Characteristics and regulatory pathway of the PrupeSEP1 SEPALLATA gene during ripening and softening in peach fruits

In-situ growth of Mn-Ni3S2 on nickel foam for catalytic ozonation of p-nitrophenol

In this study, a new catalyst for catalytic ozonation was obtained by in-situ growth of Mn-Ni3S2 nanosheets on the surface of nickel foam (NF). The full degradation of p-nitrophenol (PNP) was accomplished under optimal conditions in 40 min. The effects of material dosage, ozone dosage, pH and the presence of inorganic anions on the degradation efficiency of PNP were investigated. ESR analysis showed that singlet oxygen (1O2) and superoxide radical (O2•-) are the main contributors of PNP degradation. This study offers a new combination of supported catalysts with high efficiency and easy recovery, which provides a new idea for wastewater treatment.

Advances in genomics and genome editing for improving strawberry (Fragaria ×ananassa)

The cultivated strawberry, Fragaria ×ananassa, is a recently domesticated fruit species of economic interest worldwide. As such, there is significant interest in continuous varietal improvement. Genomics-assisted improvement, including the use of DNA markers and genomic selection have facilitated significant improvements of numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations and precision nucleotide substitutions in the target genome, revolutionizing functional genomics and crop improvement. Genome editing is beginning to gain traction in the more challenging polyploid crops, including allo-octoploid strawberry. The release of high-quality reference genomes and comprehensive subgenome-specific genotyping and gene expression profiling data in octoploid strawberry will lead to a surge in trait discovery and modification by using CRISPR/Cas. Genome editing has already been successfully applied for modification of several strawberry genes, including anthocyanin content, fruit firmness and tolerance to post-harvest disease. However, reports on many other important breeding characteristics associated with fruit quality and production are still lacking, indicating a need for streamlined genome editing approaches and tools in Fragaria ×ananassa. In this review, we present an overview of the latest advancements in knowledge and breeding efforts involving CRISPR/Cas genome editing for the enhancement of strawberry varieties. Furthermore, we explore potential applications of this technology for improving other Rosaceous plant species.

Effect of EVA film and chitosan coating on quality and physicochemical characteristics of mango fruit during postharvest storage

Mango (Mangifera indica L.) is a major tropical fruit, but a short postharvest life hampers marketing. The objective of this work is to assess the influence of a novel nanocomposite poly (ethylene-co-vinyl acetate) (EVA) film and Chitosan (CTS) affect on mango postharvest quality while stored at 20 °C. The results showed that the film coating treatment reduced the decay rate and weight loss of mangoes, maintaining good postharvest quality of mango fruit. The film coating treatment increased the antioxidant capacity of mangoes by inhibiting PPO activity and increasing the activity of antioxidant enzymes. ACS, ACO, and ethylene release were all suppressed, as well as the expression of the ethylene receptors genes ETR1, ETR2, and ERS2, thus delaying mango aging. After harvest, the EVA treatment was superior to the CTS treatment in mango preservation.

Transcription factor PpNAC1 and DNA demethylase PpDML1 synergistically regulate peach fruit ripening

Fruit ripening is accompanied by dramatic changes in color, texture, and flavor and is regulated by transcription factors (TFs) and epigenetic factors. However, the detailed regulatory mechanism remains unclear. Gene expression patterns suggest that PpNAC1 (NAM/ATAF1/2/CUC) TF plays a major role in peach (Prunus persica) fruit ripening. DNA affinity purification (DAP)-seq combined with transactivation tests demonstrated that PpNAC1 can directly activate the expression of multiple ripening-related genes, including ACC synthase1 (PpACS1) and ACC oxidase1 (PpACO1) involved in ethylene biosynthesis, pectinesterase1 (PpPME1), pectate lyase1 (PpPL1), and polygalacturonase1 (PpPG1) related to cell wall modification, and lipase1 (PpLIP1), fatty acid desaturase (PpFAD3-1), and alcohol acyltransferase1 (PpAAT1) involved in volatiles synthesis. Overexpression of PpNAC1 in the tomato (Solanum lycopersicum) nor (nonripening) mutant restored fruit ripening, and its transient overexpression in peach fruit induced target gene expression, supporting a positive role of PpNAC1 in fruit ripening. The enhanced transcript levels of PpNAC1 and its target genes were associated with decreases in their promoter mCG methylation during ripening. Declining DNA methylation was negatively associated with increased transcripts of DNA demethylase1 (PpDML1), whose promoter is recognized and activated by PpNAC1. We propose that decreased methylation of the promoter region of PpNAC1 leads to a subsequent decrease in DNA methylation levels and enhanced transcription of ripening-related genes. These results indicate that positive feedback between PpNAC1 and PpDML1 plays an important role in directly regulating expression of multiple genes required for peach ripening and quality formation.

