Nutrition metabolism plays an important role in the alternate bearing of the olive tree (Olea europaea L.)

Olive reproductive biology: implications for yield, compatibility conundrum, and environmental constraints

Olive (Olea europaea L.) is an important Mediterranean tree species with a longstanding history of cultivation, boasting a diverse array of local cultivars. While traditional olive orchards are valued for their cultural and aesthetic significance, they often face economic sustainability challenges in the modern context. The success of both traditional and newly introduced cultivars (e.g. those obtained by cross-breeding) is hindered by self-incompatibility, a prevalent issue for this species that results in low fruit set when limited genetic diversity is present. Further, biological, environmental, and agronomic factors have been shown to interlink in shaping fertilization patterns, hence impacting on the final yield. Climatic conditions during pollination, such as excessive rainfall or high temperatures, can further exacerbate the problem. In this work, we provide an overview of the various factors that trigger the phenomenon of suboptimal fruit set in olive trees. This work provides a comprehensive understanding of the interplay among these factors, shedding light on potential mechanisms and pathways that contribute to the observed outcomes in the context of self-incompatibility in olive.

Studying Parameters Affecting Accumulation of Chilling Units Required for Olive Winter Flower Induction

With global warming, mean winter temperatures are predicted to increase. Therefore, understanding how warmer winters will affect the levels of olive flower induction is essential for predicting the future sustainability of olive oil production under different climactic scenarios. Here, we studied the effect of fruit load, forced drought in winter, and different winter temperature regimes on olive flower induction using several cultivars. We show the necessity of studying trees with no previous fruit load as well as provide evidence that soil water content during winter does not significantly affect the expression of an FT-encoding gene in leaves and the subsequent rate of flower induction. We collected yearly flowering data for 5 cultivars for 9 to 11 winters, altogether 48 data sets. Analyzing hourly temperatures from these winters, we made initial attempts to provide an efficient method to calculate accumulated chill units that are then correlated with the level of flower induction in olives. While the new models tested here appear to predict the positive contribution of cold temperatures, they lack in accurately predicting the reduction in cold units caused by warm temperatures occurring during winter.

Comparative transcriptomics in alternate bearing cultivar Dashehari reveals the genetic model of flowering in mango

Flowering is a complex developmental process, with physiological and morphological phases influenced by a variety of external and internal factors. Interestingly, many mango cultivars tend to bear fruit biennially because of irregular flowering, and this has a negative impact on mango flowering and the subsequent yield, resulting in significant economic losses. In this article, transcriptome analysis was carried out on four tissues of mango cv. Dashehari (bearing tree leaf, shoot apex, inflorescence, and non-bearing tree leaf). De novo transcriptome assembly of RNA-seq reads of Dashehari using the Trinity pipeline generated 67,915 transcripts, with 25,776 genes identified. 85 flowering genes, represented by 179 transcripts, were differentially expressed in bearing vs. non-bearing leaf tissues. Gene set enrichment analysis of flowering genes identified significant upregulation of flowering related genes in inflorescence tissues compared to bearing leaf tissues. The flowering genes FT, CO, GI, ELF 4, FLD, FCA, AP1, LHY, and SCO1 were upregulated in the bearing leaf tissues. Pathway analysis of DEGs showed significant upregulation of phenylpropanoid and sucrose and starch pathways in non-bearing leaf tissue compared with bearing leaf tissue. The comparative transcriptome analysis performed in this study significantly increases the understanding of the molecular mechanisms driving the flowering process as well as alternative bearing in mango.

Influence of Drying Temperature and Harvesting Season on Phenolic Content and Antioxidant and Antiproliferative Activities of Olive (Olea europaea) Leaf Extracts

