The aim of this study was to assess the influence of the application of mycorrhizal fungal inoculum on “Cabernet Sauvignon” (Vitis vinifera L.) leaf gas exchange, yield parameters, as well as grape ...berry composition, especially regarding phenolic compounds. The experiment was conducted over two years under natural vineyard conditions of the Zagreb wine-growing area, the continental region of Croatia. “Cabernet Sauvignon” grapevines were grafted on SO4 rootstock, both being commonly used in all wine production areas in Croatia. Results obtained demonstrated that symbiotic grapevines, in general, expressed improved leaf gas exchange parameters and higher yield parameters, especially regarding the number of clusters per vine. It should be emphasized that mycorrhizal fungi affected higher total flavan-3-ols, total anthocyanins, and total polyphenols in berry skin in both experimental years. Despite variation in some yield parameters, generally, it is possible to obtain higher yields together with the improved phenolic composition of grapes.
Insect physiology and reproduction depend on several terpenoid compounds, whose biosynthesis is mainly unknown. One enigmatic group of insect monoterpenoids are mealybug sex pheromones, presumably ...resulting from the irregular coupling activity of unidentified isoprenyl diphosphate synthases (IDSs). Here, we performed a comprehensive search for IDS coding sequences of the pest mealybug Planococcus citri. We queried the available genomic and newly generated short- and long-read P. citri transcriptomic data and identified 18 putative IDS genes, whose phylogenetic analysis indicates several gene family expansion events. In vitro testing confirmed regular short-chain coupling activity with five gene products. With the candidate with highest IDS activity, we also detected low amounts of irregular coupling products, and determined amino acid residues important for chain-length preference and irregular coupling activity. This work therefore provides an important foundation for deciphering terpenoid biosynthesis in mealybugs, including the sex pheromone biosynthesis in P. citri.
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•Long- and short-read transcriptome sequence resource of Planococcus citri was built•Potential P. citri IDS coding sequences were identified•Five P. citri IDSs produced regular short polyprenyl chains•TransIDS5 produced low amounts of irregular polyprenyl chains
Biochemistry; Entomology; Omics; Phylogenetics
Progress in high-throughput molecular methods accompanied by more complex experimental designs demands novel data visualisation solutions. To specifically answer the question which parts of the ...specifical biological system are responding in particular perturbation, integrative approach in which experimental data are superimposed on a prior knowledge network is shown to be advantageous.
We have developed DiNAR, Differential Network Analysis in R, a user-friendly application with dynamic visualisation that integrates multiple condition high-throughput data and extensive biological prior knowledge. Implemented differential network approach and embedded network analysis allow users to analyse condition-specific responses in the context of topology of interest (e.g. immune signalling network) and extract knowledge concerning patterns of signalling dynamics (i.e. rewiring in network structure between two or more biological conditions). We validated the usability of software on the
and
datasets, but it is set to handle any biological instances.
DiNAR facilitates detection of network-rewiring events, gene prioritisation for future experimental design and allows capturing dynamics of complex biological system. The fully cross-platform Shiny App is hosted and freely available at https://nib-si.shinyapps.io/DiNAR. The most recent version of the source code is available at https://github.com/NIB-SI/DiNAR/ with a DOI 10.5281/zenodo.1230523 of the archived version in Zenodo.
We have witnessed a rapid advancement in high-throughput genome sequencing and the maturation of long-read technologies. However, an accurate assembly of polyploid potato genomes still remains ...challenging. Sequencing the double-monoploid genome of Solanum tuberosum Group Phureja (Xu et al., Nature 475:189-195, 2011) has enabled functional studies of polyploid potato cultivars using RNA sequencing (RNA-Seq) technologies, although with the limitation of not covering cultivar-specific gene expression. The accumulated RNA-Seq datasets from these cultivars can be leveraged to assemble tetraploid potato transcriptomes that enable the analysis of genes that are not limited to reference genome annotations. To increase transcriptomes' quality, short-read assemblies are nowadays complemented with full-length transcriptome sequencing using Pacific Biosciences or Oxford Nanopore platforms. In this chapter we give a detailed guide on a pipeline for de novo transcriptome assembly of polyploid potato genotypes and their integration into a pan-transcriptome.
