Transcriptomic events associated with internal browning of apple during postharvest storage

Sugar beet root susceptibility to storage rots and downregulation of plant defense genes increases with time in storage

Storage rots are a significant cause of postharvest losses for the sugar beet crop, however, intrinsic physiological and genetic factors that determine the susceptibility of roots to pathogen infection and disease development are unknown. Research, therefore, was carried out to evaluate the disease development in sugar beet roots caused by two common storage pathogens as a function of storage duration and storage temperature, and to identify changes in the expression of defense genes that may be influencing the root susceptibility to disease. To evaluate root susceptibility to disease, freshly harvested roots were inoculated with Botrytis cinerea or Penicillium vulpinum on the day of harvest or after 12, 40, or 120 d storage at 5 or 12 °C and the weight of rotted tissue present in the roots after incubation for 35 d after inoculation were determined. Disease susceptibility and progression to B. cinerea and P. vulpinum increased with storage duration with elevations in susceptibility occurring more rapidly to B. cinerea than P. vulpinum. Also, B. cinerea was more aggressive than P. vulpinum and caused greater rotting and tissue damage in postharvest sugar beet roots. Storage temperature had minimal effect on root susceptibility to these rot-causing pathogens. Changes in defense gene expression were determined by sequencing mRNA isolated from uninoculated roots that were similarly stored for 12, 40 or 120 d at 5 or 12 °C. As susceptibility to rot increased during storage, concurrent changes in defense-related gene expression were identified, including the differential expression of 425 pathogen receptor and 275 phytohormone signal transduction pathway-related genes. Furthermore, plant resistance and hormonal signaling genes that were significantly altered in expression coincident with the change in root susceptibility to storage rots were identified. Further investigation into the function of these genes may ultimately elucidate methods by which storage rot resistance in sugar beet roots may be improved in the future.

The relationship between cell wall and postharvest physiological deterioration of fresh produce

Postharvest physiological deterioration (PPD) reduces the availability and economic value of fresh produces, resulting in the waste of agricultural products and becoming a worldwide problem. Therefore, many studies have been carried out at the anatomical structural, physiological and biochemical levels and molecular levels of PPD of fresh produces to seek ways to manage the postharvest quality of fresh produce. The cell wall is the outermost structure of a plant cell and as such represents the first barrier to prevent external microorganisms and other injuries. Many studies on postharvest quality of crop storage organs relate to changes in plant cell wall-related components. Indeed, these studies evidence the non-negligible role of the plant cell wall in postharvest storage ability. However, the relationship between cell wall metabolism and postharvest deterioration of fresh produces has not been well summarized. In this review, we summarize the structural changes of cell walls in different types of PPD, metabolic changes, and the possible molecular mechanism regulating cell wall metabolism in PPD of fresh produce. This review provides a basis for further research on delaying the occurrence of PPD of fresh produce.

Restraining Quiescence Release-Related Ageing in Plant Cells: A Case Study in Carrot

The blackening of cut carrots causes substantial economic losses to the food industry. Blackening was not observed in carrots that had been stored underground for less than a year, but the susceptibility to blackening increased with the age of the carrots that were stored underground for longer periods. Samples of black, border, and orange tissues from processed carrot batons and slices, prepared under industry standard conditions, were analyzed to identify the molecular and metabolic mechanisms underpinning processing-induced blackening. The black tissues showed substantial molecular and metabolic rewiring and large changes in the cell wall structure, with a decreased abundance of xyloglucan, pectins (homogalacturonan, rhamnogalacturonan-I, galactan and arabinan), and higher levels of lignin and other phenolic compounds when compared to orange tissues. Metabolite profiling analysis showed that there was a major shift from primary to secondary metabolism in the black tissues, which were depleted in sugars, amino acids, and tricarboxylic acid (TCA) cycle intermediates but were rich in phenolic compounds. These findings suggest that processing triggers a release from quiescence. Transcripts encoding proteins associated with secondary metabolism were less abundant in the black tissues, but there were no increases in transcripts associated with oxidative stress responses, programmed cell death, or senescence. We conclude that restraining quiescence release alters cell wall metabolism and composition, particularly regarding pectin composition, in a manner that increases susceptibility to blackening upon processing.

Integration of transcriptome, miRNA and degradome sequencing reveals the early browning response in fresh-cut apple

Surface browning negatively impacts the shelf-life of fresh-cut apple. Herein, we found that the browning of fresh-cut apple aggravated rapidly after 24 h post-cutting, then the transcriptomic and miRNA expression profiles of fresh-cut apple immediately after cutting (T0) and 24 h post-cutting (T24) were analyzed to explore the molecular mechanism of early browning response. A total of 3156 differentially expressed mRNAs (DEGs) and 23 differentially expressed miRNAs (DEmiRNAs) were identified in T24 vs T0. Most DEGs related to respiratory, energy, antioxidant, lipid and secondary metabolism were activated in the early stage of browning. There were 63 target genes of 10 DEmiRNAs validated by degradome sequencing and among them, mdm-miR156aa_L + 1_1 targets 12-oxophytodienoate reductase, ptc-miR6478_R-1 targets patatin-like protein, mdm-miR156aa_L + 1_1 and mdm-miR156aa_L + 1_2 co-target SPLs might participate in the early browning response through regulating antioxidant, lipid and secondary metabolism. Our results will be beneficial for the technological innovation of browning amelioration for fresh-cut apple.

Biotechnological approaches for predicting and controlling apple storage disorders

Fruit storage disorders are major causes of crop losses and downgrades. Cold storage, either in air or in controlled atmospheres high in CO₂ and low in O₂, can result in chilling injury or respiratory injury (due to high internal CO₂ concentrations). Here, we review biotechnological approaches currently being used to better understand these processes, to predict to provide resistance/tolerance to them. Reducing postharvest crop losses through improved cultivars or inventory management will be a major contributor to food security.