Flower development and a functional analysis of related genes in Impatiens uliginosa

Impatiens uliginosa is a plant of the Impatiens, with peculiar flowers. In this study, we combined morphogenesis and molecular biology to explore its development of flowers. An analysis of basic observational data and paraffin sectioning showed that it took approximately 13 d for the floral organs to differentiate. An analysis of the development of inflorescences and floral organs by scanning electron microscopy showed that the inflorescence of I. uliginosa is a spiral raceme. The floral organs differentiated in the following order: lateral sepals (Ls), posterior sepal (Ps), anterior sepals (As), anterior petal (Ap), lateral petals (Lp), stamens (St) and gynoecium (Gy). I. uliginosa was found to have four sepals, and the connate stamens are caused by the fusion and growth of filament appendages. The results of fluorescence quantification and virus-induced gene silencing showed that I. uliginosa had its own unique model for flower development, and there was functional diversity of IuAP1 and IuDEF. Among them, IuAP1 controls the formation of bract s (Br), regulates the morphogenesis of posterior sepal, controls the anthocyanin precipitation of the anterior petals and the formation of lateral petals. IuDEF regulates the morphogenesis of lateral sepals, the length of development of the spur, and controls the size of yellow flower color plaques of the lateral petals. In this study, the process of flower development and the function of flower development genes of I. uliginosa were preliminarily verified. This study provides basic guidance and new concepts that can be used to study the development of Impatiens flowers.

AP3 promotes the synthesis of condensed tannin in fruit by positively regulating ANR expression

Condensed tannins are often found in fruits and nuts and have an astringent flavor. The synthesis pathway of condensed tannins is already clear, but few related regulatory factors have been explored. Previous studies about MADS-box transcription factors have mainly focused on the regulation of floral organ development. Recent studies have shown that MADS-box are also involved in fruit development, maturation, and quality. The fruit of Quercus fabri is rich in starch and nutrients in its kernel but is difficult to eat directly because of its high condensed tannin content. This study identified and functionally characterized the MADS-box transcription factor QfAP3 in Q. fabri. Functional analysis based on overexpression in Micro-Tom showed that QfAP3 promoted condensed tannin synthesis. By analyzing the expression trend of key genes in the condensed tannin synthesis pathway in Micro-Tom plants, we found that the expression trend of ANR was consistent with that of QfAP3, and QfAP3 could bind to the promoter of ANR and positively regulate it. This study has discovered new functions of MADS-box transcription factors in fruit quality formation, developed new regulatory factors for the synthesis pathway of condensed tannin, and provided a biotechnological method that can effectively reduce astringency in fruit.

Epigenomic mechanism regulating the quality and ripeness of apple fruit with differing harvest maturity

Harvest maturity significantly affects the quality of apple fruit in post-harvest storage process. Although the regulatory mechanisms underlying fruit ripening have been studied, the associated epigenetic modifications remain unclear. Thus, we compared the DNA methylation changes and the transcriptional responses of mature fruit (MF) and immature fruit (NF). There were significant correlations between DNA methylation and gene expression. Moreover, the sugar contents (sucrose, glucose, and fructose) were higher in MF than in NF, whereas the opposite pattern was detected for the starch content. The expression-level differences were due to DNA methylations and ultimately resulted in diverse fruit textures and ripeness. Furthermore, the higher ethylene, auxin, and abscisic acid levels in MF than in NF, which influenced the fruit texture and ripening, were associated with multiple differentially expressed genes in hormone synthesis, signaling, and response pathways (ACS, ACO, ZEP, NCED, and ABA2) that were regulated by DNA methylations. Multiple transcription factor genes involved in regulating fruit ripening and quality via changes in DNA methylation were identified, including MIKCC-type MADS-box genes and fruit ripening-related genes (NAP, SPL, WRKY, and NAC genes). These findings reflect the diversity in the epigenetic regulation of gene expression and may be relevant for elucidating the epigenetic regulatory mechanism underlying the ripening and quality of apple fruit with differing harvest maturity.

The apple transcription factor MdZF-HD11 regulates fruit softening by promoting Mdβ-GAL18 expression

Fruit ripening and the associated softening are major determinants of fruit quality and post-harvest shelf life. Although the mechanisms underlying fruit softening have been intensively studied, there are limited reports on the regulation of fruit softening in apples (Malus domestica). Here, we identified a zinc finger homeodomain transcription factor MdZF-HD11that trans-activates the promoter of Mdβ-GAL18, which encodes a pectin-degradation enzyme associated with cell wall metabolism. Both MdZF-HD11 and Mdβ-GAL18 genes were up-regulated by exogenous ethylene treatment and repressed by 1-methylcyclopropene treatment. Further experiments revealed that MdZF-HD11 binds directly to the Mdβ-GAL18 promoter and up-regulates its transcription. Moreover, using transgenic apple fruit calli, we found that overexpression of Mdβ-GAL18 or MdZF-HD11 significantly enhanced β-galactosidase activity, and overexpression of MdZF-HD11 induced the expression of Mdβ-GAL18. We also discovered that transient overexpression of Mdβ-GAL18 or MdZF-HD11 in 'Golden Delicious' apple significantly increased the release of ethylene, reduced fruit firmness, promoted the transformation of skin color from green to yellow, and accelerated ripening and softening of the fruit. Finally, the overexpression of MdZF-HD11 in tomato also promoted fruit softening. Collectively, these results indicate that ethylene-induced MdZF-HD11 interacts with Mdβ-GAL18 to promote the post-harvest softening of apple.

Advancing tree genomics to future proof next generation orchard production

The challenges facing tree orchard production in the coming years will be largely driven by changes in the climate affecting the sustainability of farming practices in specific geographical regions. Identifying key traits that enable tree crops to modify their growth to varying environmental conditions and taking advantage of new crop improvement opportunities and technologies will ensure the tree crop industry remains viable and profitable into the future. In this review article we 1) outline climate and sustainability challenges relevant to horticultural tree crop industries, 2) describe key tree crop traits targeted for improvement in agroecosystem productivity and resilience to environmental change, and 3) discuss existing and emerging genomic technologies that provide opportunities for industries to future proof the next generation of orchards.

