAC transcription factors (TFs) are one of the largest plant-specific gene families and play important roles in plant growth, development, and the biotic and abiotic stress response. Although the sequencing of Jojoba (Simmondsia chinensis) has been completed, the genome-wide identification and analysis of its NAC TFs has not been reported. In this study, a total of 57 genes were identified in Jojoba, which were divided into eight groups based on phylogenetic analysis. The genes clustered in the same groups have a similar gene structure and motif distribution. Based on the analysis of cis-elements in NAC TFs, nine cis-acting elements were identified in the promoter region that involved in light response, hormonal response, and stress response. Synteny analysis showed a greater collinearity between Jojoba and V. vinifera than Arabidopsis thaliana. The 24 genes in the Jojoba NAC TFs are derived from fragment replication, which may be the main source of NAC amplification. Gene expression analysis identified seven genes that were highly expressed in seeds. The differential expression analysis of NAC TFs in cotyledon and embryonic axis tissues showed that the expression of 10 genes was up-regulated and 1 gene was down-regulated. This study provides more information on the classification, gene structure, conserved motif, and evolution of NAC TFs in Jojoba, facilitating further exploration of their specific functional analysis in Jojoba seed development.

Potential Toxic Mechanisms of Neonicotinoid Insecticides in Rice: Inhibiting Auxin-Mediated Signal Transduction

Inappropriate application of pesticides not only causes sub-lethal effects on ecosystem service providers but also reduces crop yield and quality. As a xenobiotic signal molecule, pesticides may interact with signal transduction receptors in crops, resulting in oxidative damage and even metabolic perturbations. We discovered that three neonicotinoid insecticides (NIs), namely, imidacloprid, thiamethoxam, and clothianidin, at 0.06-0.12 kg ai/ha significantly inhibited the auxin signal pathway in rice leaves, thereby reducing the intracellular auxin (IAA) content. Molecular simulation further confirmed that NIs occupied the binding site where auxin transporter-like proteins 1 (LAX11) and 2 (LAX12), in which Thr253 and Asn66 of LAX11, as well as Thr244 and Asn57 of LAX12, were bound to the nitroguanidine of NIs via H-bonds. Meanwhile, Asn66 of LAX11 and Asn57 of LAX12 interacted with nitroguanidine via aromatic H-bonds. Moreover, phenylpropanoid biosynthesis was significantly disturbed because of the inhibited auxin signal pathway. Notably, peroxidase-coding genes were downregulated with a maximum value greater than 10-fold, resulting in decreased antioxidant metabolites flavone (37.82%) and lignin content (20.15%). Ultimately, rice biomass was reduced by up to 25.41% due to the decline in IAA content and antioxidant capacity. This study deeply explored the molecular mechanism of metabolic perturbations in crops stressed by pesticides, thus providing a scientific basis for pesticide environmental risk assessment and agricultural product safety.

Proanthocyanidins Delay Fruit Coloring and Softening by Repressing Related Gene Expression during Strawberry (Fragaria × ananassa Duch.) Ripening

Proanthocyanidins (PAs), also known as condensed tannins, are widespread throughout the plant kingdom, presenting diverse biological and biochemical activities. Being one of the most abundant groups of natural polyphenolic antioxidant, PAs are applied to improve plant tolerance to (a)biotic stresses and delay the senescence of fruit by scavenging the reactive oxygen species (ROS) and enhancing antioxidant responses. The effects of PAs on coloring and softening of strawberries (Fragaria × ananassa Duch.), a worldwide demanded edible fruit and typical material for studying non-climacteric fruit ripening, were firstly assessed in this work. The results showed that exogenous PAs delayed the decrease in fruit firmness and anthocyanins accumulation but improved the fruit skin brightness. Strawberries treated with PAs had similar total soluble solids, total phenolics, and total flavonoids, but lower titratable acidity content. Moreover, the contents of endogenous PAs, abscisic acid and sucrose, were somehow increased by PA treatment, while no obvious change was found in fructose and glucose content. In addition, the anthocyanin- and firmness-related genes were significantly repressed, while the PA biosynthetic gene (anthocyanin reductase, ANR) was highly up-regulated by PA treatment at the key point for fruit softening and coloring. In summary, the results presented in this study suggest that PAs slow down strawberry coloration and softening by inhibiting the expression of related genes, which could be helpful for a better understanding of the biological role of PAs and provide a new strategy to regulate strawberry ripening.

Genome-Wide Identification of the SQUAMOSA Promoter-Binding Protein-like (SPL) Transcription Factor Family in Sweet Cherry Fruit

Plant-specific SQUAMOSA promoter-binding protein-like (SPL) transcription factors play important regulatory roles during plant growth and development, fruit ripening, inflorescence branching, and biotic and abiotic stresses. However, there have been no identification or systematic studies of the SPL gene family in the sweet cherry. In this study, 12 SPL genes were identified in the sweet cherry reference genome, which were distributed over 6 chromosomes and classified into six groups according to phylogenetic relationships with other SPL gene families. Nine PavSPLs were highly expressed at green fruit stages and dramatically decreased at the onset of fruit ripening, which implied that they were important regulators during fruit development and ripening. The expression patterns of PavSPL genes under ABA, GA, and MeJA treatments showed that the PavSPLs were involved in the process of fruit ripening. A subcellular localization experiment proved that PavSPL4 and PavSPL7 proteins were localized in the nucleus. The genome-wide identification of the SPL gene family provided new insights while establishing an important foundation for sweet cherry studies.

PyuARF16/33 Are Involved in the Regulation of Lignin Synthesis and Rapid Growth in Populus yunnanensis

(1) Background: Lignin is a unique component of the secondary cell wall, which provides structural support for perennial woody plants. ARFs are the core factors of the auxin-signaling pathway, which plays an important role in promoting plant growth, but the specific relationship between auxin response factors (ARFs) and lignin has not been fully elucidated with regard to rapid plant growth in forest trees. (2) Objectives: This study aimed to investigate the relationship between ARFs and lignin with regard to rapid plant growth in forest trees. (3) Methods: We used bioinformatics analysis to investigate the PyuARF family, find genes homologous to ARF6 and ARF8 in Populus yunnanensis, and explore the changes in gene expression and lignin content under light treatment. (4) Results: We identified and characterized 35 PyuARFs based on chromosome-level genome data from P. yunnanensis. In total, we identified 92 ARF genes in P. yunnanensis, Arabidopsis thaliana, and Populus trichocarpa, which were subsequently divided into three subgroups based on phylogenetic analysis and classified the conserved exon-intron structures and motif compositions of the ARFs into the same subgroups. Collinearity analysis suggested that segmental duplication and whole-genome duplication events were majorly responsible for the expansion of the PyuARF family, and the analysis of Ka/Ks indicated that the majority of the duplicated PyuARFs underwent purifying selection. The analysis of cis-acting elements showed that PyuARFs were sensitive to light, plant hormones, and stress. We analyzed the tissue-specific transcription profiles of PyuARFs with transcriptional activation function and the transcription profiles of PyuARFs with high expression under light in the stem. We also measured the lignin content under light treatment. The data showed that the lignin content was lower, and the gene transcription profiles were more limited under red light than under white light on days 1, 7, and 14 of the light treatments. The results suggest that PyuARF16/33 may be involved in the regulation of lignin synthesis, thereby promoting the rapid growth of P. yunnanensis. (5) Conclusions: Collectively, this study firstly reports that PyuARF16/33 may be involved in the regulation of lignin synthesis and in promoting the rapid growth in P. yunnanensis.

