Two main distinct evolutionary stories describe the Italian grapevine assortment

A dataset of high-quality 7k SNP profiles of 1,038 unique Eurasian grapevine varieties was used to infer the most likely grapevine migration events, a spatial ancestry estimation, and a model about the origin of Eurasian grapevine germplasm. The comparison of putative gene flow scenarios from Caucasus throughout Europe aided to fit the more reliable spreading routes around the Mediterranean Basin. The same dataset was also used to assess the population genetic diversity, structure, and relatedness of Italian varieties. These data suggested a different history between Northern and Southern Italian grapevines, appearing clearly split into two different clusters. Interestingly, the Italian genotypes were shown to be distinguishable from all the other Eurasian populations for the first time. The same SNP panel was used to determine parental relationships, identifying the main parents of traditional Italian and closely related cultivars. The parentage network suggested that Italian germplasm largely originated from a few key parents distributed into several geographical areas of genetic influence, with more or less large overlaps. These key cultivars are ‘Bombino bianco’, ‘Garganega’/‘Grecanico’, ‘Mantonico bianco’, ‘Orsolina’/‘Coccalona nera’, ‘Muscat à petits grains blanc’, ‘Malvasia odorosissima’, ‘Sangiovese’, ‘Sciaccarello’, ‘Visparola’ and ‘Vulpea’. The pedigree reconstruction by fullsib and second-degree relationships highlighted the pivotal role of some cultivars, such as ‘Visparola’, until now scarcely known. A hypothetic migration of this variety from Southern to Northern Italy along the Eastern side, as well as ‘Sangiovese’ migration from Southern to Central Italy along the Western side might be supposed. Moreover, ‘Muscat à petits grains blanc’, mainly through its offspring ‘Malvasia odorosissima’, furnished a consistent contribution to the development of many aromatic grapes grown in the Northern-Western part of the Italian Peninsula. These results represent the most complete study of grapevine Italian population genetics that has been carried out until now on the Italian germplasm

Exploring the genetic landscape of nitrogen uptake in durum wheat: genome-wide characterization and expression profiling of NPF and NRT2 gene families

Nitrate uptake by plants primarily relies on two gene families: Nitrate transporter 1/peptide transporter (NPF) and Nitrate transporter 2 (NRT2). Here, we extensively characterized the NPF and NRT2 families in the durum wheat genome, revealing 211 NPF and 20 NRT2 genes. The two families share many Cis Regulatory Elements (CREs) and Transcription Factor binding sites, highlighting a partially overlapping regulatory system and suggesting a coordinated response for nitrate transport and utilization. Analyzing RNA-seq data from 9 tissues and 20 cultivars, we explored expression profiles and co-expression relationships of both gene families. We observed a strong correlation between nucleotide variation and gene expression within the NRT2 gene family, implicating a shared selection mechanism operating on both coding and regulatory regions. Furthermore, NPF genes showed highly tissue-specific expression profiles, while NRT2s were mainly divided in two co-expression modules, one expressed in roots (NAR2/NRT3 dependent) and the other induced in anthers and/ovaries during maturation. Our evidences confirmed that the majority of these genes were retained after small-scale duplication events, suggesting a neo- or sub-functionalization of many NPFs and NRT2s. Altogether, these findings indicate that the expansion of these gene families in durum wheat could provide valuable genetic variability useful to identify NUE-related and candidate genes for future breeding programs in the context of low-impact and sustainable agriculture

Transcriptome changes induced by Arbuscular mycorrhizal symbiosis in leaves of durum wheat (Triticum durum Desf.) promote higher salt tolerance

The salinity of soil is a relevant environmental problem around the world, with climate change raising its relevance, particularly in arid and semiarid areas. Arbuscular Mycorrhizal Fungi (AMF) positively affect plant growth and health by mitigating biotic and abiotic stresses, including salt stress. The mechanisms through which these benefits manifest are, however, still unclear. This work aimed to identify key genes involved in the response to salt stress induced by AMF using RNA-Seq analysis on durum wheat (Triticum turgidum L. subsp. durum Desf. Husn.). Five hundred sixty-three differentially expressed genes (DEGs), many of which involved in pathways related to plant stress responses, were identified. The expression of genes involved in trehalose metabolism, RNA processing, vesicle trafficking, cell wall organization, and signal transduction was significantly enhanced by the AMF symbiosis. A downregulation of genes involved in both enzymatic and non-enzymatic oxidative stress responses as well as amino acids, lipids, and carbohydrates metabolisms was also detected, suggesting a lower oxidative stress condition in the AMF inoculated plants. Interestingly, many transcription factor families, including WRKY, NAC, and MYB, already known for their key role in plant abiotic stress response, were found differentially expressed between treatments. This study provides valuable insights on AMF-induced gene expression modulation and the beneficial effects of plant-AMF interaction in durum wheat under salt stress