Comparative transcriptome and metabolite survey reveal key pathways involved in the control of the chilling injury disorder superficial scald in two apple cultivars, 'Granny Smith' and 'Ladina'

The low temperature normally applied to prevent fruit decay during the storage of apples, can also triggers the onset of a chilling injury disorder known as superficial scald. In this work, the etiology of this disorder and the mechanism of action of two preventing strategies, such as the application of 1-MCP (1-methylcyclopropene) and storage at low oxygen concentration in 'Granny Smith' and 'Ladina' apple cultivars were investigated. The metabolite assessment highlighted a reorganization of specific metabolites, in particular flavan-3-ols and unsaturated fatty acids, while the genome-wide transcriptomic analysis grouped the DEGs into four functional clusters. The KEGG pathway and GO enrichment analysis, together with the gene-metabolite interactome, showed that the treatment with 1-MCP prevented the development of superficial scald by actively promoting the production of unsaturated fatty acids, especially in 'Granny Smith'. 'Ladina', more susceptible to superficial scald and less responsive to the preventing strategies, was instead characterized by a higher accumulation of very long chain fatty acids. Storage at low oxygen concentration stimulated a higher accumulation of ethanol and acetaldehyde together with the expression of genes involved in anaerobic respiration, such as malate, alcohol dehydrogenase and pyruvate decarboxylase in both cultivars. Low oxygen concentration, likewise 1-MCP, through a direct control on ethylene prevented the onset of superficial scald repressing the expression of PPO, a gene encoding for the polyphenol oxidase enzyme responsible of the oxidation of chlorogenic acid. Moreover, in 'Granny Smith' apple, the expression of three members of the VII subgroups of ERF genes, encoding for elements coordinating the acclimation process to hypoxia in plants was observed. The global RNA-Seq pattern also elucidated a specific transcriptomic signature between the two cultivars, disclosing the effect of the different genetic background in the control of this disorder.

Phylogenesis of the Functional 1-Aminocyclopropane-1-Carboxylate Oxidase of Fungi and Plants

The 1-aminocyclopropane-1-carboxylic acid (ACC) pathway that synthesizes ethylene is shared in seed plants, fungi and probably other organisms. However, the evolutionary relationship of the key enzyme ACC oxidase (ACO) in the pathway among organisms remains unknown. Herein, we cloned, expressed and characterized five ACOs from the straw mushroom (Volvariella volvacea) and the oyster mushroom (Pleurotus ostreatus): VvACO1-4 and PoACO. The five mushroom ACOs and the previously identified AbACO of the button mushroom contained all three conserved residues that bound to Fe(II) in plant ACOs. They also had variable residues that were conserved and bound to ascorbate and bicarbonate in plant ACOs and harbored only 1-2 of the five conserved ACO motifs in plant ACOs. Particularly, VvACO2 and AbACO had only one ACO motif 2. Additionally, VvACO4 shared 44.23% sequence identity with the cyanobacterium Hapalosiphon putative functional ACO. Phylogenetic analysis showed that the functional ACOs of monocotyledonous and dicotyledonous plants co-occurred in Type I, Type II and Type III, while putative functional gymnosperm ACOs also appeared in Type III. The putative functional bacterial ACO, functional fungi and slime mold ACOs were clustered in ancestral Type IV. These results indicate that ACO motif 2, ACC and Fe(II) are essential for ACO activity. The ACOs of the other organisms may come from the horizontal transfer of fungal ACOs, which were found ordinarily in basidiomycetes. It is mostly the first case for the horizontal gene transfers from fungi to seed plants. The horizontal transfer of ACOs from fungi to plants probably facilitates the fungal-plant symbioses, plant-land colonization and further evolution to form seeds.

Cytological and proteomic evidence reveals the involvement of mitochondria in hypoxia-induced quality degradation in postharvest citrus fruit

Hypoxia frequently occurs in postharvest logistics, which greatly influences fruit storability. Here, we for the first time studied the dynamic variations of mitochondrial morphology in living citrus fruit cells, and revealed that waxing treatment-induced hypoxia strongly triggered mitochondrial fission and fragmentation. Correspondingly, hypoxia caused a decline in mitochondrial membrane potential and mobility. Besides, impairment of energetic and redox status was also found in waxed fruit. The proteomic changes of mitochondria after waxing treatment were also characterized. Using weighted gene co-expression network analysis (WGCNA), we identified 167 key hypoxia-responsive proteins, which were mainly involved in fatty acid, amino acid and organic acid metabolism. Metabolite analysis verified that waxing treatment promoted the accumulation of several hypoxic metabolites, such as ethanol, acetaldehyde, succinic acid and γ-aminobutyric acid (GABA). Taken together, our findings provide new insights into the cytological and proteomic responses of mitochondria to hypoxia during fruit storage.

Microbiological and bacterial diseases of apple fruits during storage

During storage, fruits are affected by a complex of pathogens, from which one pathogen of bacterial origin and 11 of fungal etiology have been isolated. It was determined that the treatment of apple fruits before dispatch for storage with fungicides with the following rates of application: Luna Tranquillity, SC –1.0 l/ha, Geox, WDG–0.4 kg /ha, Zato, WDG–0.15 kg /ha allows to save up to 98% of the crop yield. At the same time, the waste contained fruits with mechanical damage affected by the mold fungus Penicillium roseum LK. Biological efficacy of Luna Tranquillity, SC, Zato, WSG and combinations of these fungicides against Penicillum roseum LK. were at the level of 81-95%, no other diseases were detected in these variants. It was found that fungi were found on fruits treated with a combination of fungicides Topsin - M, WP–1.5 kg/ha in combination with Merpan, WP–2.5 kg/ha and Medea preparation, ME–1.0 l/ha; such fungi were Fusarium avenaceum (fr.) Sacc, Gloeosporium fructigenum Berk, Penicillum roseum LK.

