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Olive tree (Olea europaea L. subsp. europaea var. europaea) is one of the most important species of the Mediterranean region and one of the most ancient species domesticated. The availability of whole genome assemblies and annotations of olive tree cultivars and oleaster (O. europaea subsp. europaea var. sylvestris) has contributed to a better understanding of genetic and genomic differences between olive tree cultivars. However, compared to other plant species there is still a lack of genomic resources for olive tree popula-tions that span the entire Mediterranean region. In the present study we developed the most complete genomic variation map and the most comprehensive catalog/resource of molecular variation to date for 89 olive tree genotypes originating from the entire Mediterranean basin, revealing the genetic diversity of this commercially significant crop tree and explaining the divergence/similarity among different variants. Addi-tionally, the monumental ancient tree ‘Throuba Naxos’ was studied to characterize the potential origin or routes of olive tree domestication. Several candidate genes known to be associated with key agronomic traits, including olive oil quality and fruit yield, were uncovered by a selective sweep scan to be under selection pressure on all olive tree chromosomes. To further exploit the genomic and phenotypic resources obtained from the current work, genome-wide association analyses were performed for 23 morphological and two agronomic traits. Significant associations were detected for eight traits that provide valuable candidates for fruit tree breeding and for deeper understanding of olive tree biology. info:eu-repo/semantics/publishedVersion

Natural products are not only positioned in the heart of traditional medicine but also in modern medicine as many current drugs are coming from natural sources. Apart from the field of medicine and therapeutics, natural products are broadly used in other industrial fields such as nutrition, skincare products and nanotechnology.The aim of this study was to assess the effects of sweet cherry (Prunus avium L.) fruit extract from the Greek native cultivar 'Vasiliadi', on the human 2D and 3D in vitro models in order to investigate its potential impact on skin. We focused on 2D culture of primary normal human epidermal keratinocytes (NHEK) that were treated with sweet cherry fruit extract. In the first place, we targeted fruit extract potential cytotoxicity by determining ATP intracellular levels. Furthermore, we assessed its potential skin irritability by using 3D skin model. To better understand the bioactivity of sweet cherry fruit. extract, we used qPCR to study the expression of various genes that are implicated in the skin functions. Our experiments showed that sweet cherry fruit extract is non-toxic in 2D keratinocytes culture as well as non-irritant in 3D skin model. Our results revealed that the extract mediated important pathways for the optimum epidermis function such as cell proliferation, immune and inflammatory response.The sweet cherry fruit extracts possesses significant activity in epidermis function without any potential of cytotoxicity or skin irritability, which makes it a rather promising active agent for skincare.

Genome-wide transcriptome analysis provides systems-level insights into plant biology. Due to the limited depth of quantitative proteomics our understanding of gene-protein-complex stoichiometry is largely unknown in plants. Recently, the complexity of the proteome and its cell-/tissue-specific distribution have boosted the research community to the integration of transcriptomics and proteomics landscapes in a proteogenomic approach. Herein, we generated a quantitative proteome and transcriptome abundance atlas of 15 major sweet cherry (Prunus avium L., cv 'Tragana Edessis') tissues represented by 29 247 genes and 7584 proteins. Additionally, 199 984 alternative splicing events, particularly exon skipping and alternative 3' splicing, were identified in 23 383 transcribed regions of the analyzed tissues. Common signatures as well as differences between mRNA and protein quantities, including genes encoding transcription factors and allergens, within and across the different tissues are reported. Using our integrated dataset, we identified key putative regulators of fruit development, notably genes involved in the biosynthesis of anthocyanins and flavonoids. We also provide proteogenomic-based evidence for the involvement of ethylene signaling and pectin degradation in cherry fruit ripening. Moreover, clusters of genes and proteins with similar and different expression and suppression trends across diverse tissues and developmental stages revealed a relatively low RNA abundance-to-protein correlation. The present proteogenomic analysis allows us to identify 17 novel sweet cherry proteins without prior protein-level annotation evidenced in the currently available databases. To facilitate use by the community, we also developed the Sweet Cherry Atlas Database (https://grcherrydb.com/) for viewing and data mining these resources. This work provides new insights into the proteogenomics workflow in plants and a rich knowledge resource for future investigation of gene and protein functions in Prunus species.

SummaryThe term “terroir” has been widely employed to link differential geographic phenotypes with sensorial signatures of agricultural food products, influenced by agricultural practices, soil type and climate. Nowadays, the Geographical Indications labeling has been developed to safeguard the quality of plant-derived food that is linked to a certain terroir and is generally considered as an indication of superior organoleptic properties and phytochemical profile. As the dynamics of agroecosystems are highly intricate, consisting of tangled networks of interactions between plants, microorganisms, and the surrounding environment, the recognition of the key molecular components of terroir fingerprinting remains a great challenge to protect both the origin and the safety of food commodities. Furthermore, the contribution of microbiome as a potential driver of the terroir signature has been underestimated until recently. Herein, we present a first comprehensive view of the multi-omic landscape related to transcriptome, proteome, epigenome, and metagenome of the popular Protected Geographical Indication potatoes of Naxos.

