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The article is devoted to the study of the state of production, processing and storage of grain in the Vinnytsia region. The objectives of the research were to monitor the collected areas and gross harvests of the main crops in 2011-2021, establish the trends of their changes, analyze the capacities of transport and technological equipment and granaries of the region. The analysis was conducted on the basis of data from the State Statistics Service of Ukraine for 2011-2021. The analysis of harvested areas and gross harvests of grain of the main crops at agricultural enterprises of the region in 2011–2021 showed their tendency to increase. During this period, harvested areas increased by 1.42 times, and annual volumes of gross grain harvests had a wave-like growth pattern. Linear trend equations are proposed for forecasting harvested areas and gross grain harvests, which are characterized by coefficients of determination R2 of 0.79 and 0.65, respectively. The largest gross harvests were given by corn, wheat and sunflower, and smaller – by barley, soybeans and rapeseed. In 2018-2021, the gross harvest of these crops was within the following limits (thousand tons): corn 2015-2620, wheat 1200-1691, and sunflower 755-1001. 66 enterprises receive grain from vehicles, and 65 forward it. The average capacity of receiving grain is 3032.41 t/day, and forwarding 1183.61 t/day. There are 21 railway transport enterprises hiring, and 55 enterprises offering leave. The average capacity of receiving devices from the railway is 949.52 t/day, and the output capacity is 1448.69 t/day. 111 grain dryers from 11 producing countries are installed at the considered 53 enterprises of the region. Of them, 18.9% of enterprises have dryers of Ukrainian production only, 20.8% of enterprises have both domestic and foreign ones, but the majority of enterprises have dryers of foreign production only, which are 1.85 times more than the number of Ukrainian made dryers. It was established that 82 separators are used for grain cleaning at 37 elevators, most of which (63%) are domestically produced, which outnumber imported ones by 1.73 times. The total capacity of simultaneous storage of grain in 67 elevators of agricultural enterprises is 3554.35 thousand tons, of which 2449.41 thousand tons have harvesting elevators and 1104.94 thousand tons – production elevators. Their simultaneous storage capacity is less than the forecast values of gross grain harvests in 2022 – 6354.2 thousand tons, which requires the expansion of the elevator network of the Vinnytsia region.

At the origin of wheat-spelt breeding in Ukraine is the outstanding scientific breeder Fedir Pariy. As of today, seven varieties of wheat-spelt have been entered into the Register of plant varieties suitable for distribution in the territory of Ukraine. The first variety of spelt wheat Triticum spelta L. "Zoria Ukrainy" was entered into the register in 2011, and from that began the active study of this type of hulled wheat not only by breeders, but also by technologists, the goal of which was the introduction of hulled wheat in the domestic grain processing industry. Two years later, in 2013, the second variety of domestic spelled wheat "Yevropa" was entered into the register, the work on the selection of which was also headed by Fedir Pariy. The following varieties of spelt wheat were entered into the Register relatively recently during 2017-2021: Attergauer Dinkel (2016), Evrika (2017), Mv Martongold (2018), Vyshyvanka bilotserkivska (2018), Bilberi (2021). Considering wheat-spelt grain as a potential raw material for cereal production, it can be noted that thanks to the excellent chemical composition of the grain and its affinity with the grain of traditional wheat, it can be concluded that it can be processed at domestic grain factories of different productivity, using at the same time as the traditional available on technological equipment at the enterprise, and when building new lines and factories, use more modern solutions offered by world leaders in the production of technological equipment, such as the Buhler company. At the same time, it is possible to produce both a higher-quality product, traditional for the Ukrainian consumer, such as "Artek" and "Poltavska"groats, and to focus on the production of a new range of wheat products - the production of whole groats and flaked kernels, which in turn, with rational construction and the use of more efficient technological equipment, will give be able to produce functional and dietary food products. In addition, due to such products, the export potential of the grain processing industry can be increased, especially taking into account the small amount of spelt wheat cultivation in the countries of the European Union, with the constant increase in demand for environmentally friendly and high-quality products that are available in these countries, with the right approach, can make Ukraine an exporter of wheat-spelt processing products to EU countries and beyond.

We present the dataset “SArdinian GRAsslands” (SAGRA), a collection of georeferenced vegetation surveys sourced from different areas of Sardinia (Italy). SAGRA addresses a geographic gap in current databases, as plots from Sardinian grasslands are underrepresented. We collected vegetation data from different projects and organized it within a framework that allows for scalability to larger scales or integration into existing databases. The surveys include three categories of information: general, vegetation and management, and environmental. Overall, SAGRA comprises 1277 vegetation surveys, some of which were performed in different years in the same plots. This dataset encompasses 685 plots and 434 species, primarily therophytes.

The impact of toxic elements (TEs) contaminating the root zone of Lupinus angustifolius L. on enzymatic activities, nitrification rate, and changes in the root system was evaluated. Lupine was cultivated in a pot experiment using two types of soil - control and contamination (with a high degree of arsenic (As), cadmium (Cd), lead (Pb), and zinc (Zn) contamination). After harvesting lupine biomass, enzyme activities (β-glucosidase, acid phosphatase, arylsulphatase, lipase, chitinase, cellobiohydrolase, alanine aminopeptidase, and leucine aminopeptidase) in soils were analysed. Enzyme activities decreased with TE soil contamination. According to our results, arylsulphatase was found to be the most sensitive soil enzyme to TEs. The nitrification rate is closely related to soil contamination and plant activity, as it stimulates microbial growth and multiplication through root exudates. The close correlations confirmed this relationship (r = 0.73-0.99). An increasing trend in TE contents in the roots was observed with soil contamination. Plant hormones are crucial in regulating root growth and development under stress conditions. The levels of determined phytohormones in our experiment (auxins, abscisic acid (ABA), salicylic acid (SA), and bioactive cytokinins (bCKs)) were lower in the contamination compared to the control. Correlations confirmed a significant negative relationship between the TE content in the roots and the contents of phytohormones (auxins: r = -0.96 to -0.97; ABA: r = -0.83 to -0.86; SA: r = -0.95 to -0.99, bCKs: r = -0.87 to -0.93). The ratios of these hormones (not their absolute values) appear to be the determining factor for regulating root development and protecting plants from oxidative stress.

In this study, three insect-resistant transgenic Bacillus thuringiensis (Bt) oilseed rape events (GT1, GT5 and GT9) under field conditions were utilised to analyse the dynamics of Cry1Ac protein and the changes in soil enzyme activities in the rhizosphere soil of transgenic Bt plants during different growth stages over two successive cultivation years. The results indicated that compared to the non-transgenic control plant cv. Westar, the amount of Cry1Ac protein in the rhizosphere soil of the three transgenic oilseed rape events was significantly higher during the flowering and podding stages in the first cultivation year. Additionally, in the second cultivation year, transgenic GT1 and GT9 had significantly higher amounts of Cry1Ac protein in the rhizosphere soil during the flowering stage, and all three transgenic oilseed rape events had significantly higher amounts of Cry1Ac protein in the rhizosphere soil during the podding stage. Over the two successive cultivation years, the sucrase activity in the rhizosphere soil of transgenic events showed significant changes during bolting, flowering and podding stages, while all three transgenic events exhibited significant changes in phosphatase activity during the four different stages. Furthermore, different transgenic events showed varying significant changes in urease and protease activities during the bolting, flowering and podding stages of the first year, and all three transgenic events had significant changes in dehydrogenase activities during the four different stages of the second cultivation year. PCA and correlation analysis clearly demonstrated a strong correlation between the Cry1Ac protein and five soil enzyme activities, as well as a close interconnectedness among those five soil enzyme activities. These findings suggest that the amount of insecticidal crystal proteins in the rhizosphere soil of transgenic Bt (Cry1Ac) oilseed rape varies with different growth periods, and the enzyme activities in the rhizosphere soil of transgenic Bt oilseed rape plants undergo significant changes over two successive planting years.