Interest in plant compounds has increased, given recent evidence regarding their role in human health due to their pleiotropic effects. For example, plant bioactive compounds present in food products, including polyphenols, are associated with preventive effects in various diseases, such as cancer or inflammation. Breast and colorectal cancers are among the most commonly diagnosed cancers globally. Although appreciable advances have been made in treatments, new therapeutic approaches are still needed. Thus, in this study, up to 28 olive leaf extracts were obtained during different seasons and using different drying temperatures. The influence of these conditions on total polyphenolic content (measured using Folin-Ciocalteu assays), antioxidant activity (using Trolox Equivalent Antioxidant Capacity and Ferric Reducing Ability of Plasma assays) and antiproliferative capacity (using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, MTT assays) was tested in breast and colorectal cancer cells. Increased phenolic composition and antioxidant and antiproliferative capacity are noted in the extracts obtained from leaves harvested in autumn, followed by summer, spring and winter. Regarding drying conditions, although there is not a general trend, conditions using the highest temperatures lead to the optimal phenolic content and antioxidant and antiproliferative activities in most cases. These results confirm previously published studies and provide evidence in support of the influence of both harvesting and drying conditions on the biological activity of olive leaf extracts.

Transcriptome and Metabolome Analyses Reveal the Involvement of Multiple Pathways in Flowering Intensity in Mango

Mango (Mangifera indica L.) is famous for its sweet flavor and aroma. China is one of the major mango-producing countries. Mango is known for variations in flowering intensity that impacts fruit yield and farmers' profitability. In the present study, transcriptome and metabolome analyses of three cultivars with different flowering intensities were performed to preliminarily elucidate their regulatory mechanisms. The transcriptome profiling identified 36,242 genes. The major observation was the differential expression patterns of 334 flowering-related genes among the three mango varieties. The metabolome profiling detected 1,023 metabolites that were grouped into 11 compound classes. Our results show that the interplay of the FLOWERING LOCUS T and CONSTANS together with their upstream/downstream regulators/repressors modulate flowering robustness. We found that both gibberellins and auxins are associated with the flowering intensities of studied mango varieties. Finally, we discuss the roles of sugar biosynthesis and ambient temperature pathways in mango flowering. Overall, this study presents multiple pathways that can be manipulated in mango trees regarding flowering robustness.

The metabolic reserves, carbohydrate balance and nutritional status of jojoba (Simmondsia chinensis), in relation to its annual cycle and fruit load

Jojoba (Simmondsia chinensis (Link) Schneider) holds high industrial value and an extended cultivation trend. Despite its increased importance, there is a lack of fundamental information about its metabolic reserves and development. Our objective was to characterise metabolite allocation and fluctuations in the carbohydrate and nutrient balance of jojoba plants, as affected by fruit load and the plant's annual cycle. Metabolite profiles were performed for each organ. Soluble carbohydrates (SC) and starch concentrations were surveyed in underground and aboveground organs of high-yield and fruit-removed plants. Simultaneously, nitrogen, potassium and phosphorus were determined in the leaves to evaluate the plant's nutritional status. We found that sucrose and pinitol were the most abundant sugars in all jojoba organs. Each sugar had a 'preferred' organ: glucose was accumulated mainly in the leaves, sucrose and pinitol in woody branches, and fructose in the trunk wood. We found that fruit load significantly influenced the carbohydrate levels in green branches, trunk wood and thin roots. The phenological stage strongly affected the SC-starch balance. Among the examined minerals, only the leaf potassium level was significantly influenced by fruit load. We conclude that jojoba's nutrient and carbohydrate balance is affected by fruit load and the phenological stage, and describe the organ-specific metabolic reserves.

Olive oil consumption can prevent non-communicable diseases and COVID-19 : Review

The Mediterranean diet is appraised as the premier dietary regimen and its espousal is correlated with the prevention of degenerative diseases and extended longevity. The consumption of olive oil stands out as the most peculiar feature of the Mediterranean diet. Olive oil rich in various bioactive compounds like oleanolic acid, oleuropein, oleocanthal, and hydroxytyrosol is known for its anti-inflammatory as well as cardioprotective property. Recently in silico studies have indicated that phytochemicals present in olive oil are a potential candidate to act against SARS-CoV-2. Although extensive studies on olive oil and its phytochemical composition; still, some lacunas persist in understanding how the phytochemical composition of olive oil is dependent on upstream processing. The signaling pathways regulated by olive oil in the restriction of various diseases is also not clear. To answer these queries, a detailed search of research and review articles published between 1990 to 2019 were reviewed in this effect. Olive oil consumption was found to be advantageous for various chronic non-communicable diseases. Olive oil's constituents are having potent anti-inflammatory activities and thus restrict the progression of various inflammation-linked diseases ranging from arthritis to cancer. But it is also notable that the amount and nature of phytochemical composition of household olive oil are regulated by its upstream processing and the physicochemical properties of this oil can give a hint regarding the manufacturing method as well as its therapeutic. Moreover, daily uptake of olive oil should be monitored as excessive intake can cause body weight gain and change in the basal metabolic index. So, it can be concluded that olive oil consumption is beneficial for human health, and particularly for the prevention of cardiovascular diseases, breast cancer, and inflammation. The simple way of processing olive oil maintains the polyphenol constituents and provides more protection against non-communicable diseases and SARS-CoV-2.