Functional conservation and divergence of SEPALLATA-like genes in floral development in Cymbidium sinense

Cymbidium sinense is one of the most important traditional Chinese Orchids due to its unique and highly ornamental floral organs. Although the ABCDE model for flower development is well-established in model plant species, the precise roles of these genes in C. sinense are not yet fully understood. In this study, four SEPALLATA-like genes were isolated and identified from C. sinense. CsSEP1 and CsSEP3 were grouped into the AGL9 clade, while CsSEP2 and CsSEP4 were included in the AGL2/3/4 clade. The expression pattern of CsSEP genes showed that they were significantly accumulated in reproductive tissues and expressed during flower bud development but only mildly detected or even undetected in vegetative organs. Subcellular localization revealed that CsSEP1 and CsSEP4 were localized to the nucleus, while CsSEP2 and CsSEP3 were located at the nuclear membrane. Promoter sequence analysis predicted that CsSEP genes contained a number of hormone response elements (HREs) and MADS-box binding sites. The early flowering phenotype observed in transgenic Arabidopsis plants expressing four CsSEP genes, along with the expression profiles of endogenous genes, such as SOC1, LFY, AG, FT, SEP3 and TCPs, in both transgenic Arabidopsis and C. sinense protoplasts, suggested that the CsSEP genes played a regulatory role in the flowering transition by influencing downstream genes related to flowering. However, only transgenic plants overexpressing CsSEP3 and CsSEP4 caused abnormal phenotypes of floral organs, while CsSEP1 and CsSEP2 had no effect on floral organs. Protein-protein interaction assays indicated that CsSEPs formed a protein complex with B-class CsAP3-2 and CsSOC1 proteins, affecting downstream genes to regulate floral organs and flowering time. Our findings highlighted both the functional conservation and divergence of SEPALLATA-like genes in C. sinense floral development. These results provided a valuable foundation for future studies of the molecular network underlying floral development in C. sinense.

Comparative physiological and transcriptomic analyses provide insights into fruit softening in Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don]

Fruit softening is a complex, genetically programmed and environmentally regulated process, which undergoes biochemical and physiological changes during fruit development. The molecular mechanisms that determine these changes in Chinese cherry [Cerasus peseudocerasus (Lindl.) G.Don] fruits are still unknown. In the present study, fruits of hard-fleshed 'Hongfei' and soft-fleshed 'Pengzhoubai' varieties of Chinese cherry were selected to illustrate the fruit softening at different developmental stages. We analyzed physiological characteristics and transcriptome profiles to identify key cell wall components and candidate genes related to fruit softening and construct the co-expression networks. The dynamic changes of cell wall components (cellulose, hemicellulose, pectin, and lignin), the degrading enzyme activities, and the microstructure were closely related to the fruit firmness during fruit softening. A total of 6,757 and 3,998 differentially expressed genes (DEGs) were screened between stages and varieties, respectively. Comprehensive functional enrichment analysis supported that cell wall metabolism and plant hormone signal transduction pathways were involved in fruit softening. The majority of structural genes were significantly increased with fruit ripening in both varieties, but mainly down-regulated in Hongfei fruits compared with Pengzhoubai, especially DEGs related to cellulose and hemicellulose metabolism. The expression levels of genes involving lignin biosynthesis were decreased with fruit ripening, while mainly up-regulated in Hongfei fruits at red stage. These obvious differences might delay the cell all degrading and loosening, and enhance the cell wall stiffing in Hongfei fruits, which maintained a higher level of fruit firmness than Pengzhoubai. Co-expressed network analysis showed that the key structural genes were correlated with plant hormone signal genes (such as abscisic acid, auxin, and jasmonic acid) and transcription factors (MADS, bHLH, MYB, ERF, NAC, and WRKY). The RNA-seq results were supported using RT-qPCR by 25 selected DEGs that involved in cell wall metabolism, hormone signal pathways and TF genes. These results provide important basis for the molecular mechanism of fruit softening in Chinese cherry.

The potential of a natural iron ore residue application in the efficient removal of tetracycline hydrochloride from an aqueous solution: insight into the degradation mechanism

In the existing research, most of the heterogeneous catalysts applied in the activation of persulfate to degrade organic pollutants were synthesized from chemical reagents in the laboratory. In this paper, we have obtained a spent iron ore (IO) residue directly collecting from the iron ore plants, and efficiently activating peroxydisulfate (PS) to produce reactive free radicals. The experimental results demonstrated that the IO could effectively activate PS to degrade tetracycline hydrochloride (TCH), with TCH removal rate reaching up to 85.6% within 2 h at room temperature. The TCH removal rate was increased with increasing iron ore dosage, while the more acidic pH condition would be favorable to TCH removal process. The material characterization results demonstrated that the dominant components of IO were Fe₃O₄ and FeOOH. The transformation from Fe(II) to Fe(III) at the surface IO was observed after TCH degradation. What's more, the quenching experiment and EPR detection results confirmed that the sulfate radical (SO₄^•-) and hydroxyl radicals (•OH) would be acting as the main free radicals for TCH degradation. This study could not only explore a novel way to recycle the discarded iron ore, but also further expand its application in an effective activation of PS in an aqueous solution.