Water deficit (drought) is an important environmental factor affecting physiological processes in plants. The present work focuses on the study of changes in physiological responses of juvenile plants (plants in the vegetative phase of growth BBCH 14-16) of selected sorghum genotypes Dokok, 30485, Barnard Red and Ruzrok to water deficit and after rehydration. Water deficit affected the observed physiological parameters - gas exchange and chlorophyll fluorescence. Genotypic differences were also confirmed, with Dokok appearing to be the more sensitive genotype and Ruzrok and Barnard Red appearing to be tolerant. Following rehydration, these parameters increased but did not reach the levels of the control plants. A significant decrease in photosynthetic rate (Pn), transpiration (E) and fluorescence compared to the control was found in the water-deficient variant twice for 10 days and 6 days between rehydration periods. Only in the variant where water deficit (14 days) was followed by irrigation (10 days) transpiration increased in genotype 30485. Chlorophyll fluorescence (Fv/Fm) also decreased significantly in this cultivar. The results suggest that a rehydration period of 14 days is insufficient to restore the photosynthetic functions of stressed sorghum plants.

A suitable irrigation pattern is of great significance for reducing greenhouse gas emissions. In this study, field experiments and a denitrification-decomposition (DNDC) model were used to study the global warming potential based on CH4, N2O and CO2 fluxes under flooding irrigation and controlled irrigation in paddy fields in the Erhai Lake basin. The results showed that the average value of CH4 flux under controlled irrigation was lower than that under flooding irrigation, with a reduction range of 43.21% to 48.88%, however, the average value of the N2O and CO2 fluxes from paddy field under controlled irrigation were higher than those under flooding irrigation. Controlled irrigation patterns can significantly reduce the global warming potential in paddy fields based on CH4, N2O and CO2 fluxes. Controlled irrigation can effectively reduce the global warming potential per unit yield. For water management in the Erhai Lake basin, it is recommended the controlled irrigation treatment of soil moisture with an upper limit of 100% and a lower limit of 75-85% with irrigation, and a maximum surface water depth of 150-200 mm lasting for five days after precipitation from the jointing-booting stage to the milk stage.

In this study, Illumina MiSeq sequencing of 16S and ITS2 rRNA genes were used to determine the dynamic changes in bacterial and fungal communities and soil properties and enzyme activities in rhizosphere soil of ginseng under forest after 5, 10 and 15 years of cultivation and different growth stages. Results showed that the changes were particularly prominent in 10-year-old ginseng under forest, and the trends of organic carbon, alkaline hydrolysed nitrogen, and available potassium were extremely similar in different duration of the crop, especially in the middle stage of rapid root growth, when soil nutrient consumption was severe, and soil enzyme activities of rhizosphere were significantly reduced. The observed changes in soil properties and enzyme activities caused by the cultivation duration of the crop and growth stage could be explained by the variations in the microbiome. The microbial composition of 10-year-old ginseng under forest has undergone significant changes, at the genus level, both Acinetobacter bacteria and Kazachstania fungi exhibited a higher abundance; the abundance of Bacillota (Firmicutes), and Candidatus udaeobacter with significantly lower abundance. This study initially revealed the changes in nutrient utilisation of ginseng under forest at different cultivation duration of the crop and different growth stages, as well as the regulatory role played by microbes in this process preliminarily. We consider 10 years to be a critical stage for the long-term cultivation of ginseng in the forest, during which it is more sensitive to environmental factors and may exhibit special dynamic changes affecting its growth and quality. This provides a reference for further precision planting and harvesting of ginseng under the forest.

In this paper, I elucidated the influence of γ-aminobutyric acid (GABA) on wheat cadmium (Cd) tolerance. Research results manifested that Cd stress increased superoxide dismutase, catalase, peroxidase, ascorbate peroxidase and glutathione peroxidase activities, and ascorbic acid (AsA) and glutathione (GSH) contents. However, Cd stress decreased AsA/ dehydroascorbic acid (DHA) and GSH/oxidised glutathione (GSSG) ratios, and inhibited photosynthetic performance and plant growth. Compared to Cd alone, GABA plus Cd improved wheat Cd tolerance by increasing the activities of above antioxidant enzymes, AsA and GSH contents, and AsA/DHA and GSH/GSSG ratios. Meanwhile, compared with Cd alone, GABA plus Cd also enhanced the photosynthetic performance by improving chlorophyll (Chl) and carotenoid (Car) contents and Car/Chl ratio, photosynthetic rate, transpiration rate, stomatal conductance, intercellular carbon dioxide concentration, and Chl fluorescence parameters maximum photochemical efficiency of PSII, photochemical quenching, nonphotochemical quenching and quantum efficiency of PSII photochemistry, which further promoted plant height and biomass. Compared to control, GABA alone also improved above indicators. Current results suggested that GABA can be applied as an anti-cadmium agent in wheat production practice.

The owners of forests with water protection functions in Bulgaria do not receive compensation for their limited right to use wood and non-wood forest products from the forest areas they own. At the same time, the contribution derived from forests with water protection functions is received by water users and water consumers, whereas the costs of managing the forests are borne by their owners. The problem thus defined is not a forestry one, but an economic one, and the purpose of this paper ensues therefrom, namely to propose and test a methodology for valuating the production function of forest areas with water protection function in Bulgaria, allowing a fair distribution of income between the forest owner and the user of forest ecosystem services. The methodology is based on the form of forest management and the analytical expression of the economic relationship between a forest owner and a user of forest ecosystem services, constructed using Schenrock’s formula. It has been tested with actual data from forest areas with water protection functions falling within the administrative and territorial scope of Velingrad municipality. The obtained results are as follows: as regards the forest territories falling into Sanitary protection zone (SPZ) I of the forests with water protection functions, the economic gains from the property should be 100% realized from water consumption and the owner should receive about EUR 49.83 /ha per year; in SPZ II of the forests with water protec-tion functions, the economic gains from the property should be realized by prioritizing the water protection over the wood production function in a 75:25 ratio, i.e. the owner should receive about EUR 37.37 /ha/year; in SPZ III of the forests with water protection functions, the economic gains from the property should be realized equally in a 50:50 ratio through both production functions, i.e. about EUR 12.22 /ha/year.

