Is apomixis occurring in walnut (Juglans regia L.)? New data from progeny molecular tests and cytological investigations shed light on its reproductive system

Introduction

Persian walnut (Juglans regia) is an economically important nut fruit species cultivated worldwide for its nutritious kernel and timber quality wood. Walnut trees are mostly hetero-dichogamous and, depending on the genotype, some cultivars are protogynous, while others are protandrous. Although selfing is possible when male and female blooms overlap, the dichogamy of the species promotes outcrossing. In addition to sexual reproduction, some reports indicate that elements of apomixis may occur in commercial orchards of walnut varieties and in the last two decades, nut production by apomixis has been reported in walnut. However, there are no reliable studies on the occurrence of apomictic reproduction based on cytoembryological observations and/or molecular marker-progeny tests. This study addresses the combined use of molecular and cytological analyses to gain new insights into the population genetics and reproduction systems of J. regia.

Methods

We systematically analyzed the reproductive origin of individual progeny plants from 8 different cultivated walnut genotypes using microsatellite genotyping and carried out cytohistological investigations of 5 cultivated walnut genotypes arising seed sets from isolated flowers, to shed light on the mode of reproduction.

Results and discussion

These cytometric and genotyping analyses did not support any asexual mode of reproduction or asexual propagation by seed and all individuals studied were identified as zygotic plants produced by crossing. Likewise, the cytological findings did not confirm completely the first component of apomixis, namely apomeiosis. On the other hand, according to histological evidence, adventitious embryony seems to take place at low frequency. Overall, our findings suggest that the occurrence of gametophytic apomixis is unlikely in J. regia, but sporophytic apomixis cannot be completely ruled out.

Stability of Nanometer-Thick Layered Gallium Chalcogenides and Improvements via Hydrogen Passivation

The gallium monochalcogenides family, comprising gallium sulfide (GaS), gallium selenide (GaSe), and gallium telluride (GaTe), is capturing attention for its applications in energy storage and production, catalysis, photonics, and optoelectronics. This interest originates from their properties, which include an optical bandgap larger than those of most common transition metal dichalcogenides, efficient light absorption, and significant carrier mobility. For any application, stability to air exposure is a fundamental requirement. Here, we perform a comparative study of the stability of layered GaS, GaSe, and GaTe nanometer-thick films down to a few layers with the goal of identifying the most suitable Ga chalcogenide for future integration in photonic and optoelectronic devices. Our study unveils a trend of decreasing air stability from sulfide to selenide and finally to telluride. Furthermore, we demonstrate a hydrogen passivation process to prevent the oxidation of GaSe with a higher feasibility and durability than other state-of-the-art passivation methods proposed in the literature.

Presymptomatic geographical distribution of ALS patients suggests the involvement of environmental factors in the disease pathogenesis

BACKGROUND

Given that the pathogenetic process of ALS begins many years prior to its clinical onset, examining patients' residential histories may offer insights on the disease risk factors. Here, we analyzed the spatial distribution of a large ALS cohort in the 50 years preceding the disease onset.

METHODS

Data from the PARALS register were used. A spatial cluster analysis was performed at the time of disease onset and at 1-year intervals up to 50 years prior to that.

RESULTS

A total of 1124 patients were included. The analysis revealed a higher-incidence cluster in a large area (435,000 inhabitants) west of Turin. From 9 to 2 years before their onset, 105 cases were expected and 150 were observed, resulting in a relative risk of 1.49 (P = 0.04). We also found a surprising high number of patients pairs (51) and trios (3) who lived in the same dwelling while not being related. Noticeably, these occurrences were not observed in large dwellings as we would have expected. The probability of this occurring in smaller buildings only by chance was very low (P = 0.01 and P = 0.04 for pairs and trios, respectively).

CONCLUSIONS

We identified a higher-incidence ALS cluster in the years preceding the disease onset. The cluster area being densely populated, many exposures could have contributed to the high incidence ALS cluster, while we could not find a shared exposure among the dwellings where multiple patients had lived. However, these findings support that exogenous factors are likely involved in the ALS pathogenesis.

Genome-Wide Datasets of Chicories (Cichorium intybus L.) for Marker-Assisted Crop Breeding Applications: A Systematic Review and Meta-Analysis

Cichorium intybus L. is the most economically important species of its genus and among the most important of the Asteraceae family. In chicory, many linkage maps have been produced, several sets of mapped and unmapped markers have been developed, and dozens of genes linked to traits of agronomic interest have been investigated. This treasure trove of information, properly cataloged and organized, is of pivotal importance for the development of superior commercial products with valuable agronomic potential in terms of yield and quality, including reduced bitter taste and increased inulin production, as well as resistance or tolerance to pathogens and resilience to environmental stresses. For this reason, a systematic review was conducted based on the scientific literature published in chicory during 1980-2023. Based on the results obtained from the meta-analysis, we created two consensus maps capable of supporting marker-assisted breeding (MAB) and marker-assisted selection (MAS) programs. By taking advantage of the recently released genome of C. intybus, we built a 639 molecular marker-based consensus map collecting all the available mapped and unmapped SNP and SSR loci available for this species. In the following section, after summarizing and discussing all the genes investigated in chicory and related to traits of interest such as reproductive barriers, sesquiterpene lactone biosynthesis, inulin metabolism and stress response, we produced a second map encompassing 64 loci that could be useful for MAS purposes. With the advent of omics technologies, molecular data chaos (namely, the situation where the amount of molecular data is so complex and unmanageable that their use becomes challenging) is becoming far from a negligible issue. In this review, we have therefore tried to contribute by standardizing and organizing the molecular data produced thus far in chicory to facilitate the work of breeders.

Current insights and advances into plant male sterility: new precision breeding technology based on genome editing applications

Plant male sterility (MS) represents the inability of the plant to generate functional anthers, pollen, or male gametes. Developing MS lines represents one of the most important challenges in plant breeding programs, since the establishment of MS lines is a major goal in F1 hybrid production. For these reasons, MS lines have been developed in several species of economic interest, particularly in horticultural crops and ornamental plants. Over the years, MS has been accomplished through many different techniques ranging from approaches based on cross-mediated conventional breeding methods, to advanced devices based on knowledge of genetics and genomics to the most advanced molecular technologies based on genome editing (GE). GE methods, in particular gene knockout mediated by CRISPR/Cas-related tools, have resulted in flexible and successful strategic ideas used to alter the function of key genes, regulating numerous biological processes including MS. These precision breeding technologies are less time-consuming and can accelerate the creation of new genetic variability with the accumulation of favorable alleles, able to dramatically change the biological process and resulting in a potential efficiency of cultivar development bypassing sexual crosses. The main goal of this manuscript is to provide a general overview of insights and advances into plant male sterility, focusing the attention on the recent new breeding GE-based applications capable of inducing MS by targeting specific nuclear genic loci. A summary of the mechanisms underlying the recent CRISPR technology and relative success applications are described for the main crop and ornamental species. The future challenges and new potential applications of CRISPR/Cas systems in MS mutant production and other potential opportunities will be discussed, as generating CRISPR-edited DNA-free by transient transformation system and transgenerational gene editing for introducing desirable alleles and for precision breeding strategies.