There is a persistent interest in innovative and multifunctional ingredients in biology research. With regards to this, natural sources have an important role due to their multiple benefits. Thus, this study aims to present the pleiotropic activity of Prunus avium L. extract on human primary fibroblasts for proving its efficacy in dermis-related processes. We focused on the safety and efficacy assessments based on cytotoxicity and gene expression analysis under oxidative stress. Specifically, Prunus avium L. extract was proved non-cytotoxic in human fibroblasts. The gene expression analysis unveiled that this extract has in vitro protective properties on human dermal fibroblasts under oxidative stress related to antioxidant activity, anti-inflammatory response, cell proliferation and cell- aging. Our study demonstrated for the very first time that the Prunus avium L. extract is a multifunctional ingredient as it mediates several human dermis-related in vitro processes highlighting its potential to be used as an active ingredient in skin care products.

Οι καρποί των λαχανικών είναι απαραίτητοι για την ανθρώπινη διατροφή, καθώς παρέχουν σημαντικές βιταμίνες, μέταλλα και διαλυτές φυτικές ίνες που αναβαθμίζουν την ποιότητα τους. Λόγω της υψηλής παραλλακτικότητας που διέπει το κολοκύθι, οι καρποί του ποικίλουν σε σχήμα, μέγεθος και ποιοτικά χαρακτηριστικά. Η γενετική βάση του μεγέθους και του σχήματος των καρπών στα φυτά διερευνήθηκε για πρώτη φορά στα λαχανικά και ταυτοποιήθηκαν τα γονίδια που συνδεόνται με τη μορφολογία των καρπών. Σήμερα υπάρχουν πολλές βάσεις δεδομένων που παρέχουν πληροφορίες για το γονιδίωμα της τομάτας, του αγγουριού, του πεπονιού και του αγγουριού, σε αντίθεση με τις διαθέσιμες βάσεις δεδομένων για το κολοκύθι που είναι περιορισμένες. Στην παρούσα μελέτη δημιουργήθηκε μια βάση δεδομένων για 2 ποικιλίες του είδους Cucurbita pepo με εξαιρετικά διαφορετικό μέγεθος καρπού (ποικιλία ‘Munchkin’ (μικρόκαρπη) και ποικιλία ‘Big Moose’ (μεγαλόκαρπη)), με τη χρήση της τεχνολογίας της αλληλούχησης του μεταγραφήματος (RNA-seq). Με τη χρήση αυτής της βάσης δεδομένων πραγματοποιήθηκε συγκριτική ανάλυση των μεταγραφημάτων των δύο ποικιλιών κολοκυθιού προκειμένου να προσδιοριστούν τα γονίδια που έχουν πιθανό ρόλο στη μορφολογία του καρπού. Η ανάλυση DGE αποκάλυψε μια ποικιλία υποψήφιων γονιδίων που σχετίζονται με τη μορφολογία του καρπού με σημαντικές διαφορές στην έκφραση των γονιδίων μεταξύ των δύο υπό μελέτη ποικιλιών. Επιπλέον, δημιουργήθηκαν 13 μοριακοί δείκτες EST-SSR, που έχουν την δυνατότητα να διαχωρίζουν διαφορετικές ποικιλίες του είδους C. pepo ενώ 6 μοριακοί δείκτες EST-SSR μπορούν να χρησιμοποιηθούν και στα συγγενή είδη της οικογένειας Cucurbitaceae. Τα τελευταία χρόνια, παράγεται ένας συνεχώς αυξανόμενος αριθμός ερευνών του εμβολιασμού στις οικογένειες Cucurbitaceae και Solanaceae με στόχο τη βελτίωση της απόδοσης των καλλιεργειών αλλά και την βελτίωση των ποιοτικών χαρακτηριστικών του καρπού. Παρόλα αυτά, οι μελέτες σχετικά με την επίδραση του εμβολιασμού στη μορφολογία του καρπού και τη θρεπτική αξία στο κολοκύθι, είναι περιορισμένες. Στην παρούσα μελέτη, διευρενήθηκε η επίδραση του εμβολιασμού στην ποιότητα του καρπού σε εμβολιασμένα φυτά 4 ποικιλιών του είδους Cucurbita pepo. Συγκεκριμένα πραγματοποιήθηκαν αυτο-εμβολιασμοί και αμοιβαίοι ετεροεμβολιασμοί των ποικιλιών ‘Munchkin’ (μικρόκαρπη) και ‘Big Moose» (μεγαλόκαρπη), καθώς και ‘Round green’ (στρόγγυλοι καρποί) και ‘Princess’ (επιμήκεις καρποί). Όταν η ποικιλία ‘Big Moose’ χρησιμοποιήθηκε ως εμβόλιο, με υποκείμενο την ποικιλία ‘Munchkin’ παρουσιάστηκαν σημαντικές αλλαγές στο μέγεθος καρπού σε σύγκριση με τα αυτόριζα φυτά. Στο σχήμα του καρπού παρατηρήθηκαν μέτριες μεταβολές και στους δύο αμοιβαίους ετερο-εμβολιασμούς των ποικιλιών ‘Round green’ και ‘Princess’ σε σύγκριση με τα αυτόριζα φυτά. Είναι η πρώτη φορά που μελετώνται οι φαινοτυπικές αλλαγές μετά από ενδο-ειδικούς εμβολιασμούς στην οικογένεια Cucurbitaceae. Επιπλέον, μελετήθηκαν οι αλλαγές στην συνολική μεθυλίωση του DNA με τη χρήση των μοριακών δεικτών MSAP όπου παρατηρήθηκαν αυξομειώσεις οι οποίες φαίνεται να εξαρτώνται από την ποικιλία που θα χρησιμοποιηθεί ως υποκείμενο ή εμβόλιο. Επιπρόσθετα, έγινε ποσοτικοποίηση της έκφρασης των miRNAs των εμβολιασμένων φυτών. Τα εμβολιασμένα φυτά εμφάνισαν σημαντικές αλλαγές στα επίπεδα της γονιδιακής έκφρασης των υπό μελέτη miRNAs σε σύγκριση με τα αυτόριζα φυτά. Τέλος, για την καλύτερη διερεύνηση της ποιότητας των καρπών δημιουργήθηκαν τα μεταβολικά προφίλ των εμβολιασμένων φυτών καθώς και των αυτόριζων φυτών μαρτύρων. Στα δείγματα από τους καρπούς των ποικιλιών του είδους C. pepo με πράσινους καρπούς (ποικιλίες ‘Round green’ και ‘Princess’) και με πορτοκαλί καρπούς (ποικιλίες ‘Big Moose’ και ‘Munchkin’), εντοπίστηκαν 17 και 18 διαφορετικές ενώσεις, αντίστοιχα, οι οποίες διέφεραν στα ποσοστά παρουσίας και συγκέντρωσης. Τα αποτελέσματα αυτά συμβάλουν τόσο την περαιτέρω κατανόηση των μοριακών μηχανισμών που ρυθμίζουν τη μορφολογία καρπών όσο και στην ανάπτυξη μοριακών δεικτών που θα στοχεύουν στην επιλογή γενοτύπων με επιθυμητά μορφολογικά χαρακτηριστικά. Επίσης ανοίγουν το δρόμο για την καλύτερη κατανόηση των αλλαγών που προκαλούνται λόγω του εμβολιασμού στον φαινότυπο, τους επιγενετικούς μηχανισμούς και το μεταβολικό προφίλ των καρπών του κολοκυθιού.