Exogenous spermidine improved drought tolerance in Ilex verticillata seedlings

Winterberry (Ilex verticillata (L.) A. Gray) is a recently introduced ornamental tree species in China that has not been closely investigated for its drought resistance. In this study, we used two-year-old cuttings from I. verticillata (L.) A. Gray and two representative varieties derived from it, I. verticillata 'Oosterwijk' and I. verticillata 'Jim Dandy', as materials to investigate how this plant responds to drought stress and whether exogenous spermidine (SPD) can alleviate the negative effects caused by drought stress. The results showed that as the degree of drought stress increased, the leaves of winterberry seedlings became chlorotic, and their edges became dry. Similarly, the relative water content, specific leaf weight, chlorophyll content, leaf nitrogen content, net photosynthetic rate, stomatal conductance and transpiration rate were significantly reduced, whereas the content of malondialdehyde continuously increased with the degree of drought stress. The activities of superoxide dismutase, peroxidase, and catalase increased under moderate drought stress and then decreased under severe drought stress. The levels of soluble sugar and abscisic acid continued to increase, while those of auxin and gibberellic acid decreased. When compared with individual drought stress, an increase in the amount of external SPD clearly alleviated the effect of drought stress on winterberry seedlings. The combined phenotypes and physiological indices of the winterberry leaves under drought stress conditions revealed that the drought resistance of the native species was significantly higher than its two varieties. This finding serves as an important theoretical foundation for the popularization and application of I. verticillata (L.) A. Gray and the two varieties.

High Efficiency Regeneration System from Blueberry Leaves and Stems

The main propagation approach is tissue culture in blueberries, and tissue culture is an effective and low-cost method with higher economic efficiency in blueberries. However, there is a lack of stable and efficient production systems of industrialization of tissue culture in blueberries. In this study, the high-efficiency tissue culture and rapid propagation technology system were established based on blueberry leaves and stems. The optimal medium for callus induction was WPM (woody plant medium) containing 2.0 mg/L Forchlorfenuron (CPPU), 0.2 mg/L 2-isopentenyladenine (2-ip) with a 97% callus induction rate and a callus differentiation rate of 71% by using blueberry leaves as explants. The optimal secondary culture of the leaf callus medium was WPM containing 3.0 mg/L CPPU with an increment coefficient of 24%. The optimal bud growth medium was WPM containing 1.0 mg/L CPPU, 0.4 mg/L 2-ip, with which the growth of the bud was better, stronger and faster. The optimal rooting medium was 1/2 Murashige and Skoog (1/2MS) medium containing 2.0 mg/L naphthylacetic acid (NAA), with which the rooting rate was 90% with shorter rooting time and more adventitious root. In addition, we established a regeneration system based on blueberry stems. The optimal preculture medium in blueberry stem explants was MS medium containing 2-(N-morpholino) ethanesulfonic acid (MES) containing 0.2 mg/L indole-3-acetic acid (IAA), 0.1 mg/L CPPU, 100 mg/L NaCl, with which the germination rate of the bud was 93%. The optimal medium for fast plant growth was MS medium containing MES containing 0.4 mg/L zeatin (ZT), 1 mg/L putrescine, 1 mg/L spermidine, 1 mg/L spermidine, which had a good growth state and growth rate. The optimal cultivation for plantlet growth was MS medium containing MES containing 0.5 mg/L isopentene adenine, with which the plantlet was strong. The optimal rooting medium for the stem was 1/2MS medium containing 2.0 mg/L NAA, with which the rooting rate was 93% with a short time and more adventitious root. In conclusion, we found that stem explants had higher regeneration efficiency for a stable and efficient production system of industrialization of tissue culture. This study provides theoretical guidance and technical support in precision breeding and standardization and industrialization in the blueberry industry.

Abscisic Acid Signaling in the Regulation of Postharvest Physiological Deterioration of Sliced Cassava Tuberous Roots

Phytohormone abscisic acid (ABA) influences the shelf life of fruit, vegetables, and tubers after harvest. However, little is known about the core signaling module involved in ABA's control of the postharvest physiological process. Exogenous ABA alleviated postharvest physiological deterioration (PPD) symptoms of sliced cassava tuberous roots, increased endogenous ABA levels, and reduced endogenous H₂O₂ content. The specific ABA signaling module during the PPD process was identified as MePYL6-MePP2C16-MeSnRK2.1-MebZIP5/34. MebZIP5/MebZIP34 directly binds to and activates the promoters of MeGRX6/MeMDAR1 through ABRE elements. Exogenous ABA significantly induced the expression of genes involved in this module, glutaredoxin content, and monodehydroascorbate reductase activity. We presented a hypothesis suggesting that MePYL6-MePP2C16-MeSnRK2.1-MebZIP5/34-MeGRX6/MeMDAR1 is involved in ABA-induced antioxidative capacity, thus alleviating PPD symptoms in cassava tuberous roots. The identification of the specific signaling module involved in ABA's control of PPD provides a basis and potential targets for extending the shelf life of cassava tuberous roots.

Copper Amine Oxidase (CuAO)-Mediated Polyamine Catabolism Plays Potential Roles in Sweet Cherry (Prunus avium L.) Fruit Development and Ripening

Copper amine oxidases (CuAOs) play important roles in PA catabolism, plant growth and development, and abiotic stress response. In order to better understand how PA affects cherry fruit, four potential PavCuAO genes (PavCuAO1–PavCuAO4) that are dispersed over two chromosomes were identified in the sweet cherry genome. Based on phylogenetic analysis, they were classified into three subclasses. RNA-seq analysis showed that the PavCuAO genes were tissue-specific and mostly highly expressed in flowers and young leaves. Many cis-elements associated with phytohormones and stress responses were predicted in the 2 kb upstream region of the promoter. The PavCuAOs transcript levels were increased in response to abscisic acid (ABA) and gibberellin 3 (GA₃) treatments, as well as abiotic stresses (NaCl, PEG, and cold). Quantitative fluorescence analysis and high-performance liquid chromatography confirmed that the Put content fell, and the PavCuAO4 mRNA level rose as the sweet cherry fruit ripened. After genetically transforming Arabidopsis with PavCuAO4, the Put content in transgenic plants decreased significantly, and the expression of the ABA synthesis gene NCED was also significantly increased. At the same time, excessive H₂O₂ was produced in PavCuAO4 transiently expressed tobacco leaves. The above results strongly proved that PavCuAO4 can decompose Put and may promote fruit ripening by increasing the content of ABA and H₂O₂ while suppressing total free PA levels in the fruit.