Atmospheric Pressure Plasma Deposition of Hybrid Nanocomposite Coatings Containing TiO2 and Carbon-Based Nanomaterials

Among the different applications of TiO₂, its use for the photocatalytic abatement of organic pollutants has been demonstrated particularly relevant. However, the wide band gap (3.2 eV), which requires UV irradiation for activation, and the fast electron-hole recombination rate of this n-type semiconductor limit its photocatalytic performance. A strategy to overcome these limitations relies on the realization of a nanocomposite that combines TiO₂ nanoparticles with carbon-based nanomaterials, such as rGO (reduced graphene oxide) and fullerene (C₆₀). On the other hand, the design and realization of coatings formed of such TiO₂-based nanocomposite coatings are essential to make them suitable for their technological applications, including those in the environmental field. In this work, aerosol-assisted atmospheric pressure plasma deposition of nanocomposite coatings containing both TiO₂ nanoparticles and carbon-based nanomaterials, as rGO or C₆₀, in a siloxane matrix is reported. The chemical composition and morphology of the deposited films were investigated for the different types of prepared nanocomposites by means of FT-IR, FEG-SEM, and TEM analyses. The photocatalytic activity of the nanocomposite coatings was evaluated through monitoring the photodegradation of methylene blue (MB) as a model organic pollutant. Results demonstrate that the nanocomposite coatings embedding rGO or C₆₀ show enhanced photocatalytic performance with respect to the TiO₂ counterpart. In particular, TiO₂/C₆₀ nanocomposites allow to achieve 85% MB degradation upon 180 min of UV irradiation.

MIK2 is a candidate gene of the S-locus for sporophytic self-incompatibility in chicory (Cichorium intybus, Asteraceae)

The Cichorium genus offers a unique opportunity to study the sporophytic self-incompatibility (SSI) system, being composed of species characterized by highly efficient self-incompatibility (e.g., C. intybus) and complete self-compatibility (e.g., C. endivia). To this end, the chicory genome was used to map seven previously identified SSI locus-associated markers. The region containing the S-locus was therefore restricted to an ~4 M bp window on chromosome 5. Among the genes predicted in this region, MDIS1 INTERACTING RECEPTOR LIKE KINASE 2 (ciMIK2) was particularly promising as a candidate for SSI. Its ortholog in Arabidopsis (atMIK2) is involved in pollen-stigma recognition reactions, and its protein structure is similar to that of S-receptor kinase (SRK), a key component of the SSI system in the Brassica genus. The amplification and sequencing of MIK2 in chicory and endive accessions revealed two contrasting scenarios. In C. endivia, MIK2 was fully conserved even when comparing different botanical varieties (i.e., smooth and curly endive). In C. intybus, 387 polymorphic positions and 3 INDELs were identified when comparing accessions of different biotypes all belonging to the same botanical variety (i.e., radicchio). The polymorphism distribution throughout the gene was uneven, with hypervariable domains preferentially localized in the LRR-rich extracellular region, putatively identified as the receptor domain. The gene was hypothesized to be under positive selection, as the nonsynonymous mutations were more than double the synonymous ones (dN/dS = 2.17). An analogous situation was observed when analyzing the first 500 bp of the MIK2 promoter: no SNPs were observed among the endive samples, whereas 44 SNPs and 6 INDELs were detected among the chicory samples. Further analyses are needed to confirm the role of MIK2 in SSI and to demonstrate whether the 23 species-specific nonsynonymous SNPs in the CDS and/or the species-specific 10 bp-INDEL found in a CCAAT box region of the promoter are responsible for the contrasting sexual behaviors of chicory and endive.

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

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

Past, present, and future of genetic strategies to control tolerance to the main fungal and oomycete pathogens of grapevine

The production of high-quality wines is strictly related to the correct management of the vineyard, which guarantees good yields and grapes with the right characteristics required for subsequent vinification. Winegrowers face a variety of challenges during the grapevine cultivation cycle: the most notorious are fungal and oomycete diseases such as downy mildew, powdery mildew, and gray mold. If not properly addressed, these diseases can irremediably compromise the harvest, with disastrous consequences for the production and wine economy. Conventional defense methods used in the past involved chemical pesticides. However, such approaches are in conflict with the growing attention to environmental sustainability and shifts from the uncontrolled use of chemicals to the use of integrated approaches for crop protection. Improvements in genetic knowledge and the availability of novel biotechnologies have created new scenarios for possibly producing grapes with a reduced, if not almost zero, impact. Here, the main approaches used to protect grapevines from fungal and oomycete diseases are reviewed, starting from conventional breeding, which allowed the establishment of new resistant varieties, followed by biotechnological methods, such as transgenesis, cisgenesis, intragenesis, and genome editing, and ending with more recent perspectives concerning the application of new products based on RNAi technology. Evidence of their effectiveness, as well as potential risks and limitations based on the current legislative situation, are critically discussed.

Pipeline to Design Inbred Lines and F1 Hybrids of Leaf Chicory (Radicchio) Using Male Sterility and Genotyping-by-Sequencing

Chicory, a horticultural crop cultivated worldwide, presents many botanical varieties and local biotypes. Among these, cultivars of the Italian radicchio group of the pure species Cichorium intybus L. and its interspecific hybrids with Cichorium endivia L.-as the "Red of Chioggia" biotype-includes several phenotypes. This study uses a pipeline to address the marker-assisted breeding of F1 hybrids: it presents the genotyping-by-sequencing results of four elite inbred lines using a RADseq approach and an original molecular assay based on CAPS markers for screening mutants with nuclear male sterility in the radicchio of Chioggia. A total of 2953 SNP-carrying RADtags were identified and used to compute the actual estimates of homozygosity and overall genetic similarity and uniformity of the populations, as well as to determine their genetic distinctiveness and differentiation. Molecular data were further used to investigate the genomic distribution of the RADtags among the two Cichorium species, allowing their mapping in 1131 and 1071 coding sequences in chicory and endive, respectively. Paralleling this, an assay to screen the genotype at the male sterility locus Cims-1 was developed to discriminate wild-type and mutant alleles of the causative gene myb80-like. Moreover, a RADtag mapped close to this genomic region proved the potential application of this method for future marker-assisted selection tools. Finally, after combining the genotype information of the core collection, the best 10 individuals from each inbred line were selected to compute the observed genetic similarity as a measure of uniformity as well as the expected homozygosity and heterozygosity estimates scorable by the putative progenies derived from selfing (pollen parent) and full-sibling (seed parent) or pair-wise crossing (F1 hybrids). This predictive approach was conducted as a pilot study to understand the potential application of RADseq in the fine tuning of molecular marker-assisted breeding strategies aimed at the development of inbred lines and F1 hybrids in leaf chicory.