A Complex Gene Network Mediated by Ethylene Signal Transduction TFs Defines the Flower Induction and Differentiation in Olea europaea L

The olive tree (Olea europaea L.) is a typical Mediterranean crop, important for olive and oil production. The high tendency to bear fruits in an uneven manner, defined as irregular or alternate bearing, results in a significant economic impact for the high losses in olives and oil production. Buds from heavy loaded (‘ON’) and unloaded (‘OFF’) branches of a unique olive tree were collected in July and the next March to compare the transcriptomic profiles and get deep insight into the molecular mechanisms regulating floral induction and differentiation. A wide set of DEGs related to ethylene TFs and to hormonal, sugar, and phenylpropanoid pathways was identified in buds collected from ‘OFF’ branches. These genes could directly and indirectly modulate different pathways, suggesting their key role during the lateral bud transition to flowering stage. Interestingly, several genes related to the flowering process appeared as over-expressed in buds from March ‘OFF’ branches and they could address the buds towards flower differentiation. By this approach, interesting candidate genes related to the switch from vegetative to reproductive stages were detected and analyzed. The functional analysis of these genes will provide tools for developing breeding programs to obtain olive trees characterized by more constant productivity over the years.

Differential expression of genes in olive leaves and buds of ON- versus OFF-crop trees

Alternate bearing (AB) refers to the tendency of trees to have an irregular crop load from 1 year (ON) to the next year (OFF). Despite its economic importance, it is not fully understood how gene networks and their related metabolic pathways may influence the irregular bearing in olive trees. To unravel molecular mechanisms of this phenomenon in olive (cv. Conservalia), the whole transcriptome of leaves and buds from ON and OFF-trees was sequenced using Illumina next generation sequencing approach. The results indicated that expressed transcripts were involved in metabolism of carbohydrates, polyamins, phytohormones and polyphenol oxidase (POD) related to antioxidant system. Expression of POD was increased in leaf samples of ON- versus OFF-trees. The expression pattern of the greater number of genes was changed more in buds than in leaves. Up-regulation of gene homologues to the majority of enzymes that were involved in photorespiration metabolism pathway in buds of ON-trees was remarkable that may support the hypotheses of an increase in photorespiratory metabolism in these samples. The results indicated changes in expression pattern of homologous to those taking part of abscisic acid and cytokinin synthesis which are connected to photorespiration. Our data did not confirm expression of homologue (s) to those of chlorogenic acid metabolism, which has been addressed earlier that have a probable role in biennial bearing in olive. Current findings provide new candidate genes for further functional analysis, gene cloning and exploring of molecular basses of AB in olive.

Comparative RNA sequencing based transcriptome profiling of regular bearing and alternate bearing mango (Mangifera indica L.) varieties reveals novel insights into the regulatory mechanisms underlying alternate bearing

OBJECTIVE

This study is to understand a comprehensive perspective on the molecular mechanisms underlying alternate bearing in mango (Mangifera indica L.) via transcriptome wide gene expression profiling of both regular and irregular mango varieties.