A novel strategy for improving watermelon resistance to cucumber green mottle mosaic virus by exogenous boron application

The molecular mode controlling cucumber green mottle mosaic virus (CGMMV)-induced watermelon blood flesh disease (WBFD) is largely unknown. In this study, we have found that application of exogenous boron suppressed CGMMV infection in watermelon fruit and alleviated WBFD symptoms. Our transcriptome analysis showed that the most up-regulated differentially expressed genes (DEGs) were associated with polyamine and auxin biosynthesis, abscisic acid catabolism, defence-related pathways, cell wall modification, and energy and secondary metabolism, while the down-regulated DEGs were mostly involved in ethylene biosynthesis, cell wall catabolism, and plasma membrane functions. Our virus-induced gene silencing results showed that silencing of SPDS expression in watermelon resulted in a higher putrescine content and an inhibited CGMMV infection correlating with no WBFD symptoms. SBT and TUBB1 were also required for CGMMV infection. In contrast, silencing of XTH23 and PE/PEI7 (low-level lignin, cellulose and pectin) and ATPS1 (low-level glutathione) promoted CGMMV accumulation. Furthermore, RAP2-3, MYB6, WRKY12, H2A, and DnaJ11 are likely to participate in host antiviral resistance. In addition, a higher (spermidine + spermine):putrescine ratio, malondialdehyde content, and lactic acid content were responsible for fruit decay and acidification. Our results provide new knowledge on the roles of boron in watermelon resistance to CGMMV-induced WBFD. This new knowledge can be used to design better control methods for CGMMV in the field and to breed CGMMV resistant watermelon and other cucurbit crops.

Ripening of Pomegranate Skin as Revealed by Developmental Transcriptomics

The appearance of pomegranate (Punica granatum L.) fruit is highly important for its marketing. The primary concerns are obtaining sufficient red pigment accumulation and minimal cracking of the fruit skin (the outer red layer of the peel). We analyzed the skin transcriptome of pomegranate cv. Wonderful at distinct time points of fruit development to characterize the processes that occur in the skin during fruit ripening and which may reflect on processes in the whole fruit, such as the non-climacteric nature of pomegranate. The data suggested a ripening mechanism in pomegranate skin that differs from that in strawberry—the model plant for non-climacteric fruit where abscisic acid is the growth regulator that drives ripening—involving ethylene, polyamine, and jasmonic acid pathways. The biosynthetic pathways of important metabolites in pomegranate—hydrolyzable tannins and anthocyanins—were co-upregulated at the ripening stage, in line with the visual enhancement of red coloration. Interestingly, cuticle- and cell-wall-related genes that showed differential expression between the developmental stages were mainly upregulated in the skin of early fruit, with lower expression at mid-growth and ripening stages. Nevertheless, lignification may be involved in skin hardening in the mature fruit.

Genome-Wide Identification and Analysis of the NAC Transcription Factor Gene Family in Garden Asparagus (Asparagus officinalis)

As a large plant-specific gene family, the NAC (NAM, ATAF1/2, and CUC2) transcription factor is related to plant growth, development, and response to abiotic stresses. Although the draft genome of garden asparagus (Asparagus officinalis) has been released, the genome-wide investigation of the NAC gene family is still unavailable. In this study, a total of 85 A. officinalis NAC genes were identified, and a comprehensive analysis of the gene family was performed, including physicochemical properties, phylogenetic relationship, chromosome localization, gene structure, conserved motifs, intron/exon, cis-acting elements, gene duplication, syntenic analysis, and differential gene expression analysis. The phylogenetic analysis demonstrated that there were 14 subgroups in both A. officinalis and Arabidopsis thaliana, and the genes with a similar gene structure and motif distribution were clustered in the same group. The cis-acting regulatory analysis of AoNAC genes indicated four types of cis-acting elements were present in the promoter regions, including light-responsive, hormone-responsive, plant-growth-and-development-related, and stress-responsive elements. The chromosomal localization analysis found that 81 NAC genes in A. officinalis were unevenly distributed on nine chromosomes, and the gene duplication analysis showed three pairs of tandem duplicated genes and five pairs of segmental duplications, suggesting that gene duplication is possibly associated with the amplification of the A. officinalis NAC gene family. The differential gene expression analysis revealed one and three AoNAC genes that were upregulated and downregulated under different types of salinity stress, respectively. This study provides insight into the evolution, diversity, and characterization of NAC genes in garden asparagus and will be helpful for future understanding of their biological roles and molecular mechanisms in plants.

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.

Exogenously applied spermidine alleviates hypoxia stress in Phyllostachys praecox seedlings via changes in endogenous hormones and gene expression

BACKGROUND

Hypoxia stress is thought to be one of the major abiotic stresses that inhibits the growth and development of higher plants. Phyllostachys pracecox is sensitive to oxygen and suffers soil hypoxia during cultivation; however, the corresponding solutions to mitigate this stress are still limited in practice. In this study, Spermidine (Spd) was tested for regulating the growth of P. praecox seedlings under the hypoxia stress with flooding.

RESULTS

A batch experiment was carried out in seedlings treated with 1 mM and 2 mM Spd under flooding for eight days. Application of 1 mM and 2 mM Spd could alleviate plant growth inhibition and reduce oxidative damage from hypoxia stress. Exogenous Spd significantly (P < 0.05) increased proline, soluble protein content, catalase (CAT), superoxide dismutase (SOD), and S-adenosylmethionine decarboxylase (SAMDC) activity, enhanced abscisic acid (ABA) and indole-3-acetic acid (IAA) content, and reduced ethylene emission, hydrogen peroxide (H₂O₂), superoxide radical (O₂^·-) production rate, ACC oxidase (ACO) and ACC synthase (ACS) to protect membranes from lipid peroxidation under flooding. Moreover, exogenous Spd up-regulated the expression of auxin-related genes auxin responsive factor1 (ARF1), auxin1 protein (AUX1), auxin2 protein (AUX2), auxin3 protein (AUX3) and auxin4 protein (AUX4), and down-regulated the expression of ethylene-related ACO and ACS genes during flooding.

CONCLUSION

The results indicated that exogenous Spd altered hormone concentrations and the expression of hormone-related genes, thereby protecting the bamboo growth under flooding. Our data suggest that Spd can be used to reduce hypoxia-induced cell damage and improve the adaptability of P. praecox to flooding stress.