Metabolic Profiling and Post-harvest Behavior of “Dottato” Fig (Ficus carica L.) Fruit Covered With an Edible Coating From O. ficus-indica

Fig fruits are usually highly sensitive to some physiopathological disorders during post-harvest life, such as softening and skin cracking. Indeed, the use of edible coating (EC) has been evaluated in several fruit crops to reduce fruit post-harvest transpiration and to maintain fruit visual quality. The aim of this study was to determine the post-harvest metabolic response of breba figs treated with mucilage extract from O puntia ficus-indica cladodes, using an untargeted metabolomic approach. Coated and non-coated (control) fruit were sealed in plastic bags, and stored at 4°C for 7 days. The effect of the ECs on their quality fruit during cold storage and qualitative attributes were evaluated by analyzing the fruit primary metabolism and other qualitative parameters such as total soluble solids (TSS) content, titratable acidity (TA), fresh weight loss and firmness. Results underlined that EC was effective in maintaining fruit fresh weight, and fruit firmness. Stepwise discriminant analysis was able to discriminate fruit conditions. Alanine, xylulose, aspartic acid, glutamic, acid and 2,5-dihydroxypyrazine showed a significant role on discriminating edible coated fruit from untreated ones. Principal component analysis (PCA) was able to highlight clear differences in the overall metabolism changes between untreated and treated fruit. The application of EC significantly mitigated the decrease of most of the aminoacid content during cold storage. EC treatment caused the changes of several organic acids in comparison to untreated control, increasing the amount of carbohydrates and other key metabolites, such as beta-sitosterol, glycerol, and uracil. These results clearly showed the drastic effects of EC on fig metabolism during post-harvest and shed light on the beneficial mechanisms of this treatment

Genetic differentiation of the Capparis spinosa group in the Mediterranean area

The Capparis spinosa group is represented in the Mediterranean by a complex of taxa widespread in North Africa, the Middle East, and southern Europe. The taxonomy of this group used to be based on morphological characters with little work on the genetics of the group, and there is still much to be learned about its evolutionary history and diversification. We sampled 431 individuals of two subspecies and five varieties of C. spinosa and analysed them using highly informative EST-SSR markers to evaluate the population genetic diversity, structure and differentiation of the species in the Mediterranean. In addition, comparisons with the genetic profiles of C. spinosa subsp. cartilaginea, the putative ancestral taxon were made to investigate the phylogeographic history and possible gene flow across taxa. Integrated Bayesian approaches showed: i) a high divergence among C. spinosa subsp. spinosa var. canescens, C. spinosa subsp. spinosa var. aegyptia and the three varieties belonging to C. spinosa subsp. rupestris (var. rupestris, var. ovata and var. myrtifolia), with a clear separation between var. aegyptia and var. canescens which allows to consider var. aegyptia as a subspecies of C. spinosa; ii) a significant correlation between genetic divergence and geographic distance between the five varieties studied; iii) that the different varieties in the Mediterranean may have been derived from C. spinosa subsp. cartilaginea. Further genomic investigations are required to confirm our results. However, the findings presented allows us to suggest the genus Capparis can be considered a model for the study of the gene flow and differentiation in species occurring in a wide range of habitats

Integrated Bayesian Approaches Shed Light on the Dissemination Routes of the Eurasian Grapevine Germplasm

