Analysis of ripening-related gene expression in papaya using an Arabidopsis-based microarray

Dissecting the effect of soil on plant phenology and berry transcriptional plasticity in two Italian grapevine varieties (Vitis vinifera L.)

Grapevine embodies a fascinating species as regards phenotypic plasticity and genotype-per-environment interactions. The terroir, namely the set of agri-environmental factors to which a variety is subjected, can influence the phenotype at the physiological, molecular, and biochemical level, representing an important phenomenon connected to the typicality of productions. We investigated the determinants of plasticity by conducting a field-experiment where all terroir variables, except soil, were kept as constant as possible. We isolated the effect of soils collected from different areas, on phenology, physiology, and transcriptional responses of skin and flesh of a red and a white variety of great economic value: Corvina and Glera. Molecular results, together with physio-phenological parameters, suggest a specific effect of soil on grapevine plastic response, highlighting a higher transcriptional plasticity of Glera in respect to Corvina and a marked response of skin compared to flesh. Using a novel statistical approach, we identified clusters of plastic genes subjected to the specific influence of soil. These findings could represent an issue of applicative value, posing the basis for targeted agricultural practices to enhance the desired characteristics for any soil/cultivar combination, to improve vineyards management for a better resource usage and to valorize vineyards uniqueness maximizing the terroir-effect.

Whole Transcriptome Analyses of Apricots and Japanese Plum Fruits after 1-MCP (Ethylene-Inhibitor) and Ethrel (Ethylene-Precursor) Treatments Reveal New Insights into the Physiology of the Ripening Process

The physiology of Prunus fruit ripening is a complex and not completely understood process. To improve this knowledge, postharvest behavior during the shelf-life period at the transcriptomic level has been studied using high-throughput sequencing analysis (RNA-Seq). Monitoring of fruits has been analyzed after different ethylene regulator treatments, including 1-MCP (ethylene-inhibitor) and Ethrel (ethylene-precursor) in two contrasting selected apricot (Prunus armeniaca L.) and Japanese plum (P. salicina L.) cultivars, ‘Goldrich’ and ‘Santa Rosa’. KEEG and protein–protein interaction network analysis unveiled that the most significant metabolic pathways involved in the ripening process were photosynthesis and plant hormone signal transduction. In addition, previously discovered genes linked to fruit ripening, such as pectinesterase or auxin-responsive protein, have been confirmed as the main genes involved in this process. Genes encoding pectinesterase in the pentose and glucuronate interconversions pathway were the most overexpressed in both species, being upregulated by Ethrel. On the other hand, auxin-responsive protein IAA and aquaporin PIP were both upregulated by 1-MCP in ‘Goldrich’ and ‘Santa Rosa’, respectively. Results also showed the upregulation of chitinase and glutaredoxin 3 after Ethrel treatment in ‘Goldrich’ and ‘Santa Rosa’, respectively, while photosystem I subunit V psaG (photosynthesis) was upregulated after 1-MCP in both species. Furthermore, the overexpression of genes encoding GDP-L-galactose and ferredoxin in the ascorbate and aldarate metabolism and photosynthesis pathways caused by 1-MCP favored antioxidant activity and therefore slowed down the fruit senescence process.

Biochemical, Sensory, and Molecular Evaluation of Flavour and Consumer Acceptability in Australian Papaya (Carica papaya L.) Varieties

Inconsistency in flavour is one of the major challenges to the Australian papaya industry. However, objectively measurable standards of the compound profiles that provide preferable taste and aroma, together with consumer acceptability, have not been set. In this study, three red-flesh papayas (i.e., ‘RB1’, ‘RB4’, and ‘Skybury’) and two yellow-flesh papayas (i.e., ‘1B’ and ‘H13’) were presented to a trained sensory panel and a consumer panel to assess sensory profiles and liking. The papaya samples were also examined for sugar components, total soluble solids, and 14 selected volatile compounds. Additionally, the expression patterns of 10 genes related to sweetness and volatile metabolism were assessed. In general, red papaya varieties had higher sugar content and tasted sweeter than yellow varieties, while yellow varieties had higher concentrations of citrus floral aroma volatiles and higher aroma intensity. Higher concentrations of glucose, linalool oxide, and terpinolene were significantly associated with decreased consumer liking. Significant differences were observed in the expression profiles of all the genes assessed among the selected papaya varieties. Of these, cpGPT2 and cpBGLU31 were positively correlated to glucose production and were expressed significantly higher in ‘1B’ than in ‘RB1’ or ‘Skybury’. These findings will assist in the strategic selective breeding for papaya to better match consumer and, hence, market demand.