Management of genetic erosion: The (successful) case study of the pear (Pyrus communis L.) germplasm of the Lazio region (Italy)

Pyrus communis L. is an important temperate fruit with high nutritional and economic value. Italy, as the largest pear producer in the EU and second in the world, has a particularly rich germplasm characterized by hundreds of local varieties. The Lazio Region was the first Italian region to start programs focused on safeguarding varieties at risk of extinction and has started a massive census of fruit varieties by combining molecular data and productive-territorial information. In this study, 311 pear accessions collected from the five provinces of the Lazio region were genetically characterized by the means of nine simple sequence repeat (SSR) markers, eight of which were recommended by the European Cooperative Programme for Plant Genetic Resources (ECPGR). The SSR analysis revealed 250 unique genotypes and 14 cases of synonymies, namely, accessions with different names but identical molecular profiles (100% genetic similarity). The microsatellite set showed a high polymorphism information content (PIC; mean PIC=0.77) and an exceptionally high discrimination power (DP = 0.99), making it particularly efficient both for the study of genetic diversity and for the prediction of the degree of ploidy. Notably, 20% of the accessions displayed triallelic profiles (i.e., accessions having ≥2 loci with a third allele), while the remaining accessions were diploids. These results were further confirmed by flow cytometry data analysis. Standardization of the molecular analyses at the national and international levels and harmonization of the SSR sets used for germplasm characterization are of paramount importance for producing molecular profiles useful for registration and variety maintenance.

Photocatalytic Investigation of Aerosol-Assisted Atmospheric Pressure Plasma Deposited Hybrid TiO2 Containing Nanocomposite Coatings

We report on the aerosol-assisted atmospheric-pressure plasma deposition onto a stainless-steel woven mesh of a thin nanocomposite coating based on TiO2 nanoparticles hosted in a hybrid organic−inorganic matrix, starting from nanoparticles dispersed in a mixture of hexamethyldisiloxane and isopropyl alcohol. The stainless-steel mesh was selected as an effective support for the possible future technological application of the coating for photocatalytically assisted water depollution. The prepared coatings were thoroughly investigated from the chemical and morphological points of view and were demonstrated to be photocatalytically active in the degradation of an organic molecule, used as a pollutant model, in water upon UV light irradiation. In order to optimize the photocatalytic performance, different approaches were investigated for the coating’s realization, namely (i) the control of the deposition time and (ii) the application of a postdeposition O2 plasma treatment on the pristine coatings. Both strategies were found to be able to increase the photocatalytic activity, and, remarkably, their combination resulted in a further enhancement of the photoactivity. Indeed, the proposed combined approach allowed a three-fold increase in the kinetic constant of the degradation reaction of the model dye methylene blue with respect to the pristine coating. Interestingly, the chemical and morphological characterizations of all the prepared coatings were able to account for the enhancement of the photocatalytic performance. Indeed, the presence of the TiO2 nanoparticles on the outmost surface of the film confirmed the accessibility of the photocatalytic sites in the nanocomposite and reasonably explained the enhanced photocatalytic performance. In addition, the sustained photoactivity (>5 cycles of use) of the nanocomposites was demonstrated.

Observing and modeling long-term persistence of P. noctiluca in coupled complementary marine systems (Southern Tyrrhenian Sea and Messina Strait)

In the Mediterranean Sea, the Strait of Messina (MS) is a very peculiar area, connecting highly different regions and representing a privileged observatory for an early comprehension and assessment of ecosystems shifts. It is hypothesized that the outbreaks observed near the coast of many sites in the Mediterranean Sea may be the result of transport of permanent populations of P. noctiluca in pelagic waters to the coast, caused by specific hydrodynamic conditions. By both visual observations and numerical experiments our objective is twofold: (A) to help clarify whether the basin of the Aeolian Islands Archipelago (AIA), in the Southern Tyrrhenian Sea (STS), may be the site from which large populations of P. noctiluca are transported to the MS, and (B) to evaluate whether the upwelling turbulent system of the MS can be an energetic opportunity for this species. It should offer a rich habitat without jeopardizing the overall survival of the population, that is subject to stranding due to strong currents. Although very different, the two involved ecosystems (AIA and MS ) are complementary for the success of Pelagia noctiluca life cycle. Outputs obtained by coupling the 3D hydrodynamic model (SHYFEM) with a Lagrangian particle tracking model support the hypothesis of a connectivity between these two ecosystems, particularly in the first half of the year, indicating the coastal areas around the AIA as potential optimal source location for Pelagia larval stages. We support the very attractive hypothesis that two connected systems exist, the former one favours Pelagia's reproduction and acts as a nursery and the latter favours its growth due to higher productivity. We speculate that the reproductive population of the AIA is not permanent, but is renewed every year by individuals who have fed and quickly grown in the MS and who are passively transported by downwelling along canyon "corridors".

First genomic insights into the Mandevilla genus

Mandevilla (Apocynaceae) is a greatly appreciated genus in the world ornamental market. In this study, we attempted to address the poor genetic knowledge and the huge taxonomic gaps existing in this genus by analyzing a collection of 55 accessions. After cytometrically determining the triploid genome size (1,512.64 Mb) of a reference sample (variety "Mandevilla 2001"), the plastidial genome (cpDNA, 0.18 Mb) and a draft of the nuclear genome (nuDNA, 207 Mb) were assembled. While cpDNA was effective in reconstructing the phylogenesis of the Apocynaceae family based on a DNA superbarcoding approach, the nuDNA assembly length was found to be only 41% of the haploid genome size (506 Mb, predicted based on the K-mer frequency distribution). Its annotation enabled the prediction of 37,811 amino acid sequences, of which 10,562 resulted full length proteins. Among them, we identified nine proteins whose orthologs (in Catharanthus roseus) are involved in the biosynthesis of monoterpene indole alkaloids (MIAs), including catharanthine, tabersonine, and vincadifformine. The nuclear genome draft was also useful to develop a highly informative (average polymorphism information content, PIC = 0.62) set of 23 simple sequence repeat (SSR) markers that was validated on the Mandevilla collection. These results were integrated with cytometric measurements, nuclear ITS1 haplotyping and chloroplast DNA barcoding analyses to assess the origin, divergence and relationships existing among the 55 accessions object of the study. As expected, based on the scarce information available in the literature, the scenario was extremely intricate. A reasonable hypothesis is that most of the accessions represent interspecific hybrids sharing the same species as maternal parent (i.e., Mandevilla sanderi).

Layered gallium sulfide optical properties from monolayer to CVD crystalline thin films

Interest in layered van der Waals semiconductor gallium monosulfide (GaS) is growing rapidly because of its wide band gap value between those of two-dimensional transition metal dichalcogenides and of insulating layered materials such as hexagonal boron nitride. For the design of envisaged optoelectronic, photocatalytic and photonic applications of GaS, the knowledge of its dielectric function is fundamental. Here we present a combined theoretical and experimental investigation of the dielectric function of crystalline 2H-GaS from monolayer to bulk. Spectroscopic imaging ellipsometry with micron resolution measurements are corroborated by first principle calculations of the electronic structure and dielectric function. We further demonstrate and validate the applicability of the established dielectric function to the analysis of the optical response of c-axis oriented GaS layers grown by chemical vapor deposition (CVD). These optical results can guide the design of novel, to our knowledge, optoelectronic and photonic devices based on low-dimensional GaS.

Chunk-wise regularised PCA-based imputation of missing data

Standard multivariate techniques like Principal Component Analysis (PCA) are based on the eigendecomposition of a matrix and therefore require complete data sets. Recent comparative reviews of PCA algorithms for missing data showed the regularised iterative PCA algorithm (RPCA) to be effective. This paper presents two chunk-wise implementations of RPCA suitable for the imputation of “tall” data sets, that is, data sets with many observations. A “chunk” is a subset of the whole set of available observations. In particular, one implementation is suitable for distributed computation as it imputes each chunk independently. The other implementation, instead, is suitable for incremental computation, where the imputation of each new chunk is based on all the chunks analysed that far. The proposed procedures were compared to batch RPCA considering different data sets and missing data mechanisms. Experimental results showed that the distributed approach had similar performance to batch RPCA for data with entries missing completely at random. The incremental approach showed appreciable performance when the data is missing not completely at random, and the first analysed chunks contain sufficient information on the data structure.