Sweet cherry germplasm contains a high variety of phenotypes which are associated with fruit size and shape as well as sugar content, etc. High phenotypic variation can be a result of genetic or epigenetic diversity that may interact through time. Recent studies have provided evidence that besides allelic variation, epiallelic variation can establish new heritable phenotypes. Herein we conducted a genetic and an epigenetic study (using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) markers, respectively), accompanied by phenotypic traits correlation analysis in sweet cherry gene pools. The mean genetic diversity was greater than the epigenetic diversity (hgen = 0.193, hepi = 0.185), while no significant relationship was found between genetic and epigenetic distance according to a Mantel test. Furthermore, according to correlation analyses our results provided evidence that epigenetic diversity in predefined populations of sweet cherry had a stronger impact on phenotypic traits than their rich genetic diversity.

The current study characterizes the physicochemical, sensory and bioactive compound traits of twenty-two sweet cherry accessions, namely breeding lines, landraces and modern cultivars, embodying the majority of Greek germplasm. The evaluated accessions differ in several quality traits including colour parameters and textural properties as well as sensory attributes, such as taste intensity and overall acceptance. Significant differences in primary metabolites, including fructose, glucose, sorbitol, malic acid were recorded among tested accessions. All genotypes were rich in polyphenols, primarily in quercetin-3,4-O-diglucoside, esculetin, rutin and neochlorogenic acid. An anthocyanins-related discrimination among accessions was also obtained based on cyanidin-3-O-rutinoside and peonidin glycosides content. Overall, the cultivars 'Tsolakeika' and 'Bakirtzeika' exhibited the higher consumer acceptance while the cultivars 'Vasiliadi' and 'Tragana Edessis-Naousis' and especially the breeding line 'TxAg33' contained high polyphenol levels. These results represent a valuable resource for future breeding efforts for sweet cherry cultivars with improved nutritional quality traits.