RESULTS

Transcriptome data of regular (Neelam) and irregular (Dashehari) mango varieties revealed a total of 42,397 genes. Out of that 12,557 significantly differentially expressed genes were identified, of which 6453 were found to be up-regulated and 6104 were found to be down-regulated genes. Further, many of the common unigenes which were involved in hormonal regulation, metabolic processes, oxidative stress, ion homeostasis, alternate bearing etc. showed significant differences between these two different bearing habit varieties. Pathway analysis showed the highest numbers of differentially expressed genes were related with the metabolic processes (523). A total of 26 alternate bearing genes were identified and principally three genes viz; SPL-like gene (GBVX01015803.1), Rumani GA-20-oxidase-like gene (GBVX01019650.1) and LOC103420644 (GBVX01016070.1) were significantly differentially expressed (at log2FC and pval less than 0.05) while, only single gene (gbGBVW01004309.1) related with flowering was found to be differentially expressed. A total of 15 differentially expressed genes from three important pathways viz; alternate bearing, carbohydrate metabolism and hormone synthesis were validated using Real time PCR and results were at par with in silico analysis.

CONCLUSIONS

Deciphering the differentially expressed genes (DEGs) and potential candidate genes associated with alternate bearing, hormone and carbohydrate metabolism pathways will help for illustrating the molecular mechanisms underlying the bearing tendencies in mango.

Dynamic Cytosine DNA Methylation Patterns Associated with mRNA and siRNA Expression Profiles in Alternate Bearing Apple Trees

Cytosine DNA methylation plays an important role in plants: it can mediate gene expression to affect plant growth and development. However, little is known about the potential involvement of cytosine DNA methylation in apple trees as well as in response to alternate bearing. Here, we performed whole-genome bisulfate sequencing to investigate genomic CG, CHG, and CHH methylation patterns, together with their global mRNA accumulation and small RNA expression in "Fuji" apple trees. Results showed that "Fuji" apple trees have a higher CHH methylation than Arabidopsis. Moreover, genomic methylation analysis revealed that CG and CHG methylation were robustly maintained at the early stage of flower induction. Additionally, differentially methylated regions (DMRs), including hypermethylated and hypomethylated DMRs, were also characterized in alternate bearing (AB) apple trees. Intriguingly, the DMRs were enriched in hormones, redox state, and starch and sucrose metabolism, which affected flowering. Further global gene expression evaluation based on methylome analysis revealed a negative correlation between gene body methylation and gene expression. Subsequent small RNA analyses showed that 24-nucleotide small interfering RNAs were activated and maintained in non-CG methylated apple trees. Our whole-genome DNA methylation analysis and RNA and small RNA expression profile construction provide valuable information for future studies.

Regulation of On-Tree Vitamin E Biosynthesis in Olive Fruit during Successive Growing Years: The Impact of Fruit Development and Environmental Cues

The term vitamin E refers to a group of eight lipophilic compounds known as tocochromanols. The tocochromanols are divided into two groups, that is, tocopherols and tocotrienols, with four forms each, namely α-, β-, γ-, and δ-. In order to explore the temporal biosynthesis of tocochromanols in olive (Olea europaea cv. 'Koroneiki') fruit during on-tree development and ripening over successive growing years, a combined array of analytical, molecular, bioinformatic, immunoblotting, and antioxidant techniques were employed. Fruits were harvested at eight successive developmental stages [10-30 weeks after flowering (WAF)], over three consecutive years. Intriguingly, climatic conditions affected relative transcription levels of vitamin E biosynthetic enzymes; a general suppression to induction pattern (excluding VTE5) was monitored moving from the 1st to the 3rd growing year, probably correlated to decreasing rainfall levels and higher temperature, particularly at the fruit ripening stage. A gradual diminution of VTE5 protein content was detected during the fruit development of each year, with a marked decrease occurring after 16 WAF. Alpha-tocopherol was the most abundant metabolite with an average percentage of 96.82 ± 0.23%, 91.13 ± 0.95%, and 88.53 ± 0.96% (during the 1st, 2nd, and 3rd year, respectively) of total vitamin E content in 10-30 WAF. The concentrations of α-tocopherol revealed a generally declining pattern, both during the on-tree ripening of the olive fruit and across the 3 years, accompanied by a parallel decline of the total antioxidant capacity of the drupe. Contrarily, all other tocochromanols demonstrated an inverse pattern with lowest levels being recorded during the 1st year. It is likely that, in a defense attempt against water deficit conditions and increased air temperature, transcription of genes involved in vitamin E biosynthesis (excluding VTE5) is up-regulated in olive fruit, probably leading to the blocking/deactivating of the pathway through a negative feedback regulatory mechanism.