PAs Regulate Early Somatic Embryo Development by Changing the Gene Expression Level and the Hormonal Balance in Dimocarpus longan Lour

Polyamines (PAs) play an important regulatory role in many basic cellular processes and physiological and biochemical processes. However, there are few studies on the identification of PA biosynthesis and metabolism family members and the role of PAs in the transition of plant embryogenic calli (EC) into globular embryos (GE), especially in perennial woody plants. We identified 20 genes involved in PA biosynthesis and metabolism from the third-generation genome of longan (Dimocarpus longan Lour.). There were no significant differences between longan and other species regarding the number of members, and they had high similarity with Citrus sinensis. Light, plant hormones and a variety of stress cis-acting elements were found in these family members. The biosynthesis and metabolism of PAs in longan were mainly completed by DlADC2, DlSAMDC2, DlSAMDC3, DlSPDS1A, DlSPMS, DlCuAOB, DlCuAO3A, DlPAO2 and DlPAO4B. In addition, 0.01 mmol∙L⁻¹ 1-aminocyclopropane-1-carboxylic acid (ACC), putrescine (Put) and spermine (Spm), could promote the transformation of EC into GE, and Spm treatment had the best effect, while 0.01 mmol∙L⁻¹ D-arginine (D-arg) treatment inhibited the process. The period between the 9th and 11th days was key for the transformation of EC into GE in longan. There were higher levels of gibberellin (GA), salicylic acid (SA) and abscisic acid (ABA) and lower levels of indole-3-acetic acid (IAA), ethylene and hydrogen peroxide (H₂O₂) in this key period. The expression levels in this period of DlADC2, DlODC, DlSPDS1A, DlCuAOB and DlPAO4B were upregulated, while those of DlSAMDC2 and DlSPMS were downregulated. These results showed that the exogenous ACC, D-arg and PAs could regulate the transformation of EC into GE in longan by changing the content of endogenous hormones and the expression levels of PA biosynthesis and metabolism genes. This study provided a foundation for further determining the physicochemical properties and molecular evolution characteristics of the PA biosynthesis and metabolism gene families, and explored the mechanism of PAs and ethylene for regulating the transformation of plant EC into GE.

Characterization and regulation mechanism analysis of ubiquitin-conjugating family genes in strawberry reveals a potential role in fruit ripening

BACKGROUND

E2 ubiquitin-conjugating (UBC) enzymes are an integral component of the ubiquitin proteasome system that play an important role in plant development, growth, and external stress responses. Several UBC genes have been identified in various plants. However, no studies exploring the functions of UBC genes in regulating fruit of strawberry have been reported. In the present study, a systematic analysis of the entire UBC family members were conducted in the genome of strawberry (Fragaria ×ananassa) based on bioinformatics method, and the gene functioning in strawberry ripening was explored.

RESULTS

A total of 191 UBC genes were identified in the genome of cultivated strawberry. These genes were unevenly distributed across the 28 chromosomes from the 4 subgenomes of cultivated strawberry, ranging from 3 to 11 genes per chromosome. Moreover, the expansion of FaUBC genes in strawberry was mainly driven by WGD. All the FaUBC genes were clarified into 13 groups and most of them were included in the group VI. The gene structure analysis showed that the number of exons varied from 1 to 23, and the structure of genes had few differences within the same groups but a distinction in different groups. Identification of the cis-acting elements of the promoter revealed multiple regulatory elements that responded to plant growth and development, phytohormone responsive, and abiotic and biotic stress. Data from functional annotation indicated that FaUBC genes play a role in a variety of biological processes. The RNA-seq data showed that FaUBC genes displayed different expression pattern during the fruit ripening process and clarified into 6 clusters. In particular, cluster 3 exhibiting a sudden expression increase in the turning red stage were speculated to be involved in fruit ripening. Hence, two FaUBC genes (FaUBC76 and FaUBC78) were selected for gene function analysis by transient over-expression method. The results indicated that FaUBC76 has a positive effect on the fruit development and ripening in strawberry by up-regulating accumulation of anthocyanins. Moreover, expression of some maturity-related genes were also significantly increased, further supporting a role for FaUBC76 in the regulation of fruit ripening or softening. On the contrary, the overexpression of FaUBC78 significantly increased the firmness of strawberry fruit, indicating that FaUBC78 had a positive role in inhibiting the decrease of strawberry fruit firmness.

CONCLUSION

Our study not only provide comprehensive information on system evolution and function on UBC genes, but also give a new insight into explore the roles of FaUBC genes in the regulation of strawberry ripening.

Horticultural innovation by viral-induced gene regulation of carotenogenesis

Multipartite viral vectors provide a simple, inexpensive and effective biotechnological tool to transiently manipulate (i.e. reduce or increase) gene expression in planta and characterise the function of genetic traits. The development of virus-induced gene regulation (VIGR) systems usually involve the targeted silencing or overexpression of genes involved in pigment biosynthesis or degradation in plastids, thereby providing rapid visual assessment of success in establishing RNA- or DNA-based VIGR systems in planta. Carotenoids pigments provide plant tissues with an array of yellow, orange, and pinkish-red colours. VIGR-induced transient manipulation of carotenoid-related gene expression has advanced our understanding of carotenoid biosynthesis, regulation, accumulation and degradation, as well as plastid signalling processes. In this review, we describe mechanisms of VIGR, the importance of carotenoids as visual markers of technology development, and knowledge gained through manipulating carotenogenesis in model plants as well as horticultural crops not always amenable to transgenic approaches. We outline how VIGR can be utilised in plants to fast-track the characterisation of gene function(s), accelerate fruit tree breeding programs, edit genomes, and biofortify plant products enriched in carotenoid micronutrients for horticultural innovation.

Conjugated Polyamines in Root Plasma Membrane Enhanced the Tolerance of Plum Seedling to Osmotic Stress by Stabilizing Membrane Structure and Therefore Elevating H+-ATPase Activity

Polyamines are small positively charged molecules in plants and play important functions in many biological processes under various environmental stresses. One of the most confounding problems relating to polyamines (PAs) in stresses is the lack of understanding of the mechanisms underlying their function(s). Furthermore, a limited number of studies have addressed this issue at the sub-cellular level, especially in tree plants under drought stress. Therefore, in this research, by simulating natural drought stress with polyethylene glycol (PEG) osmotic stress, the relationship between the levels of conjugated polyamines and the activity of H⁺-ATPase in the plasma membrane was elucidated with the roots of two plum (Prunus salicina L.) cultivars, which were different in drought tolerance, as experimental materials. Furthermore, free PA levels and the activities of S-adenosylmethionine decarboxylase (SAMDC) and transglutaminase (TGase), which were closely associated with the levels of free and conjugated PAs, were also detected. Results showed that under osmotic stress, the increases of the levels of non-covalently conjugated (non-CC) spermidine (Spd) and spermine (Spm), covalently conjugated (CC) putrescine (Put) and Spd in the plasma membrane of drought-tolerant Ganli No. 5 were more significant than those of drought-sensitive Suli No. 3, indicating that these conjugated PAs might be involved in the tolerance of plum seedlings to stress. Furthermore, the conjugated PAs were closely correlated with plum seedling growth, water retention capacity, plasma membrane damage degree, and hydrogen (H⁺)-ATPase activity in the plasma membrane. To get more complementary pieces of evidence, we subjected plum seedlings to combined treatments of PEG and exogenous PA (Spd and Spm), and an inhibitor of SAMDC [methylglyoxal-bis (guanylhydrazone), (MGBG)] or TGase (o-phenanthroline). These results collectively suggested that non-CC Spd and Spm, CC Put and Spd in plasma membrane might function in enhancing the tolerance of plum seedlings to osmotic stress by stabilizing membrane structure and therefore elevating H⁺-ATPase activity.