[EN] Background Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages. Here, we present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots. Results In total, 27,868 genes and 2352 novel transcripts were annotated from these 16 tissues, with over 18,000 genes common to all tissue groups. Of these, 3812 were identified as housekeeping genes, half of which assigned to known gene ontologies. Flowers, seeds, and young fruits had the largest number of specific genes, whilst intermediate-age fruits the fewest. There also were genes that were differentially expressed in the various tissues, the male flower being the tissue with the most differentially expressed genes in pair-wise comparisons with the remaining tissues, and the leaf stem the least. The largest expression change during fruit development was early on, from female flower to fruit two days after pollination. A weighted correlation network analysis performed on the global gene expression dataset assigned 25,413 genes to 24 coexpression groups, and some of these groups exhibited strong tissue specificity. Conclusions These findings enrich our understanding about the transcriptomic events associated with summer squash development and ripening. This comprehensive gene expression atlas is expected not only to provide a global view of gene expression patterns in all major tissues in C. pepo but to also serve as a valuable resource for functional genomics and gene discovery in Cucurbitaceae., BP was funded by Ministerio de Ciencia, Innovacion y Universidades, cofunded with FEDER funds (Project No. AGL2017-85563-C2-1-R) and by PROMETEO project 2017/078 (to promote excellence groups) by the Conselleria d'Educacio, Investigacio, Cultura vertical bar Esports (Generalitat Valenciana).

Parsley (Petroselinum crispum) aromatic, edible leaves are used fresh or dried as a herb, but also for their pharmaceutical properties. Given the profound concern to high nutritious and pharmaceutical value of superior plant’s germplasm, a survey is presented in this study on the phenotypic, genetic and phytochemical characterization of fifteen Greek parsley landraces in comparison to nine commercial cultivars, all grown under the same conditions in Greece. Our data reported high differences between the Greek landraces and most of the commercial cultivars in a majority of morphological traits investigated according to the International Union for the Protection of New Varieties of Plants descriptors list. The genetic diversity of all landraces and commercial cultivars were investigated using Inter Simple Sequence Repeat and Amplified Fragment Length Polymorphism molecular markers. The percentage of polymorphic loci was 63.83 % for the cultivars, and all loci were polymorphic (100 %) for the Greek landraces, while considerably higher values of unbiased haploid gene diversity were revealed in the landraces compared with the commercial cultivars. The essential oil yield of the landraces and cultivars of parsley studied ranged from 0.11−0.26 mL 100 g−1 leaf FW. The major compounds in the parsley essential oils as determined by gas-chromatography were α-pinene (0.6–11.8%), β-pinene (0.2–8.2%), myrcene (1.3–13.5%), β-phellandrene (9.6–39.1 %), terpinolene (1.4–8.9 %), 1, 3, 8-p-menthatriene (0.1–43.4 %), cis-carveol (0.2–8.1 %), iso-dihydro carveol acetate (0.2–6.9 %), myristicin (0.51–44.4%) and apiole (0.01–35.2 %). According to the targeted liquid chromatographic analysis coumarin derivatives, hydrocinnamic acids, flavanones, flavones and flavonols were identified in parsley methanolic extracts. Flavones were represented by apigenin and luteolin derivatives, and flavonols by kaempferol, quercetin, galangin and morin. Apiin was the major flavone in all parsley samples ranging from 1732.57 to 3676.43 mg 100 g -1 dry weight. The wide variation in phenotypic, genetic and phytochemical profiles observed for the landraces, indicate that the Greek germplasm collection could serve as an important source of genetic material for plant breeding and selection towards the development of new cultivars with superior traits regarding their aroma quality and polyphenolic content but also to support ongoing studies on flavonoid biosynthesis in this culinary herb.

Sweet cherries, Prunus avium L. (Rosaceae), are gaining importance due to their perenniallity and nutritional attributes beneficial for human health. Interestingly, sweet cherry cultivars exhibit a wide range of phenotypic diversity in important agronomic traits, such as flowering time and defense reactions against pathogens. In this study, whole-genome resequencing (WGRS) was employed to characterize genetic variation, population structure and allelic variants in a panel of 20 sweet cherry and one wild cherry genotypes, embodying the majority of cultivated Greek germplasm and a representative of a local wild cherry elite phenotype. The 21 genotypes were sequenced in an average depth of coverage of 33.91×. and effective mapping depth, to the genomic reference sequence of ‘Satonishiki’ cultivar, between 22.21× to 36.62×. Discriminant analysis of principal components (DAPC) with SNPs revealed two clusters of genotypes. There was a rapid linkage disequilibrium decay, as the majority of SNP pairs with r2 in near complete disequilibrium (>0.8) were found at physical distances less than 10 kb. Functional analysis of the variants showed that the genomic ratio of non-synonymous/synonymous (dN/dS) changes was 1.78. The higher dN frequency in the Greek cohort of sweet cherry could be the result of artificial selection pressure imposed by breeding, in combination with the vegetative propagation of domesticated cultivars through grafting. The majority of SNPs with high impact (e.g., stop codon gaining, frameshift), were identified in genes involved in flowering time, dormancy and defense reactions against pathogens, providing promising resources for future breeding programs. Our study has established the foundation for further large scale characterization of sweet cherry germplasm, enabling breeders to incorporate diverse germplasm and allelic variants to fine tune flowering and maturity time and disease resistance in sweet cherry cultivars.