Transcript Analysis and Regulative Events during Flower Development in Olive (Olea europaea L.)

The identification and characterization of transcripts involved in flower organ development, plant reproduction and metabolism represent key steps in plant phenotypic and physiological pathways, and may generate high-quality transcript variants useful for the development of functional markers. This study was aimed at obtaining an extensive characterization of the olive flower transcripts, by providing sound information on the candidate MADS-box genes related to the ABC model of flower development and on the putative genetic and molecular determinants of ovary abortion and pollen-pistil interaction. The overall sequence data, obtained by pyrosequencing of four cDNA libraries from flowers at different developmental stages of three olive varieties with distinct reproductive features (Leccino, Frantoio and Dolce Agogia), included approximately 465,000 ESTs, which gave rise to more than 14,600 contigs and approximately 92,000 singletons. As many as 56,700 unigenes were successfully annotated and provided gene ontology insights into the structural organization and putative molecular function of sequenced transcripts and deduced proteins in the context of their corresponding biological processes. Differentially expressed genes with potential regulatory roles in biosynthetic pathways and metabolic networks during flower development were identified. The gene expression studies allowed us to select the candidate genes that play well-known molecular functions in a number of biosynthetic pathways and specific biological processes that affect olive reproduction. A sound understanding of gene functions and regulatory networks that characterize the olive flower is provided.

Insights into the proteomic response of soybean towards Al₂O₃, ZnO, and Ag nanoparticles stress

Understanding the complex mechanisms involved in plant response to nanoparticles is indispensable in assessing the impact of nano-pollutants on environment. The present study compares the phytotoxicity of three different metal-based nanoparticles (Al2O3, ZnO, and Ag) in soybean seedling at proteome level. Plant growth, rigidity of roots, and root cell viability were markedly affected by ZnO- and Ag-NPs stress; while, Al2O3-NPs challenged soybean maintained normal seedling growth like control. Moreover, severe oxidative burst was evident in ZnO-NPs and Ag-NPs treatments. Gel-free proteomic analysis of NPs stressed soybean roots revealed 104 commonly changed proteins primarily associated with secondary metabolism, cell organization, and hormone metabolism. Oxidation-reduction cascade related genes, such as GDSL motif lipase 5, SKU5 similar 4, galactose oxidase, and quinone reductase were up-regulated in Al2O3-NPs challenged roots and down-regulated in ZnO- and Ag-NPs treatments. In comparison to root, 16 common proteins were found to be significantly changed in leaves of NPs exposed soybean that were predominantly associated to photosystem and protein degradation. The proteomic findings suggest that high abundance of proteins involved in oxidation-reduction, stress signaling, hormonal pathways related to growth and development might be the principal key for optimum growth of soybean under Al2O3-NPs stress.

Fruit load governs transpiration of olive trees

We tested the hypothesis that whole-tree water consumption of olives (Olea europaea L.) is fruit load-dependent and investigated the driving physiological mechanisms. Fruit load was manipulated in mature olives grown in weighing-drainage lysimeters. Fruit was thinned or entirely removed from trees at three separate stages of growth: early, mid and late in the season. Tree-scale transpiration, calculated from lysimeter water balance, was found to be a function of fruit load, canopy size and weather conditions. Fruit removal caused an immediate decline in water consumption, measured as whole-plant transpiration normalized to tree size, which persisted until the end of the season. The later the execution of fruit removal, the greater was the response. The amount of water transpired by a fruit-loaded tree was found to be roughly 30% greater than that of an equivalent low- or nonyielding tree. The tree-scale response to fruit was reflected in stem water potential but was not mirrored in leaf-scale physiological measurements of stomatal conductance or photosynthesis. Trees with low or no fruit load had higher vegetative growth rates. However, no significant difference was observed in the overall aboveground dry biomass among groups, when fruit was included. This case, where carbon sources and sinks were both not limiting, suggests that the role of fruit on water consumption involves signaling and alterations in hydraulic properties of vascular tissues and tree organs.