Climate change has a significant impact on the agricultural sector, negatively affecting plants’ growth and development, with predicted strong consequences on food availability in the future. ...Although we are experiencing more frequent and intense heavy rainfall events, a major contributor to field flooding, there is still not much known about the impact of these events on different crops. In this study, we investigated the effects of waterlogging on a model plant white cabbage (Brassica oleracea var. capitata f. alba), with the aim to follow its response to both single and recurrent short-term (72-h length) waterlogging, as well as to track difference in the sensitivity between plants in different growth stages (38- and 48-day-old plants). In our 22-day experiment, settled under fully controlled conditions (16 h day/8 h night, 25 °C day/20 °C night, 60–70% relative air humidity, 250 µmol m−2 s−1 photosynthetic active radiation), with the aim to more comprehensively recognize consequences of waterlogging on plants, we measured changes in plants on multiple levels: (i) within its morphological traits (number and length of leaves, leaf area, and blade width), (ii) within chlorophyll fluorescence and multispectral traits (20 parameters), (iii) following the levels of plant stress parameters (salicylic acid, abscisic acid, proline, and total polyphenols), and (iv) following changes in the plants’ elemental and mineral composition. According to our results, white cabbage was shown not to be very sensitive to waterlogging, with only plants exposed to repeated waterlogging showing signs of the congestion stress. These signs, observed in the changes of molecular stress parameters salicylic and abscisic acids, were not so clearly evident at the aboveground level. We did not observe changes in the plants’ morphologies, nor their photosynthetic performance. In addition, removal of waterlogging stress resulted in complete recovery of our model plants, suggesting a prompt adaptation response of white cabbage. With the projected increased frequency of occurrence of flooding events, it will become increasingly more important to recognize crops being highly sensitive to flooding with the aim to try to adapt to the changing climate.
Extreme events have produced more rain and became more frequent in many regions around the world, and these trends will rise with the warming of the planet. The vulnerable agricultural sectors, ...directly dependent on the climate, is predicted to be significantly affected by climate change, with an expected decline in future crop yields. We provide data on the effects of floods, because of excessive rain, on the agricultural sector in Croatia, with emphasis on its northern Pannonian region. Data collected for the period 2015-2020 are based on a 34-question survey, conducted among farmers previously reporting on climate-related damages to their crops. With almost 80% of farmers having experienced flooding on their field plots in the last 5 years (mostly short-term flooding, i.e. waterlogging of up to seven days), it is clear that this type of investigation needs further attention. Data suggested that floods most often occurred in the plant germination phase (before the 5th leaf) representing a risk for plant damage and consequent reduction in yields. A combination of mitigation and adaptation measures could minimize water retention in the fields and reduce damage, however, our survey implied that farmers scarcely use such measures. Knowledge gained in this study represents the first step toward understanding potential negative effects of the extreme events on the fragile agricultural sector in Croatia and could help authorities in decision making with the aim to reduce the degree of uncertainty associated with climate change effects.
Plant defence signalling response against various pathogens, including viruses, is a complex phenomenon. In resistant interaction a plant cell perceives the pathogen signal, transduces it within the ...cell and performs a reprogramming of the cell metabolism leading to the pathogen replication arrest. This work focuses on signalling pathways crucial for the plant defence response, i.e., the salicylic acid, jasmonic acid and ethylene signal transduction pathways, in the Arabidopsis thaliana model plant. The initial signalling network topology was constructed manually by defining the representation formalism, encoding the information from public databases and literature, and composing a pathway diagram. The manually constructed network structure consists of 175 components and 387 reactions. In order to complement the network topology with possibly missing relations, a new approach to automated information extraction from biological literature was developed. This approach, named Bio3graph, allows for automated extraction of biological relations from the literature, resulting in a set of (component1, reaction, component2) triplets and composing a graph structure which can be visualised, compared to the manually constructed topology and examined by the experts. Using a plant defence response vocabulary of components and reaction types, Bio3graph was applied to a set of 9,586 relevant full text articles, resulting in 137 newly detected reactions between the components. Finally, the manually constructed topology and the new reactions were merged to form a network structure consisting of 175 components and 524 reactions. The resulting pathway diagram of plant defence signalling represents a valuable source for further computational modelling and interpretation of omics data. The developed Bio3graph approach, implemented as an executable language processing and graph visualisation workflow, is publically available at http://ropot.ijs.si/bio3graph/and can be utilised for modelling other biological systems, given that an adequate vocabulary is provided.