The Complex Biological Effects of Pectin: Galectin-3 Targeting as Potential Human Health Improvement?

Galectin-3 is the only chimeric representative of the galectin family. Although galectin-3 has ubiquitous regulatory and physiological effects, there is a great number of pathological environments where galectin-3 cooperatively participates. Pectin is composed of different chemical structures, such as homogalacturonans, rhamnogalacturonans, and side chains. The study of pectin's major structural aspects is fundamental to predicting the impact of pectin on human health, especially regarding distinct molecular modulation. One of the explored pectin's biological activities is the possible galectin-3 protein regulation. The present review focuses on revealing the structure/function relationship of pectins, their fragments, and their biological effects. The discussion highlighted by this review shows different effects described within in vitro and in vivo experimental models, with interesting and sometimes contradictory results, especially regarding galectin-3 interaction. The review demonstrates that pectins are promissory food-derived molecules for different bioactive functions. However, galectin-3 inhibition by pectin had been stated in literature before, although it is not a fully understood, experimentally convincing, and commonly agreed issue. It is demonstrated that more studies focusing on structural analysis and its relation to the observed beneficial effects, as well as substantial propositions of cause and effect alongside robust data, are needed for different pectin molecules' interactions with galectin-3.

Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content

The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here.

Papaya (Carica papaya L.) Flavour Profiling

A major challenge to the papaya industry is inconsistency in fruit quality and, in particular, flavour, which is a complex trait that comprises taste perception in the mouth (sweetness, acidity, or bitterness) and aroma produced by several volatile compounds. Current commercial varieties vary greatly in their taste, likely due to historical prioritised selection for fruit appearance as well as large environmental effects. Therefore, it is important to better understand the genetic and biochemical mechanisms and biosynthesis pathways underpinning preferable flavour in order to select and breed for better tasting new commercial papaya varieties. As an initial step, objectively measurable standards of the compound profiles that provide papaya's taste and aroma, together with 'mouth feel', are required. This review presents an overview of the approaches to characterise the flavour profiles of papaya through sugar component determination, volatile compound detection, sensory panel testing, as well as genomics-based studies to identify the papaya flavour.

Systems Biology Applied to the Study of Papaya Fruit Ripening: The Influence of Ethylene on Pulp Softening

Papaya is a fleshy fruit that undergoes fast ethylene-induced modifications. The fruit becomes edible, but the fast pulp softening is the main factor that limits the post-harvest period. Papaya fast pulp softening occurs due to cell wall disassembling coordinated by ethylene triggering that massively expresses pectinases. In this work, RNA-seq analysis of ethylene-treated and non-treated papayas enabled a wide transcriptome overview that indicated the role of ethylene during ripening at the gene expression level. Several families of transcription factors (AP2/ERF, NAC, and MADS-box) were differentially expressed. ACO, ACS, and SAM-Mtase genes were upregulated, indicating a high rate of ethylene biosynthesis after ethylene treatment. The correlation among gene expression and physiological data demonstrated ethylene treatment can indeed simulate ripening, and regulation of changes in fruit color, aroma, and flavor could be attributed to the coordinated expression of several related genes. Especially about pulp firmness, the identification of 157 expressed genes related to cell wall metabolism demonstrated that pulp softening is accomplished by a coordinated action of several different cell wall-related enzymes. The mechanism is different from other commercially important fruits, such as strawberry, tomato, kiwifruit, and apple. The observed behavior of this new transcriptomic data confirms ethylene triggering is the main event that elicits fast pulp softening in papayas.