Interlaboratory study on Sb2S3 interplay between structure, dielectric function, and amorphous-to-crystalline phase change for photonics

Antimony sulfide, Sb₂S₃, is interesting as the phase-change material for applications requiring high transmission from the visible to telecom wavelengths, with its band gap tunable from 2.2 to 1.6 eV, depending on the amorphous and crystalline phase. Here we present results from an interlaboratory study on the interplay between the structural change and resulting optical contrast during the amorphous-to-crystalline transformation triggered both thermally and optically. By statistical analysis of Raman and ellipsometric spectroscopic data, we have identified two regimes of crystallization, namely 250°C ≤ T < 300°C, resulting in Type-I spherulitic crystallization yielding an optical contrast Δn ∼ 0.4, and 300 ≤ T < 350°C, yielding Type-II crystallization bended spherulitic structure with different dielectric function and optical contrast Δn ∼ 0.2 below 1.5 eV. Based on our findings, applications of on-chip reconfigurable nanophotonic phase modulators and of a reconfigurable high-refractive-index core/phase-change shell nanoantenna are designed and proposed.

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Study of the dielectric function of amorphous and crystalline Sb2S3 phase change material

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Identification of two crystallization regimes for the phase change of Sb2S3

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Design of Sb2S3 on-chip reconfigurable photonic phase modulator

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Design of reconfigurable high-refractive index core/phase-change shell nanoantenna

First Genomic Insights Into The <em>Mandevilla</em> Genus.. [DOI: 10.20944/preprints202204.0255.v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Mandevilla (Apocynaceae) is a greatly appreciated genus in the world ornamental market. In this study, we attempted to address the poor genetic knowledge and the huge taxonomic gaps existing in this genus by analyzing the germplasm of 55 accessions. After cytometrically determining the triploid genome size (1,512.64 Mb) of a reference sample (variety &ldquo;Mandevilla 2001&rdquo;), the plastidial genome (cpDNA, 0,18 Mb) and a draft of the nuclear genome (nuDNA, 207 Mb) were assembled. While cpDNA was effective in reconstructing the phylogenesis of the Apocynaceae family based on a DNA superbarcoding approach, the nuDNA assembly length was found to be only 41% of the haploid genome size (506 Mb, predicted based on the K-mer frequency distribution). Its annotation enabled the prediction of thousands of genes, of which 5,275 resulted in full CDS. Among them, we identified nine genes whose orthologs (in Catharanthus roseus) encode enzymes involved in the biosynthesis of monoterpene indole alkaloids (MIAs), including catharanthine, tabersonine and vincadifformine. The nuclear genome draft was also useful to develop a highly informative (mean PIC=0.62) set of 23 SSR markers that was validated on the Mandevilla collection. These results were integrated with cytometric measurements, nuclear ITS1 haplotyping and chloroplast DNA barcoding analyses to assess the origin, divergence and relationships existing among the 55 accessions object of the study. As expected, based on the scarce information available in the literature, the scenario was extremely intricate. A reasonable hypothesis is that most of the accessions represent interspecific hybrids sharing the same species as maternal parent (i.e., Mandevilla sanderi).

Polydopamine coating of living diatom microalgae

Many microorganisms produce specific structures, known as spores or cysts, to increase their resistance to adverse environmental conditions. Scientists have started to produce biomimetic materials inspired by these natural membranes, especially for industrial and biomedical applications. Here, we present biological data on the biocompatibility of a polydopamine-based artificial coating for diatom cells. In this work, living Thalassiosira weissflogii diatom cells are coated on their surface with a polydopamine layer mimicking mussel adhesive protein. Polydopamine does not affect diatoms growth kinetics, it enhances their resistance to degradation by treatment with detergents and acids, and it decreases the uptake of model staining emitters. These outcomes pave the way for the use of living diatom cells bearing polymer coatings for sensors based on living cells, resistant to artificial microenvironments, or acting as living devices for cells interface study.

Graphical abstract

Trends in Apomixis Research: The 10 Most Cited Research Articles Published in the Pregenomic and Genomic Eras

Apomixis, or asexual reproduction by seed, represents an easy shortcut for life cycle renewal based on maternal embryo production without ploidy reduction (meiosis) and ploidy restitution (syngamy). Although the first studies officially published on this topic in scientific journals date back to the early 1930s, the identification and introduction of genes involved in asexual reproduction in species of agronomic interest still represent a major challenge. Through a bibliometric analysis of the research programs implemented in apomixis over the last 40 years, the present study was aimed to discuss not only the main findings achieved but also the investigational methods and model species used. We split the critical survey of the most cited original articles into pregenomic and genomic eras to identify potential trends and depict scenarios that have emerged in the scientific community working on apomixis, as well as to determine any correlation between the exponential increase in acquired basic knowledge and the development of advanced analytical technologies. This review found a substantial stagnation in the use of the same model species, with few exceptions, for at least 40 years. In contrast, the development of new molecular techniques, genomic platforms, and repositories has directly affected the approaches used in research, which has been directed toward an increasingly focused study of the genetic and epigenetic determinants of apomixis.

Exploring the Thickness-Dependence of the Properties of Layered Gallium Sulfide

Group III layered monochalcogenide gallium sulfide, GaS, is one of the latest additions to the two-dimensional (2D) materials family, and of particular interest for visible-UV optoelectronic applications due to its wide bandgap energy in the range 2.35–3.05 eV going from bulk to monolayer. Interestingly, when going to the few-layer regime, changes in the electronic structure occur, resulting in a change in the properties of the material. Therefore, a systematic study on the thickness dependence of the different properties of GaS is needed. Here, we analyze mechanically exfoliated GaS layers transferred to glass substrates. Specifically, we report the dependence of the Raman spectra, photoluminescence, optical transmittance, resistivity, and work function on the thickness of GaS. Those findings can be used as guidance in designing devices based on GaS.

Genotyping Analysis by RAD-Seq Reads Is Useful to Assess the Genetic Identity and Relationships of Breeding Lines in Lavender Species Aimed at Managing Plant Variety Protection

Lavender species are widely distributed in their wild forms around the Mediterranean Basin and they are also cultivated worldwide as improved and registered clonal varieties. The economic interest of the species belonging to the Lavandula genus is determined by their use as ornamental plants and important source of essential oils that are destinated to the production of cosmetics, pharmaceuticals and foodstuffs. Because of the increasing number of cases of illegal commercialization of selected varieties, the protection of plant breeders’ rights has become of main relevance for the recognition of breeding companies’ royalties. With this aim, genomic tools based on molecular markers have been demonstrated to be very reliable and transferable among laboratories, and also much more informative than morphological descriptors. With the rising of the next-generation sequencing (NGS) technologies, several genotyping-by-sequencing approaches are now available. This study deals with a deep characterization of 15 varietal clones, belonging to two distinct Lavandula species, by means of restriction-site associated DNA sequencing (RAD-Seq). We demonstrated that this technology screens single nucleotide variants that enable to assess the genetic identity of individual accessions, to reconstruct genetic relationships among related breeding lines, to group them into genetically distinguishable main subclusters, and to assign their molecular lineages to distinct ancestors. Moreover, a number of polymorphic sites were identified within genes putatively involved in biosynthetic pathways related to both tissue pigmentation and terpene production, useful for breeding and/or protecting newly registered varieties. Overall, the results highlighted the presence of pure ancestries and interspecific hybrids for the analyzed Lavandula species, and demonstrated that RAD-Seq analysis is very informative and highly reliable for characterizing Lavandula clones and managing plant variety protection.