During a phytosociological field-work campaign aimed at studying some relict Scheuchzerio-Caricetea boreal mires of the montane and subalpine belts of the Laga Mountains, the highest and largest siliceous massif of the Apennine range, several bryophyte taxa of particular biogeographic interest were collected. Among these taxa, Schljakovia kunzeana and Ptychostomum cernuum were found to be new records for the whole Apennine range while Hamatocaulis vernicosus (taxon included in annex II of Habitats Directive) and Scorpidium cossonii as new for the Central-Southern Apennines. Two further species, Bryum canariense, Plagiomnium cuspidatum, were found to be confirmations of old records for the Central Apennines dating back to the early 1900s. At the national and regional level, nine, out of the forty-four bryophyte taxa identified in this study, were found to be new for the Lazio administrative Region, and one taxon as new for the Abruzzo Region. The majority of these new records belong to the boreal chorotype, the Laga Mountains being one of the most important conservation sites for the relict circumboreal and arctic-alpine flora in the whole Mediterranean area. According to both the EUNIS Habitat classification and the EU Habitats Directive Annex I, several, out of the 44 bryophytes identified in this study, act as diagnostic species for European Community Habitats. Nevertheless, a complete correspondence between bryophyte taxon and habitat type was not found upon comparing these two environmental policy systems.

Abstract 'Candidatus Phytoplasma solani’ (CPs), a phytoplasma endemic to the Euro-Mediterranean basin is a causative agent of several plant diseases, including the grapevine yellows disease “bois noir” (BN). As different CPs strains have been shown to have different ecological reservoirs and pathways for spread, the genetic characterization of CPs strains is a prerequisite, and better control of BN relies on the identification of reservoir plants. The variability of the phytoplasma genotypes involved in the BN pathosystem in Croatian vineyards was assessed by a multilocus sequence typing (MLST) approach. The genotyping was performed on selected grapevine, wild plants, and insects collected within the eleven years of national survey conducted in all Croatian viticultural regions. The extensive tuf, secY, stamp, and vmp1 genes-based MLST analyses revealed two new genotypes for stamp and vmp1 genes, designated as ST59 and V28, respectively, and overall identified 28 different CPs MLST genotypes. The prevalent MLST genotype in grapevine CPsSqt21 (S6/ST6/V18/tuf-b2) was widespread in nine counties across Uplands, Slavonia, and Danube wine regions and was affiliated to the known vector Hyalesthes obsoletus and to Urtica dioica. The other two most frequent genotypes were the U. dioica-associated CPsSqt28 (S39/ST46/V3/tuf-a) and the C. arvensis-associated CPsSqt2 (S1/ST9/V4/tuf-b1). CPs of different vmp1 genotypes was also detected in Cixius wagneri specimens originating from different parts of Croatia. In addition, CPs was detected in several Dichtyophara europaea insects and in two new potential plant reservoirs Ailanthus altissima and Robinia pseudoacacia. The substantial number of found MLST genotypes indicates the presence of several independent epidemiological cycles and is certainly a consequence of a unique geographical position of Croatia, bridging the different eco-climatic areas of central and south-eastern Europe.

Abstract Fungal diseases are the main factors affecting the quality and production of vegetables. Rapid and accurate detection of pathogenic spores is of great practical significance for early prediction and prevention of diseases. However, there are some problems with microscopic images collected in the natural environment, such as complex backgrounds, more disturbing materials, small size of spores, and various forms. Therefore, this study proposed an improved detection method of GCS-YOLOv8 (Global context and CARFAE and Small detector-optimized YOLOv8), effectively improving the detection accuracy of small-target pathogen spores in natural scenes. Firstly, by adding a small target detection layer in the network, the network’s sensitivity to small targets is enhanced, and the problem of low detection accuracy of the small target is effectively improved. Secondly, Global Context attention is introduced in Backbone to optimize the CSPDarknet53 to 2-Stage FPN (C2F) module and model global context information. At the same time, the feature up-sampling module Content-Aware Reassembly of Features (CARAFE) was introduced into Neck to enhance the ability of the network to extract spore features in natural scenes further. Finally, we used an Explainable Artificial Intelligence (XAI) approach to interpret the model’s predictions. The experimental results showed that the improved GCS-YOLOv8 model could detect the spores of the three fungi with an accuracy of 0.926 and a model size of 22.8 MB, which was significantly superior to the existing model and showed good robustness under different brightness conditions. The test on the microscopic images of the infection structure of cucumber down mildew also proved that the model had good generalization. Therefore, this study realized the accurate detection of pathogen spores in natural scenes and provided feasible technical support for early predicting and preventing fungal diseases.

Abstract Soybean seeds are susceptible to damage from the Riptortus pedestris, which is a significant factor affecting the quality of soybean seeds. Currently, manual screening methods for soybean seeds are limited to visual inspection, making it difficult to identify seeds that are phenotypically defect-free but have been punctured by stink bugs on the sub-surface. To facilitate the convenient and efficient identification of healthy soybean seeds, this paper proposes a soybean seed pest detection method based on spatial frequency domain imaging combined with RL-SVM. Firstly, soybean optical data is obtained using single integration sphere technique, and the vigor index of soybean seeds is obtained through germination experiments. Then, based on the above two data items using feature extraction algorithms (the successive projections algorithm and the competitive adaptive reweighted sampling algorithm), the characteristic wavelengths of soybeans are identified. Subsequently, the spatial frequency domain imaging technique is used to obtain the sub-surface images of soybean seeds in a forward manner, and the optical coefficients such as the reduced scattering coefficient $${{\mu }{\prime}}_{s}$$ μ ′ s and absorption coefficient $${\mu }_{a}$$ μ a of soybean seeds are inverted. Finally, RL-MLR, RL-GRNN, and RL-SVM prediction models are established based on the ratio of the area of insect-damaged sub-surface to the entire seed, soybean varieties, and $${\mu }_{a}$$ μ a at three wavelengths (502 nm, 813 nm, and 712 nm) for predicting and identifying soybean the stinging and sucking pest damage levels of soybean seeds. The experimental results show that the spatial frequency domain imaging technique yields small errors in the optical coefficients of soybean seeds, with errors of less than 15% for $${\mu }_{a}$$ μ a and less than 10% for $${{\mu }{\prime}}_{s}$$ μ ′ s . After parameter adjustment through reinforcement learning, the Macro-Recall metrics of each model have improved by 10%-15%, and the RL-SVM model achieves a high Macro-Recall value of 0.9635 for classifying the pest damage levels of soybean seeds.

Abstract Background This study explores the use of Unmanned Aerial Vehicles (UAVs) for estimating wheat biomass, focusing on the impact of phenotyping and analytical protocols in the context of late-stage variety selection programs. It emphasizes the importance of variable selection, model specificity, and sampling location within the experimental plot in predicting biomass, aiming to refine UAV-based estimation techniques for enhanced selection accuracy and throughput in variety testing programs. Results The research uncovered that integrating geometric and spectral traits led to an increase in prediction accuracy, whilst a recursive feature elimination (RFE) based variable selection workflowled to slight reductions in accuracy with the benefit of increased interpretability. Models, tailored to specific experiments were more accurate than those modelling all experiments together, while models trained for broad-growth stages did not significantly increase accuracy. The comparison between a permanent and a precise region of interest (ROI) within the plot showed negligible differences in biomass prediction accuracy, indicating the robustness of the approach across different sampling locations within the plot. Significant differences in the within-season repeatability (w2) of biomass predictions across different experiments highlighted the need for further investigation into the optimal timing of measurement for prediction. Conclusions The study highlights the promising potential of UAV technology in biomass prediction for wheat at a small plot scale. It suggests that the accuracy of biomass predictions can be significantly improved through optimizing analytical and modelling protocols (i.e., variable selection, algorithm selection, stage-specific model development). Future work should focus on exploring the applicability of these findings under a wider variety of conditions and from a more diverse set of genotypes.