Transcriptional regulation of fleshy fruit texture

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

Characterization and functional analysis of the MADS-box EgAGL9 transcription factor from the mesocarp of oil palm (Elaeis guineensis Jacq.)

Oil palm (Elaeis guineensis Jacq.) is one of the most important oil crops in the world, and compared to all oil crops, it has the highest productive efficiency. In the present study, a MADS-box transcription factor of the AGAMOUS class, named EgAGL9, was identified by expression profile analysis in the different developmental stages of oil palm mesocarp. Real-time quantitative PCR results confirmed that the expression of EgAGL9 increased rapidly during the last stages of oil palm mesocarp development. Then, three downstream genes, including EgSAD (Stearoyl-ACP desaturase), EgTSA (Tryptophan synthase) and EgSDH (Succinate dehydrogenase), were screened by ChIP-Seq and data analysis. EMSA analysis verified that EgAGL9 interacted with the promoter regions of EgSAD, EgTSA and EgSDH. Moreover, the expression levels of EgSAD, EgTSA and EgSDH were downregulated in EgAGL9-overexpressing protoplasts and calli of oil palm. Compared to WT, the total lipid content and ratio of unsaturated fatty acids in transgenic calli (including oleic acid, linoleic acid and linolenic acid) were significantly decreased. Together, these results revealed that these three EgAGL9-regulated genes are involved in regulatory pathways in the oil palm mesocarp. Compared with previous studies, the present study provides a new research strategy for understanding of the molecular regulatory pathways of lipid metabolism in mesocarp of oil palm. The obtained results will bring a new perspective for a comprehensive understanding of the regulation of the metabolic accumulation in the oil palm mesocarp.

Transcriptome analysis of peach fruit under 1-MCP treatment provides insights into regulation network in melting peach softening

Peach (Prunus persica L.) displays distinguish texture phenotype during postharvest, which could be classified into three types, including melting flesh (MF), non-melting flesh (NMF) and stony-hard (SH). Of that MF peach would soften rapidly with an outbreak of ethylene production, which cause a huge waste during fruit transportation and storage. 1-methylcyclopropene (1-MCP) was used to alleviate fruit softening. In this study, we performed RNA-sequencing on two MF peach cultivars (‘YuLu’ and ‘Yanhong’) after 1-MCP treatment to identify the candidate genes participating in peach fruit softening. 167 genes were identified by WGCNA and correlation analysis, which could respond to 1-MCP treatment and might be related to softening. Among them, 5 auxin related genes including 2 IAAs, 1 ARF and 2 SAURs, and 4 cell wall modifying genes (PpPG1, PpPG2, PpPG24 and PpPMEI) were characterized as key genes participating in MF peach softening. Furthermore, 2 transcription factors, which belong to HD-ZIP and MYB were predicted as candidates regulating softening process by constructing transcriptional network of these 4 cell wall modifying genes combined with expression pattern analysis, of that the HD-ZIP could trans-activate promoter of PpPG1.

Genome-wide identification and characterization of long noncoding RNAs during peach (Prunus persica) fruit development and ripening

LncRNAs represent a class of RNA transcripts of more than 200 nucleotides (nt) in length without discernible protein-coding potential. The expression levels of lncRNAs are significantly affected by stress or developmental cues. Recent studies have shown that lncRNAs participate in fruit development and ripening processes in tomato and strawberry; however, in other fleshy fruits, the association between lncRNAs and fruit ripening remains largely elusive. Here, we constructed 9 ssRNA-Seq libraries from three different peach (Prunus persica) fruit developmental stages comprising the first and second exponential stages and the fruit-ripening stage. In total, 1500 confident lncRNAs from 887 loci were obtained according to the bioinformatics analysis. The lncRNAs identified in peach fruits showed distinct characteristics compared with protein-coding mRNAs, including lower expression levels, lower complexity of alternative splicing, shorter isoforms and smaller numbers of exons. Expression analysis identified 575 differentially expressed lncRNAs (DELs) classified into 6 clusters, among which members of Clusters 1, 2, 4 and 5 were putatively associated with fruit development and ripening processes. Quantitative real-time PCR revealed that the DELs indeed had stage-specific expression patterns in peach fruits. GO and KEGG enrichment analysis revealed that DELs might be associated with fruit-ripening-related physiological and metabolic changes, such as flavonoid biosynthesis, fruit texture softening, chlorophyll breakdown and aroma compound accumulation. Finally, the similarity analysis of lncRNAs within different plant species indicated the low sequence conservation of lncRNAs. Our study reports a large number of fruit-expressed lncRNAs and identifies fruit development phase-specific expressed lncRNA members, which highlights their potential functions in fruit development and ripening processes and lays the foundations for future functional research.