Roles of abscisic acid in regulating ripening and quality of strawberry, a model non-climacteric fruit

Abscisic acid (ABA) is a dominant regulator of ripening and quality in non-climacteric fruits. Strawberry is regarded as a model non-climacteric fruit due to its extensive genetic studies and proven suitability for transgenic approaches to understanding gene function. Strawberry research has contributed to studies on color, flavor development, and fruit softening, and in recent years ABA has been established as a core regulator of strawberry fruit ripening, whereas ethylene plays this role in climacteric fruits. Despite this major difference, several components of the interacting genetic regulatory network in strawberry, such as MADS-box and NAC transcription factors, are similar to those that operate in climacteric fruit. In this review, we summarize recent advances in understanding the role of ABA biosynthesis and signaling and the regulatory network of transcription factors and other phytohormones in strawberry fruit ripening. In addition to providing an update on its ripening, we discuss how strawberry research has helped generate a broader and more comprehensive understanding of the mechanism of non-climacteric fruit ripening and focus attention on the use of strawberry as a model platform for ripening studies.

Roles of abscisic acid in regulating ripening and quality of strawberry, a model non-climacteric fruit

Abscisic acid (ABA) is a dominant regulator of ripening and quality in non-climacteric fruits. Strawberry is regarded as a model non-climacteric fruit due to its extensive genetic studies and proven suitability for transgenic approaches to understanding gene function. Strawberry research has contributed to studies on color, flavor development, and fruit softening, and in recent years ABA has been established as a core regulator of strawberry fruit ripening, whereas ethylene plays this role in climacteric fruits. Despite this major difference, several components of the interacting genetic regulatory network in strawberry, such as MADS-box and NAC transcription factors, are similar to those that operate in climacteric fruit. In this review, we summarize recent advances in understanding the role of ABA biosynthesis and signaling and the regulatory network of transcription factors and other phytohormones in strawberry fruit ripening. In addition to providing an update on its ripening, we discuss how strawberry research has helped generate a broader and more comprehensive understanding of the mechanism of non-climacteric fruit ripening and focus attention on the use of strawberry as a model platform for ripening studies.

Polyamines conjugated to plasma membrane functioned in enhancing the tolerance of cucumber seedlings to osmotic stress via elevating H+-ATPase activity

Polyamine (PA), one of the important plant growth regulators, is closely associated with drought stress. However, the function of conjugated PA is not still clear in the roots of cucumber seedlings under polyethylene glycol (PEG) osmotic stress. Therefore, in this study the relationship between the levels of conjugated polyamines and the activity of H⁺-ATPase in plasma membrane was elucidated with the roots of two cucumber (Cucumis sativus L.) cultivars, which were different in drought tolerance, as experimental materials. Furthermore, the contents of free PAs and the activities of S-adenosylmethionine decarboxylase (SAMDC) and transglutaminase (TGase), which were closely related to the levels of conjugated polyamines, were also determined. Results showed that under osmotic stress, the increases of the levels of non-covalently conjugated (non-CC) spermidine (Spd) and spermine (Spm), covalently conjugated (CC) putrescine (Put) and Spd in plasma membrane of drought-tolerant Tangshan 5 were more obvious than those of drought-sensitive Jinyou 1. Furthermore, the conjugated PAs mentioned above were closely correlated with increase rate of seedling dry weight, plasma membrane permeability, water content and H⁺-ATPase activity in plasma membrane. Results of the additional tests, in which exogenous Spd, Spm and two inhibitors, MGBG and phenanthrolin were used, were complementary to the results above. From these results, it could be concluded that non-CC Spd and Spm, CC Put and Spd in plasma membrane functioned in enhancing the tolerance of cucumber seedlings to osmotic stress via elevating H⁺-ATPase activity.

Comprehensive Analysis of Jumonji Domain C Family from Citrus grandis and Expression Profilings in the Exocarps of “Huajuhong” (Citrus grandis “Tomentosa”) during Various Development Stages

Citrus grandis “Tomentosa” (“Huajuhong”) is a famous Traditional Chinese Medicine. In this study, a total of 18 jumonji C (JMJC) domain-containing proteins were identified from C. grandis. The 18 CgJMJCs were unevenly located on six chromosomes of C. grandis. Phylogenetic analysis revealed that they could be classified into five groups, namely KDM3, KDM4, KDM5, JMJC, and JMJD6. The domain structures and motif architectures in the five groups were diversified. Cis-acting elements on the promoters of 18 CgJMJC genes were also investigated, and the abscisic acid-responsive element (ABRE) was distributed on 15 CgJMJC genes. Furthermore, the expression profiles of 18 CgJMJCs members in the exocarps of three varieties of “Huajuhong”, for different developmental stages, were examined. The results were validated by quantitative real-time PCR (qRT-PCR). The present study provides a comprehensive characterization of JMJC domain-containing proteins in C. grandis and their expression patterns in the exocarps of C. grandis “Tomentosa” for three varieties with various development stages.

Tomato SlPP2C5 Is Involved in the Regulation of Fruit Development and Ripening

Abscisic acid (ABA) regulates plant development mainly through its signaling, in which ABA binds to receptors to inhibit type 2C protein phosphatases (PP2Cs). The exact roles of PP2Cs in fruit development are still unclear. In this work, we verify that tomato SlPP2C5 works as a negative regulator in ABA signaling during fruit development. SlPP2C5 was inhibited by both monomeric and dimeric ABA receptors SlPYLs through ABA dose-dependent way, and it interacted physically with SlPYLs and SlSnRK2s. SlPP2C5 was highly expressed in fruits induced by exogenous ABA. Plants with overexpressed SlPP2C5 had lower sensitivity to ABA, which showed faster seed germination and primary root growth compared to Wild type (WT), while SlPP2C5-suppressed plants were more sensitive to ABA. SlPP2C5-over-expression (OE) delayed fruit ripening onset, while SlPP2C5-RNAi advanced fruit ripening. Alteration of SlPP2C5 expression impacts fruit quality parameters as well, including pericarp thickness, fruit shape index, seed number and weight and the soluble solid content. RNA-seq analysis revealed that there were significant expression differences of genes related to ethylene release and lycopene synthesis between WT and both SlPP2C5-OE and SlPP2C5-RNAi lines with an inversed variation. Taken together, our findings demonstrate that SlPP2C5 plays an important role in the regulation of fruit development, ripening and quality.

Different regulatory mechanisms of plant hormones in the ripening of climacteric and non-climacteric fruits: a review

This review contains the regulatory mechanisms of plant hormones in the ripening process of climacteric and non-climacteric fruits, interactions between plant hormones and future research directions. The fruit ripening process involves physiological and biochemical changes such as pigment accumulation, softening, aroma and flavor formation. There is a great difference in the ripening process between climacteric fruits and non-climacteric fruits. The ripening of these two types of fruits is affected by endogenous signals and exogenous environments. Endogenous signaling plant hormones play an important regulatory role in fruit ripening. This paper systematically reviews recent progress in the regulation of plant hormones in fruit ripening, including ethylene, abscisic acid, auxin, jasmonic acid (JA), gibberellin, brassinosteroid (BR), salicylic acid (SA) and melatonin. The role of plant hormones in both climacteric and non-climacteric fruits is discussed, with emphasis on the interaction between ethylene and other adjustment factors. Specifically, the research progress and future research directions of JA, SA and BR in fruit ripening are discussed, and the regulatory network between JA and other signaling molecules remains to be further revealed. This study is meant to expand the understanding of the importance of plant hormones, clarify the hormonal regulation network and provide a basis for targeted manipulation of fruit ripening.