Abstract Background Previous research literature reported different results regarding the long-term effects that cannabis use can exert on the frontal lobe neurocognitive functions of its users. Another body of research suggested that cannabis use negatively affects the person’s general level of occupational and psychosocial functioning consequently to these alterations. Some other research results did not support these findings. To date, it is still debatable whether chronic cannabis use triggers negative neurocognitive effects in chronic users even after a period of abstinence. Research data exploring consequent adverse outcomes on the general individual occupational and psychosocial functioning is not yet conclusive. Results We conducted this study to examine the residual neurocognitive effects of cannabis use, whether it is affected by duration of cannabis use before abstinence, and its relation to individual’s global assessment of functioning exhibited in the person’s occupational and social life whether it’s family or friends. Our sample comprised 80 male participants (18–45 years old) who were grouped into 4 groups (3 groups with different durations of use and a control group), with no significant difference between the four studied groups regarding age, education, and socioeconomic level. The Kruskal Wallis test was used to test the significance of differences in the distribution of total frontal lobe battery results and the general assessment of function scores using GAF scores between study groups. Post hoc testing was performed to adjust for multiple comparisons using Bonferroni method. Conclusion Data analysis showed that cannabis users experienced general functional disturbances that encompass impairments in social and occupational life aspects. These impairments in function are correlated with the presence of neurocognitive deficits even after a period of abstinence. Both having significant positive correlation with longer duration of cannabis use.

Abstract Potato is the most widely grown non-grain crop and ranks as the third most significant global food crop following rice and wheat. Despite its long history of cultivation over vast areas, slow breeding progress and environmental stress have led to a scarcity of high-yielding potato varieties. Enhancing the quality and yield of potato tubers remains the ultimate objective of potato breeding. However, conventional breeding has faced challenges due to tetrasomic inheritance, high genomic heterozygosity, and inbreeding depression. Recent advancements in molecular biology and functional genomic studies of potato have provided valuable insights into the regulatory network of physiological processes and facilitated trait improvement. In this review, we present a summary of identified factors and genes governing potato growth and development, along with progress in potato genomics and the adoption of new breeding technologies for improvement. Additionally, we explore the opportunities and challenges in potato improvement, offering insights into future avenues for potato research.

Weed diversity is crucial for supporting ecological services, but weed control methods significantly influence weed species dominance and diversity. The present study was conducted in southwestern Nigeria’s rainforest-savanna transitional agroecological zone during the 2017 and 2018 rainy seasons. Different weed management techniques were assessed, including applying cyanide-сontaining cassava effluent (CE@3WAS), pendimethalin (P), and hoe weeding (HW@3WAS), as well as repeated applications of HW and CE (HW@3&5WAS, CE@3&5WAS), and integrated approaches (P + CE@5WAS, P + HW@5WAS, CE@3WAS + HW@5WAS). A control treatment, where the weeds were left unmanaged, was also included. The experiment followed a randomized complete block design with three replications. Weed samples were collected using 25 cm x 25 cm quadrats placed randomly along the plot diagonals. Weed diversity was assessed using the ShannonWiener index and descriptive statistics. Results indicated that the control methods influenced weed species composition. Specifically, the presence of broad-leaf weeds was prominent in the P + HW@5WAS (2017) and P + CE@5WAS (2018) treatments, while grasses dominated in the weedy check (2017) and HW@3WAS (2018), suggesting that these strategies favour specific morphological groups of the weeds. Weed diversity decreased across various management practices, with the rankings in ascending order: CE@3&5WAP, CE@3WAP, P+CE@5WAS, CE@3WAP + HW@5WAP, P + HW@5WAP, Pendimethalin, HW@3WAP, and HW@3&5WAP. These findings underscore the importance of selecting weed management strategies based on weed ecological significance. Integrated weed management emerged as a more ecologically sustainable approach for okra fields compared to sole herbicide application or manual weeding.

Abstract Xanthomonas campestris pv. campestris (Xcc) is the causal agent of black rot in Brassica vegetables, which can induce the host plant to produce salicylic acid and 4-hydroxybenzoic acid (4-HBA) during infection. Xcc was previously shown to sense and degrade host plant-derived 4-HBA via the sensor PobR and a PobA-dependent pathway. The degradation of 4-HBA is associated with Xcc virulence in cabbage. The present study generated a reporter strain XC1::PpobA-gusA to monitor pobA transcription. 4-HBA-like compounds were screened for their ability to interfere with pobA transcription. Benzoic acid (BA) was found to efficiently decrease pobA transcription in a dose-dependent manner. Xcc neither produced nor degraded BA; however, the exogenous addition of BA to the 4-HBA-containing Xcc culture significantly decreased the 4-HBA degradation rate. Furthermore, addition of BA into the Xcc culture did not significantly affect the transcription of pobA or pobR; however, addition of BA into the 4-HBA-containing culture significantly decreased the transcription of both genes. Isothermal titration calorimetry and an electrophoretic mobility shift assay revealed that BA binds to PobR with a moderate affinity, which interfered with the binding of 4-HBA/PobR complex to the pobA promoter and thereby inhibiting pobA transcription and 4-HBA degradation. The endogenous BA level of the infected cabbage leaves increased in response to Xcc infection. In the presence of BA, the virulence of Xcc on cabbage decreased significantly. Taken together, these results suggest that cabbage utilizes BA to interfere with 4-HBA degradation, thereby reducing Xcc virulence. Thus, BA has the potential to be developed as a bactericide against Xcc infection.

Abstract Purpose Wood comprises different cell types, such as fibers, tracheids and vessels, defining its properties. Studying cells’ shape, size, and arrangement in microscopy images is crucial for understanding wood characteristics. Typically, this involves macerating (soaking) samples in a solution to separate cells, then spreading them on slides for imaging with a microscope that covers a wide area, capturing thousands of cells. However, these cells often cluster and overlap in images, making the segmentation difficult and time-consuming using standard image-processing methods. Results In this work, we developed an automatic deep learning segmentation approach that utilizes the one-stage YOLOv8 model for fast and accurate segmentation and characterization of macerated fiber and vessel form aspen trees in microscopy images. The model can analyze 32,640 x 25,920 pixels images and demonstrate effective cell detection and segmentation, achieving a $$\hbox {mAP}_{0.5-0.95}$$ mAP 0.5 - 0.95 of 78 %. To assess the model’s robustness, we examined fibers from a genetically modified tree line known for longer fibers. The outcomes were comparable to previous manual measurements. Additionally, we created a user-friendly web application for image analysis and provided the code for use on Google Colab. Conclusion By leveraging YOLOv8’s advances, this work provides a deep learning solution to enable efficient quantification and analysis of wood cells suitable for practical applications.