Developing and Testing Molecular Markers in Cannabis sativa (Hemp) for Their Use in Variety and Dioecy Assessments

Cannabis sativa (2n = 2x = 20) is a popular species belonging to the Cannabaceae family. Despite its use for medical, recreational, and industrial purposes as well as its long history, the genetic research on this species is in its infancy due to the legal implications and the prohibition campaigns. The recent legalization of Cannabis in many countries along with the use of genomics boosted the approaches aimed at marker-assisted selection, germplasm management, genetic discrimination, and authentication of cultivars. Nonetheless, the exploitation of molecular markers for the development of commercial varieties through marker-assisted breeding schemes is still rare. The present study aimed to develop an informative panel of simple sequence repeat markers to be used for the genotyping of high breeding value C. sativa lines. Starting from 41 nuclear SSR designated by in silico analyses, we selected 20 highly polymorphic and discriminant loci that were tested in 104 individuals belonging to 11 distinct hemp varieties. The selected markers were successful in accessing homozygosity, genetic uniformity, and genetic variation within and among varieties. Population structure analysis identified eight genetic groups, clustering individuals based on sexual behaviors (dioecious and monoecious) and geographical origins. Overall, this study provides important tools for the genetic characterization, authentication, conservation of biodiversity, genetic improvement and traceability of this increasingly important plant species.

Synthesis of Tailored Perfluoro Unsaturated Monomers for Potential Applications in Proton Exchange Membrane Preparation

The aim of the present work is the synthesis and characterization of new perfluorinated monomers bearing, similarly to Nafion^®, acidic groups for proton transport for potential and future applications in proton exchange membrane (PEM) fuel cells. To this end, we focused our attention on the synthesis of various molecules with (i) sufficient volatility to be used in vacuum polymerization techniques (e.g., PECVD)), (ii) sulfonic, phosphonic, or carboxylic acid functionalities for proton transport capacity of the resulting membrane, (iii) both aliphatic and aromatic perfluorinated tags to diversify the membrane polarity with respect to Nafion^®, and (iv) a double bond to facilitate the polymerization under vacuum giving a preferential way for the chain growth of the polymer. A retrosynthetic approach persuaded us to attempt three main synthetic strategies: (a) organometallic Heck-type cross-coupling, (b) nucleophilic displacement, and (c) Wittig–Horner reaction (carbanion approach). Preliminary results on the plasma deposition of a polymeric film are also presented. The variation of plasma conditions allowed us to point out that the film prepared in the mildest settings (20 W) shows the maximum monomer retention in its structure. In this condition, plasma polymerization likely occurs mainly by rupture of the π bond in the monomer molecule.

Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies

The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family.

The grapevine (Vitis vinifera L.) floral transcriptome in Pinot noir variety: identification of tissue-related gene networks and whorl-specific markers in pre- and post-anthesis phases

The comprehension of molecular processes underlying the development and progression of flowering in plants is a hot topic, not only because that often the products of interest for human and animal nutrition are linked to the development of fruits or seeds, but also because the processes of gametes formation occurring in sexual organs are at the basis of recombination and genetic variability which constitutes the matter on which evolution acts, whether understood as natural or human driven. In the present study, we used an NGS approach to produce a grapevine flower transcriptome snapshot in different whorls and tissues including calyx, calyptra, filament, anther, stigma, ovary, and embryo in both pre- and post-anthesis phases. Our investigation aimed at identifying hub genes that unequivocally distinguish the different tissues providing insights into the molecular mechanisms that are at the basis of floral whorls and tissue development. To this end we have used different analytical approaches, some now consolidated in transcriptomic studies on plants, such as pairwise comparison and weighted-gene coexpression network analysis, others used mainly in studies on animals or human's genomics, such as the tau (τ) analysis aimed at isolating highly and absolutely tissue-specific genes. The intersection of data obtained by these analyses allowed us to gradually narrow the field, providing evidence about the molecular mechanisms occurring in those whorls directly involved in reproductive processes, such as anther and stigma, and giving insights into the role of other whorls not directly related to reproduction, such as calyptra and calyx. We believe this work could represent an important genomic resource for functional analyses of grapevine floral organ growth and fruit development shading light on molecular networks underlying grapevine reproductive organ determination.

Molecular Hallmarks, Agronomic Performances and Seed Nutraceutical Properties to Exploit Neglected Genetic Resources of Common Beans Grown by Organic Farming in Two Contrasting Environments

Common bean (Phaseolus vulgaris L.) is an essential source of food proteins and an important component of sustainable agriculture systems around the world. Thus, conserving and exploiting the genetic materials of this crop species play an important role in achieving global food safety and security through the preservation of functional and serependic opportunities afforded by plant species diversity. Our research aimed to collect and perform agronomic, morpho-phenological, molecular-genetic, and nutraceutical characterizations of common bean accessions, including lowland and mountain Venetian niche landraces (ancient farmer populations) and Italian elite lineages (old breeder selections). Molecular characterization with SSR and SNP markers grouped these accessions into two well-separated clusters that were linked to the original Andean and Mesoamerican gene pools, which was consistent with the outputs of ancestral analysis. Genetic diversity in the two main clusters was not distributed equally the Andean gene pool was found to be much more uniform than the Mesoamerican pool. Additional subdivision resulted in subclusters, supporting the existence of six varietal groups. Accessions were selected according to preliminary investigations and historical records and cultivated in two contrasting Venetian environments: sea-level and mountain territories. We found that the environment significantly affected some nutraceutical properties of the seeds, mainly protein and starch contents. The antioxidant capacity was found significantly greater at sea level for climbing accessions and in the mountains for dwarf accessions. The seed yield at sea level was halved than mountain due to a seeds reduction in weight, volume, size and density. At sea level, bean landraces tended to have extended flowering periods and shorter fresh pod periods. The seed yield was positively correlated with the length of the period during which plants had fresh pods and negatively correlated with the length of the flowering period. Thus, the agronomic performance of these genetic resources showed their strong connection and adaptation to mountainous environments. On the whole, the genetic-molecular information put together for these univocal bean entries was combined with overall results from plant and seed analyses to select and transform the best accessions into commercial varieties (i.e., pure lines) suitable for wider cultivation.