Ascorbic Acid Content and Transcriptional Profiling of Genes Involved in Its Metabolism during Development of Petals, Leaves, and Fruits of Orange (Citrus sinensis cv. Valencia Late)

Citrus fruit is one of the most important contributors to the ascorbic acid (AsA) intake in humans. Here, we report a comparative analysis of AsA content and transcriptional changes of genes related to its metabolism during development of petals, leaves and fruits of Valencia Late oranges (Citrus sinensis). Petals of close flowers and at anthesis contained the highest concentration of AsA. In fruits, AsA content in the flavedo reached a maximum at color break, whereas the pulp accumulated lower levels and experienced minor fluctuations during development. AsA levels in leaves were similar to those in the flavedo at breaker stage. The transcriptional profiling of AsA biosynthetic, degradation, and recycling genes revealed a complex and specific interplay of the different pathways for each tissue. The D-galacturonic acid pathway appeared to be relevant in petals, whereas in leaves the L-galactose pathway (GGP and GME) also contributed to AsA accumulation. In the flavedo, AsA content was positively correlated with the expression of GGP of the L-galactose pathway and negatively with DHAR1 gene of the recycling pathway. In the pulp, AsA appeared to be mainly controlled by the coordination among the D-galacturonic acid pathway and the MIOX and GalDH genes. Analysis of the promoters of AsA metabolism genes revealed a number of cis-acting elements related to developmental signals, but their functionalities remain to be investigated.

De novo sequencing and analysis of the transcriptome of two highbush blueberry (Vaccinium corymbosum L.) cultivars 'Bluecrop' and 'Legacy' at harvest and following post-harvest storage

Fruit firmness and in particular the individual components of texture and moisture loss, are considered the key quality traits when describing blueberry fruit quality, and whilst these traits are genetically regulated, the mechanisms governing their control are not clearly understood. In this investigation, RNAseq was performed on fruits of two blueberry cultivars with very different storage properties, 'Bluecrop' and 'Legacy', at harvest, three weeks storage in a non-modified environment at 4 °C and after three weeks storage at 4 °C followed by three days at 21 °C, with the aim of understanding the transcriptional changes that occur during storage in cultivars with very different post-harvest fruit quality. De novo assemblies of the transcriptomes of the two cultivars were performed separately and a total of 39,335 and 41,896 unigenes for 'Bluecrop' and 'Legacy' respectively were resolved. Differential gene expression analyses were grouped into four cluster profiles based on changes in transcript abundance between harvest and 24 days post-harvest. A total of 290 unigenes were up-regulated in 'Legacy' only, 685 were up-regulated in 'Bluecrop', 252 were up-regulated in both cultivars and 948 were down-regulated in both cultivars between harvest and 24 days post-harvest. Unigenes showing significant differential expression between harvest and following post-harvest cold-storage were grouped into classes of biological processes including stress responses, cell wall metabolism, wax metabolism, calcium metabolism, cellular components, and biological processes. In total 21 differentially expressed unigenes with a putative role in regulating the response to post-harvest cold-storage in the two cultivars were identified from the de novo transcriptome assemblies performed. The results presented provide a stable foundation from which to perform further analyses with which to functionally validate the candidate genes identified, and to begin to understand the genetic mechanisms controlling changes in firmness in blueberry fruits post-harvest.

Transcriptomic changes associated with husk scald incidence on pomegranate fruit peel during cold storage

Pomegranate fruit is valued for its social, economic, aesthetic and health benefits. The fruit rapidly loses quality after harvest due to continued metabolic responses and physiological disorders under sub-optimal conditions. The incidence of physiological disorder such as husk scald manifests during storage and commercial shipping, which affects the appearance and limits marketability. Despite the importance of pomegranate husk scald, little information is available about the origin and molecular mechanisms. Therefore, the aim of this study was to investigate the scald incidence of pomegranate fruit at molecular level using RNA-Seq (Ion Proton™ Next Generation Sequencing) by analyzing peel transcriptomic changes. The RNA-seq analysis generated 98,441,278 raw reads. 652 Differentially Expressed Genes (DEGs) with a fold change of > |2|, a p value ≤ 0.05 and a false discovery rate (FDR) of <0.05 were identified between healthy and scald fruit peels. An analysis of the gene ontologies of these DEGs revealed the 432 genes were assigned with molecular functions, 272 as cellular components and 205 as part of biological processes. In this analysis, genes (Pgr023188 and Pgr025081) that encode uncharacterized protein and gene (Pgr007593) that encodes glycosyltransferase showed significantly highest fold changes. Genes (Pgr003448, Pgr006024 and Pgr023696) involved in various iron binding and oxidoreductase activities were significantly suppressed. This is the first transcriptome analysis of pomegranate fruit peel related to husk scald development. Results obtained from this study will add valuable information on husk scald related changes on pomegranate fruit at genomic level and provide insight on other related physiological disorders.

Dynamics of ascorbic acid content in apple (Malus x domestica) during fruit development and storage

Vitamin C is a crucial antioxidant and cofactor for both plants and humans. Apple fruits generally contain low levels of vitamin C, making vitamin C content an interesting trait for apple crop improvement. With the aim of breeding high vitamin C apple cultivars it is important to get an insight in the natural biodiversity of vitamin C content in apple fruits. In this study, quantification of ascorbic acid (AsA), dehydroascorbic acid (DHA), and total AsA (AsA + DHA) in apple pulp of 79 apple accessions at harvest revealed significant variation, indicating a large genetic biodiversity. High density genotyping using an 8 K SNP array identified 21 elite and 58 local cultivars in this germplasm, with local accessions showing similar levels of total AsA but higher amounts of DHA compared to elite varieties. Out of the 79 apple cultivars screened, ten genotypes with either the highest or the lowest concentration of total AsA at harvest were used for monitoring vitamin C dynamics during fruit development and storage. For all these cultivars, the AsA/DHA ratio in both apple pulp and peel increased throughout fruit development, whereas the AsA/DHA balance always shifted towards the oxidized form during storage and shelf life, putatively reflecting an abiotic stress response. Importantly, at any point during apple fruit development and storage, the apple peel contained a higher level of vitamin C compared to the pulp, most likely because of its direct exposure to abiotic and biotic stresses.