Abstract Virus-Induced Gene Silencing (VIGS) is a versatile tool in plant science, yet its application to non-model species like sunflower demands extensive optimization due to transformation challenges. In this study, we aimed to elucidate the factors that significantly affect the efficiency of Agrobacterium-VIGS in sunflowers. After testing a number of approaches, we concluded that the seed vacuum technique followed by 6 h of co-cultivation produced the most efficient VIGS results. Genotype-dependency analysis revealed varying infection percentages (62–91%) and silencing symptom spreading in different sunflower genotypes. Additionally, we explored the mobility of tobacco rattle virus (TRV) and phenotypic silencing manifestation (photo-bleaching) across different tissues and regions of VIGS-infected sunflower plants. We showed the presence of TRV is not necessarily limited to tissues with observable silencing events. Finally, time-lapse observation demonstrated a more active spreading of the photo-bleached spots in young tissues compared to mature ones. This study not only offers a robust VIGS protocol for sunflowers but also provides valuable insights into genotype-dependent responses and the dynamic nature of silencing events, shedding light on TRV mobility across different plant tissues.

Abstract Background Ripeness is a phenotype that significantly impacts the quality of fruits, constituting a crucial factor in the cultivation and harvesting processes. Manual detection methods and experimental analysis, however, are inefficient and costly. Results In this study, we propose a lightweight and efficient melon ripeness detection method, MRD-YOLO, based on an improved object detection algorithm. The method combines a lightweight backbone network, MobileNetV3, a design paradigm Slim-neck, and a Coordinate Attention mechanism. Additionally, we have created a large-scale melon dataset sourced from a greenhouse based on ripeness. This dataset contains common complexities encountered in the field environment, such as occlusions, overlapping, and varying light intensities. MRD-YOLO achieves a mean Average Precision of 97.4% on this dataset, achieving accurate and reliable melon ripeness detection. Moreover, the method demands only 4.8 G FLOPs and 2.06 M parameters, representing 58.5% and 68.4% of the baseline YOLOv8n model, respectively. It comprehensively outperforms existing methods in terms of balanced accuracy and computational efficiency. Furthermore, it maintains real-time inference capability in GPU environments and demonstrates exceptional inference speed in CPU environments. The lightweight design of MRD-YOLO is anticipated to be deployed in various resource constrained mobile and edge devices, such as picking robots. Particularly noteworthy is its performance when tested on two melon datasets obtained from the Roboflow platform, achieving a mean Average Precision of 85.9%. This underscores its excellent generalization ability on untrained data. Conclusions This study presents an efficient method for melon ripeness detection, and the dataset utilized in this study, alongside the detection method, will provide a valuable reference for ripeness detection across various types of fruits.

Abstract Background CRISPR Cas9 and Cas12a are the two most frequently used programmable nucleases reported in plant systems. There is now a wide range of component parts for both which likely have varying degrees of effectiveness and potentially applicability to different species. Our aim was to develop and optimise Cas9 and Cas12a based systems for highly efficient genome editing in the monocotyledons barley and wheat and produce a user-friendly toolbox facilitating simplex and multiplex editing in the cereal community. Results We identified a Zea mays codon optimised Cas9 with 13 introns in conjunction with arrayed guides driven by U6 and U3 promoters as the best performer in barley where 100% of T0 plants were simultaneously edited in all three target genes. When this system was used in wheat > 90% of T0 plants were edited in all three subgenome targets. For Cas12a, an Arabidopsis codon optimised sequence with 8 introns gave the best editing efficiency in barley when combined with a tRNA based multiguide array, resulting in 90% mutant alleles in three simultaneously targeted genes. When we applied this Cas12a system in wheat 86% & 93% of T0 plants were mutated in two genes simultaneously targeted. We show that not all introns contribute equally to enhanced mutagenesis when inserted into a Cas12a coding sequence and that there is rationale for including multiple introns. We also show that the combined effect of two features which boost Cas12a mutagenesis efficiency (D156R mutation and introns) is more than the sum of the features applied separately. Conclusion Based on the results of our testing, we describe and provide a GoldenGate modular cloning system for Cas9 and Cas12a use in barley and wheat. Proven Cas nuclease and guide expression cassette options found in the toolkit will facilitate highly efficient simplex and multiplex mutagenesis in both species. We incorporate GRF-GIF transformation boosting cassettes in wheat options to maximise workflow efficiency.

Abstract Background Stalk lodging (the premature breaking of plant stalks or stems prior to harvest) is a persistent agricultural problem that causes billions of dollars in lost yield every year. Three-point bending tests, and rind puncture tests are common biomechanical measurements utilized to investigate crops susceptibility to lodging. However, the effect of testing rate on these biomechanical measurements is not well understood. In general, biological specimens (including plant stems) are well known to exhibit viscoelastic mechanical properties, thus their mechanical response is dependent upon the rate at which they are deflected. However, there is very little information in the literature regarding the effect of testing rate (aka displacement rate) on flexural stiffness, bending strength and rind puncture measurements of plant stems. Results Fully mature and senesced maize stems and wheat stems were tested in three-point bending at various rates. Maize stems were also subjected to rind penetration tests at various rates. Testing rate had a small effect on flexural stiffness and bending strength calculations obtained from three-point bending tests. Rind puncture measurements exhibited strong rate dependent effects. As puncture rate increased, puncture force decreased. This was unexpected as viscoelastic materials typically show an increase in resistive force when rate is increased. Conclusions Testing rate influenced three-point bending test results and rind puncture measurements of fully mature and dry plant stems. In green stems these effects are expected to be even larger. When conducting biomechanical tests of plant stems it is important to utilize consistent span lengths and displacement rates within a study. Ideally samples should be tested at a rate similar to what they would experience in-vivo.

Abstract Background As genomes of many eukaryotic species, especially plants, are large and complex, their de novo sequencing and assembly is still a difficult task despite progress in sequencing technologies. An alternative to genome assembly is the assembly of transcriptome, the set of RNA products of the expressed genes. While a bunch of de novo transcriptome assemblers exists, the challenges of transcriptomes (the existence of isoforms, the uneven expression levels across genes) complicates the generation of high-quality assemblies suitable for downstream analyses. Results We developed Trans2express – a web-based tool and a pipeline of de novo hybrid transcriptome assembly and postprocessing based on rnaSPAdes with a set of subsequent filtrations. The pipeline was tested on Arabidopsis thaliana cDNA sequencing data obtained using Illumina and Oxford Nanopore Technologies platforms and three non-model plant species. The comparison of structural characteristics of the transcriptome assembly with reference Arabidopsis genome revealed the high quality of assembled transcriptome with 86.1% of Arabidopsis expressed genes assembled as a single contig. We tested the applicability of the transcriptome assembly for gene expression analysis. For both Arabidopsis and non-model species the results showed high congruence of gene expression levels and sets of differentially expressed genes between analyses based on genome and based on the transcriptome assembly. Conclusions We present Trans2express – a protocol for de novo hybrid transcriptome assembly aimed at recovering of a single transcript per gene. We expect this protocol to promote the characterization of transcriptomes and gene expression analysis in non-model plants and web-based tool to be of use to a wide range of plant biologists.