Discovery of SNPs and InDels in papaya genotypes and its potential for marker assisted selection of fruit quality traits

Papaya is a tropical and climacteric fruit that is recognized for its nutritional benefits and medicinal applications. Its fruits ripen quickly and show a drastic fruit softening, leading to great post-harvest losses. To overcome this scenario, breeding programs of papaya must invest in exploring the available genetic variation to continue developing superior cultivars with improved fruit quality traits. The objective of this study was to perform a whole-genome genotyping (WGG) of papaya, predict the effects of the identified variants, and develop a list of ripening-related genes (RRGs) with linked variants. The Formosa elite lines of papaya Sekati and JS-12 were submitted to WGG with an Illumina Miseq platform. The effects of variants were predicted using the snpEff program. A total of 28,451 SNPs having Ts/Tv (Transition/Transversion) ratio of 2.45 and 1,982 small insertions/deletions (InDels) were identified. Most variant effects were predicted in non-coding regions, with only 2,104 and 138 effects placed in exons and splice site regions, respectively. A total of 106 RRGs were found to be associated with 460 variants, which may be converted into PCR markers to facilitate genetic mapping and diversity studies and to apply marker-assisted selection (MAS) for specific traits in papaya breeding programs.

Ethylene and Auxin: Hormonal Regulation of Volatile Compound Production During Tomato (Solanum lycopersicum L.) Fruit Ripening

As the auxin-ethylene interaction in climacteric fruit ripening has been highlighted, the hormonal regulation of aroma changes in climacteric fruits requires clarification. The influence of both phytohormones on the volatile organic compound (VOC) metabolism was evaluated during tomato (Solanum lycopersicum L.) fruit ripening. Tomato fruits cv. Micro-Tom and Sweet Grape at the mature green stage were randomly grouped according to treatment with ethylene (ETHY), auxin (IAA), or both (ETHY + IAA). At middle ripening, Micro-Tom ETHY + IAA fruits present VOC profiles similar to those of ETHY fruits, while Sweet Grape presents VOC profiles closer to those of IAA fruits. At full ripeness, Micro-Tom and Sweet Grape ETHY + IAA fruits show profiles closer to those of IAA fruits, suggesting that the auxin overlaps the ethylene effects. Aroma compounds positively correlated with consumer preferences (2-isobutylthiazole, 6-methyl-5-hepten-2-one, and others) are identified in both cultivars and have their contents affected by both hormone treatments. The transcription of genes related to the biosynthesis of important tomato VOCs that have fatty-acid and carotenoid precursors evidences their regulation by both plant hormones. Additionally, the results indicate that the observed effects on the VOC metabolism are not restricted to the Micro-Tom cultivar, as these are also observed in the Sweet Grape cultivar. In conclusion, ethylene and auxin directly regulate the metabolic pathways related to VOC formation, impacting tomato aroma formation during ripening since Micro-Tom fruits apparently at the same maturation stage have different aromas.

Metabolome and proteome of ethylene-treated papayas reveal different pathways to volatile compounds biosynthesis

Papayas undergo fast postharvest changes triggered by the plant hormone ethylene. Some important pathways have been analyzed in limited studies (transcriptomics and targeted metabolomics); however, broad use of proteomics or untargeted metabolomics have not yet been used in papayas. In this study, two groups of green papayas (150 days after anthesis-physiological maturity for papayas) were treated with ethylene at different times (6 and 12 h) and their metabolic changes in fruit pulp were evaluated with untargeted metabolomics (general metabolites and volatile compounds) and proteomics. Polar metabolites exhibited distinct patterns, especially with regard to some amino and fatty acids during stimulated ripening. In particular, glutamate increased through a possible gamma aminobutyric acid (GABA) shunt and/or proteases activity. Moreover, the stimulated ripening altered the volatile compounds and the protein profiles. The results suggest that changes in membrane breakdown and the resulting oxidative processes could be responsible for volatile compound production, altering some sensorial qualities of papayas, such as pulp softening and the specific papaya linalool volatile compound increment. Thus, GABA levels could also be a strong biological marker for papaya development and ripening stages. This study applied two "omic" techniques that provided insight into how the plant hormone ethylene could influence papaya postharvest quality.