PpSAUR43, an Auxin-Responsive Gene, Is Involved in the Post-Ripening and Softening of Peaches

Auxin’s role in the post-ripening of peaches is widely recognized as important. However, little is known about the processes by which auxin regulates fruit post-ripening. As one of the early auxin-responsive genes, it is critical to understand the role of small auxin-up RNA (SAUR) genes in fruit post-ripening and softening. Herein, we identified 72 PpSAUR auxin-responsive factors in the peach genome and divided them into eight subfamilies based on phylogenetic analysis. Subsequently, the members related to peach post-ripening in the PpSAUR gene family were screened, and we targeted PpSAUR43. The expression of PpSAUR43 was decreased with fruit post-ripening in melting flesh (MF) fruit and was high in non-melting flesh (NMF) fruit. The overexpression of PpSAUR43 showed a slower rate of firmness decline, reduced ethylene production, and a delayed fruit post-ripening process. The MADS-box gene family plays an important regulatory role in fruit ripening. In this study, we showed with yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BIFC) experiments that PpSAUR43 can interact with the MADS-box transcription factor PpCMB1(PpMADS2), which indicates that PpSAUR43 may inhibit fruit ripening by suppressing the function of the PpCMB1 protein. Together, these results indicate that PpSAUR43 acts as a negative regulator involved in the peach post-ripening process.

PpePL1 and PpePL15 Are the Core Members of the Pectate Lyase Gene Family Involved in Peach Fruit Ripening and Softening

Pectin is the major component in the primary cell wall and middle lamella, maintaining the physical stability and mechanical strength of the cell wall. Pectate lyase (PL), a cell wall modification enzyme, has a major influence on the structure of pectin. However, little information and no comprehensive analysis is available on the PL gene family in peach (Prunus persica L. Batsch). In this study, 20 PpePL genes were identified in peach. We characterized their physicochemical characteristics, sequence alignments, chromosomal locations, and gene structures. The PpePL family members were classified into five groups based on their phylogenetic relationships. Among those, PpePL1, 9, 10, 15, and 18 had the higher expression abundance in ripe fruit, and PpePL1, 15, and 18 were upregulated during storage. Detailed RT-qPCR analysis revealed that PpePL1 and PpePL15 were responsive to ETH treatment (1 g L^-1 ethephon) with an abundant transcript accumulation, which suggested these genes were involved in peach ripening and softening. In addition, virus-induced gene silencing (VIGS) technology was used to identify the roles of PpePL1 and PpePL15. Compared to controls, the RNAi fruit maintained greater firmness in the early storage stage, increased acid-soluble pectin (ASP), and reduced water-soluble pectin (WSP). Moreover, transmission electron microscopy (TEM) showed that cell wall degradation was reduced in the fruit of RNAi-1 and RNAi-15, which indicated that softening of the RNAi fruit has been delayed. Our results indicated that PpePL1 and PpePL15 play an important role in peach softening by depolymerizing pectin and degrading cell wall.

Selection and Validation of Reliable Reference Genes for Gene Expression Studies in Different Genotypes and TRV-Infected Fruits of Peach (Prunus persica L. Batsch) during Ripening

Real-time quantitative PCR (RT-qPCR) is a powerful tool to detect and quantify transcription abundance, and the stability of the reference gene determines its success. However, the most suitable reference gene for different genotypes and tobacco rattle virus (TRV) infected fruits was unclear in peach (Prunus persica L. Batsch). In this study, 10 reference genes were selected and gene expression was characterized by RT-qPCR across all samples, including different genotypes and TRV-infected fruits during ripening. Four statistical algorithms (geNorm, NormFinder, BestKeeper, and RefFinder) were used to calculate the stability of 10 reference genes. The geNorm analysis indicated that two suitable reference genes should be used for gene expression normalization. In general, the best combination of reference genes was CYP2 and Tua5 for TRV-infected fruits and CYP2 and Tub1 for different genotypes. In 18S, GADPH, and TEF2, there is an unacceptable variability of gene expression in all experimental conditions. Furthermore, to confirm the validity of the reference genes, the expression levels of PpACO1, PpEIN2, and PpPL were normalized at different fruit storage periods. In summary, our results provide guidelines for selecting reliable reference genes in different genotypes and TRV-infected fruits and lay the foundation for accurate evaluation of gene expression for RT-qPCR analysis in peach.

The Roles of Floral Organ Genes in Regulating Rosaceae Fruit Development

The function of floral organ identity genes, APETALA1/2/3, PISTILLATA, AGAMOUS, and SEPALLATA1/2/3, in flower development is highly conserved across angiosperms. Emerging evidence shows that these genes also play important roles in the development of the fruit that originates from floral organs following pollination and fertilization. However, their roles in fruit development may vary significantly between species depending on the floral organ types contributing to the fruit tissues. Fruits of the Rosaceae family develop from different floral organ types depending on the species, for example, peach fruit flesh develops from carpellary tissues, whereas apple and strawberry fruit flesh develop from extra-carpellary tissues, the hypanthium and receptacle, respectively. In this review, we summarize recent advances in understanding floral organ gene function in Rosaceae fruit development and analyze the similarities and diversities within this family as well as between Rosaceae and the model plant species Arabidopsis and tomato. We conclude by suggesting future research opportunities using genomics resources to rapidly dissect gene function in this family of perennial plants.

Relying on the non-radical degradation of oxytetracycline by peroxymonosulfate activated with a magnetic Cu/Fe composite: performance and mechanism

CuFe-1 nanoparticles were successfully synthesized, and they could effectively activate peroxymonosulfate to assist the degradation of oxytetracycline.