Abstract Background Chinese Cymbidium orchids, cherished for their deep-rooted cultural significance and significant economic value in China, have spawned a rich tapestry of cultivars. However, these orchid cultivars are facing challenges from insufficient cultivation practices and antiquated techniques, including cultivar misclassification, complex identification, and the proliferation of counterfeit products. Current commercial techniques and academic research primarily emphasize species identification of orchids, rather than delving into that of orchid cultivars within species. Results To bridge this gap, the authors dedicated over a year to collecting a cultivar image dataset for Chinese Cymbidium orchids named Orchid2024. This dataset contains over 150,000 images spanning 1,275 different categories, involving visits to 20 cities across 12 provincial administrative regions in China to gather pertinent data. Subsequently, we introduced various visual parameter-efficient fine-tuning (PEFT) methods to expedite model development, achieving the highest top-1 accuracy of 86.14% and top-5 accuracy of 95.44%. Conclusion Experimental results demonstrate the complexity of the dataset while highlighting the considerable promise of PEFT methods within flower image classification. We believe that our work not only provides a practical tool for orchid researchers, growers and market participants, but also provides a unique and valuable resource for further exploring fine-grained image classification tasks. The dataset and code are available at https://github.com/pengyingshu/Orchid2024 .

Abstract Grain-filling of rice spikelets (particularly for the later flowering inferior spikelets) is an important characteristic that affects both quality and yield. Rice ratooning technology is used to cultivate a second crop from dormant buds that sprout from stubble left after the first harvest. This study used two rice varieties, the conventional indica rice ‘Jinhui 809’ and the hybrid indica-japonica rice ‘Yongyou 1540’, to assess the impact of rice ratooning on grain-filling. The results indicated that the grain-filling process in inferior spikelets of ratoon season rice (ISR) showed significant improvement compared to inferior spikelets of main crop (late season) rice (ISL). This improvement was evident in the earlier onset of rapid grain-filling, higher seed-setting percentage, and improved grain quality. A label-free quantitative proteomic analysis using mass spectrometry identified 1724 proteins with significant abundance changes, shedding light on the molecular mechanisms behind the improved grain-filling in ISR. The functional analysis of these proteins indicated that ratooning stimulated the metabolic processes of sucrose-starch, trehalose, and hormones in rice inferior spikelets, leading to enhanced enzyme activities related to starch synthesis, elevated concentrations of trehalose-6-phosphate (T6P), indole-3-acetic acid (IAA) and zeatin riboside (ZR) during the active grain-filling phase. This research highlighted the importance of the GF14f protein as a key regulator in the grain-filling process of ISR. It revealed that GF14f transcriptional and protein levels declined more rapidly in ISR compared to ISL during grain-filling. Additionally, the GF14f-RNAi plants specific to the endosperm exhibited improved quality in inferior spikelets. These findings suggest that the enhancement of starch synthesis, increased levels of IAA, ZR, and T6P, along with the rapid decrease in GF14f protein, play a role in enhancing grain-filling in ratoon season rice.

Abstract Plants NADP-malic enzymes (NADP-MEs) act as a class of oxidative decarboxylase to mediate malic acid metabolism in organisms. Despite NADP-MEs have been demonstrated to play pivotal roles in regulating diverse biological processes, the role of NADP-MEs involving in plant growth and development remains rarely known. Here, we characterized the function of rice cytosolic OsNADP-ME2 in regulating plant height. The results showed that RNAi silencing and knock-out of OsNADP-ME2 in rice results in a dwarf plant structure, associating with significant expression inhibition of genes involving in phytohormone Gibberellin (GA) biosynthesis and signaling transduction, but with up-regulation for the expression of GA signaling suppressor SLR1. The accumulation of major bioactive GA1, GA4 and GA7 are evidently altered in RNAi lines, and exogenous GA treatment compromises the dwarf phenotype of OsNADP-ME2 RNAi lines. RNAi silencing of OsNADP-ME2 also causes the reduction of NADP-ME activity associating with decreased production of pyruvate. Thus, our data revealed a novel function of plant NADP-MEs in modulation of rice plant height through regulating bioactive GAs accumulation and GA signaling, and provided a valuable gene resource for rice plant architecture improvement.

Abstract Background The identification of spotted leaf 50 (spl50), a novel lesion mimic mutant (LMM) in rice, provides critical insights into the mechanisms underlying programmed cell death (PCD) and innate immunity in plants. Results Based on ethyl methane sulfonate (EMS)-induced mutagenesis, the spl50 mutant mimics hypersensitive responses in the absence of pathogen by displaying spontaneous necrotic lesions after the tillering phase. SPL50, an ARM repeat protein essential for controlling reactive oxygen species (ROS) metabolism and boosting resistance to blast disease, was identified by map-based cloning techniques. This work also demonstrates the detrimental effects of spl50 on photosynthetic efficiency and chloroplast development. The crucial significance of SPL50 in cellular signaling and stress response is shown by its localization to the cytoplasm and constitutive expression in various plant tissues. In light of growing concerns regarding global food security, this study highlights the pivotal role of SPL50 in regulating programmed cell death (PCD) and enhancing the immune response in plants, contributing to strategies for improving crop disease resistance. Conclusions The novel identification of the SPL50 gene in rice, encoding an ARM repeat protein, reveals its pivotal role in regulating PCD and innate immune responses independently of pathogen attack.

Under abiotic stresses, such as salt stress, abscisic acid (ABA) production is induced and enhances stress tolerance. ABA is also an important plant hormone that regulates vital biological responses, including seed gemination delay. However, the interplay between stress conditions and biological responses is not well understood. Previously, we reported a wide salt tolerance variation among Brassica napus varieties. This range of salt tolerance makes B. napus ideal for exploring the relationship between salt tolerance and ABA-induced seed germination delay. First, we investigated the ABA-induced seed-germination delay of 22 B. napus varieties, each with different salt tolerances. We observed that highly salt-tolerant varieties exhibited significant seed-germination delays when exposed to increasing ABA concentrations. Additionally, among the varieties, exogenous ABA induced a range of different germination delays, suggesting a significant correlation between germination delay and salt tolerance at the seedling stage. Expression analysis, with and without ABA treatment, for several genes involved in the ABA signalling pathway and downstream was also performed at seed germination. The results suggest the potential involvement of ABI5 and SOS1 in both germination regulation and salt tolerance.