The recent sequencing of many Rosaceae complete genomes, including that of sweet cherry (Prunus avium L.), along with the availability of high-throughput resources offers new challenges and opportunities for cherry breeders in the genomic era towards improvement of climate-smart traits and diseases resistance against the main pathogens, which are consistently plagued the crop. Conventional breeding approaches are laborious, time-consuming and inefficient to fulfil increasing demands, especially in terms of climate change. The advances both in marker-assisted and genomics-assisted breeding, high-throughput sequencing technologies and bioinformatics tools should enable the sweet cherry breeding at a faster pace. These genomics technologies will certainly generate a large amount of data, and this new knowledge might be efficiently employed in cherry breeding towards the development of varieties with elevated adaptation to climatic challenges, including disease resistance against pathogens. The rapidly accumulating genomic resources will enable the development of molecular markers associated with many important quantitative trait loci, deciphering the genomic variations in various germplasms towards the development of climate-smart and disease resistant sweet cherries. Furthermore, an integrated approach based on a full range of plant omics sciences and their outcomes would result in the development of efficient genomics-based trait selection and identification of allelic variations involved in flowering time, dormancy and defence reactions against pathogens. Especially climate change alters dramatically the susceptibility of sweet cherry cultivars to rapidly evolved pathogens, and although the recent advances in genomics resources, there are still only a few reports of genomics applications for diseases resistance evaluation in germplasm collections. In this chapter, we discuss and summarize the advances through genomics-assisted breeding towards improvement of climate-smart traits and diseases resistance in sweet cherry.

Tobacco is an economically important crop with leaves that are a significant source of aromatic, bioactive compounds such as phenolics and alkaloids. In the present study un-biased transcriptomics and metabolomics approaches were employed to identify and quantify individual changes in transcript and metabolite profiles in leaves of three oriental tobacco varieties. Based on next generation sequencing (NGS) and gas chromatography mass spectrometry (GC–MS) technologies, a wide variety of transcripts and metabolites was detected and the metabolic diversity among varieties was determined. Genes with largest expression differences were identified in the leaves of the three varieties; among them three were commonly over-expressed in two varieties in comparison with the third variety. Notably, significant expression differences were recorded in phenylalanine ammonia lyase (PAL) genes that are key genes of phenylpropanoid biosynthesis. Following transcriptomics, metabolomics analysis has shown that polyphenolic compounds varied widely among the three varieties. Furthermore, statistically significant differences in soluble sugars, alcohols, organic acids, amino acids and other metabolites were also revealed. The integration of the two -omics datasets in determining diversity of tobacco varieties offers important readouts for the genetic control of metabolite production and constitutes a resource for future studies in the area of plant biotechnology for improving tobacco specific traits.

To further understand the impact of grafting on fruit characteristics and to comprehend the mechanisms involved in graft-induced changes we studied homo- and hetero- grafted Cucurbita pepo cultivars (cv.) that vary in fruit size and shape. C. pepo cv. ‘Munchkin’ and cv. ‘Big Moose’ as well as cv. ‘Round green’ and cv. ‘Princess’ were homo-grafted and reciprocally hetero-grafted. The results show significant changes in fruit size when ‘Big Moose’ was grafted onto ‘Munchkin’ rootstocks in comparison to homo-grafted controls. Statistically significant changes were also observed in fruit shape when cv. ‘Princess’ was grafted on cv. ‘Round green’. This is the first report of such phenotypic changes after intra-species/inter-cultivar grafting in Cucurbitaceae. Additionally, we found significant changes in (i) secondary metabolite profile, (ii) global DNA methylation pattern and (iii) miRNA expression patterns in grafted scions and (iv) DNA methylation on graft-induced phenotypic changes in grafted plants. Our results contribute to further understanding graft-induced effects on fruit morphology in intra-species grafting. Furthermore, our results pave the way for understanding the role of phenolic metabolites and epigenetic molecular mechanisms on the phenotypic changes recorded.