Comparative proteomic analysis provides novel insights into the regulation mechanism underlying papaya (Carica papaya L.) exocarp during fruit ripening process

BACKGROUND

Papaya (Carica papaya L.) is a popular climacteric fruit, undergoing various physico-chemical changes during ripening. Although papaya is widely cultivated and consumed, few studies on the changes in metabolism during its ripening process at the proteasome level have been performed. Using a newly developed TMT-LCMS analysis, proteomes of papaya fruit at different ripening stages were investigated.

RESULTS

In total, 3220 proteins were identified, of which 2818 proteins were quantified. The differential accumulated proteins (DAPs) exhibited various biological functions and diverse subcellular localizations. The KEGG enrichment analysis showed that various metabolic pathways were significantly altered, particularly in flavonoid and fatty acid metabolisms. The up-regulation of several flavonoid biosynthesis-related proteins may provide more raw materials for pigment biosynthesis, accelerating the color variation of papaya fruit. Variations in the fatty acid metabolism- and cell wall degradation-related proteins were investigated during the ripening process. Furthermore, the contents of several important fatty acids were determined, and increased unsaturated fatty acids may be associated with papaya fruit volatile formation.

CONCLUSIONS

Our data may give an intrinsic explanation of the variations in metabolism during the ripening process of papaya fruit.

Fast and Furious: Ethylene-Triggered Changes in the Metabolism of Papaya Fruit During Ripening

Papaya is a climacteric fleshy fruit characterized by fast ripening after harvest. During the relatively short postharvest period, papaya fruit undergoes several changes in metabolism that result in pulp softening and sweetening, as well as the development of a characteristic aroma. Since papaya is one of the most cultivated and appreciated tropical fruit crops worldwide, extensive research has been conducted to not only understand the formation of the quality and nutritional attributes of ripe fruit but also to develop methods for controlling the ripening process. However, most strategies to postpone papaya ripening, and therefore to increase shelf life, have failed to maintain fruit quality. Ethylene blockage precludes carotenoid biosynthesis, while cold storage can induce chilling injury and negatively affect the volatile profile of papaya. As a climacteric fruit, the fast ripening of papaya is triggered by ethylene biosynthesis. The generation of the climacteric ethylene positive feedback loop is elicited by the expression of a specific transcription factor that leads to an up-regulation of 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS) and ACC-oxidase (ACO) expression, triggering the system II ethylene biosynthesis. The ethylene burst occurs about 3 to 4 days after harvest and induces pectinase expression. The disassembling of the papaya cell wall appears to help in fruit sweetness, while glucose and fructose are also produced by acidic invertases. The increase in ethylene production also results in carotenoid accumulation due to the induction of cyclases and hydroxylases, leading to yellow and red/orange-colored pulp phenotypes. Moreover, the production of volatile terpene linalool, an important biological marker for papaya's sensorial quality, is also induced by ethylene. All these mentioned processes are related to papaya's sensorial and nutritional quality. We describe the understanding of ethylene-triggered events that influence papaya quality and nutritional traits, as these characteristics are a consequence of an accelerated metabolism during fruit ripening.

Timing and Order of the Molecular Events Marking the Onset of Berry Ripening in Grapevine

Grapevine (Vitis vinifera) is a model for the investigation of physiological and biochemical changes during the formation and ripening of nonclimacteric fleshy fruits. However, the order and complexity of the molecular events during fruit development remain poorly understood. To identify the key molecular events controlling berry formation and ripening, we created a highly detailed transcriptomic and metabolomic map of berry development, based on samples collected every week from fruit set to maturity in two grapevine genotypes for three consecutive years, resulting in 219 samples. Major transcriptomic changes were represented by coordinated waves of gene expression associated with early development, veraison (onset of ripening)/midripening, and late-ripening and were consistent across vintages. The two genotypes were clearly distinguished by metabolite profiles and transcriptional changes occurring primarily at the veraison/midripening phase. Coexpression analysis identified a core network of transcripts as well as variations in the within-module connections representing varietal differences. By focusing on transcriptome rearrangements close to veraison, we identified two rapid and successive shared transitions involving genes whose expression profiles precisely locate the timing of the molecular reprogramming of berry development. Functional analyses of two transcription factors, markers of the first transition, suggested that they participate in a hierarchical cascade of gene activation at the onset of ripening. This study defined the initial transcriptional events that mark and trigger the onset of ripening and the molecular network that characterizes the whole process of berry development, providing a framework to model fruit development and maturation in grapevine.