Abstract Background Understanding the mechanism of male sterility is crucial for producing hybrid seeds and developing sterile germplasm resources. However, only a few cytoplasmic male sterility (CMS) lines of cotton have been produced due to several challenges, like inadequate variation of agronomic traits, incomplete sterility, weak resilience of restorer lines, and difficulty in combining strong dominance. Therefore, the morphological and cytological identification of CMS in cotton will facilitate hybrid breeding. Results Two F2 segregating populations of cotton were constructed from cytoplasmic male sterile lines (HaA and 01A, maternal) and restorer lines (HaR and 26R, paternal). Genetic analysis of these populations revealed a segregation ratio of 3:1 for fertile to sterile plants. Phenotypic analysis indicated no significant differences in traits of flower bud development between sterile and fertile plants. However, sterile plants exhibited smaller floral organs, shortened filament lengths, and anther atrophy on the flowering day in comparison with the fertile plants. When performed scanning electron microscopy (SEM), the two F2 populations revealed morphological variations in the anther epidermis. Cellular analysis showed no significant differences in pollen development before pollen maturation. Interestingly, between the pollen maturation and flowering stages, the tapetum layer of sterile plants degenerated prematurely, resulting in abnormal pollen grains and gradual pollen degradation. Conclusion The results of this study suggest that fertility-restoring genes are controlled by a single dominant gene. Sterile plants exhibit distinctive floral morphology, which is characterized by stamen atrophy and abnormal anthers. Pollen abortion occurs between pollen maturity and flowering, indicating that premature tapetum degradation may be the primary cause of pollen abortion. Overall, our study provides a theoretical basis for utilizing CMS in hybrid breeding and in-depth investigation of the dominant configuration of cotton hybrid combinations, mechanisms of sterility, and the role of sterile and restorer genes.

Abstract Lessons learned from past experiences push for an alternate way of crop production. In India, adopting high density planting system (HDPS) to boost cotton yield is becoming a growing trend. HDPS has recently been considered a replacement for the current Indian production system. It is also suitable for mechanical harvesting, which reducing labour costs, increasing input use efficiency, timely harvesting timely, maintaining cotton quality, and offering the potential to increase productivity and profitability. This technology has become widespread in globally cotton growing regions. Water management is critical for the success of high density cotton planting. Due to the problem of freshwater availability, more crops should be produced per drop of water. In the high-density planting system, optimum water application is essential to control excessive vegetative growth and improve the translocation of photoassimilates to reproductive organs. Deficit irrigation is a tool to save water without compromising yield. At the same time, it consumes less water than the normal evapotranspiration of crops. This review comprehensively documents the importance of growing cotton under a high-density planting system with deficit irrigation. Based on the current research and combined with cotton production reality, this review discusses the application and future development of deficit irrigation, which may provide theoretical guidance for the sustainable advancement of cotton planting systems.

Abstract Seeds, considered as the foundation of agriculture, are invaded by a broad spectrum of seed-borne pathogens. The current study aimed to control seed-borne fungal pathogens of wheat, Aspergillus flavus and A. niger, by using Ag+ nanochitosan (Ag-NC) for nano-priming of seeds and enhancing seed quality. Nanochitosan (NC) and Ag-NC were synthesized using the gelation method and characterized by UV–vis spectrophotometry, FESEM, EDXS, and HRTEM. NC and Ag-NC showed irregular surface topography with an average particle size of 275 and 325 nm, respectively. Antifungal activity of both the nanoparticles at 0.1, 0.2, 0.3, 0.4, and 0.5 mg/mL revealed that Ag-NC at 0.5 mg/mL has completely terminated the mycelial growth of both pathogens. Malonaldehyde content increased to 77.77% in A. flavus and 82.66% in A. niger when exposed to 0.5 mg/mL Ag-NC. High-intensity fluorescence due to oxidative stress was observed in Ag-NC-treated pathogens. Ultra-structural changes in Ag-NC treated pathogenic spores under SEM displayed pronounced membrane damages. Wheat seeds were nano-primed with NC and Ag-NC at 0.5 mg/mL, and fungal load was examined to evaluate the mitigation of pathogenic stress and its effect on seedling growth promotion activity. Ag-NC priming reduced the fungal load and allowed successful seed germination. Ag-NC priming increased the albumin, gliadin, gluten, and glutenin content along with total phenol, reducing sugar and starch levels. Ag-NC priming increased the overall protein levels traced through SDS-PAGE. Seed priming with Ag-NC promotes seed germination, mean germination time, stress tolerance index, vigour, etc. NC and Ag-NC at 0.5 mg/mL showed no cytotoxic effect on the Human Embryonic Kidney (HEK293) cell line that ensures the nanoparticles are non-toxic. Thus, the synthesized nanoparticles exhibit a dual role in antifungal activity and plant growth promotion.

Abstract Background Structural genomic variants (SVs) are prevalent in plant genomes and have played an important role in evolution and domestication, as they constitute a significant source of genomic and phenotypic variability. Nevertheless, most methods in quantitative genetics focusing on crop improvement, such as genomic prediction, consider only Single Nucleotide Polymorphisms (SNPs). Deep Learning (DL) is a promising strategy for genomic prediction, but its performance using SVs and SNPs as genetic markers remains unknown. Results We used rice to investigate whether combining SVs and SNPs can result in better trait prediction over SNPs alone and examine the potential advantage of Deep Learning (DL) networks over Bayesian Linear models. Specifically, the performances of BayesC (considering additive effects) and a Bayesian Reproducible Kernel Hilbert space (RKHS) regression (considering both additive and non-additive effects) were compared to those of two different DL architectures, the Multilayer Perceptron, and the Convolution Neural Network, to explore their prediction ability by using various marker input strategies. We found that exploiting structural and nucleotide variation slightly improved prediction ability on complex traits in 87% of the cases. DL models outperformed Bayesian models in 75% of the studied cases, considering the four traits and the two validation strategies used. Finally, DL systematically improved prediction ability of binary traits against the Bayesian models. Conclusions Our study reveals that the use of structural genomic variants can improve trait prediction in rice, independently of the methodology used. Also, our results suggest that Deep Learning (DL) networks can perform better than Bayesian models in the prediction of binary traits, and in quantitative traits when the training and target sets are not closely related. This highlights the potential of DL to enhance crop improvement in specific scenarios and the importance to consider SVs in addition to SNPs in genomic selection.

Abstract As a typical bulb flower, lily is widely cultivated worldwide because of its high ornamental, medicinal and edible value. Although breeding efforts evolved over the last 10000 years, there are still many problems in the face of increasing consumer demand. The approach of biotechnological methods would help to solve this problem and incorporate traits impossible by conventional breeding. Target traits are dormancy, development, color, floral fragrance and resistances against various biotic and abiotic stresses, so as to improve the quality of bulbs and cut flowers in planting, cultivation, postharvest, plant protection and marketing. Genetic transformation technology is an important method for varietal improvement and has become the foundation and core of plant functional genomics research, greatly assisting various plant improvement programs. However, achieving stable and efficient genetic transformation of lily has been difficult worldwide. Many gene function verification studies depend on the use of model plants, which greatly limits the pace of directed breeding and germplasm improvement in lily. Although significant progress has been made in the development and optimization of genetic transformation systems, shortcomings remain. Agrobacterium-mediated genetic transformation has been widely used in lily. However, severe genotypic dependence is the main bottleneck limiting the genetic transformation of lily. This review will summarizes the research progress in the genetic transformation of lily over the past 30 years to generate the material including a section how genome engineering using stable genetic transformation system, and give an overview about recent and future applications of lily transformation. The information provided in this paper includes ideas for optimizing and improving the efficiency of existing genetic transformation methods and for innovation, provides technical support for mining and identifying regulatory genes for key traits, and lays a foundation for genetic improvement and innovative germplasm development in lily.