The local scale genetic diversity of Thymus sibthorbii, an aromatic species of the Greek flora, was studied both in relation to its habitat characteristics. The study was conducted in Cholomontas mountain, northern Greece at altitudes of 760–870 m. Genetic material from Southern and Northwestern exposures and from different grazing intensities within each exposure, was studied using ISSR molecular markers. The plant cover at each study site was measured and the floristic composition of the site was calculated. The grazing intensity affected the species composition and reduced the abundance of T. sibthorpii. The floristic diversity in terms of species richness, evenness and Shannon index (IF) was higher at the southern sites. Within population gene diversity (HE) ranged from 0.203 to 0.245 and Shannon index (IG) from 0.311 to 0.377. Most of the genetic diversity resided within populations (88%). Significant genetic differentiation was detected among the populations from the southern and northwestern sites, as well as among populations of each exposure. Genetic diversity of T. sibthorpii was not correlated to species diversity (richness and evenness), either within or between populations. Instead, genetic diversity was found to be positively correlated with environmental factors, such as N soil content and soil moisture.

Nutrients in the form of fertilizers and/or other additives such as amino acids, dramatically influence plant development and growth, plant nutrient composition and the level of soil pollution. Moreover, the treatment of soil microbiota is emerging as a new strategy in plant breeding to achieve desirable traits. Thus, integrated study of fertilizer application and soil microbiota might lead to a better understanding of soil-plant interactions and inform the design of novel ways to fertilize plants. Herein we report metagenomics data for soil microbiota in lettuce ( Lactuca sativa ) treated with fertilizer, amino acids or their combinations as follows: N-fertilizer + Amino16®, Amino16®, N-fertilizer and no treatment control. Data have been deposited in the NCBI Sequence Read Archive (SRA) (accession number: PRJNA388765).

Molecular taxonomic studies have been performed in the past in order to identify different wheat species and construct a molecular phylogeny. These were based on universal but sufficiently divergent sequences from both the nuclear and chloroplastic genomes of wheat. They included two short plastid sequences from the plastid genes rbcL and matK which have been proposed as the core “barcode” sequences by the “barcoding” guidelines for general plant identification. Historically, in molecular plant taxonomy, plastidic sequences had been favored over nuclear sequences, due to their uniparental inheritance and consequently lower intra-molecular recombination. However recently, the short nuclear sequence from the internal transcribed spacer 2 (ITS2) has been used successfully for the accurate identification of many medicinal and other plant species. Herein, we have used the plastidic matK, rbcL trnL, and the nuclear ITS2 region for the identification of different wheat species of Triticum L. and goatgrass species of Aegilops L. We have successfully discriminated all species that were examined from both genera, thus, validating the ITS2 region as a ‘barcode tool’ for accurate distinction of plants in the genus Triticum L. and Aegilops L. The success rate of PCR amplification and sequencing of the ITS2 region was 100%. We report also that matK, rbcL and trnL regions could not discriminate all species in contrast to the ITS2 region which demonstrated full discriminatory capacity.

The genetic basis of fruit size and shape was investigated for the first time in Cucurbita species and genetic loci associated with fruit morphology have been identified. Although extensive genomic resources are available at present for tomato (Solanum lycopersicum), cucumber (Cucumis sativus), melon (Cucumis melo) and watermelon (Citrullus lanatus), genomic databases for Cucurbita species are limited. Recently, our group reported the generation of pumpkin (Cucurbita pepo) transcriptome databases from two contrasting cultivars with extreme fruit sizes. In the current study we used these databases to perform comparative transcriptome analysis in order to identify genes with potential roles in fruit morphology and fruit size. Differential Gene Expression (DGE) analysis between cv. 'Munchkin' (small-fruit) and cv. 'Big Moose' (large-fruit) revealed a variety of candidate genes associated with fruit morphology with significant differences in gene expression between the two cultivars. In addition, we have set the framework for generating EST-SSR markers, which discriminate different C. pepo cultivars and show transferability to related Cucurbitaceae species. The results of the present study will contribute to both further understanding the molecular mechanisms regulating fruit morphology and furthermore identifying the factors that determine fruit size. Moreover, they may lead to the development of molecular marker tools for selecting genotypes with desired morphological traits.

Sweet cherries, Prunus avium L. (Rosaceae), are gaining importance due to their perenniallity and nutritional attributes beneficial for human health. Interestingly, sweet cherry cultivars exhibit a wide range of phenotypic diversity in important agronomic traits, such as flowering time and defense reactions against pathogens. In this study, whole-genome resequencing (WGRS) was employed to characterize genetic variation, population structure and allelic variants in a panel of 20 sweet cherry and one wild cherry genotypes, embodying the majority of cultivated Greek germplasm and a representative of a local wild cherry elite phenotype. The 21 genotypes were sequenced in an average depth of coverage of 33.91×. and effective mapping depth, to the genomic reference sequence of ‘Satonishiki’ cultivar, between 22.21× to 36.62×. Discriminant analysis of principal components (DAPC) with SNPs revealed two clusters of genotypes. There was a rapid linkage disequilibrium decay, as the majority of SNP pairs with r2 in near complete disequilibrium (>0.8) were found at physical distances less than 10 kb. Functional analysis of the variants showed that the genomic ratio of non-synonymous/synonymous (dN/dS) changes was 1.78. The higher dN frequency in the Greek cohort of sweet cherry could be the result of artificial selection pressure imposed by breeding, in combination with the vegetative propagation of domesticated cultivars through grafting. The majority of SNPs with high impact (e.g., stop codon gaining, frameshift), were identified in genes involved in flowering time, dormancy and defense reactions against pathogens, providing promising resources for future breeding programs. Our study has established the foundation for further large scale characterization of sweet cherry germplasm, enabling breeders to incorporate diverse germplasm and allelic variants to fine tune flowering and maturity time and disease resistance in sweet cherry cultivars.

