Whole genome scanning of a Mediterranean basin hotspot collection provides new insights into olive tree biodiversity and biology

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 populations 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. Additionally, 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.This research was financed by Greek Public Investments Program (PIP) of General Secretariat for Research & Technology (GSRT), under the Emblematic Action ‘The Olive Road’ (project code:2018ΣE01300000). Sebastián Ramos-Onsins is supported by the grant PID2020-119255GB-I00 (MICINN, Spain) and the CERCA Programme/Generalitat de Catalunya and acknowledges financial support from the Spanish Ministry of Economy and Competitiveness, through the Severo Ochoa Programme for Centres of Excellence in R&D 2016–2019 and 2020–2023 (SEV-2015-0533, CEX2019-000917) and the European Regional Development Fund (ERDF).The publication of the article in OA mode was financially supported by HEAL-Link.With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000917).Peer reviewe

Study of the morphological and qualitative fruit changes in the grafted squash plants with -omics technology

Fruits are essential for the human diet as they provide important vitamins, minerals and soluble dietary fibre. The genetic basis of fruit size and shape was investigated for the first time in vegetables and genes associated with fruit morphology have been identified. Although extensive genomic resources are available at present for tomato, cucumber, melon and watermelon, genomic databases for Cucurbita species are limited. 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 showing significant differences in gene expression between the two cultivars. In addition, we have generated EST-SSR markers, which discriminate different C. pepo cultivars and show transferability to related Cucurbitaceae species. In the last few years, a growing number of investigations in Cucurbitaceae and Solanaceae grafting aimed at improving horticultural crop performance in terms of fruit yield and quality. Nevertheless, studies concerning the effect of grafting on fruit morphology, nutritional value, fruit size and shape in particular, are scarce. To further understand, the impact of grafting on fruits and to comprehend mechanisms involved in the graft-induced changes we studied homo- and reciprocally hetero- grafted Cucurbita pepo cultivars (cv.) with vary in fruit size and shape. In this direction, C. pepo cv. ‘Munchkin’ (small fruit) and cv. ‘Big Moose’ (large fruit) as well as cv. ‘Round green’ (round fruit) and cv. ‘Princess’ (elongated fruit) were homografted and reciprocally heterografted. The results shown, by comparison to homo-grafting, significant changes in fruit size when ‘Big Moose’ scion was hetero-grafted onto ‘Munchkin’ rootstocks. While moderate changes in fruit shape were observed when both reciprocal grafting combinations of cv. ‘Round green’ and cv. ‘Princess’ were performed. This is the first report of such phenotypic changes after intra-species/inter-cultivar grafting in Cucurbitaceae. Additionally, we reveal significant changes i) in secondary metabolite profile, ii) in global DNA methylation and iii) in miRNA expression patterns in grafted scions and in DNA methylation and miRNAs on graft-induced fruit morphology changes. The results of the present study will contribute to further understanding the molecular mechanisms regulating fruit morphology and to 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. Our results contribute to understanding of the graft-induced effects on fruit architecture in intra-species grafting as well. They pave the way for understanding the role of phenolic metabolites and epigenetic molecular mechanisms, like DNA methylation and miRNAs, in the phenotypic changes recorded.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

Could Causal Discovery in Proteogenomics Assist in Understanding Gene–Protein Relations? A Perennial Fruit Tree Case Study Using Sweet Cherry as a Model

Genome-wide transcriptome analysis is a method that produces important data on plant biology at a systemic level. The lack of understanding of the relationships between proteins and genes in plants necessitates a further thorough analysis at the proteogenomic level. Recently, our group generated a quantitative proteogenomic atlas of 15 sweet cherry (Prunus avium L.) cv. ‘Tragana Edessis’ tissues represented by 29,247 genes and 7584 proteins. The aim of the current study was to perform a targeted analysis at the gene/protein level to assess the structure of their relation, and the biological implications. Weighted correlation network analysis and causal modeling were employed to, respectively, cluster the gene/protein pairs, and reveal their cause–effect relations, aiming to assess the associated biological functions. To the best of our knowledge, this is the first time that causal modeling has been employed within the proteogenomics concept in plants. The analysis revealed the complex nature of causal relations among genes/proteins that are important for traits of interest in perennial fruit trees, particularly regarding the fruit softening and ripening process in sweet cherry. Causal discovery could be used to highlight persistent relations at the gene/protein level, stimulating biological interpretation and facilitating further study of the proteogenomic atlas in plants