Metabolite Changes during Postharvest Storage: Effects on Fruit Quality Traits

Metabolic changes occurring in ripe or senescent fruits during postharvest storage lead to a general deterioration in quality attributes, including decreased flavor and ‘off-aroma’ compound generation. As a consequence, measures to reduce economic losses have to be taken by the fruit industry and have mostly consisted of storage at cold temperatures and the use of controlled atmospheres or ripening inhibitors. However, the biochemical pathways and molecular mechanisms underlying fruit senescence in commercial storage conditions are still poorly understood. In this sense, metabolomic platforms, enabling the profiling of key metabolites responsible for organoleptic and health-promoting traits, such as volatiles, sugars, acids, polyphenols and carotenoids, can be a powerful tool for further understanding the biochemical basis of postharvest physiology and have the potential to play a critical role in the identification of the pathways affected by fruit senescence. Here, we provide an overview of the metabolic changes during postharvest storage, with special attention to key metabolites related to fruit quality. The potential use of metabolomic approaches to yield metabolic markers useful for chemical phenotyping or even storage and marketing decisions is highlighted.

Regulation of the Central Carbon Metabolism in Apple Fruit Exposed to Postharvest Low-Oxygen Stress

After harvest, fruit remain metabolically active and continue to ripen. The main goal of postharvest storage is to slow down the metabolic activity of the detached fruit. In many cases, this is accomplished by storing fruit at low temperature in combination with low oxygen (O2) and high carbon dioxide (CO2) partial pressures. However, altering the normal atmospheric conditions is not without any risk and can induce low-O2 stress. This review focuses on the central carbon metabolism of apple fruit during postharvest storage, both under normal O2 conditions and under low-O2 stress conditions. While the current review is focused on apple fruit, most research on the central carbon metabolism, low-O2 stress, and O2 sensing has been done on a range of different model plants (e.g., Arabidopsis, potato, rice, and maize) using various plant organs (e.g., seedlings, tubers, roots, and leaves). This review pulls together this information from the various sources into a coherent overview to facilitate the research on the central carbon metabolism in apple fruit exposed to postharvest low-O2 stress.

Impact of elevated O2 and CO2 atmospheres on chemical attributes and quality of strawberry (Fragaria × ananassa Duch.) during storage

Modified atmosphere has widely been evident to contribute to fruit quality maintenance, however the correlation among these quality traits was less known. To explore main factors of elevated atmosphere and reduce the detection indexes, we exposed strawberry to either high O₂ (80% O₂ + 20% N₂) or CO₂ (20% CO₂ + 20% O₂ + 60% N₂) atmosphere and compared quality characteristics. It was demonstrated that both atmospheres well maintained the fruit firmness, alleviated weight loss and decay rate. Elevated O₂ maintained the polyphenolic contents and cell integrity by significantly decreasing superoxide and hydrogen peroxide levels. PCA analysis implied that HO treatment mainly affected oxygen metabolism while HCO affected carbon metabolism more. Significantly positive correlation was observed between weight loss, anthocyanin content and decay rate in elevated O₂ and control groups. This study provided new insights into correlation and difference between impact of elevated O₂ and CO₂ to postharvest preservation.

Transcriptome analysis provides insights into the stress response crosstalk in apple (Malus × domestica) subjected to drought, cold and high salinity

Drought, cold, and high salinity are three major abiotic stresses effecting apple tree growth and fruit production. Understanding the genetic mechanisms of crosstalk between stress responses signalling networks and identifying the genes involved in apple has potential importance for crop improvement and breeding strategies. Here, the transcriptome profiling analysis of in vitro-grown apple plants subjected to drought, cold and high salinity stress, showed a total of 377 upregulated and 211 downregulated common differentially expressed genes (DEGs) to all 3 stress treatments compared with the control. Gene Ontology (GO) analysis indicated that these common DEGs were enriched in ‘metabolic process’ under the ‘biological process’ category, as well as in ‘binding’ and ‘catalytic activity’ under the ‘molecular function’ category. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that common DEGs were mainly belong to the ‘biological functions’ category and 17 DEGs were identified in ‘environmental information processing’ sub-category which may act as signal transduction components in response crosstalk regulation. Overexpression of 5 upregulated genes individually, out of these 17 common DEGs in apple calli promoted the consistent upregulation of DREB6, CBF1 and ZAT10 and increased the mass weight and antioxidase ability, implying these five common DEGs involved in multiple pathways and improved comprehensive resistance to stress.

Vitamin C Content in Fruits: Biosynthesis and Regulation

Throughout evolution, a number of animals including humans have lost the ability to synthesize ascorbic acid (ascorbate, vitamin C), an essential molecule in the physiology of animals and plants. In addition to its main role as an antioxidant and cofactor in redox reactions, recent reports have shown an important role of ascorbate in the activation of epigenetic mechanisms controlling cell differentiation, dysregulation of which can lead to the development of certain types of cancer. Although fruits and vegetables constitute the main source of ascorbate in the human diet, rising its content has not been a major breeding goal, despite the large inter- and intraspecific variation in ascorbate content in fruit crops. Nowadays, there is an increasing interest to boost ascorbate content, not only to improve fruit quality but also to generate crops with elevated stress tolerance. Several attempts to increase ascorbate in fruits have achieved fairly good results but, in some cases, detrimental effects in fruit development also occur, likely due to the interaction between the biosynthesis of ascorbate and components of the cell wall. Plants synthesize ascorbate de novo mainly through the Smirnoff-Wheeler pathway, the dominant pathway in photosynthetic tissues. Two intermediates of the Smirnoff-Wheeler pathway, GDP-D-mannose and GDP-L-galactose, are also precursors of the non-cellulosic components of the plant cell wall. Therefore, a better understanding of ascorbate biosynthesis and regulation is essential for generation of improved fruits without developmental side effects. This is likely to involve a yet unknown tight regulation enabling plant growth and development, without impairing the cell redox state modulated by ascorbate pool. In certain fruits and developmental conditions, an alternative pathway from D-galacturonate might be also relevant. We here review the regulation of ascorbate synthesis, its close connection with the cell wall, as well as different strategies to increase its content in plants, with a special focus on fruits.