Genome-wide characterization and expression analysis of common bean bHLH transcription factors in response to excess salt concentration

Members of basic helix-loop-helix (bHLH) gene family found in all eukaryotes play crucial roles in response to stress. Though, most eukaryotes carry the proteins of this family, biological functions of the most bHLH family members are not deeply evaluated in plants. In this study, we conducted a comprehensive genome-wide analysis of bHLH transcription factors in salt tolerant common bean. We identified 155 bHLH protein-encoding genes (PvbHLH) by using in silico comparative genomics tools. Based on the phylogenetic tree, PvbHLH genes were classified into 8 main groups with 21 subfamilies. Exon-intron analysis indicated that proteins belonging to same main groups exhibited a closely related gene structure. While, the PvbHLH gene family has been mainly expanded through segmental duplications, a total of 11 tandem duplication were detected. Genome-wide expression analysis of bHLH genes showed that 63 PvbHLH genes were differentially expressed in at least one tissue. Three of them displayed higher expression values in both leaf and root tissues. The in silico micro-RNA target transcript analyses revealed that totally 100 PvHLH genes targeted by 86 plant miRNAs. The most abundant transcripts, which were targeted by all 18 plant miRNA, were belonging to PvHLH-22 and PvHLH-44 genes. The expression of 16 PvbHLH genes in the root and leaf tissues of salt-stressed common bean was evaluated using qRT-PCR. Among them, two of PvbHLHs, PvbHLH-54, PvbHLH-148, were found to be up-regulated in both tissues in correlation with RNA-seq measurements. The results of this study could help improve understanding of biological functions of common bean bHLH family under salt stress. Additionally, it may provide basic resources for analyzing bHLH protein function for improving economic, agronomic and ecological benefit in common bean and other species.

ReprOlive: a database with linked data for the olive tree (Olea europaea L.) reproductive transcriptome

Plant reproductive transcriptomes have been analyzed in different species due to the agronomical and biotechnological importance of plant reproduction. Here we presented an olive tree reproductive transcriptome database with samples from pollen and pistil at different developmental stages, and leaf and root as control vegetative tissues http://reprolive.eez.csic.es). It was developed from 2,077,309 raw reads to 1,549 Sanger sequences. Using a pre-defined workflow based on open-source tools, sequences were pre-processed, assembled, mapped, and annotated with expression data, descriptions, GO terms, InterPro signatures, EC numbers, KEGG pathways, ORFs, and SSRs. Tentative transcripts (TTs) were also annotated with the corresponding orthologs in Arabidopsis thaliana from TAIR and RefSeq databases to enable Linked Data integration. It results in a reproductive transcriptome comprising 72,846 contigs with average length of 686 bp, of which 63,965 (87.8%) included at least one functional annotation, and 55,356 (75.9%) had an ortholog. A minimum of 23,568 different TTs was identified and 5,835 of them contain a complete ORF. The representative reproductive transcriptome can be reduced to 28,972 TTs for further gene expression studies. Partial transcriptomes from pollen, pistil, and vegetative tissues as control were also constructed. ReprOlive provides free access and download capability to these results. Retrieval mechanisms for sequences and transcript annotations are provided. Graphical localization of annotated enzymes into KEGG pathways is also possible. Finally, ReprOlive has included a semantic conceptualisation by means of a Resource Description Framework (RDF) allowing a Linked Data search for extracting the most updated information related to enzymes, interactions, allergens, structures, and reactive oxygen species.