Global DNA methylation changes in Cucurbitaceae inter-species grafting

Grafting has been used to improve yield, fruit quality and disease resistance in a range of tree and vegetable species. The molecular mechanisms underpinning grafting responses have only recently started to be delineated. One of those mechanisms involves long distance transfer of genetic material from rootstock to scion alluding to an epigenetic component to the grafting process. In the research presented herein we extended published work on heritable changes in the DNA methylation pattern of Solanaceae scion genomes, in Cucurbitaceae inter-species grafting. Specifically, we examined global DNA methylation changes in scions of cucumber, melon and watermelon heterografted onto pumpkin rootstocks using MSAP analysis. We observed a significant increase of global DNA methylation in cucumber and melon scions pointing to an epigenetic effect in Cucurbitaceae heterografting. Exploitation of differential epigenetic marking in different rootstock-scion combinations could lead to development of epi-molecular markers for generation and selection of superior quality grafted vegetables

Genetic diversity of Barbary fig (Opuntia ficus-indica) collection in Greece with ISSR molecular markers

AbstractBarbary fig (Opuntia ficus indica) could be an economically important species as it could be an alternative crop extremely tolerant to dry condition and water deficiency. Moreover, it could be used in alternative sustainable cultivation systems and landscape conservation. In this work, we report the analysis of the genetic diversity of Greek Barbary fig genotypes using ISSR molecular markers. Six primers were screened to assess their ability to detect polymorphisms within twenty-two Barbary fig accessions and generated 57 markers (bands), with an average of 9.5 markers per primer. The percentage of polymorphic bands (50.21%) and the resolving power (RP) (28.85) showed the efficiency of the used primers. Mean values for GD (gene diversity) and I (Shannon index) were found as 0.215 and 0.355, respectively. The revealed ISSR markers allow distinguishing all accessions analyzed except for one case. UPGMA dendrogram and PCoA (Principal Coordinate Analysis) were performed to access patterns of diversity among genotypes. The high genetic diversity existing in the Greek germplasm suggests that it would be beneficial to utilize this pool in Barbary fig breeding programs and germplasm management activities

De novo transcriptome assembly of two contrasting pumpkin cultivars

Cucurbita pepo (squash, pumpkin, gourd), a worldwide-cultivated vegetable of American origin, is extremely variable in fruit characteristics. However, the information associated with genes and genetic markers for pumpkin is very limited. In order to identify new genes and to develop genetic markers, we performed a transcriptome analysis (RNA-Seq) of two contrasting pumpkin cultivars. Leaves and female flowers of cultivars, ‘Big Moose’ with large round fruits and ‘Munchkin’ with small round fruits, were harvested for total RNA extraction. We obtained a total of 6 GB (Big Moose; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3056882) and 5 GB (Munchkin; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3056883) sequence data (NCBI SRA database SRX1502732 and SRX1502735, respectively), which correspond to 18,055,786 and 14,824,292 150-base reads. After quality assessment, the clean sequences where 17,995,932 and 14,774,486 respectively. The numbers of total transcripts for ‘Big Moose’ and ‘Munchkin’ were 84,727 and 68,051, respectively. TransDecoder identified possible coding regions in assembled transcripts. This study provides transcriptome data for two contrasting pumpkin cultivars, which might be useful for genetic marker development and comparative transcriptome analyses. Keywords: RNA-Seq, Pumpkin, Contrasting cultivars, Cucurbita pep

Comparative metagenomics reveals alterations in the soil bacterial community driven by N-fertilizer and Amino 16® application in lettuce

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)