AcERF1B and AcERF073 Positively Regulate Indole-3-acetic Acid Degradation by Activating AcGH3.1 Transcription during Postharvest Kiwifruit Ripening

Ethylene can accelerate the postharvest ripening process of kiwifruit, while indole-3-acetic acid (IAA) delays it. However, the molecular mechanism by which ethylene regulates IAA degradation is unclear. Here, we found that ethephon promotes the degradation of free IAA in kiwifruit. Furthermore, ethylene can promote the expression of AcGH3.1 and enhance its promoter activity. Two ethylene response factors (ERFs), AcERF1B and AcERF073, were obtained using an AcGH3.1 promoter as bait for a yeast one-hybrid screening library. Both AcERF1B and AcERF073 bind to the AcGH3.1 promoter to activate it. Also, AcERF1B/073 enhanced AcGH3.1 expression, decreased the free IAA content, and increased the IAA-Asp content in kiwifruit. In addition, we found that the AcERF1B and AcERF073 proteins directly interact, and this interaction enhanced their binding to the AcGH3.1 promoter. In summary, our results suggest that AcERF1B and AcERF073 positively regulate IAA degradation by activating AcGH3.1 transcription, which accelerated postharvest kiwifruit ripening.

Biologia futura: the role of polyamine in plant science

Polyamines (PAs) are positively charged amines such as putrescine, spermidine and spermine that ubiquitously exist in all organisms. They have been considered as a new type of plant biostimulants, with pivotal roles in many physiological processes. Polyamine levels are controlled by intricate regulatory feedback mechanisms. PAs are directly or indirectly regulated through interaction with signaling metabolites (H₂0₂, NO), aminobutyric acid (GABA), phytohormones (abscisic acid, gibberellins, ethylene, cytokinins, auxin, jasmonic acid and brassinosteroids) and nitrogen metabolism (maintaining the balance of C:N in plants). Exogenous applications of PAs enhance the stress resistance, flowering and fruit set, synthesis of bioactive compounds and extension of agricultural crops shelf life. Up-regulation of PAs biosynthesis by genetic manipulation can be a novel strategy to increase the productivity of agricultural crops. Recently, the role of PAs in symbiosis relationships between plants and beneficial microorganisms has been confirmed. PA metabolism has also been targeted to design new harmless fungicides.

The NAC transcription factor FaRIF controls fruit ripening in strawberry

In contrast to climacteric fruits such as tomato, the knowledge on key regulatory genes controlling the ripening of strawberry, a nonclimacteric fruit, is still limited. NAC transcription factors (TFs) mediate different developmental processes in plants. Here, we identified and characterized Ripening Inducing Factor (FaRIF), a NAC TF that is highly expressed and induced in strawberry receptacles during ripening. Functional analyses based on stable transgenic lines aimed at silencing FaRIF by RNA interference, either from a constitutive promoter or the ripe receptacle-specific EXP2 promoter, as well as overexpression lines showed that FaRIF controls critical ripening-related processes such as fruit softening and pigment and sugar accumulation. Physiological, metabolome, and transcriptome analyses of receptacles of FaRIF-silenced and overexpression lines point to FaRIF as a key regulator of strawberry fruit ripening from early developmental stages, controlling abscisic acid biosynthesis and signaling, cell-wall degradation, and modification, the phenylpropanoid pathway, volatiles production, and the balance of the aerobic/anaerobic metabolism. FaRIF is therefore a target to be modified/edited to control the quality of strawberry fruits.

N6-methyladenosine RNA modification regulates strawberry fruit ripening in an ABA-dependent manner

BACKGROUND

Epigenetic mark such as DNA methylation plays pivotal roles in regulating ripening of both climacteric and non-climacteric fruits. However, it remains unclear whether mRNA m6A methylation, which has been shown to regulate ripening of the tomato, a typical climacteric fruit, is functionally conserved for ripening control among different types of fruits.

RESULTS

Here we show that m6A methylation displays a dramatic change at ripening onset of strawberry, a classical non-climacteric fruit. The m6A modification in coding sequence (CDS) regions appears to be ripening-specific and tends to stabilize the mRNAs, whereas m6A around the stop codons and within the 3' untranslated regions is generally negatively correlated with the abundance of associated mRNAs. We identified thousands of transcripts with m6A hypermethylation in the CDS regions, including those of NCED5, ABAR, and AREB1 in the abscisic acid (ABA) biosynthesis and signaling pathway. We demonstrate that the methyltransferases MTA and MTB are indispensable for normal ripening of strawberry fruit, and MTA-mediated m6A modification promotes mRNA stability of NCED5 and AREB1, while facilitating translation of ABAR.

CONCLUSION

Our findings uncover that m6A methylation regulates ripening of the non-climacteric strawberry fruit by targeting the ABA pathway, which is distinct from that in the climacteric tomato fruit.

Chitosan and putrescine modulate reactive oxygen species metabolism and physiological responses during chili fruit ripening

We investigated the combined effect of chitosan (CHT) and putrescine (PUT) on the postharvest shelf life of Capsicum fruit concerning the metabolism of reactive oxygen species (ROS) through direct and indirect effects on ripening characters cell wall hydrolyzing enzyme and ROS metabolism. The PUT and CHT directly affected quality indices like color, firmness and water loss with a concomitant oxidative bust in the development of O₂^•- and H₂O₂ in fruit pulp. This was accompanied by significant suppression of respiratory flux, a decrease of total soluble solids and ascorbic acid content throughout postharvest storage. PUT applied with CHT modified the oxidative metabolism of fruits by a significant reduction in the level of O₂^•- and H₂O₂ content. In addition, a significant accumulation of total polyamine under respective treatment was reasonably correlated with both ROS producing enzyme as well as H₂O₂ and O₂^•-. Wall hydrolyzing enzymes like pectin methyl esterase and cellulase had marked downregulation both under PUT and CHT + PUT treatment. Moreover, on close observation, the combinational effects of PUT and CHT had better effects in the regulation of those enzymes as compared to individual treatment. Fruits restore higher antioxidative capacities as evident with superoxide dismutase (SOD), guaiacol peroxidases (GPX), ascorbate peroxidase (APX) catalase (CAT), glutathione peroxidase (GPX), NADPH oxidase (NOX) and glutathione reductase (GR), indicating their roles on fruit coat softening. Finally, the treatment of PUT and CHT in combination increased shelf life vis-à-vis the quality of fruit.