Transcriptome analysis of wheat inoculated with Fusarium graminearum

Plants are frequently exposed to microorganisms like fungi, bacteria, and viruses that cause biotic stresses. Fusarium head blight (FHB) is an economically risky wheat disease, which occurs upon Fusarium graminearum (Fg) infection. Moderately susceptible (cv. "Mizrak 98") and susceptible (cv. "Gun 91") winter type bread wheat cultivars were subjected to transcriptional profiling after exposure to Fg infection. To examine the early response to the pathogen in wheat, we measured gene expression alterations in mock and pathogen inoculated root crown of moderately susceptible (MS) and susceptible cultivars at 12 hours after inoculation (hai) using 12X135K microarray chip. The transcriptome analyses revealed that out of 39,179 transcripts, 3668 genes in microarray were significantly regulated at least in one time comparison. The majority of differentially regulated transcripts were associated with disease response and the gene expression mechanism. When the cultivars were compared, a number of transcripts and expression alterations varied within the cultivars. Especially membrane related transcripts were detected as differentially expressed. Moreover, diverse transcription factors showed significant fold change values among the cultivars. This study presented new insights to understand the early response of selected cultivars to the Fg at 12 hai. Through the KEGG analysis, we observed that the most altered transcripts were associated with starch and sucrose metabolism and gluconeogenesis pathways.

Genome-wide fungal stress responsive miRNA expression in wheat

MicroRNAs (miRNAs) are small non-coding class of RNAs. They were identified in many plants with their diverse regulatory roles in several cellular and metabolic processes. A number of miRNAs were involved in biotic and abiotic stress responses. Here, fungal stress responsive wheat miRNAs were analyzed by using miRNA-microarray strategy. Two different fungi (Fusarium culmorum and Bipolaris sorokiniana) were inoculated on resistant and sensitive wheat cultivars. A total of 87 differentially regulated miRNAs were detected in the 8 × 15 K array including all of the available plant miRNAs. Using bioinformatics tools, the target transcripts of responsive miRNAs were predicted, and related biological processes and mechanisms were assessed. A number of the miRNAs such as miR2592s, miR869.1, miR169b were highly differentially regulated showing more than 200-fold change upon fungal-inoculation. Some of the miRNAs were identified as fungal-inoculation responsive for the first time. The analyses showed that some of the differentially regulated miRNAs targeted resistance-related genes such as LRR, glucuronosyl transferase, peroxidase and Pto kinase. The comparison of the two miRNA-microarray analyses indicated that fungal-responsive wheat miRNAs were differentially regulated in pathogen- and cultivar-specific manners.

Transcriptome and metabolome analysis of plant sulfate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulfur, nitrogen and phosphorus nutritional responses in Arabidopsis

Sulfur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulfur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulfate starvation have been studied in the past, knowledge of the regulation of sulfur metabolism is still fragmentary. This work focuses on the discovery of candidates for regulatory genes such as transcription factors (TFs) using 'omics technologies. For this purpose a short term sulfate-starvation/re-supply approach was used. ATH1 microarray studies and metabolite determinations yielded 21 TFs which responded more than 2-fold at the transcriptional level to sulfate starvation. Categorization by response behaviors under sulfate-starvation/re-supply and other nutrient starvations such as nitrate and phosphate allowed determination of whether the TF genes are specific for or common between distinct mineral nutrient depletions. Extending this co-behavior analysis to the whole transcriptome data set enabled prediction of putative downstream genes. Additionally, combinations of transcriptome and metabolome data allowed identification of relationships between TFs and downstream responses, namely, expression changes in biosynthetic genes and subsequent metabolic responses. Effect chains on glucosinolate and polyamine biosynthesis are discussed in detail. The knowledge gained from this study provides a blueprint for an integrated analysis of transcriptomics and metabolomics and application for the identification of uncharacterized genes.

Quantifying key parameters as elicitors for alternate fruit bearing in cv. 'Elstar' apple trees

The commonly known alternate bearing, i.e. year-to-year change of large and small yields of fruit tree crops worldwide, is often induced by abiotic stress such as late frost, which will eliminate flowers or fruitlets. This study presents an alternative form, biotic biennial bearing, i.e. change of large and small yields of the same trees within the same tree row in the same year. Three methods were developed or modified for the analysis of the number of flower clusters and yield of 2086 apple (Malus domestica Borkh.) cv. 'Elstar' trees. The first method, i.e., based on intersect between yield in year x and year x+1 and flower clusters in year x, yielded 91-106 flower clusters, whereas the second method, i.e., mean yield in year x and year x+1, resulted in a range of 72-133 flower clusters, or 9.6kg/tree necessary for sustainable cultivation of apple cv. 'Elstar'. The third 'biennial bearing index' (BBI), was calculated in three ways as the ratio of differences in tree yields to cumulative tree yield, for individual trees (rather than orchard average) to demonstrate the tree-to-tree alternation. A scheme for the possible underlying regulatory mechanisms was developed, which includes potential elicitors such as light deprivation and subsequent lack of flower initiation, are discussed as a possible result of polar basipetal GA7 transport, cytokinin level in the xylem and phloem and down-regulation of the gene expression of the flowering gene. Suggested countermeasures included early chemical or mechanical thinning.