[EN] Cucurbita pepo contains two cultivated subspecies, each of which encompasses four fruit-shape morphotypes (cultivar groups). The Pumpkin, Vegetable Marrow, Cocozelle, and Zucchini Groups are of subsp. pepo and the Acorn, Crookneck, Scallop, and Straightneck Groups are of subsp. ovifera. Recently, a de novo assembly of the C. pepo subsp. pepo Zucchini genome was published, providing insights into its evolution. To expand our knowledge of evolutionary processes within C. pepo and to identify variants associated with particular morphotypes, we performed whole-genome resequencing of seven of these eight C. pepo morphotypes. We report for the first time whole-genome resequencing of the four subsp. pepo (Pumpkin, Vegetable Marrow, Cocozelle, green Zucchini, and yellow Zucchini) morphotypes and three of the subsp. ovifera (Acorn, Crookneck, and Scallop) morphotypes. A high-depth resequencing approach was followed, using the BGISEQ-500 platform that enables the identification of rare variants, with an average of 33.5X. Approximately 94.5% of the clean reads were mapped against the reference Zucchini genome. In total, 3,823,977 high confidence single-nucleotide polymorphisms (SNPs) were identified. Within each accession, SNPs varied from 636,918 in green Zucchini to 2,656,513 in Crookneck, and were distributed homogeneously along the chromosomes. Clear differences between subspecies pepo and ovifera in genetic variation and linkage disequilibrium are highlighted. In fact, comparison between subspecies pepo and ovifera indicated 5710 genes (22.5%) with Fst > 0.80 and 1059 genes (4.1%) with Fst = 1.00 as potential candidate genes that were fixed during the independent evolution and domestication of the two subspecies. Linkage disequilibrium was greater in subsp. ovifera than in subsp. pepo, perhaps reflective of the earlier differentiation of morphotypes within subsp. ovifera. Some morphotype-specific genes have been localized. Our results offer new clues that may provide an improved understanding of the underlying genomic regions involved in the independent evolution and domestication of the two subspecies. Comparisons among SNPs unique to particular subspecies or morphotypes may provide candidate genes responsible for traits of high economic importance., This work has been supported by Hellenic Agricultural Organization (ELGO) Demeter. Furthermore, we thank the Conselleria de Educacio, Investigacio, Cultura i Esport (Generalitat Valenciana) for funding Project Prometeo 2017/078 "Seleccion de Variedades Tradicionales y Desarrollo de Nuevas Variedades de Cucurbitaceas Adaptadas a la Produccion Ecologica". Also, this work was supported by Chiang Mai University.

Alternaria core rot and Alternaria black heart rot of apple and pomegranate fruit, respectively, are major pre- and postharvest diseases worldwide. However, it is very difficult to differentiate the rot related Alternaria species in the Alternaria complex as they are not always correlate to species-groups based upon morphological characteristics and due to the limited genetic variation these species exhibit among each other. Therefore, it is crucial to exploit novel assays towards the accurate identification and differentiation of these Alternaria species. We have developed, a real-time PCR assay [using species specific primers targeting the endopolygalacturonase ( EndoPG ) gene] combined with a high-resolution melting (HRM) curve analysis for discrimination of the 14 single nucleotide polymorphisms (SNPs)-based Alternaria haplotypes, which were assigned based on the aligned sequence profiles of 138 Alternaria spp. strains previously isolated from apple and pomegranate rotted fruit. This analysis specifically generated 14 unique HRM curve haplotype profiles among the Alternaria complex species tested. The results showed that HRM curve analysis allows the rapid and adequate identification and genotyping of the three Alternaria species ( A. alternata, A. tenuissima and A. arborescens ) responsible mostly for the apple and pomegranate fruit rot diseases.