Papaya CpEIN3a and CpNAC2 Co-operatively Regulate Carotenoid Biosynthesis-Related Genes CpPDS2/4, CpLCY-e and CpCHY-b During Fruit Ripening

Papaya is an important tropical fruit with a rich source of carotenoids. The ripening of papaya is a physiological and metabolic process with remarkable changes including accumulation of carotenoids, which depends primarily on the action of ethylene. Ethylene response is mediated by a transcriptional cascade involving the transcription factor families of EIN3/EILs and ERFs. Although ERF members have been reported to control carotenoid production in Arabidopsis and tomato, whether EIN3/EILs are also involved in carotenoid biosynthesis during fruit ripening remains unclear. In this work, two EIN3 genes from papaya fruit, namely CpEIN3a and CpEIN3b, were studied, of which CpEIN3a was increased during fruit ripening, concomitant with the increase of transcripts of carotenoid biosynthesis-related genes including CpPDS2/4, CpZDS, CpLCY-e and CpCHY-b, and carotenoid content. Electrophoretic mobility shift assays (EMSAs) and transient expression analyses revealed that CpEIN3a was able to bind to the promoters of CpPDS4 and CpCHY-b, and promoted their transcription. Protein-protein interaction assays indicated that CpEIN3a physically interacted with another transcription factor CpNAC2, which acted as a transcriptional activator of CpPDS2/4, CpZDS, CpLCY-e and CpCHY-b by directly binding to their promoters. More importantly, the transcriptional activation abilities of CpPDS2/4, CpLCY-e and CpCHY-b were more pronounced following their interaction. Collectively, our findings suggest that CpEIN3a interacts with CpNAC2 and, individually or co-operatively, activates the transcription of a subset of carotenoid biosynthesis-related genes, providing new insights into the regulatory networks of carotenoid biosynthesis during papaya fruit ripening.

Isolation of ripening-related genes from ethylene/1-MCP treated papaya through RNA-seq

BACKGROUND

Since papaya is a typical climacteric fruit, exogenous ethylene (ETH) applications can induce premature and quicker ripening, while 1-methylcyclopropene (1-MCP) slows down the ripening processes. Differential gene expression in ETH or 1-MCP-treated papaya fruits accounts for the ripening processes. To isolate the key ripening-related genes and better understand fruit ripening mechanisms, transcriptomes of ETH or 1-MCP-treated, and non-treated (Control Group, CG) papaya fruits were sequenced using Illumina Hiseq2500.

RESULTS

A total of 18,648 (1-MCP), 19,093 (CG), and 15,321 (ETH) genes were detected, with the genes detected in the ETH-treatment being the least. This suggests that ETH may inhibit the expression of some genes. Based on the differential gene expression (DGE) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, 53 fruit ripening-related genes were selected: 20 cell wall-related genes, 18 chlorophyll and carotenoid metabolism-related genes, four proteinases and their inhibitors, six plant hormone signal transduction pathway genes, four transcription factors, and one senescence-associated gene. Reverse transcription quantitative PCR (RT-qPCR) analyses confirmed the results of RNA-seq and verified that the expression pattern of six genes is consistent with the fruit senescence process. Based on the expression profiling of genes in carbohydrate metabolic process, chlorophyll metabolism pathway, and carotenoid metabolism pathway, the mechanism of pulp softening and coloration of papaya was deduced and discussed. We illustrate that papaya fruit softening is a complex process with significant cell wall hydrolases, such as pectinases, cellulases, and hemicellulases involved in the process. Exogenous ethylene accelerates the coloration of papaya changing from green to yellow. This is likely due to the inhibition of chlorophyll biosynthesis and the α-branch of carotenoid metabolism. Chy-b may play an important role in the yellow color of papaya fruit.