Fig fruit ripening is regulated by the interaction between ethylene and abscisic acid

Fleshy fruit ripening is typically regulated by ethylene in climacteric fruits and abscisic acid (ABA) in non-climacteric fruits. Common fig (Ficus carica) shows a dual-ripening mechanism, which is not fully understood. Here, we detected separate peaks of ethylene and ABA in fig fruits at the onset- and on-ripening stages, in conjunction with a sharp rise in glucose and fructose contents. In a newly-designed split-fruit system, exogenous ethylene failed to rescue fluridone-inhibited fruit ripening, whereas exogenous ABA rescued 2-amino-ethoxy-vinyl glycine (AVG)-inhibited fruit ripening. Transcriptome analysis revealed changes in the expression of genes key to both ABA and ethylene biosynthesis and perception during fig fruit ripening. At the de-greening stage, downregulation of FcACO2 or FcPYL8 retarded ripening, but downregulation of FcETR1/2 did not; unexpectedly, downregulation of FcAAO3 promoted ripening, but it inhibited ripening only before the de-greening stage. Furthermore, we detected an increase in ethylene emissions in the FcAAO3-RNAi ripening fruit and a decrease in ABA levels in the FcACO2-RNAi unripening fruit. Importantly, FcPYL8 can bind to ABA, suggesting that it functions as an ABA receptor. Our findings support the hypothesis that ethylene regulates the fig fruit ripening in an ABA-dependent manner. We propose a model for the role of the ABA-ethylene interaction in climacteric/non-climacteric processes.

Reannotation of the cultivated strawberry genome and establishment of a strawberry genome database

Cultivated strawberry (Fragaria × ananassa) is an important fruit crop species whose fruits are enjoyed by many worldwide. An octoploid of hybrid origin, the complex genome of this species was recently sequenced, serving as a key reference genome for cultivated strawberry and related species of the Rosaceae family. The current annotation of the F. ananassa genome mainly relies on ab initio predictions and, to a lesser extent, transcriptome data. Here, we present the structure and functional reannotation of the F. ananassa genome based on one PacBio full-length RNA library and ninety-two Illumina RNA-Seq libraries. This improved annotation of the F. ananassa genome, v1.0.a2, comprises a total of 108,447 gene models, with 97.85% complete BUSCOs. The models of 19,174 genes were modified, 360 new genes were identified, and 11,044 genes were found to have alternatively spliced isoforms. Additionally, we constructed a strawberry genome database (SGD) for strawberry gene homolog searching and annotation downloading. Finally, the transcriptome of the receptacles and achenes of F. ananassa at four developmental stages were reanalyzed and qualified, and the expression profiles of all the genes in this annotation are also provided. Together, this study provides an updated annotation of the F. ananassa genome, which will facilitate genomic analyses across the Rosaceae family and gene functional studies in cultivated strawberry.

Grafting Delays Watermel on Fruit Ripening by Altering Gene Expression of ABA Centric Phytohormone Signaling

Grafting cultivation is implemented worldwide mainly to resist abiotic and biotic stresses and is an effective method to improve watermelon production. However, grafting may affect fruit development and quality. In our experiment, pumpkin-grafted (PG) watermelon fruits developed slower and the ripening period was extended compared to self-grafted (SG) fruits. We found that the concentrations of abscisic acid (ABA) among endogenous phytohormones were dramatically reduced by pumpkin grafting. In order to understand these changes at the gene expression level, we performed a comprehensive analysis of the fruit flesh transcriptomes between PG and SG during fruit development and ripening. A total of 1,675 and 4,102 differentially expressed genes (DEGs) were identified between PG and SG. Further functional enrichment analysis revealed that these DEGs were associated with carbohydrate biosynthesis, phytohormone signaling transmission, and cell wall metabolism categories. ABA centric phytohormone signaling and fruit quality-related genes including ABA receptor, PP2C proteins, AP2-EREBP transcription factors, sucrose transporter, and carotenoid isomerase were co-expressed with fruit ripening. These results provide the valuable resource for understanding the mechanism of pumpkin grafting effect on watermelon fruit ripening and quality development.

Update on the Roles of Polyamines in Fleshy Fruit Ripening, Senescence, and Quality

Ripening of fleshy fruits involves complex physiological, biochemical, and molecular processes that coincide with various changes of the fruit, including texture, color, flavor, and aroma. The processes of ripening are controlled by ethylene in climacteric fruits and abscisic acid (ABA) in non-climacteric fruits. Increasing evidence is also uncovering an essential role for polyamines (PAs) in fruit ripening, especially in climacteric fruits. However, until recently breakthroughs have been made in understanding PA roles in the ripening of non-climacteric fruits. In this review, we compare the mechanisms underlying PA biosynthesis, metabolism, and action during ripening in climacteric and non-climacteric fruits at the physiological and molecular levels. The PA putrescine (Put) has a role opposite to that of spermidine/spermine (Spd/Spm) in cellular metabolism. Arginine decarboxylase (ADC) is crucial to Put biosynthesis in both climacteric and non-climacteric fruits. S-adenosylmethionine decarboxylase (SAMDC) catalyzes the conversion of Put to Spd/Spm, which marks a metabolic transition that is concomitant with the onset of fruit ripening, induced by Spd in climacteric fruits and by Spm in non-climacteric fruits. Once PA catabolism is activated by polyamine oxidase (PAO), fruit ripening and senescence are facilitated by the coordination of mechanisms that involve PAs, hydrogen peroxide (H₂O₂), ABA, ethylene, nitric oxide (NO), and calcium ions (Ca²⁺). Notably, a signal derived from PAO5-mediated PA metabolism has recently been identified in strawberry, a model system for non-climacteric fruits, providing a deeper understanding of the regulatory roles played by PAs in fleshy fruit ripening.

Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression patterns during somatic embryogenesis in Dimocarpus longan Lour

The NAM, ATAF1/2, and CUC2 form a huge plant-specific gene family of NAC TFs that are involved in the growth, development, and regulation of biotic and abiotic stress responses. Although the draft genome of longan (Dimocarpus longan Lour.) has been published, however the comprehensive data regarding the functions, evolution, and expression patterns of the NAC family are still unavailable. In this study, a comprehensive analysis of the NAC transcription factor family in longan was performed, and a total of 114 NAC genes were found. We investigated the NAC gene family exploring the phylogeny, domain conservation, intron/exon, motifs, cis-regulatory elements, protein-protein interaction, and expression profiles of RNA-seq samples in different tissues and early somatic embryogenesis of longan. Phylogenetic analysis showed that the genes with similar gene structure and motif distribution were clustered in the same group. Cis-element identification indicates the possible role of NAC genes in biological and physiological processes. Protein-protein interaction identified the DlNACs homologous with Arabidopsis proteins. We further investigated the expression pattern of DlNAC genes in different tissues (pulp, stem, large fruit, young fruit, and flower) during somatic embryogenesis at embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), and globular embryos (GE) stages. The qRT-PCR results showed that the DlNAC genes were expressed higher at EC and GE stage compared with ICpEC stage. In conclusion, our results provide insight into the evolution, diversity, and characterization of NAC genes in the longan and provide a base for understanding their biological roles and molecular mechanisms in plants.