The MADS-box gene FveSEP3 plays essential roles in flower organogenesis and fruit development in woodland strawberry

Flower and fruit development are two key steps for plant reproduction. The ABCE model for flower development has been well established in model plant species; however, the functions of ABCE genes in fruit crops are less understood. In this work, we identified an EMS mutant named R27 in woodland strawberry (Fragaria vesca), showing the conversion of petals, stamens, and carpels to sepaloid organs in a semidominant inheritance fashion. Mapping by sequencing revealed that the class E gene homolog FveSEP3 (FvH4_4g23530) possessed the causative mutation in R27 due to a G to E amino acid change in the conserved MADS domain. Additional fvesep3^CR mutants generated by CRISPR/Cas9 displayed similar phenotypes to fvesep3-R27. Overexpressing wild-type or mutated FveSEP3 in Arabidopsis suggested that the mutation in R27 might cause a dominant-negative effect. Further analyses indicated that FveSEP3 physically interacted with each of the ABCE proteins in strawberry. Moreover, both R27 and fvesep3^CR mutants exhibited parthenocarpic fruit growth and delayed fruit ripening. Transcriptome analysis revealed that both common and specific differentially expressed genes were identified in young fruit at 6-7 days post anthesis (DPA) of fvesep3 and pollinated wild type when compared to unpollinated wild type, especially those in the auxin pathway, a key hormone regulating fruit set in strawberry. Together, we provided compelling evidence that FveSEP3 plays predominant E functions compared to other E gene homologs in flower development and that FveSEP3 represses fruit growth in the absence of pollination and promotes fruit ripening in strawberry.

Functional conservation and divergence of SEPALLATA-like genes in the development of two-type florets in marigold

Marigold (Tagetes erecta), as one member of Asteraceae family, bears a typical capitulum with two morphologically distinct florets. The SEPALLATA genes are involved in regulating the floral meristem determinacy, organ identity, fruit maturation, seed formation, and plant architecture. Here, five SEP-like genes were cloned and identified from marigold. Sequence alignment and phylogenetic analysis demonstrated that TeSEP3-1, TeSEP3-2, and TeSEP3-3 proteins were grouped into SEP3 clade, and TeSEP1 and TeSEP4 proteins were clustered into SEP1/2/4 clade. Quantitative real-time PCR analysis revealed that TeSEP1 and TeSEP3-3 were broadly expressed in floral organs, and that TeSEP3-2 and TeSEP4 were mainly expressed in pappus and corollas, while TeSEP3-1 was mainly expressed in two inner whorls. Ectopic expression of TeSEP1, TeSEP3-2, TeSEP3-3, and TeSEP4 in arabidopsis and tobacco resulted in early flowering. However, overexpression of TeSEP3-1 in arabidopsis and tobacco caused no visible phenotypic changes. Notably, overexpression of TeSEP4 in tobacco decreased the number of petals and stamens. Overexpression of TeSEP1 in tobacco led to longer sepals and simpler inflorescence architecture. The comprehensive pairwise interaction analysis suggested that TeSEP proteins had a broad interaction with class A, C, D, E proteins to form dimers. The yeast three-hybrid analysis suggested that in ternary complexes, class B proteins interacted with TeSEP3 by forming heterodimer TePI-TeAP3-2. The regulatory network analysis of MADS-box genes in marigold further indicated that TeSEP proteins played a "glue" role in regulating floral organ development, implying functional conservation and divergence of MADS box genes in regulating two-type floret developments. This study provides an insight into the formation mechanism of floral organs of two-type florets, thus broadening our knowledge of the genetic basis of flower evolution.

Applications of virus-induced gene silencing for identification of gene function in fruit

With the development of bioinformatics, it is easy to obtain information and data about thousands of genes, but the determination of the functions of these genes depends on methods for rapid and effective functional identification. Virus-induced gene silencing (VIGS) is a mature method of gene functional identification developed over the last 20 years, which has been widely used in many research fields involving many species. Fruit quality formation is a complex biological process, which is closely related to ripening. Here, we review the progress and contribution of VIGS to our understanding of fruit biology and its advantages and disadvantages in determining gene function.

Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

BACKGROUND

Fruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences between the mesocarp of mature and ripe fruit, it would be possible to highlight critical molecular processes involved in the fruit ripening.

RESULTS

To accomplish this goal, the proteome from mature and ripe fruit was assessed from the variety O'Henry through shotgun proteomics using 1D-gel (PAGE-SDS) as fractionation method followed by LC/MS-MS analysis. Data from the 131,435 spectra could be matched to 2740 proteins, using the peach genome reference v1. After data pre-treatment, 1663 proteins could be used for comparison with datasets assessed using transcriptomic approaches and for quantitative protein accumulation analysis. Close to 26% of the genes that code for the proteins assessed displayed higher expression at ripe fruit compared to other fruit developmental stages, based on published transcriptomic data. Differential accumulation analysis between mature and ripe fruit revealed that 15% of the proteins identified were modulated by the ripening process, with glycogen and isocitrate metabolism, and protein localization overrepresented in mature fruit, as well as cell wall modification in ripe fruit. Potential biomarkers for the ripening process, due to their differential accumulation and gene expression pattern, included a pectin methylesterase inhibitor, a gibbellerin 2-beta-dioxygenase, an omega-6 fatty acid desaturase, a homeobox-leucine zipper protein and an ACC oxidase. Transcription factors enriched in NAC and Myb protein domains would target preferentially the genes encoding proteins more abundant in mature and ripe fruit, respectively.