CONCLUSIONS

Comparing the differential gene expression in ETH/1-MCP-treated papaya using RNA-seq is a sound approach to isolate ripening-related genes. The results of this study can improve our understanding of papaya fruit ripening molecular mechanism and reveal candidate fruit ripening-related genes for further research.

Physiological Degradation of Pectin in Papaya Cell Walls: Release of Long Chains Galacturonans Derived from Insoluble Fractions during Postharvest Fruit Ripening

Papaya (Carica papaya L.) is a fleshy fruit that presents a rapid pulp softening during ripening. However, the timeline on how papaya pectinases act in polysaccharide solubilization and the consequent modification of the cell wall fractions during ripening is still not clear. In this work, the gene expression correlations between, on one hand, 16 enzymes potentially acting during papaya cell wall disassembling and, on the other hand, the monosaccharide composition of cell wall fractions during papaya ripening were evaluated. In order to explain differences in the ripening of papaya samplings, the molecular mass distribution of polysaccharides from water-soluble and oxalate-soluble fractions (WSF and OSF, respectively), as well as the oligosaccharide profiling from the WSF fraction, were evaluated by high performance size exclusion chromatography coupled to a refractive index detector and high performance anion-exchange chromatography coupled to pulse amperometric detection analyses, respectively. Results showed that up-regulated polygalacturonase and β-galactosidase genes were positively correlated with some monosaccharide profiles. In addition, an overall increase in the retention time of high molecular weight (HMW) and low molecular weight (LMW) polysaccharides in WSF and OSF was shown. The apparent disappearance of one HMW peak of the OSF may result from the conversion of pectin that were crosslinked with calcium into more soluble forms through the action of PGs, which would increase the solubilization of polysaccharides by lowering their molecular weight. Thus, the results allowed us to propose a detailed process of papaya cell wall disassembling that would affect sensorial properties and post-harvesting losses of this commercially important fruit.

Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis

Bambara groundnut (Vigna subterranea (L.) Verdc.) is an African legume and is a promising underutilized crop with good seed nutritional values. Low temperature stress in a number of African countries at night, such as Botswana, can effect the growth and development of bambara groundnut, leading to losses in potential crop yield. Therefore, in this study we developed a computational pipeline to identify and analyze the genes and gene modules associated with low temperature stress responses in bambara groundnut using the cross-species microarray technique (as bambara groundnut has no microarray chip) coupled with network-based analysis. Analyses of the bambara groundnut transcriptome using cross-species gene expression data resulted in the identification of 375 and 659 differentially expressed genes (p<0.01) under the sub-optimal (23°C) and very sub-optimal (18°C) temperatures, respectively, of which 110 genes are commonly shared between the two stress conditions. The construction of a Highest Reciprocal Rank-based gene co-expression network, followed by its partition using a Heuristic Cluster Chiseling Algorithm resulted in 6 and 7 gene modules in sub-optimal and very sub-optimal temperature stresses being identified, respectively. Modules of sub-optimal temperature stress are principally enriched with carbohydrate and lipid metabolic processes, while most of the modules of very sub-optimal temperature stress are significantly enriched with responses to stimuli and various metabolic processes. Several transcription factors (from MYB, NAC, WRKY, WHIRLY & GATA classes) that may regulate the downstream genes involved in response to stimulus in order for the plant to withstand very sub-optimal temperature stress were highlighted. The identified gene modules could be useful in breeding for low-temperature stress tolerant bambara groundnut varieties.