Herbal infusions, commonly referred to as herbal teas are among the most widely consumed hot beverages. Herbal tea authenticity is an issue of food safety. Reliable test methods, which could identify the botanical origin of herbal tea products, are required in order to protect the consumer from fraud and authenticate genuine products considering also the potential medical use of the herbs. Herein, we present a method that enables the simultaneous and reliable identification of 9 herbal species of sage, Greek sage, chamomile, mountain-tea, oregano, Cretan oregano, yarrow, lemon balm and rosemary. A high resolution melting (HRM) assay, targeting a fragment of the internal transcribed spacer 2 (ITS2) gene, was developed in order to authenticate the botanical origin of the herbal teas and their mixtures. Species-specific primers were designed and combined in a multiplex PCR resulting in fragments of different length and therefore different melting behavior for each species. The method was developed using dried tissue from each of the nine species. The multiplex HRM assay proposed in this work can be applied as routine tests for the verification of botanical origin in herbal teas and can be extended to authenticate all types of herbal foodstuffs.

The phenotypic and genetic analysis of apple (Malus × domestica Borkh) genotypes is essential for breeding species. Information on the morphology and genetic structure of apple offers significant help for germplasm maintenance and selection of suitable material to breed superior cultivars. This study shows the results of an investigation on the morphology and the genetic diversity for 19 apple cultivars, which are preserved in an ex situ collection in Naoussa, Central Macedonia, Greece. Information was recorded over a 5-year period for 47 traits describing plant morphology and phenotype, as well as leaf and fruit quality. Data were analyzed using the principal component analysis (PCA) method. The Euclidean distance metric and the Ward’s agglomeration method were used in an unsupervised hierarchical cluster analysis of all cultivars. The cultivars were grouped into four main clusters, suggesting that the characterized apple collection has a high potential for specific breeding goals. Furthermore, the cultivars were genotyped using seven microsatellite primers. Moderate levels of polymorphism were detected, and 38 distinctive alleles (5.4 alleles per primer pair) were identified. Both multivariate clustering approach (phenotypic data) and the genetic distance clustering approach (genetic data) grouped the apple cultivars according to their type. Hence, these data could be used for protection or patenting processes of existing or new apple cultivars carried out by the EU-Community Plant Variety Office.

Beans are one of the most important staple crops in the world. Runner bean (Phaseolus coccineus L.) is a small-scale agriculture crop compared to common bean (Phaseolusvulgaris). Beans have been introduced to Europe from the Central America to Europe and since then they have been scattered to different geographical regions. This has resulted in the generation of numerous local cultivars and landraces with distinguished characters and adaptive potential. To identify and characterize the underlying genomic variation of two very closely related runner bean cultivars, we performed RNA-Seq with de novo transcriptome assembly in two landraces of P. coccineus, ‘Gigantes’ and ‘Elephantes’ phenotypically distinct, differing in seed size and shape. The cleaned reads generated 37,379 and 37,774 transcripts for ‘Gigantes’ and ‘Elephantes,’ respectively. A total of 1896 DEGs were identified between the two cultivars, 1248 upregulated in ‘Elephantes’ and 648 upregulated in ‘Gigantes.’ A significant upregulation of defense-related genes was observed in ‘Elephantes,’ among those, numerous members of the AP2-EREBP, WRKY, NAC, and bHLH transcription factor families. In total, 3956 and 4322 SSRs were identified in ‘Gigantes’ and ‘Elephantes,’ respectively. Trinucleotide repeats were the most dominant repeat motif, accounting for 41.9% in ‘Gigantes’ and 40.1% in ‘Elephantes’ of the SSRs identified, followed by dinucleotide repeats (29.1% in both cultivars). Additionally, 19,281 putative SNPs were identified, among those 3161 were non-synonymous, thus having potential functional implications. High-confidence non-synonymous SNPs were successfully validated with an HRM assay, which can be directly adopted for P. coccineus molecular breeding. These results significantly expand the number of polymorphic markers within P. coccineus genus, enabling the robust identification of runner bean cultivars, the construction of high-resolution genetic maps, potentiating genome-wide association studies. They finally contribute to the genetic reservoir for the improvement of the closely related and intercrossable Phaseolus vulgaris.

An increasing demand for cherry production (Prunus avium L.) in Greece led to the development of new high quality sweet cherry cultivars. Self-incompatibility in cherry is one of the most challenging issues for the species’ cultivation and top breeding priority. Τhe present study focuses on the development of new hybrids with improved traits such as productivity, fruit size, organoleptic characteristics and self-compatibility. For this purpose, thirty different cultivars were crossed and produced hybrids that were evaluated according to 34 morpho-physiological characteristics. The results were analyzed using the XLSTAT (version 2014.1) software and a dendrogram was constructed using the agglomerative hierarchical clustering method. Optimal hybrid clustering was achieved when characteristics of great economic importance such as fruit shape and size, growth habit and days to blooming were included in the analysis. Based on the results, new sweet cherry hybrids with the special character of self-compatibility were developed. Our findings provide crucial new information for sweet cherry future breeding programs and cultivation.