Red to Brown: An Elevated Anthocyanic Response in Apple Drives Ethylene to Advance Maturity and Fruit Flesh Browning

The elevation of anthocyanin contents in fruits and vegetables is a breeding target for many crops. In some fruit, such as tomato, higher anthocyanin concentrations enhance storage and shelf life. In contrast, highly anthocyanic red-fleshed apples (Malus x domestica) have an increased incidence of internal browning flesh disorder (IBFD). To determine the mechanisms underlying this, 'Royal Gala' cultivar apples over-expressing the anthocyanin-related transcription factor (TF) MYB10 (35S:MYB10), which produces fruit with highly pigmented flesh, were compared with standard 'Royal Gala' Wild Type (WT) grown under the same conditions. We saw no incidence of IBFD in WT 'Royal Gala' but the over-expression of MYB10 in the same genetic background resulted in a high rate of IBDF. We assessed concentrations of potential substrates for IBDF and a comparison of metabolites in these apples showed that anthocyanins, chlorogenic acid, pro-cyanidins, flavon-3-ols, and quercetin were all higher in the MYB10 lines. For the flavol-3-ols sub-group, epicatechin rather than catechin was elevated in MYB10 lines compared with the control fruit. Internal ethylene concentrations were measured throughout fruit development and were significantly higher in 35S:MYB10 lines, and ethylene was detected at an earlier developmental stage pre-harvest. Expression analysis of key genes associated with ethylene biosynthesis (aminocyclopropane-1-carboxylic acid synthase and oxidase; ACS and ACO) and polyphenol oxidase (PPO) showed the potential for increased ethylene production and the mechanism for enhanced PPO-mediated browning. The expression of a transcription factor of the ethylene response factor (ERF) class, ERF106, was elevated in red flesh. Analysis of transcriptional activation by MYB10 showed that this transcription factor could activate the expression of apple ACS, ACO, and ERF106 genes. Our data show a link between the elevation of anthocyanin-related transcription factors and an undesirable fruit disorder. The accelerated advancement of maturity via premature ethylene induction has implications for the breeding and storage of these more highly pigmented plant products.

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

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

Metabolic Alterations in Postharvest Pear Fruit As Influenced by 1-Methylcyclopropene and Controlled Atmosphere Storage

This study assessed the impact of 1-methylcyclopropene (1-MCP) and controlled atmosphere (CA) on the metabolism of targeted amino acids, organic acids, and antioxidants in stored 'AC Harrow Crisp' pears and their relationships to storage disorders. Pears were treated with 0 or 300 nL L^-1 1-MCP and stored at 0 °C under ambient air or CA. Spectrophotometric assays demonstrated that glutathione levels fluctuated with storage and were most preserved by 1-MCP under ambient air. HPLC analysis revealed that ascorbate concentrations declined with storage and were little affected by 1-MCP and CA. Citrate, lactate, and fumarate accumulated with storage but were differentially affected by 1-MCP. Aspartate and glutamate concentrations were greater with 1-MCP; γ-aminobutyrate accumulated in disordered fruit. Principal component analysis demonstrated that alterations in citrate and fumarate were, respectively, correlated with internal breakdown and senescent scald. γ-Aminobutyrate and alanine were associated with internal cavities. All disorders were associated with antioxidant depletion.

Progress toward Understanding the Molecular Basis of Fruit Response to Hypoxia

Oxygen has shaped life on Earth as we know it today. Molecular oxygen is essential for normal cellular function, i.e., plants need oxygen to maintain cellular respiration and for a wide variety of biochemical reactions. When oxygen levels in the cell are lower than levels needed for respiration, then the cell experiences hypoxia. Plants are known to experience root hypoxia during natural environmental conditions like flooding. Fruit, on the other hand, is known to be hypoxic under normal oxygen conditions. This observation could be explained (at least partially) as a consequence of diffusional barriers, low tissue diffusivity, and high oxygen consumption by respiration. From the physiological point of view, hypoxia is known to have a profound impact on fruit development, since it is well documented that a low oxygen environment can significantly delay ripening and senescence of some fruit. This effect of a low-oxygen environment is readily used for optimizing storage conditions and transport, and for prolonging the shelf life of several fruit commodities. Therefore, further understanding of the complex relationship between oxygen availability within the cell and fruit development could assist postharvest management.

De novo sequencing and analysis of the transcriptome during the browning of fresh-cut Luffa cylindrica 'Fusi-3' fruits

Fresh-cut luffa (Luffa cylindrica) fruits commonly undergo browning. However, little is known about the molecular mechanisms regulating this process. We used the RNA-seq technique to analyze the transcriptomic changes occurring during the browning of fresh-cut fruits from luffa cultivar 'Fusi-3'. Over 90 million high-quality reads were assembled into 58,073 Unigenes, and 60.86% of these were annotated based on sequences in four public databases. We detected 35,282 Unigenes with significant hits to sequences in the NCBInr database, and 24,427 Unigenes encoded proteins with sequences that were similar to those of known proteins in the Swiss-Prot database. Additionally, 20,546 and 13,021 Unigenes were similar to existing sequences in the Eukaryotic Orthologous Groups of proteins and Kyoto Encyclopedia of Genes and Genomes databases, respectively. Furthermore, 27,301 Unigenes were differentially expressed during the browning of fresh-cut luffa fruits (i.e., after 1-6 h). Moreover, 11 genes from five gene families (i.e., PPO, PAL, POD, CAT, and SOD) identified as potentially associated with enzymatic browning as well as four WRKY transcription factors were observed to be differentially regulated in fresh-cut luffa fruits. With the assistance of rapid amplification of cDNA ends technology, we obtained the full-length sequences of the 15 Unigenes. We also confirmed these Unigenes were expressed by quantitative real-time polymerase chain reaction analysis. This study provides a comprehensive transcriptome sequence resource, and may facilitate further studies aimed at identifying genes affecting luffa fruit browning for the exploitation of the underlying mechanism.