The must used to make sparkling wine has a low pH value and moderate sugar content, and its potassium content can have a strong influence. An excess of potassium often leads to an insufficient supply ...of magnesium, since potassium has a strong antagonistic effect on magnesium, and, consequently, to poorer photosynthesis and a poorer quality of the must. The aim of this study was to determine whether the application of foliar fertilizers based on magnesium, phosphorus, and amino acids could reduce leaf potassium content, affecting the reductions in sugar content and pH value and increasing the total acidity of the must. A fertilizer trial with three replicates was conducted on the cultivar Istrian Malvasia (TCtrl—NPK, TMg—NPK + Agromag (6% MgO), TMgP—NPK + Agromag + Fosforo (30% P2O5) i TMgPBS—NPK + Agromag + Fosforo + Bio Prot) in a random complete block design. The NPK fertilizer was applied in the autumn. Foliar fertilization was applied three times during the growing season (31 May, 7 July, and 22 August 2014), and leaf samples were collected for leaf analysis before each application. The results show that foliar fertilization significantly reduced leaf potassium content, especially when treated with magnesium alone (treatment TMg). In addition, foliar fertilization significantly lowered the pH and increased the sugar content of the must. The results obtained in this research give a scientific contribution to the creation of fertilizer treatments for vines with a positive effect on the basic chemical composition of the base wine and provide a good basis for further research in reducing the use of certain enological practices during production.
Motar ili petrovac, Crithmum maritimum L. biljka je slanih staništa supralitorala, uglavnom uz obale europskog Sredozemlja. Sadrži vrijedne tvari kao što su, eterična ulja, masne kiseline i fenolni ...spojevi. Jedini je halofit koji sintetizira polifenolni antioksidant klorogensku kiselinu – derivat kafeoil kininske kiseline. Eterična ulja motra imaju antimikrobno djelovanje, a masne kiseline snažan potencijal u regeneraciji epitela. Biljka se koristi kao svježi i sušeni sastojak u gastronomiji. Eksperiment klijavosti ex vitro trajao je 45 dana, uz temperaturu 15-32 °C i vlagu zraka 50-88 % u razdoblju od svibnja do lipnja. Klijavost sjemenki na univerzalnom supstratu Florafin pomiješanim s vrtnim tlom, bila je 80 %, a kasniji rast presadnica u vrtnom tlu bio je bujan u uvjetima jadranske klime. Rezultati potvrđuju da bi se Crithmum maritimum mogao uspješno uzgajati u vrtnom tlu iznad supralitorala i tako biti dostupniji za berbu.
Sea fennel, Crithmum maritimum L., is a halophyte appearing in the splash zone, mainly on rocky shores of the European Mediterranean. Crithmum maritimum contains valuable substances such as essential oils, fatty acids and phenolic compounds. It is the only halophyte that synthesizes the polyphenolic antioxidant chlorogenic acid – derivative of caffeoyl quinic acid. Essential oils of sea fennel have an antimicrobial effect, and fatty acids have a strong potential in the regeneration of the epithelium. It is also a plant that is used as a fresh and dried ingredient in gastronomy. The experiment ex vitro lasted 45 days under the Adriatic climate with temperature range of 15-32°C and air humidity 50-88%, in the period from May to June. The germination rate of the seeds on the universal substrate Florafin was 80%, and the subsequent growth of the seedlings in the garden soil was lush under the conditions of the Adriatic climate. The results confirm that Crithmum maritimum could be successfully grown in garden soil above the supralittoral and thus be more available for harvesting.
Up to date, there are no reports on the effects of combined sulfur (S) and nitrogen (N) foliar application in olive orchards on volatile compounds and sensory characteristics of virgin olive oil ...(VOO). In this work, the effects of increasing the fertilizer S and N concentration on volatile compound composition and odor and taste attributes of monovarietal VOOs of Istarska bjelica and Leccino cultivars were investigated. The volatile compounds were analyzed by gas chromatography with flame ionization and mass spectrometric detection after isolation by solid-phase microextraction, while sensory attributes were assessed by a professional panel. In all the investigated VOO samples, aldehydes were the most represented group of compounds, with (E)-2-hexenal as the most abundant, followed by (Z)-3-hexenal and 1-penten-3-one. Significant differences in the volatile profiles and sensory attributes were observed between VOOs from different treatments, mainly attributable to the interactions between all the factors that were investigated: treatment, cultivar, and year. Although significant interactions were noted for sensory attributes as well, the score for overall quality was generally lower for Leccino VOOs and for VOOs from both cultivars that were obtained after the highest SN dose treatment. All the samples were graded by overall sensory scores that were higher than eight and were characterized by well-pronounced fruitiness and the absence of sensory defects. The results of this study showed that foliar application of S and N significantly affects the quality of VOO, confirming that such a practice can modulate the characteristic olive oil odor and taste attributes and thus possibly influence its acceptability and preference among consumers.
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