The domestication and spreading of grapevine as well as the gene flow history had been described in many studies. We used a high-quality 7k SNP dataset of 1,038 Eurasian grape varieties with unique profiles to assess the population genetic diversity, structure, and relatedness, and to infer the most likely migration events. Comparisons of putative scenarios of gene flow throughout Europe from Caucasus helped to fit the more reliable migration routes around the Mediterranean Basin. Approximate Bayesian computation (ABC) approach made possible to provide a response to several questions so far remaining unsolved. Firstly, the assessment of genetic diversity and population structure within a well-covered dataset of ancient Italian varieties suggested the different histories between the Northern and Southern Italian grapevines. Moreover, Italian genotypes were shown to be distinguishable from all the other Eurasian populations for the first time. The entire Eurasian panel confirmed the east-to-west gene flow, highlighting the Greek role as a “bridge” between the Western and Eastern Eurasia. Portuguese germplasm showed a greater proximity to French varieties than the Spanish ones, thus being the main route for gene flow from Iberian Peninsula to Central Europe. Our findings reconciled genetic and archaeological data for one of the most cultivated and fascinating crops in the world

Integrated omics approach reveals the molecular pathways activated in tomato by Kocuria rhizophila, a soil plant growth-promoting bacterium

Plant microbial biostimulants application has become a promising and eco-friendly agricultural strategy to improve crop yields, reducing chemical inputs for more sustainable cropping systems. The soil dwelling bacterium Kocuria rhizophila was previously characterized as Plant Growth Promoting Bacteria (PGPB) for its multiple PGP traits, such as indole-3-acetic acid production, phosphate solubilization capability and salt and drought stress tolerance. Here, we evaluated by a multi-omics approach, the PGP activity of K. rhizophila on tomato, revealing the molecular pathways by which it promotes plant growth. Transcriptomic analysis showed several up-regulated genes mainly related to amino acid metabolism, cell wall organization, lipid and secondary metabolism, together with a modulation in the DNA methylation profile, after PGPB inoculation. In agreement, proteins involved in photosynthesis, cell division, and plant growth were highly accumulated by K. rhizophila. Furthermore, "amino acid and peptides", "monosaccharides", and "TCA" classes of metabolites resulted the most affected by PGPB treatment, as well as dopamine, a catecholamine neurotransmitter mediating plant growth through S-adenosylmethionine decarboxylase (SAMDC), a gene enhancing the vegetative growth, up-regulated in tomato by K. rhizophila treatment. Interestingly, eight gene modules well correlated with differentially accumulated proteins (DAPs) and metabolites (DAMs), among which two modules showed the highest correlation with nine proteins, including a nucleoside diphosphate kinase, and cytosolic ascorbate peroxidase, as well as with several amino acids and metabolites involved in TCA cycle. Overall, our findings highlighted that sugars and amino acids, energy regulators, involved in tomato plant growth, were strongly modulated by the K. rhizophila-plant interaction

Bioactive Metabolite Survey of Actinobacteria Showing Plant Growth Promoting Traits to Develop Novel Biofertilizers

The use of chemical fertilizers and pesticides has caused harmful impacts on the environment with the increase in economic burden. Biofertilizers are biological products containing living microorganisms capable of improving plant growth through eco-friendly mechanisms. In this work, three actinobacterial strains Streptomyces violaceoruber, Streptomyces coelicolor, and Kocuria rhizophila were characterized for multiple plant growth promoting (PGP) traits such as indole acetic acid production, phosphate solubilization, N-2-fixation, and drought and salt tolerance. Then, these strains were investigated for their secreted and cellular metabolome, revealing a rich arsenal of bioactive molecules, including antibiotics and siderophores, with S. violaceoruber being the most prolific strain. Furthermore, the in vivo assays, performed on tomato (Solanum lycopersicum L.), resulted in an improved germination index and the growth of seedlings from seeds treated with PGP actinobacteria, with a particular focus on S. violaceoruber cultures. In particular, this last strain, producing volatile organic compounds having antimicrobial activity, was able to modulate volatilome and exert control on the global DNA methylation of tomato seedlings. Thus, these results, confirming the efficacy of the selected actinobacteria strains in promoting plant growth and development by producing volatile and non-volatile bioactive molecules, can promote eco-friendly alternatives in sustainable agriculture

The asparagus genome sheds light on the origin and evolution of a young Y chromosome

Several models have been proposed to explain the emergence of sex chromosomes. Here, through comparative genomics and mutant analysis, Harkess et al. show that linked but separate genes on the Y chromosome are responsible for sex determination in Asparagus, supporting a two-gene model for sex chromosome evolution