Genetic Control of Ascorbic Acid Biosynthesis and Recycling in Horticultural Crops

Ascorbic acid (AsA) is an essential compound present in almost all living organisms that has important functions in several aspects of plant growth and development, hormone signaling, as well as stress defense networks. In recent years, the genetic regulation of AsA metabolic pathways has received much attention due to its beneficial role in human diet. Despite the great variability within species, genotypes, tissues and developmental stages, AsA accumulation is considered to be controlled by the fine orchestration of net biosynthesis, recycling, degradation/oxidation, and/or intercellular and intracellular transport. To date, several structural genes from the AsA metabolic pathways and transcription factors are considered to significantly affect AsA in plant tissues, either at the level of activity, transcription or translation via feedback inhibition. Yet, all the emerging studies support the notion that the steps proceeding through GDP-_L-galactose phosphorylase and to a lesser extent through GDP-_D-mannose-3,5-epimerase are control points in governing AsA pool size in several species. In this mini review, we discuss the current consensus of the genetic regulation of AsA biosynthesis and recycling, with a focus on horticultural crops. The aspects of AsA degradation and transport are not discussed herein. Novel insights of how this multifaceted trait is regulated are critical to prioritize candidate genes for follow-up studies toward improving the nutritional value of fruits and vegetables.

A practical examination of RNA isolation methods for European pear (Pyrus communis)

Objective

With the goal of identifying fast, reliable, and broadly applicable RNA isolation methods in European pear fruit for downstream transcriptome analysis, we evaluated several commercially available kit-based RNA isolation methods, plus our modified version of a published cetyl trimethyl ammonium bromide (CTAB)-based method.

Results

We confirmed previous work indicating chaotropic agent-based kits produced sufficient, high-quality RNA in freshly harvested, mature ‘Bartlett’ fruit. However, RNA isolation from ‘d’Anjou’ pear peel and especially cortical tissues of fruit stored for 11 months proved challenging to all but our modified CTAB-based method. Generally, more RNA was recovered from peel tissues than cortical tissues. Less toxic dithiothreitol was confirmed to be an acceptable reducing agent as its substitution for 2-mercaptoethanol often yielded high quality RNA. Finally, we present evidence that erroneous signals in the 5S region of Bioanalyzer RNA size plot histograms, that interfered with RNA integrity number calculation, were small RNA fragments that are reduced by simple cleanup procedures, not artifacts as previously reported.

Electronic supplementary material

The online version of this article (doi:10.1186/s13104-017-2564-2) contains supplementary material, which is available to authorized users.

Delayed response to cold stress is characterized by successive metabolic shifts culminating in apple fruit peel necrosis

BACKGROUND

Superficial scald is a physiological disorder of apple fruit characterized by sunken, necrotic lesions appearing after prolonged cold storage, although initial injury occurs much earlier in the storage period. To determine the degree to which the transition to cell death is an active process and specific metabolism involved, untargeted metabolic and transcriptomic profiling was used to follow metabolism of peel tissue over 180 d of cold storage.

RESULTS

The metabolome and transcriptome of peel destined to develop scald began to diverge from peel where scald was controlled using antioxidant (diphenylamine; DPA) or rendered insensitive to ethylene using 1-methylcyclopropene (1-MCP) beginning between 30 and 60 days of storage. Overall metabolic and transcriptomic shifts, representing multiple pathways and processes, occurred alongside α-farnesene oxidation and, later, methanol production alongside symptom development.

CONCLUSIONS

Results indicate this form of peel necrosis is a product of an active metabolic transition involving multiple pathways triggered by chilling temperatures at cold storage inception rather than physical injury. Among multiple other pathways, enhanced methanol and methyl ester levels alongside upregulated pectin methylesterases are unique to peel that is developing scald symptoms similar to injury resulting from mechanical stress and herbivory in other plants.

Gaining Insight into Exclusive and Common Transcriptomic Features Linked with Biotic Stress Responses in Malus

Identifying key information in transcriptomic data is very important, especially when the "omic" study deals with plant responses to stresses in field conditions where a high number of variables and disturbing factors may affect the analysis. In this meta-analysis we collected 12 transcriptomic works in Malus in order to identify which key genes, proteins, gene categories are involved in general plant pathological conditions and those features linked with exclusive biotic stress responses. Those genes that are only related with molecular responses to pathogen attacks and those linked with other plant physiological processes were identified. A pipeline composed by pathway and gene set enrichment analysis, protein-protein interaction networks and gene visualization tools was employed. A total of 13,230 genes of the 12 studies were analyzed with functional data mining tools: 5,215 were upregulated, 8,015 were downregulated. Gene set enrichment analysis pointed out that photosynthesis was inhibited by Erwinia amylovora and fungal pathogens. Different hormonal crosstalk was linked with responses to different pathogens. Gibberellin-related pathways, ABA-related were mostly repressed by fungal pathogens. Relating to transcription factors, genes encoding MYBs and WRKY2 were downregulated by fungal pathogens and 12 WRKYs were commonly regulated by different biotic stresses The protein-protein interaction analysis discovered the presence of several proteins affected by more than one biotic stress including a WRKY40 and some highly interactive proteins such as heat shock proteins. This study represents a first preliminary curated meta-analysis of apple transcriptomic responses to biotic stresses.

Transcriptomic Response of Resistant (PI613981-Malus sieversii) and Susceptible ("Royal Gala") Genotypes of Apple to Blue Mold (Penicillium expansum) Infection

Malus sieversii from Central Asia is a progenitor of the modern domesticated apple (Malus × domestica). Several accessions of M. sieversii are highly resistant to the postharvest pathogen Penicillium expansum. A previous study identified the qM-Pe3.1 QTL on LG3 for resistance to P. expansum in the mapping population GMAL4593, developed using the resistant accession, M. sieversii -PI613981, and the susceptible cultivar "Royal Gala" (RG) (M. domestica), as parents. The goal of the present study was to characterize the transcriptomic response of susceptible RG and resistant PI613981 apple fruit to wounding and inoculation with P. expansum using RNA-Seq. Transcriptomic analyses 0-48 h post inoculation suggest a higher basal level of resistance and a more rapid and intense defense response to wounding and wounding plus inoculation with P. expansum in M. sieversii -PI613981 than in RG. Functional analysis showed that ethylene-related genes and genes involved in "jasmonate" and "MYB-domain transcription factor family" were over-represented in the resistant genotype. It is suggested that the more rapid response in the resistant genotype (Malus sieversii-PI613981) plays a major role in the resistance response. At least twenty DEGs were mapped to the qM-Pe3.1 QTL (M × d v.1: 26,848,396-28,424,055) on LG3, and represent potential candidate genes responsible for the observed resistance QTL in M. sieversii-PI613981. RT-qPCR of several of these genes was used to validate the RNA-Seq data and to confirm their higher expression in MS0.