Gene selection heuristic algorithm for nutrigenomics studies

Large datasets from -omics studies need to be deeply investigated. The aim of this paper is to provide a new method (LEM method) for the search of transcriptome and metabolome connections. The heuristic algorithm here described extends the classical canonical correlation analysis (CCA) to a high number of variables (without regularization) and combines well-conditioning and fast-computing in "R." Reduced CCA models are summarized in PageRank matrices, the product of which gives a stochastic matrix that resumes the self-avoiding walk covered by the algorithm. Then, a homogeneous Markov process applied to this stochastic matrix converges the probabilities of interconnection between genes, providing a selection of disjointed subsets of genes. This is an alternative to regularized generalized CCA for the determination of blocks within the structure matrix. Each gene subset is thus linked to the whole metabolic or clinical dataset that represents the biological phenotype of interest. Moreover, this selection process reaches the aim of biologists who often need small sets of genes for further validation or extended phenotyping. The algorithm is shown to work efficiently on three published datasets, resulting in meaningfully broadened gene networks.

Isolation and expression analysis of cDNAs that are associated with alternate bearing in Olea europaea L. cv. Ayvalık

Background

Olive cDNA libraries to isolate candidate genes that can help enlightening the molecular mechanism of periodicity and / or fruit production were constructed and analyzed. For this purpose, cDNA libraries from the leaves of trees in “on year” and in “off year” in July (when fruits start to appear) and in November (harvest time) were constructed. Randomly selected 100 positive clones from each library were analyzed with respect to sequence and size. A fruit-flesh cDNA library was also constructed and characterized to confirm the reliability of each library’s temporal and spatial properties.

Results

Quantitative real-time RT-PCR (qRT-PCR) analyses of the cDNA libraries confirmed cDNA molecules that are associated with different developmental stages (e. g. “on year” leaves in July, “off year” leaves in July, leaves in November) and fruits. Hence, a number of candidate cDNAs associated with “on year” and “off year” were isolated. Comparison of the detected cDNAs to the current EST database of GenBank along with other non - redundant databases of NCBI revealed homologs of previously described genes along with several unknown cDNAs. Of around 500 screened cDNAs, 48 cDNA elements were obtained after eliminating ribosomal RNA sequences. These independent transcripts were analyzed using BLAST searches (cutoff E-value of 1.0E-5) against the KEGG and GenBank nucleotide databases and 37 putative transcripts corresponding to known gene functions were annotated with gene names and Gene Ontology (GO) terms. Transcripts in the biological process were found to be related with metabolic process (27%), cellular process (23%), response to stimulus (17%), localization process (8.5%), multicellular organismal process (6.25%), developmental process (6.25%) and reproduction (4.2%).

Conclusions

A putative P450 monooxigenase expressed fivefold more in the “on year” than that of “off year” leaves in July. Two putative dehydrins expressed significantly more in “on year” leaves than that of “off year” leaves in November. Homologs of UDP – glucose epimerase, acyl - CoA binding protein, triose phosphate isomerase and a putative nuclear core anchor protein were significant in fruits only, while a homolog of an embryo binding protein / small GTPase regulator was detected in “on year” leaves only. One of the two unknown cDNAs was specific to leaves in July while the other was detected in all of the libraries except fruits. KEGG pathway analyses for the obtained sequences correlated with essential metabolisms such as galactose metabolism, amino sugar and nucleotide sugar metabolisms and photosynthesis. Detailed analysis of the results presents candidate cDNAs that can be used to dissect further the genetic basis of fruit production and / or alternate bearing which causes significant economical loss for olive growers.