Involvement of the Putative N-Acetylornithine Deacetylase from Arabidopsis thaliana in Flowering and Fruit Development

In eukaryotic cells, the non-proteinogenic amino acid ornithine is the precursor of arginine and polyamines (PAs). The final step of ornithine biosynthesis occurs in plants via a cyclic pathway catalyzed by N(2)-acetylornithine:N-acetylglutamate acetyltransferase (NAOGAcT). An alternative route for ornithine formation, the linear pathway, has been reported for enteric bacteria and a few other organisms; the acetyl group of N(2)-acetylornithine is released as acetate by N(2)-acetylornithine deacetylase (NAOD). NAOD activity has never been demonstrated in plants, although many putative NAOD-like genes have been identified. In this investigation, we examined the effect of down-regulation of the putative Arabidopsis thaliana NAOD gene by using AtNAOD-silenced (sil#17) and T-DNA insertional mutant (atnaod) plants. The ornithine content was consistently reduced in sil#17 and atnaod plants compared with wild-type plants, suggesting that in addition to NAOGAcT action, AtNAOD contributes to the regulation of ornithine levels in plant cells. Ornithine depletion was associated with altered levels of putrescine and spermine. Reduced AtNAOD expression resulted in alterations at the reproductive level, causing early flowering and impaired fruit setting. In this regard, the highest level of AtNAOD expression was observed in unfertilized ovules. Our findings suggest that AtNAOD acts as a positive regulator of fruit setting and agree with those obtained in tomato auxin-synthesizing parthenocarpic plants, where induction of SlNAOD was associated with the onset of ovary growth. Thus, here we have uncovered the first hints of the functions of AtNAOD by connecting its role in flower and fruit development with the regulation of ornithine and PA levels.

Integrated network analysis identifies fight-club nodes as a class of hubs encompassing key putative switch genes that induce major transcriptome reprogramming during grapevine development

We developed an approach that integrates different network-based methods to analyze the correlation network arising from large-scale gene expression data. By studying grapevine (Vitis vinifera) and tomato (Solanum lycopersicum) gene expression atlases and a grapevine berry transcriptomic data set during the transition from immature to mature growth, we identified a category named "fight-club hubs" characterized by a marked negative correlation with the expression profiles of neighboring genes in the network. A special subset named "switch genes" was identified, with the additional property of many significant negative correlations outside their own group in the network. Switch genes are involved in multiple processes and include transcription factors that may be considered master regulators of the previously reported transcriptome remodeling that marks the developmental shift from immature to mature growth. All switch genes, expressed at low levels in vegetative/green tissues, showed a significant increase in mature/woody organs, suggesting a potential regulatory role during the developmental transition. Finally, our analysis of tomato gene expression data sets showed that wild-type switch genes are downregulated in ripening-deficient mutants. The identification of known master regulators of tomato fruit maturation suggests our method is suitable for the detection of key regulators of organ development in different fleshy fruit crops.

Development of a gene-centered ssr atlas as a resource for papaya (Carica papaya) marker-assisted selection and population genetic studies

Carica papaya (papaya) is an economically important tropical fruit. Molecular marker-assisted selection is an inexpensive and reliable tool that has been widely used to improve fruit quality traits and resistance against diseases. In the present study we report the development and validation of an atlas of papaya simple sequence repeat (SSR) markers. We integrated gene predictions and functional annotations to provide a gene-centered perspective for marker-assisted selection studies. Our atlas comprises 160,318 SSRs, from which 21,231 were located in genic regions (i.e. inside exons, exon-intron junctions or introns). A total of 116,453 (72.6%) of all identified repeats were successfully mapped to one of the nine papaya linkage groups. Primer pairs were designed for markers from 9,594 genes (34.5% of the papaya gene complement). Using papaya-tomato orthology assessments, we assembled a list of 300 genes (comprising 785 SSRs) potentially involved in fruit ripening. We validated our atlas by screening 73 SSR markers (including 25 fruit ripening genes), achieving 100% amplification rate and uncovering 26% polymorphism rate between the parental genotypes (Sekati and JS12). The SSR atlas presented here is the first comprehensive gene-centered collection of annotated and genome positioned papaya SSRs. These features combined with thousands of high-quality primer pairs make the atlas an important resource for the papaya research community.

Analysis of papaya cell wall-related genes during fruit ripening indicates a central role of polygalacturonases during pulp softening

Papaya (Carica papaya L.) is a climacteric fleshy fruit that undergoes dramatic changes during ripening, most noticeably a severe pulp softening. However, little is known regarding the genetics of the cell wall metabolism in papayas. The present work describes the identification and characterization of genes related to pulp softening. We used gene expression profiling to analyze the correlations and co-expression networks of cell wall-related genes, and the results suggest that papaya pulp softening is accomplished by the interactions of multiple glycoside hydrolases. The polygalacturonase cpPG1 appeared to play a central role in the network and was further studied. The transient expression of cpPG1 in papaya results in pulp softening and leaf necrosis in the absence of ethylene action and confirms its role in papaya fruit ripening.