CONCLUSIONS

Shotgun proteomics is an unbiased approach to get deeper into the proteome allowing to detect differences in protein abundance between samples. This technique provided a resolution so that individual gene products could be identified. Many proteins likely involved in cell wall and sugar metabolism, aroma and color, change their abundance during the transition from mature to ripe fruit.

PaMADS7, a MADS-box transcription factor, regulates sweet cherry fruit ripening and softening

E-class MADS-box transcription factors, SEPALLATA (SEP) genes have an important role in floral organ initiation and development and fruit ripening. In this study, four sweet cherry SEP-like genes (PaMADS2, PaMADS4, PaMADS5, and PaMADS7) were cloned and functionally characterized. Gene expression analysis showed that the differential expression levels of PaMADS4 and PaMADS7 coincided with fruit ripening, and expression of PaMADS2 and PaMADS5 did not. Expression of PaMADS7 was affected by ABA and IAA. Subcellular localization assay demonstrated that four sweet cherry SEP-like proteins were all localized inside the nucleus. Silencing PaMADS7 using TRV-mediated virus-induced gene silencing inhibited fruit ripening and influenced major ripening-related physiological processes, such as ABA content, soluble sugar contents, fruit firmness, and anthocyanin content, as well as expression of ripening-related genes. In addition, silencing of PaMADS7 induced phenotype defects that suppressed fruit ripening, which were rescued by exogenous ABA. Furthermore, yeast one-hybrid assay (Y1H) and transient expression analyses revealed that PaMADS7 directly binds to the promoter of PaPG1, which is involved in sweet cherry fruit softening, and positively activated PaPG1expression. These results showed that PaMADS7 is an indispensable positive regulator of sweet cherry fruit ripening and softening.

Auxin and Its Interaction With Ethylene Control Adventitious Root Formation and Development in Apple Rootstock

Adventitious root (AR) formation is indispensable for vegetative asexual propagation. Indole-3-butyric acid (IBA) functioned indirectly as precursor of IAA in regulating AR formation. Ethylene affects auxin synthesis, transport, and/or signaling processes. However, the interactions between auxin and ethylene that control AR formation in apple have not been elucidated. In this study, we investigated the effects of IBA and its interaction with ethylene on AR development in apple. The results revealed that IBA stimulated the formation of root primordia, increased the number of ARs, and upregulated expression of genes (MdWOX11, MdLBD16, and MdLBD29) involved in AR formation. Comparison of different periods of IBA application indicated that IBA was necessary for root primordium formation, while long time IBA treatment obviously inhibited root elongation. RNA-seq analysis revealed that many plant hormone metabolism and signal transduction related genes were differentially expressed. IBA stimulated the production of ethylene during AR formation. Auxin inhibiting ARs elongation depended on ethylene. Together, our results suggest that the inhibitory role of auxin on AR elongation in apples is partially mediated by stimulated ethylene production.

A critical evaluation of the role of ethylene and MADS transcription factors in the network controlling fleshy fruit ripening

Contents Summary 1724 I. Introduction 1725 II. Ripening genes 1725 III. The importance of ethylene in controlling ripening 1727 IV. The importance of MADS-RIN in controlling ripening 1729 V. Interactions between components of the ripening regulatory network 1734 VI. Conclusions 1736 Acknowledgements 1738 Author contributions 1738 References 1738 SUMMARY: Understanding the regulation of fleshy fruit ripening is biologically important and provides insights and opportunities for controlling fruit quality, enhancing nutritional value for animals and humans, and improving storage and waste reduction. The ripening regulatory network involves master and downstream transcription factors (TFs) and hormones. Tomato is a model for ripening regulation, which requires ethylene and master TFs including NAC-NOR and the MADS-box protein MADS-RIN. Recent functional characterization showed that the classical RIN-MC gene fusion, previously believed to be a loss-of-function mutation, is an active TF with repressor activity. This, and other evidence, has highlighted the possibility that MADS-RIN itself is not important for ripening initiation but is required for full ripening. In this review, we discuss the diversity of components in the control network, their targets, and how they interact to control initiation and progression of ripening. Both hormones and individual TFs affect the status and activity of other network participants, which changes overall network signaling and ripening outcomes. MADS-RIN, NAC-NOR and ethylene play critical roles but there are still unanswered questions about these and other TFs. Further attention should be paid to relationships between ethylene, MADS-RIN and NACs in ripening control.

Effects of hot air treatment in combination with Pichia guilliermondii on postharvest preservation of peach fruit

BACKGROUND

Antagonistic yeast and hot air treatment are two promising methods for conferring resistance to pathogenic fungi. The study assessed the effectiveness of hot-air treatment (45 °C, 4 h) and antagonistic yeast (Pichia guilliermondii at 10⁸ CFU mL^-1 ) alone or in combination on the two major postharvest diseases (Rhizopus stolonifer and Penicillium expansum), as well as the quality and antioxidant parameters in harvested peaches.

RESULTS

The combination of hot-air treatment and Pichia guilliermondii had notable inhibitory effects on infections in peach fruit wounds. In addition, the individual hot-air treatment or Pichia guilliermondii could improve quality indexes to varying degrees, but the combination of the above two treatments could achieve the highest efficacy. Furthermore, compared with other groups, the combined treatment induced the highest activities of superoxide dismutase and catalase, improved the content of total phenolics and reduced glutathione most obviously. Lastly, the most significant reductions in malondialdehyde content and relative electrical conductivity were observed in the combination-treated fruit.