Gene expression and metabolism preceding soft scald, a chilling injury of 'Honeycrisp' apple fruit

BACKGROUND

'Honeycrisp' is an apple cultivar that is susceptible to soft scald, a chilling injury expressed as necrotic patches on the peel. Improved understanding of metabolism associated with the disorder would improve our understanding of soft scald and contribute to developing more effective management strategies for apple storage. It was expected that specific gene expression and specific metabolite levels in the peel would be linked with soft scald risk at harvest and/or specific time points during cold storage.

RESULTS

Fruit from nine 'Honeycrisp' apple orchards that would eventually develop different incidences of soft scald between 4 and 8 weeks of cold air storage were used to contrast and determine differential transcriptomic and metabolomic changes during storage. Untargeted metabolic profiling revealed changes in a number of distinct pathways preceding and concurrent with soft scald symptom development, including elevated γ-aminobutryic acid (GABA), 1-hexanol, acylated steryl glycosides, and free p-coumaryl acyl esters. At harvest, levels of sesquiterpenoid and triterpenoid acyl esters were relatively higher in peel of fruit that did not later develop the disorder. RNA-seq driven gene expression profiling highlighted possible involvement of genes and associated metabolic processes with soft scald development. These included elevated expression of genes involved in lipid peroxidation and phenolic metabolism in fruit with soft scald, and isoprenoid/brassinosteroid metabolism in fruit that did not develop soft scald. Expression of other stress-related genes in fruit that developed soft scald included chlorophyll catabolism, cell wall loosening, and lipid transport while superoxide dismutases were up-regulated in fruit that did not develop the disorder.

CONCLUSIONS

This study delineates the sequential transcriptomic and metabolomic changes preceding soft scald symptom development. Changes were differential depending on susceptibility of fruit to the disorder and could be attributed to key stress related and mediating pathways.

Hypobaric Treatment Effects on Chilling Injury, Mitochondrial Dysfunction, and the Ascorbate-Glutathione (AsA-GSH) Cycle in Postharvest Peach Fruit

In this study, hypobaric treatment effects were investigated on chilling injury, mitochondrial dysfunction, and the ascorbate-glutathione (AsA-GSH) cycle in peach fruit stored at 0 °C. Internal browning of peaches was dramatically reduced by applying 10-20 kPa pressure. Hypobaric treatment markedly inhibited membrane fluidity increase, whereas it kept mitochondrial permeability transition pore (MPTP) concentration and cytochrome C oxidase (CCO) and succinic dehydrogenase (SDH) activity relatively high in mitochondria. Similarly, 10-20 kPa pressure treatment reduced the level of decrease observed in AsA and GSH concentrations, while it enhanced ascorbate peroxidase (APX), glutathione reductase (GR), and monodehydroascorbate reductase (MDHAR) activities related to the AsA-GSH cycle. Furthermore, comparative transcriptomic analysis showed that differentially expressed genes (DEGs) associated with the metabolism of glutathione, ascorbate, and aldarate were up-regulated in peaches treated with 10-20 kPa for 30 days at 0 °C. Genes encoding GR, MDHAR, and APX were identified and exhibited higher expression in fruits treated with low pressure than in fruits treated with normal atmospheric pressure. Our findings indicate that the alleviation of chilling injury by hypobaric treatment was associated with preventing mitochondrial dysfunction and triggering the AsA-GSH cycle by the transcriptional up-regulation of related enzymes.

Biochemical Basis of CO2-Related Internal Browning Disorders in Pears (Pyrus communis L. cv. Rocha) during Long-Term Storage

This study aimed at understanding the biochemical basis of internal browning disorders (IBDs) in 'Rocha' pear. For this purpose, the effects of storage under normal controlled atmosphere (CA) (3 kPa of O2 + 0.5 kPa of CO2) and IBD-inducing CA (1 kPa of O2 + 10 kPa of CO2) on the antioxidant and fermentative metabolisms and polyphenol oxidase (PPO) activity and phenolics concentration were studied. The higher IBD incidence in high CO2-stored fruits was positively correlated with fermentative metabolites and negatively with ascorbate and H2O2 concentrations, and it was linked to PPO activation. These results indicate that both the antioxidant and fermentative metabolisms are involved in the occurrence of IBD in 'Rocha' pear. From the integration of the biochemical and enzymatic data, a schematic model illustrating the effects of high CO2 and low O2 in 'Rocha' pears during long-term storage was constructed.

Oxidative metabolism is associated with physiological disorders in fruits stored under multiple environmental stresses

In combination with low temperature, controlled atmosphere storage and 1-methylcyclopropene (ethylene antagonist) application are used to delay senescence of many fruits and vegetables. Controlled atmosphere consists of low O2 and elevated CO2. When sub-optimal partial pressures are used, these practices represent multiple abiotic stresses that can promote the development of physiological disorders in pome fruit, including flesh browning and cavities, although there is some evidence for genetic differences in susceptibility. In the absence of surface disorders, fruit with flesh injuries are not easily distinguished from asymptomatic fruit until these are consumed. Oxidative stress metabolites tend to accumulate (e.g., γ-aminobutyrate) or rapidly decline (e.g., ascorbate and glutathione) in vegetative tissues exposed to hypoxic and/or elevated CO2 environments. Moreover, these phenomena can be associated with altered energy and redox status. Biochemical investigations of Arabidopsis and tomato plants with genetically-altered levels of enzymes associated with the γ-aminobutyrate shunt and the ascorbate-glutathione pathway indicate that these metabolic processes are functionally related and critical for dampening the oxidative burst in vegetative and fruit tissues, respectively. Here, we hypothesize that γ-aminobutyrate accumulation, as well energy and antioxidant depletion are associated with the development of physiological injury in pome fruit under multiple environmental stresses. An improved understanding of this relationship could assist in maintaining the quality of stored fruit.