A multi-kingdom metabarcoding study on cattle grazing Alpine pastures discloses intra-seasonal shifts in plant selection and faecal microbiota

Diet selection by grazing livestock may affect animal performance as well as the biodiversity of grazed areas. Recent DNA barcoding techniques allow to assess dietary plant composition in faecal samples, which may be additionally integrated by the description of gut microbiota. In this high throughput metabarcoding study, we investigated the diversity of plant, fungal and bacterial taxa in faecal samples of lactating cows of two breeds grazing an Alpine semi-natural grassland during summer. The estimated plant composition of the diet comprised 67 genera and 39 species, which varied remarkably during summer, suggesting a decline of the diet forage value with the advancing of the vegetative season. The fungal community included Neocallimastigomycota gut symbionts, but also Ascomycota and Basidiomycota plant parasite and coprophilous taxa, likely ingested during grazing. The proportion of ingested fungi was remarkably higher than in other studies, and varied during summer, although less than that observed for plants. Some variation related to breed was also detected. The gut bacterial taxa remained stable through the summer but displayed a breed-specific composition. The study provided insights in the reciprocal organisms' interactions affecting, and being affected by, the foraging behaviour: plants showed a high temporal variation, fungi a smaller one, while bacteria had practically none; conversely, the same kingdoms showed the opposite gradient of variation as respect to the animal host breed, as bacteria revealed to be the group mostly characterized by host-specificity.

Synthesis of antibacterial composite coating containing nanocapsules in an atmospheric pressure plasma

Antibacterial coating is an important strategy preventing bacterial colonization and biofilm formation. One-step synthesis of nanocapsule-containing antibacterial coatings with controlled release of Ag⁺ ions was achieved in the current work by aerosol-assisted atmospheric pressure plasma deposition. The experimental parameters of deposition including the discharge power, silver nitrate concentration, aerosol flow rate, continuous and pulsed mode of operation were studied in order to analyze their effects on surface morphology and chemical composition of the coating. Formation of nanocapsules embedded in the polymeric coating was observed. A core-shell structure was found for nanocapsule with silver in the core and polymer in the shell. Antibacterial coatings on polyethylene terephthalate film were studied in terms of Ag⁺ ion release, antibacterial properties against Escherichia coli and Staphylococcus aureus, and cytotoxicity with murine fibroblasts. Two-phase release kinetics of Ag⁺ ions was observed as initially a short-term burst release followed by a long-term slow release. It was revealed that high antibacterial efficiency of the coatings deposited on polyethylene terephthalate films can be coupled with low cytotoxicity. These biocompatible antibacterial coatings are very promising in different fields including biological applications.

A Reappraisal of the Evolutionary and Developmental Pathway of Apomixis and Its Genetic Control in Angiosperms

Apomixis sensu stricto (agamospermy) is asexual reproduction by seed. In angiosperms it represents an easy byway of life cycle renewal through gamete-like cells that give rise to maternal embryos without ploidy reduction (meiosis) and ploidy restitution (syngamy). The origin of apomixis still represents an unsolved problem, as it may be either evolved from sex or the other way around. This review deals with a reappraisal of the origin of apomixis in order to deepen knowledge on such asexual mode of reproduction which seems mainly lacking in the most basal angiosperm orders (i.e., Amborellales, Nymphaeales and Austrobaileyales, also known as ANA-grade), while it clearly occurs in different forms and variants in many unrelated families of monocots and eudicots. Overall findings strengthen the hypothesis that apomixis as a whole may have evolved multiple times in angiosperm evolution following different developmental pathways deviating to different extents from sexuality. Recent developments on the genetic control of apomixis in model species are also presented and adequately discussed in order to shed additional light on the antagonist theories of gain- and loss-of-function over sexuality.

The Mitochondrial Genome Assembly of Fennel (Foeniculum vulgare) Reveals Two Different atp6 Gene Sequences in Cytoplasmic Male Sterile Accessions

Cytoplasmic male sterility (CMS) has always aroused interest among researchers and breeders, being a valuable resource widely exploited not only to breed F1 hybrid varieties but also to investigate genes that control stamen and pollen development. With the aim of identifying candidate genes for CMS in fennel, we adopted an effective strategy relying on the comparison between mitochondrial genomes (mtDNA) of both fertile and sterile genotypes. mtDNA raw reads derived from a CMS genotype were assembled in a single molecule (296,483 bp), while a draft mtDNA assembly (166,124 nucleotides, 94 contigs) was performed using male fertile sample (MF) sequences. From their annotation and alignment, two atp6-like sequences were identified. atp6-, the putative mutant copy with a 300 bp truncation at the 5'-end, was found only in the mtDNA of CMS samples, while the wild type copy (atp6+) was detected only in the MF mtDNA. Further analyses (i.e., reads mapping and Sanger sequencing), revealed an atp6+ copy also in CMS samples, probably in the nuclear DNA. However, qPCRs performed on different tissues proved that, despite its availability, atp6+ is expressed only in MF samples, while apt6- mRNA was always detected in CMS individuals. In the light of these findings, the energy deficiency model could explain the pollen deficiency observed in male sterile flower. atp6- could represent a gene whose mRNA is translated into a not-fully functional protein leading to suboptimal ATP production that guarantees essential cellular processes but not a high energy demand process such as pollen development. Our study provides novel insights into the fennel mtDNA genome and its atp6 genes, and paves the way for further studies aimed at understanding their functional roles in the determination of male sterility.

The Effect of Soil on the Biochemical Plasticity of Berry Skin in Two Italian Grapevine (V. vinifera L.) Cultivars

Grapevine represents a particularly interesting species as concerns phenotypic plasticity, considering that the terroir, meaning the contribution of the geography, geology, and climate of a certain place, together with the agronomical practices utilized, may deeply influence the berry phenotype at the physiological, molecular, and biochemical levels. This phenomenon leads to the production of wines that, although produced from the same variety, exhibit different enological profiles and represents an issue of increasing interest from both a biological and an economic point of view. The main objective of the present study was to deepen the understanding of phenotypic plasticity in grapevine, trying to dissect the role of one its important components - the soil - by investigating the singular effect that different physico-chemical soil properties can produce in terms of berry plasticity at the phenological, physiological, and biochemical levels in a red and a white variety of great economic importance in Italy and overseas: Corvina and Glera. The results indicated a genotype-dependent response to the soil factor, with higher biochemical plasticity in Corvina with respect to Glera and suggested a key role of specific soil properties, including the skeleton, texture, and mineral composition, on the metabolite profile of berry skin.

Sustainable and Tunable Mg/MgO Plasmon-Catalytic Platform for the Grand Challenge of SF6 Environmental Remediation

Sulfur hexafluoride (SF₆) is one of the most harmful greenhouse gases producing environmental risks. Therefore, developing ways of degrading SF₆ without forming hazardous products is increasingly important. Herein, we demonstrate for the first time the plasmon-catalytic heterogeneous degradation of SF₆ into nonhazardous MgF₂ and MgSO₄ products by nontoxic and sustainable plasmonic magnesium/magnesium oxide (Mg/MgO) nanoparticles, which are also effective as a plasmon-enhanced SF₆ chemometric sensor. The main product depends on the excitation wavelength; when the localized surface plasmon resonance (LSPR) is in the ultraviolet, then MgF₂ forms, while visible light LSPR results in MgSO₄. Furthermore, Mg/MgO platforms can be regenerated in few seconds by hydrogen plasma treatment and can be reused in a new cycle of air purification. Therefore, this research first demonstrates effectiveness of Mg/MgO plasmon-catalysis enabling environmental remediation with the concurrent functionalities of monitoring, degrading, and detecting sulfur and fluorine gases in the atmosphere.