CONCLUSIONS

The combined treatment could control fungal diseases, besides delay the decline of quality and antioxidant parameters, so as to achieve the purpose of fresh keeping for harvested peach fruit. © 2018 Society of Chemical Industry.

Identification of genes preferentially expressed in wild strawberry receptacle fruit and demonstration of their promoter activities

Fragaria vesca (F. vesca), the wild strawberry, is a diploid model for the commercial, octoploid strawberry as well as other members of the economically relevant Rosaceae family. Unlike the fruits of tomato and Arabidopsis, the fleshy fruit of strawberry is unique in that it is derived from the floral receptacle and has an external seed configuration. Thus, identification and subsequent characterization of receptacle-expressed genes may shed light on novel developmental processes or provide insight into how developmental regulation differs between receptacle-derived and ovary-derived fruits. Further, since fruit and flower tissues are the last organs to form on a plant, the development of receptacle fruit-specific promoters may provide useful molecular tools for research and application. In this work, we mined previously generated RNA-Seq datasets and identified 589 genes preferentially expressed in the strawberry receptacle versus all other profiled tissues. Promoters of a select subset of the 589 genes were isolated and their activities tested using a GUS transcriptional reporter. These promoters may now be used by the F. vesca research community for a variety of purposes, including driving expression of tissue-specific reporters, RNAi constructs, or specific genes to manipulate fruit development. Further, identified genes with receptacle-specific expression patterns, including MADS-Box and KNOX family transcription factors, are potential key regulators of fleshy fruit development and attractive candidates for functional characterization.

Lignin Involvement in Programmed Changes in Peach-Fruit Texture Indicated by Metabolite and Transcriptome Analyses

Texture is an important component of peach-fruit quality. In the present study, an analysis of metabolite and transcriptome profiles during storage of a nonmelting-flesh cultivar, 'Baili', and a melting-flesh cultivar, 'Hongli', was conducted to explore the molecular mechanisms underlying different fruit textures in peach. Results indicated that higher levels of anthocyanins were present in 'Hongli' peach, whereas lignin monomers and ethylene precursors were higher in 'Baili'. A transcriptome analysis indicated that genes associated with lignin synthesis were more highly expressed in 'Baili' than in 'Hongli', especially Pp4CL2, Pp4CL3, and PpCOMT2. Texture differences between the two varieties may be the result of differential expression of two branches of the phenylpropanoid metabolic pathway. One branch regulates flavonoid metabolism and was highly active in 'Hongli' fruit, whereas the other branch regulates lignin synthesis and was more highly active in 'Baili' fruit.

Down-Regulation of PpBGAL10 and PpBGAL16 Delays Fruit Softening in Peach by Reducing Polygalacturonase and Pectin Methylesterase Activity

β-galactosidases are cell wall hydrolases that play an important role in fruit softening. However, PpBGALs mechanism impacting on ethylene-dependent peach fruit softening was still unclear. In this study, we found that PpBGAL4, -6, -8, -10, -16, and -17 may be required for ethylene-dependent peach softening and PpBGAL10, -16 may make a main contribution to it among 17 PpBGALs. Utilization of virus-induced gene silencing (VIGS) showed that fruits were firmer than those of the control at 4 and 6 days after harvest (DAH) when PpBGAL10 and PpBGAL16 expression was down-regulated. Suppression of PpBGAL10 and PpBGAL16 expression also reduced PpPG21 and PpPME3 transcription, and polygalacturonase (PG) and pectinmethylesterases (PME) activity. Overall, total cell wall material and protopectin slowly declined, water-soluble pectin slowly increased, and cellulose and hemicellulose was altered significantly at 4 DAH, relative to control fruit. In addition, PpACO1 expression and ethylene production were also suppressed at 4 DAH because of inhibiting PpBGAL10 and PpBGAL16 expression. These results suggested that down-regulation of PpBGAL10 and PpBGAL16 expression delays peach fruit softening by decreasing PG and PME activity, which inhibits cell wall degradation and ethylene production.

Transcriptome profiling by RNA-Seq reveals differentially expressed genes related to fruit development and ripening characteristics in strawberries (Fragaria × ananassa)

Strawberry (Fragaria × ananassa) is an ideal plant for fruit development and ripening research due to the rapid substantial changes in fruit color, aroma, taste, and softening. To gain deeper insights into the genes that play a central regulatory role in strawberry fruit development and ripening characteristics, transcriptome profiling was performed for the large green fruit, white fruit, turning fruit, and red fruit stages of strawberry. A total of 6,608 differentially expressed genes (DEGs) with 2,643 up-regulated and 3,965 down-regulated genes were identified in the fruit development and ripening process. The DEGs related to fruit flavonoid biosynthesis, starch and sucrose biosynthesis, the citrate cycle, and cell-wall modification enzymes played important roles in the fruit development and ripening process. Particularly, some candidate genes related to the ubiquitin mediated proteolysis pathway and MADS-box were confirmed to be involved in fruit development and ripening according to their possible regulatory functions. A total of five ubiquitin-conjugating enzymes and 10 MADS-box transcription factors were differentially expressed between the four fruit ripening stages. The expression levels of DEGs relating to color, aroma, taste, and softening of fruit were confirmed by quantitative real-time polymerase chain reaction. Our study provides important insights into the complicated regulatory mechanism underlying the fruit ripening characteristics in Fragaria × ananassa.