Genomic resources in fruit plants: an assessment of current status

The availability of many genomic resources such as genome sequences, functional genomics resources including microarrays and RNA-seq, sufficient numbers of molecular markers, express sequence tags (ESTs) and high-density genetic maps is causing a rapid acceleration of genetics and genomic research of many fruit plants. This is leading to an increase in our knowledge of the genes that are linked to many horticultural and agronomically important traits. Recently, some progress has also been made on the identification and functional analysis of miRNAs in some fruit plants. This is one of the most active research fields in plant sciences. The last decade has witnessed development of genomic resources in many fruit plants such as apple, banana, citrus, grapes, papaya, pears, strawberry etc.; however, many of them are still not being exploited. Furthermore, owing to lack of resources, infrastructure and research facilities in many lesser-developed countries, development of genomic resources in many underutilized or less-studied fruit crops, which grow in these countries, is limited. Thus, research emphasis should be given to those fruit crops for which genomic resources are relatively scarce. The development of genomic databases of these less-studied fruit crops will enable biotechnologists to identify target genes that underlie key horticultural and agronomical traits. This review presents an overview of the current status of the development of genomic resources in fruit plants with the main emphasis being on genome sequencing, EST resources, functional genomics resources including microarray and RNA-seq, identification of quantitative trait loci and construction of genetic maps as well as efforts made on the identification and functional analysis of miRNAs in fruit plants.

Comparative transcriptional profiling analysis of olive ripe-fruit pericarp and abscission zone tissues shows expression differences and distinct patterns of transcriptional regulation

BACKGROUND

In fleshy fruit, abscission of fully ripe fruit is a process intimately linked to the ripening process. In many fruit-tree species, such as olive (Olea europaea L. cv. Picual), there is a coupling of the full ripening and the activation of the abscission-zone (AZ). Although fully ripe fruit have marked physiological differences with respect to their AZs, dissimilarities in gene expression have not been thoroughly investigated. The present study examines the transcriptome of olive fruit and their AZ tissues at the last stage of ripening, monitored using mRNA-Seq.

RESULTS

Roche-454 massive parallel pyrosequencing enabled us to generate 397,457 high-quality EST sequences, among which 199,075 were from ripe-fruit pericarp and 198,382 from AZ tissues. We assembled these sequences into 19,062 contigs, grouped as 17,048 isotigs. Using the read amounts for each annotated isotig (from a total of 15,671), we identified 7,756 transcripts. A comparative analysis of the transcription profiles conducted in ripe-fruit pericarp and AZ evidenced that 4,391 genes were differentially expressed genes (DEGs) in fruit and AZ. Functional categorization of the DEGs revealed that AZ tissue has an apparently higher response to external stimuli than does that of ripe fruit, revealing a higher expression of auxin-signaling genes, as well as lignin catabolic and biosynthetic pathway, aromatic amino acid biosynthetic pathway, isoprenoid biosynthetic pathway, protein amino acid dephosphorylation, amino acid transport, and photosynthesis. By contrast, fruit-enriched transcripts are involved in ATP synthesis coupled proton transport, glycolysis, and cell-wall organization. Furthermore, over 150 transcripts encoding putative transcription-factors (TFs) were identified (37 fruit TFs and 113 AZ TFs), of which we randomly selected eight genes and we confirmed their expression patterns using quantitative RT-PCR.

CONCLUSION

We generated a set of EST sequences from olive fruit at full ripening, and DEGs between two different olive tissues, ripe fruit and their AZ, were also identified. Regarding the cross-talk between fruit and AZ, using qRT-PCR, we confirmed a set of TF genes that were differentially expressed, revealing profiles of expression that have not previously been reported, this offering a promising beginning for studies on the different transcription regulation in such tissues.