Initiated Chemical Vapor Deposition of Crosslinked Organic Coatings for Controlling Gentamicin Delivery

A coating consisting of a copolymer of methacrylic acid and ethylene glycol dimethacrylate was deposited over a gentamicin film by initiated chemical vapor deposition with the aim of controlling the drug release. Gentamicin release in water was monitored by means of conductance measurements and of UV-vis Fluorescence Spectroscopy. The influence of the polymer chemical composition, specifically of its crosslinking density, has been investigated as a tool to control the swelling behavior of the initiated chemical vapor deposition (iCVD) coating in water, and therefore its ability to release the drug. Agar diffusion test and microbroth dilution assays against Staphylococcus aureus and Pseudomonas aeruginosa on cellulose coated substrates confirmed that the antibacterial activity of the drug released by the coating was retained, though the release of gentamicin was not complete.

Potentials and Challenges of Genomics for Breeding Cannabis Cultivars

Cannabis (Cannabis sativa L.) is an influential yet controversial agricultural plant with a very long and prominent history of recreational, medicinal, and industrial usages. Given the importance of this species, we deepened some of the main challenges-along with potential solutions-behind the breeding of new cannabis cultivars. One of the main issues that should be fixed before starting new breeding programs is the uncertain taxonomic classification of the two main taxa (e.g., indica and sativa) of the Cannabis genus. We tried therefore to examine this topic from a molecular perspective through the use of DNA barcoding. Our findings seem to support a unique species system (C. sativa) based on two subspecies: C. sativa subsp. sativa and C. sativa subsp. indica. The second key issue in a breeding program is related to the dioecy behavior of this species and to the comprehension of those molecular mechanisms underlying flower development, the main cannabis product. Given the role of MADS box genes in flower identity, we analyzed and reorganized all the genomic and transcriptomic data available for homeotic genes, trying to decipher the applicability of the ABCDE model in Cannabis. Finally, reviewing the limits of the conventional breeding methods traditionally applied for developing new varieties, we proposed a new breeding scheme for the constitution of F₁ hybrids, without ignoring the indisputable contribution offered by genomics. In this sense, in parallel, we resumed the main advances in the genomic field of this species and, ascertained the lack of a robust set of SNP markers, provided a discriminant and polymorphic panel of SSR markers as a valuable tool for future marker assisted breeding programs.

The Molecular Determination of Hybridity and Homozygosity Estimates in Breeding Populations of Lettuce (Lactuca sativa L.)

The development of new varieties of horticultural crops benefits from the integration of conventional and molecular marker-assisted breeding schemes in order to combine phenotyping and genotyping information. In this study, a selected panel of 16 microsatellite markers were used in different steps of a breeding programme of lettuce (Lactuca sativa L., 2 n = 18). Molecular markers were first used to genotype 71 putative parental lines and to plan 89 controlled crosses designed to maximise recombination potentials. The resulting 871 progeny plants were then molecularly screened, and their marker allele profiles were compared with the profiles expected based on the parental lines. The average cross-pollination success rate was 68 ± 33%, so 602 F1 hybrids were completely identified. Unexpected genotypes were detected in 5% of cases, consistent with this species' spontaneous out-pollination rate. Finally, in a later step of the breeding programme, 47 different F3 progenies, selected by phenotyping for a number of morphological descriptors, were characterised in terms of their observed homozygosity and within-population genetic uniformity and stability. Ten of these populations had a median homozygosity above 90% and a median genetic similarity above 95% and are, therefore, particularly suitable for pre-commercial trials. In conclusion, this study shows the synergistic effects and advantages of conventional and molecular methods of selection applied in different steps of a breeding programme aimed at developing new varieties of lettuce.

Diversity Analysis of Sweet Potato Genetic Resources Using Morphological and Qualitative Traits and Molecular Markers

The European Union (EU) market for sweet potatoes has increased by 100% over the last five years, and sweet potato cultivation in southern European countries is a new opportunity for the EU to exploit and introduce new genotypes. In view of this demand, the origins of the principal Italian sweet potato clones, compared with a core collection of genotypes from Central and Southern America, were investigated for the first time. This was accomplished by combining a genetic analysis, exploiting 14 hypervariable microsatellite markers, with morphological and chemical measurements based on 16 parameters. From the molecular analyses, Italian accessions were determined to be genetically very similar to the South American germplasm, but they were sub-clustered into two groups. This finding was subsequently confirmed by the morphological and chemical measurements. Moreover, the analysis of the genetic structure of the population suggested that one of the two groups of Italian genotypes may have descended from one of the South American accessions, as predicted on the basis of the shared morphological characteristics and molecular fingerprints. Overall, the combination of two different characterization methods, genetic markers and agronomic traits, was effective in differentiating or clustering the sweet potato genotypes, in agreement with their geographical origin or phenotypic descriptors. This information could be exploited by both breeders and farmers to detect and protect commercial varieties, and hence for traceability purposes.

Genetic Structure of Cultivated Varieties of Radicchio (Cichorium intybus L.): A Comparison between F1 Hybrids and Synthetics

Cichorium intybus L., well known in Italy with the common name “Radicchio”, is an important leafy vegetable that is prevalently reproduced by allogamy due to very efficient barriers of self-incompatibility. Marker-assisted breeding is widely used by seed firms to develop new hybrid varieties that manifest genetic distinctiveness, uniformity and stability. A total of 29 mapped microsatellite markers were used for genotyping 504 samples of the Red of Chioggia biotype: First, two synthetics, four F1 hybrids and two derived F2 populations were compared to assess the distinctiveness of their gene pool and structure; then, the uniformity and stability of 3 years of production of a commercial F1 variety were also investigated. Genetic similarity and diversity statistics as well as the genetic structure of populations were analysed, including allele and genotype frequencies. The mean estimates and ranges of genetic similarity enabled the molecular discrimination of OP synthetics from F1 varieties and their F2 progenies and the determination of individual plant memberships. Moreover, the genetic structure of F1 hybrids produced in 3 years unexpectedly revealed two main clusters that discriminate the first 2 years from the 3rd, mainly because of the presence of uncommon specific alleles and different allele frequencies. Overall, this molecular information will enable breeders to determine the genetic distinctness, uniformity and stability of commercial and experimental varieties, as well as their genetic relationships and relatedness. Hence, this work provides a useful tool for achieving the molecular characterisation and genetic identification of different radicchio populations.

Data from in vivo functionalization of diatom mesoporous biosilica with bisphosphonates

Diatoms are unicellular photosynthetic microalgae that produce a sophisticated mesoporous biosilica shell called frustule. Easy to achieve and extract, diatom frustules represent a low-cost source of mesoporous biocompatible biosilica. In this paper, the possibility to in vivo functionalize the diatom biosilica with bisphosphonates (BPs) was investigated. In particular, two BPs were tested: the amino-containing sodium alendronate (ALE) and the amino-lacking sodium etidronate (ETI). According to first SEM-EDX analysis, the presence of the amino-moiety in ALE structure allowed a better incorporation of this BP into living diatom biosilica, compared to ETI. Then, diatom growth was deeply investigated in presence of ALE. After extraction of functionalized frustules, ALE-biosilica was further characterized by XPS and microscopy, and ALE release was evaluated by ferrochelation assay. Moreover, the bone regeneration performances of ALE-functionalized frustules were preliminarily investigated on bone osteoblast-like cells, via Comassie staining. Data are related to the research article "In vivo functionalization of diatom biosilica with sodium alendronate as osteoactive material".