Omics studies of citrus, grape and rosaceae fruit trees

Recent advance of bioinformatics and analytical apparatuses such as next generation DNA sequencer (NGS) and mass spectrometer (MS) has brought a big wave of comprehensive study to biology. Comprehensive study targeting all genes, transcripts (RNAs), proteins, metabolites, hormones, ions or phenotypes is called genomics, transcriptomics, proteomics, metabolomics, hormonomics, ionomics or phenomics, respectively. These omics are powerful approaches to identify key genes for important traits, to clarify events of physiological mechanisms and to reveal unknown metabolic pathways in crops. Recently, the use of omics approach has increased dramatically in fruit tree research. Although the most reported omics studies on fruit trees are transcriptomics, proteomics and metabolomics, and a few is reported on hormonomics and ionomics. In this article, we reviewed recent omics studies of major fruit trees, i.e. citrus, grapevine and rosaceae fruit trees. The effectiveness and prospects of omics in fruit tree research will as well be highlighted.

Extreme Hypoxic Conditions Induce Selective Molecular Responses and Metabolic Reset in Detached Apple Fruit

The ripening physiology of detached fruit is altered by low oxygen conditions with profound effects on quality parameters. To study hypoxia-related processes and regulatory mechanisms, apple (Malus domestica, cv Granny Smith) fruit, harvested at commercial ripening, were kept at 1°C under normoxic (control) and hypoxic (0.4 and 0.8 kPa oxygen) conditions for up to 60 days. NMR analyses of cortex tissue identified eight metabolites showing significantly different accumulations between samples, with ethanol and alanine displaying the most pronounced difference between hypoxic and normoxic treatments. A rapid up-regulation of alcohol dehydrogenase and pyruvate-related metabolism (lactate dehydrogenase, pyruvate decarboxylase, alanine aminotransferase) gene expression was detected under both hypoxic conditions with a more pronounced effect induced by the lowest (0.4 kPa) oxygen concentration. Both hypoxic conditions negatively affected ACC synthase and ACC oxidase transcript accumulation. Analysis of RNA-seq data of samples collected after 24 days of hypoxic treatment identified more than 1000 genes differentially expressed when comparing 0.4 vs. 0.8 kPa oxygen concentration samples. Genes involved in cell-wall, minor and major CHO, amino acid and secondary metabolisms, fermentation and glycolysis as well as genes involved in transport, defense responses, and oxidation-reduction appeared to be selectively affected by treatments. The lowest oxygen concentration induced a higher expression of transcription factors belonging to AUX/IAA, WRKY, HB, Zinc-finger families, while MADS box family genes were more expressed when apples were kept under 0.8 kPa oxygen. Out of the eight group VII ERF members present in apple genome, two genes showed a rapid up-regulation under hypoxia, and western blot analysis showed that apple MdRAP2.12 proteins were differentially accumulated in normoxic and hypoxic samples, with the highest level reached under 0.4 kPa oxygen. These data suggest that ripe apple tissues finely and specifically modulate sensing and regulatory mechanisms in response to different hypoxic stress conditions.

Omics data input for metabolic modeling

Recent advancements in high-throughput large-scale analytical methods to sequence genomes of organisms, and to quantify gene expression, proteins, lipids and metabolites have changed the paradigm of metabolic modeling. The cost of data generation and analysis has decreased significantly, which has allowed exponential increase in the amount of omics data being generated for an organism in a very short time. Compared to progress made in microbial metabolic modeling, plant metabolic modeling still remains limited due to its complex genomes and compartmentalization of metabolic reactions. Herein, we review and discuss different omics-datasets with potential application in the functional genomics. In particular, this review focuses on the application of omics-datasets towards construction and reconstruction of plant metabolic models.

Genome-wide transcriptome and expression profile analysis of Phalaenopsis during explant browning

Background

Explant browning presents a major problem for in vitro culture, and can lead to the death of the explant and failure of regeneration. Considerable work has examined the physiological mechanisms underlying Phalaenopsis leaf explant browning, but the molecular mechanisms of browning remain elusive. In this study, we used whole genome RNA sequencing to examine Phalaenopsis leaf explant browning at genome-wide level.

Methodology/Principal Findings

We first used Illumina high-throughput technology to sequence the transcriptome of Phalaenopsis and then performed de novo transcriptome assembly. We assembled 79,434,350 clean reads into 31,708 isogenes and generated 26,565 annotated unigenes. We assigned Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, and potential Pfam domains to each transcript. Using the transcriptome data as a reference, we next analyzed the differential gene expression of explants cultured for 0, 3, and 6 d, respectively. We then identified differentially expressed genes (DEGs) before and after Phalaenopsis explant browning. We also performed GO, KEGG functional enrichment and Pfam analysis of all DEGs. Finally, we selected 11 genes for quantitative real-time PCR (qPCR) analysis to confirm the expression profile analysis.

Conclusions/Significance

Here, we report the first comprehensive analysis of transcriptome and expression profiles during Phalaenopsis explant browning. Our results suggest that Phalaenopsis explant browning may be due in part to gene expression changes that affect the secondary metabolism, such as: phenylpropanoid pathway and flavonoid biosynthesis. Genes involved in photosynthesis and ATPase activity have been found to be changed at transcription level; these changes may perturb energy metabolism and thus lead to the decay of plant cells and tissues. This study provides comprehensive gene expression data for Phalaenopsis browning. Our data constitute an important resource for further functional studies to prevent explant browning.