Beyond Ethylene: New Insights Regarding the Role of Alternative Oxidase in the Respiratory Climacteric

Climacteric fruits are characterized by a dramatic increase in autocatalytic ethylene production that is accompanied by a spike in respiration at the onset of ripening. The change in the mode of ethylene production from autoinhibitory to autostimulatory is known as the System 1 (S1) to System 2 (S2) transition. Existing physiological models explain the basic and overarching genetic, hormonal, and transcriptional regulatory mechanisms governing the S1 to S2 transition of climacteric fruit. However, the links between ethylene and respiration, the two main factors that characterize the respiratory climacteric, have not been examined in detail at the molecular level. Results of recent studies indicate that the alternative oxidase (AOX) respiratory pathway may play an essential role in mediating cross-talk between ethylene response, carbon metabolism, ATP production, and ROS signaling during climacteric ripening. New genomic, metabolic, and epigenetic information sheds light on the interconnectedness of ripening metabolic pathways, necessitating an expansion of the current, ethylene-centric physiological models. Understanding points at which ripening responses can be manipulated may reveal key, species- and cultivar-specific targets for regulation of ripening, enabling superior strategies for reducing postharvest wastage.

Transcriptome analysis of strawberry fruit in response to exogenous arginine

Transcriptome and physiological analysis showed that exogenous arginine can delay the ripening process of postharvest strawberry fruit. Arginine (Arg) plays an important role in the growth and development of plants, but its growth and development regulatory mechanisms in strawberry fruit are unknown. In this study, we found that the content of Arg decreased after the onset of fruit coloration and exogenous Arg inhibited fruit coloration. We comprehensively analyzed the transcriptome of 'Sweet Charlie' strawberry fruit with or without Arg treatment and identified a large number of differential genes and metabolites. Based on the transcriptome data, we also found that Arg inhibited ripening, which coincided with changes in several physiological parameters and their corresponding gene transcripts, including firmness, anthocyanin content, sugar content, Arg content, indole-acetic acid (IAA) content, abscisic acid (ABA) content, and ethylene emissions. We also found that Arg induced the expression of heat-shock proteins (HSPs) and antioxidant enzyme genes, which improved strawberry stress resistance. This study elucidated the molecular mechanism by which exogenous Arg delays strawberry fruit ripening, providing some genetic information to help guide the future improvement and cultivation of strawberry.

Auxin regulates anthocyanin biosynthesis through the auxin repressor protein MdIAA26

Auxin plays an important role in plant growth and development; for example, it regulates the elongation and division of plant cells, the formation of plantlet's geotropism and phototropism, and the growth of main lateral roots and hypocotyl. IAA gene is associated with auxin and can response to biotic and abiotic stress in plants. However, the regulatory effect of auxin on anthocyanin accumulation has been rarely reported. In this study, we show that auxin inhibites the accumulation of anthocyanin and decreases the expression of genes related to anthocyanin synthesis in calli, leaves, and seedlings of apple. The expression levels of MdIAA family genes were determined, and we found that MdIAA26 significantly responded to auxin, which also induced MdIAA26 degradation. Functional analysis of MdIAA26 showed that overexpressing MdIAA26 in apple calli and Arabidopsis could promote the accumulation of anthocyanin and up-regulate the genes related to anthocyanin synthesis. Furthermore, the MdIAA26-overexpressing Arabidopsis could counteract auxin-induced inhibition on anthocyanin accumulation, which indicates that auxin inhibits the accumulation of anthocyanin in apple by degrading MdIAA26 protein.

LbNR-Derived Nitric Oxide Delays Lycium Fruit Coloration by Transcriptionally Modifying Flavonoid Biosynthetic Pathway

Anthocyanin-derived fleshy fruit pigmentation has become an excellent system for studying the regulatory network underlying fruit ripening and quality. The transcriptional control of anthocyanin biosynthesis by MYB-bHLH-WDR complexes has been well established, but the intermediate signals through which the environmental or developmental cues regulate these transcription factors remain poorly understood. Here we found that nitric oxide (NO) production during Lycium fruit ripening decreased progressively presenting a negative relationship with anthocyanins. After cloning of the nitric reductase (NR) gene from Lycium barbarum (LbNR) plants, we demonstrated that LbNR-derived NO partially inhibited anthocyanin biosynthesis but enhanced proanthocyanidin (PA) accumulation, and delayed fruit coloration. Application of the NO donor, sodium nitroprusside (SNP), produced a similar effect. The endogenous or exogenous NO downregulated the transcripts both of the regulatory genes and the structural genes that related to anthocyanin biosynthesis, while upregulated both of those genes that related to PA biosynthesis. Given there is a significant negative relationship between the levels of anthocyanins and PAs during Lycium fruit ripening, NO not only inhibited anthocyanin de novo biosynthesis but redirected the flavonoid biosynthetic pathway from anthocyanins to PA production. Two types of LrMYB transcription factors of opposite nature, namely anthocyanin-specific and PA-specific, which belong to the R2R3-MYB subfamily and 1R-MYB subfamily, respectively, were identified from L. ruthenicum fruits. It was further found that NO acts by antagonizing the ABA signaling, a phytohormone we have previously shown playing a positive role in Lycium fruit coloration. Our results provided particularly novel information about NO-ABA-anthocyanin interplay during Lycium fruit development and ripening, which may fill a gap between the developmental cues and the transcriptional regulation of anthocyanin biosynthesis.

CpARF2 and CpEIL1 interact to mediate auxin-ethylene interaction and regulate fruit ripening in papaya

Papaya (Carica papaya L.) is a commercially important fruit crop. Various phytohormones, particularly ethylene and auxin, control papaya fruit ripening. However, little is known about the interaction between auxin and ethylene signaling during the fruit ripening process. In the present study, we determined that the interaction between the CpARF2 and CpEIL1 mediates the interaction between auxin and ethylene signaling to regulate fruit ripening in papaya. We identified the ethylene-induced auxin response factor CpARF2 and demonstrated that it is essential for fruit ripening in papaya. CpARF2 interacts with an important ethylene signal transcription factor CpEIL1, thus increasing the CpEIL1-mediated transcription of the fruit ripening-associated genes CpACS1, CpACO1, CpXTH12 and CpPE51. Moreover, CpEIL1 is ubiquitinated by CpEBF1 and is degraded through the 26S proteasome pathway. However, CpARF2 weakens the CpEBF1-CpEIL1 interaction and interferes with CpEBF1-mediated degradation of CpEIL1, promoting fruit ripening. Therefore, CpARF2 functions as an integrator in the auxin-ethylene interaction and regulates fruit ripening by stabilizing CpEIL1 protein and promoting the transcriptional activity of CpEIL1. To our knowledge, we have revealed a novel module of CpARF2/CpEIL1/CpEBF1 that fine-tune fruit ripening in papaya. Manipulating this mechanism could help growers tightly control papaya fruit ripening and prolong shelf life.