Genomics of Flower Identity in Grapevine (Vitis vinifera L.)

The identity of the four characteristic whorls of typical eudicots, namely, sepals, petals, stamens, and carpels, is specified by the overlapping action of homeotic genes, whose single and combined contributions have been described in detail in the so-called ABCDE model. Continuous species-specific refinements and translations resulted in this model providing the basis for understanding the genetic and molecular mechanisms of flower development in model organisms, such as Arabidopsis thaliana and other main plant species. Although grapevine (Vitis vinifera L.) represents an extremely important cultivated fruit crop globally, studies related to the genetic determinism of flower development are still rare, probably because of the limited interest in sexual reproduction in a plant that is predominantly propagated asexually. Nonetheless, several studies have identified and functionally characterized some ABCDE orthologs in grapevine. The present study is intended to provide a comprehensive screenshot of the transcriptional behavior of 18 representative grapevine ABCDE genes encoding MADS-box transcription factors in a developmental kinetic process, from preanthesis to the postfertilization stage and in different flower organs, namely, the calyx, calyptra, anthers, filaments, ovary, and embryos. The transcript levels found were compared with the proposed model for Arabidopsis to evaluate their biological consistency. With a few exceptions, the results confirmed the expression pattern expected based on the Arabidopsis data.

Optically addressing interaction of Mg/MgO plasmonic systems with hydrogen

Magnesium-based films and nanostructures are being studied in order to improve hydrogen reversibility, storage capacity, and kinetics, because of their potential in the hydrogen economy. Some challenges with magnesium (Mg) samples are their unavoidable oxidation by air exposure and lack of direct in situ real time measurements of hydrogen interaction with Mg and MgO surfaces and Mg plasmonic nanoparticles. Given these challenges, the present article investigates direct interaction of Mg with hydrogen, as well as implications of its inevitable oxidation by real-time spectroscopic ellipsometry for exploiting the optical properties of Mg, MgH₂ and MgO. The direct hydrogenation measurements have been performed in a reactor that combines a remote hydrogen plasma source with an in situ spectroscopic ellipsometer, which allows optical monitoring of the hydrogen interaction and results in optical property modification. The hydrogen plasma dual use is to provide the hydrogen-atoms and to reduce barriers to heterogeneous hydrogen reactions.

Construction of the First SNP-Based Linkage Map Using Genotyping-by-Sequencing and Mapping of the Male-Sterility Gene in Leaf Chicory

We report the first high-density linkage map construction through genotyping-by-sequencing (GBS) in leaf chicory (Cichorium intybus subsp. intybus var. foliosum, 2n = 2x = 18) and the SNP-based fine mapping of the linkage group region carrying a recessive gene responsible for male-sterility (ms1). An experimental BC₁ population, segregating for the male sterility trait, was specifically generated and 198 progeny plants were preliminary screened through a multiplexed SSR genotyping analysis for the identification of microsatellite markers linked to the ms1 locus. Two backbone SSR markers belonging to linkage group 4 of the available Cichorium consensus map were found genetically associated to the ms1 gene at 5.8 and 12.1 cM apart. A GBS strategy was then used to produce a high-density SNP-based linkage map, containing 727 genomic loci organized into 9 linkage groups and spanning a total length of 1,413 cM. 13 SNPs proved to be tightly linked to the ms1 locus based on a subset of 44 progeny plants analyzed. The map position of these markers was further validated by sequence-specific PCR experiments using an additional set of 64 progeny plants, enabling to verify that four of them fully co-segregated with male-sterility. A mesosynteny analysis revealed that 10 genomic DNA sequences encompassing the 13 selected SNPs of chicory mapped in a peripheral region of chromosome 5 of lettuce (Lactuca sativa L.) spanning about 18 Mbp. Since a MYB103-like gene, encoding for a transcription factor involved in callose dissolution of tetrads and exine development of microspores, was found located in the same chromosomal region, this orthologous was chosen as candidate for male-sterility. The amplification and sequencing of its CDS using accessions with contrasting phenotypes/genotypes (i.e., 4 male sterile mutants, ms1ms1, and 4 male fertile inbreds, Ms1Ms1) enabled to detect an INDEL of 4 nucleotides in its second exon, responsible for an anticipated stop codon in the male sterile mutants. This polymorphism was subsequently validated through allele-specific PCR assays and found to fully co-segregate with male-sterility, using 64 progeny plants of the same mapping BC₁ population. Overall, our molecular data could be practically exploited for genotyping plant materials and for marker-assisted breeding schemes in leaf chicory.

Single step synthesis of Janus nano-composite membranes by atmospheric aerosol plasma polymerization for solvents separation

Solvent permeation across membranes is limited due to physical resistance to diffusion from the selective layer within the membrane and to plasticizing effects generated by the solvent molecules onto the polymeric macromolecular matrix. Nano-composite thin film membranes provide promising routes to generate controlled microstructural separation materials with higher selectivities and permeabilities. Here, the fabrication of nano-composite based on octamethyl-polyhedral oligomeric silsesquioxane - hexamethyldisiloxane thin film membranes is demonstrated by aerosol assisted atmospheric plasma deposition onto pre-formed nano-porous membrane supports for the first time. Stable, atomically smooth and continuous solid films with controllable thickness down to 50 nm were achieved. The deposition process allowed for the control of the wettability of the surfaces to water and organic solvents, leading to the generation of hydrophobic but alcohol-philic surfaces. The liquid entry pressure of the films to water was found to be 8 bar from plasma polymerization as oppose to 3 bar for the bare nano-porous support only. In addition, the ideal separation selectivity for ethanol to water, up to 6.5, highlight the impact of both the surface energy and level of cross-linking of the hexamethyldisiloxane nanostructures on the diffusion mechanisms. This new atmospheric plasma deposition strategy opens-up cost-effective and environmentally friendly routes for the design of the smart Janus membrane with customizable properties and performance.

Mapping the transition to superwetting state for nanotextured surfaces templated from block-copolymer self-assembly

Adding roughness to hydrophilic surfaces is generally expected to enhance their wetting by water. Indeed, global free energy minimization predicts decreasing contact angles when roughness factor or surface energy increases. However, experimentally it is often found that water spreading on rough surfaces is impeded by pinning effects originating from local free energy minima; an effect, largely neglected in scientific literature. Here, we utilize Laplace pressure as a proxy for these local minima, and we map the transition to a superwetting state of hydrophilic nano-textured surfaces in terms of surface chemistry and texture geometry. We demonstrate the effect for polymer model surfaces templated from block-copolymer self-assembly comprising dense, nano-pillar arrays exhibiting strong pinning in their pristine state. By timed argon plasma exposure, we tune surface chemistry to map the transition into the superwetting state of low contact angle, which we show coincide with the surface supporting hemiwicking flow. For the near-ideal model surfaces, the transition to the superwetting state occurs below a critical material contact angle of ∼50°. We show that superwetting surfaces possess anti-fogging properties, and demonstrate long term stability of the superwetting effect by coating the nanotextured surfaces with ∼10 nm thin films of either tungsten or silica.