Abstract Background Oak wilt disease, caused by Bretziella fagacearum is a significant threat to oak (Quercus spp.) tree health in the United States and Eastern Canada. The disease may cause dramatic damage to natural and urban ecosystems without management. Early and accurate diagnosis followed by timely treatment increases the level of disease control success. Results A rapid assay based on loop mediated isothermal amplification (LAMP) was first developed with fluorescence detection of B. fagacearum after 30-minute reaction time. Six different primers were designed to specifically bind and amplify the pathogen’s DNA. To simplify the use of this assay in the field, gold nanoparticles (AuNPs) were designed to bind to the DNA amplicon obtained from the LAMP reaction. Upon inducing precipitation, the AuNP-amplicons settle as a red pellet visible to the naked eye, indicative of pathogen presence. Both infected and healthy red oak samples were tested using this visualization method. The assay was found to have high diagnostic sensitivity and specificity for the B. fagacearum isolate studied. Moreover, the developed assay was able to detect the pathogen in crude DNA extracts of diseased oak wood samples, which further reduced the time required to process samples. Conclusions In summary, the LAMP assay coupled with oligonucleotide-conjugated gold nanoparticle visualization is a promising method for accurate and rapid molecular-based diagnosis of B. fagacearum in field settings. The new method can be adapted to other forest and plant diseases by simply designing new primers.

Abstract It is essential to find environment-friendly agrochemicals to cope with the problems of nutrient imbalance, fruit quality decline, and physiological disorders during apple fruit production, which is beneficial for improving the quality and yield of apple. A natural extract from Paecilomyces variotii (ZNC), an endophytic fungus, has been used widely to enhance crop performance. However, an understanding of the mechanism underlying ZNC-triggered growth and alleviation of nutrient deficiency-associated symptoms in apples remains elusive. Here, the photosynthesis, leaf growth, and fruit quality were enhanced by adding ZNC. In addition, ZNC relieved nutrient deficiency-related symptoms promoted the differentiation of root morphology and vitality, and reduced the accumulation of osmoprotectants and reactive oxygen species, thereby promoting growth under normal and nutrient-deficient conditions. Finally, genome-wide RNA sequencing reveals the ZNC-regulated mechanisms involved in hormone and metal ion pathways. Our study reveals the role of ZNC in promoting growth and improving the quality of apple, providing a new direction for reducing the use of chemical fertilizers and pesticides.

Abstract Mitogen-activated protein kinase (MAPK) cascades have been discovered to play a fundamental role in regulating organ abscission. However, the identity of protein substrates targeted by MAPK cascades, as well as whether the role of MAPK protein cascades in the abscission process is conserved across different plant species, remain unknown. Here, the role of homologs of MPK3 and MPK6 in regulating fruit abscission were characterized in litchi. Ectopic expression of LcMPK3 or LcMPK6 in Arabidopsis mpk3 mpk6 mutant rescued the deficiency in floral organ abscission, while silencing of LcMPK3 or LcMPK6 in litchi significantly decreased fruitlet abscission. Importantly, a total of 49 proteins interacting with LcMPK3 were identified through yeast two-hybrid screening, including two components of the MAPK signaling cascade, five transcription factors, and two aquaporins. Furthermore, the interaction between LcMPK3/6 with LcBZR1/2, core components in brassinosteroids signaling that suppress litchi fruitlet abscission, was confirmed using in vitro and in vivo assays. Moreover, phos-tag assays demonstrated that LcMPK3/6 could phosphorylate LcBZR1/2, with several phosphorylation residues identified. Together, our findings suggest that LcMPK3 and LcMPK6 play a positive regulatory role in fruitlet abscission in litchi, and offer crucial information for the investigation of mechanisms underlying MPK3/6-mediated organ abscission in plants.

Abstract Rice grain is widely consumed as a staple food, providing essential nutrition for households, particularly marginalized families. It plays a crucial role in ensuring food security, promoting human nutrition, supporting good health, and contributing to global food and nutritional security. Addressing the diverse quality demands of emerging diverse and climate-risked population dietary needs requires the development of a single variety of rice grain that can meet the various dietary and nutritional requirements. However, there is a lack of concrete definition for rice grain quality, making it challenging to cater to the different demands. The lack of sufficient genetic study and development in improving rice grain quality has resulted in widespread malnutrition, hidden hunger, and micronutrient deficiencies affecting a significant portion of the global population. Therefore, it is crucial to identify genetically evolved varieties with marked qualities that can help address these issues. Various factors account for the declining quality of rice grain and requires further study to improve their quality for healthier diets. We characterized rice grain quality using Lancastrians descriptor and a multitude of intrinsic and extrinsic quality traits. Next, we examined various components of rice grain quality favored in the Asia–Pacific region. This includes preferences by different communities, rice industry stakeholders, and value chain actors. We also explored the biological aspects of rice grain quality in the region, as well as specific genetic improvements that have been made in these traits. Additionally, we evaluated the factors that can influence rice grain quality and discussed the future directions for ensuring food and nutritional security and meeting consumer demands for grain quality. We explored the diverse consumer bases and their varied preferences in Asian-Pacific countries including India, China, Nepal, Bhutan, Vietnam, Sri Lanka, Pakistan, Thailand, Cambodia, Philippines, Bangladesh, Indonesia, Korea, Myanmar and Japan. The quality preferences encompassed a range of factors, including rice head recovery, grain shape, uniform size before cooking, gelatinization, chalkiness, texture, amylose content, aroma, red-coloration of grain, soft and shine when cooked, unbroken when cooked, gelatinization, less water required for cooking, gelatinization temperature (less cooking time), aged rice, firm and dry when cooked (gel consistency), extreme white, soft when chewed, easy-to-cook rice (parboiled rice), vitamins, and minerals. These preferences were evaluated across high, low, and medium categories. A comprehensive analysis is provided on the enhancement of grain quality traits, including brown rice recovery, recovery rate of milled rice, head rice recovery, as well as morphological traits such as grain length, grain width, grain length–width ratio, and grain chalkiness. We also explored the characteristics of amylose, gel consistency, gelatinization temperature, viscosity, as well as the nutritional qualities of rice grains such as starch, protein, lipids, vitamins, minerals, phytochemicals, and bio-fortification potential. The various factors that impact the quality of rice grains, including pre-harvest, post-harvest, and genotype considerations were explored. Additionally, we discussed the future direction and genetic strategies to effectively tackle these challenges. These qualitative characteristics represent the fundamental focus of regional and national breeding strategies employed by different countries to meet consumer preference. Given the significance of rice as a staple food in Asia–Pacific countries, it is primarily consumed domestically, with only a small portion being exported internationally. All the important attributes must be clearly defined within specific parameters. It is crucial for geneticists and breeders to develop a rice variety that can meet the diverse demands of consumers worldwide by incorporating multiple desirable traits. Thus, the goal of addressing global food and nutritional security, and human healthy can be achieved. Graphical Abstract

Abstract Strong early growth vigor is an essential target in both direct seeded rice breeding and high-yielding rice breeding for rice varieties with relatively short growth duration in the double-cropping region. Shoot dry weight (SDW) is one of the important traits associated with early growth vigor, and breeders have been working to improve this trait. Finding stable QTLs or functional genes for SDW is crucial for improving the early growth vigor by implementing molecular breeding in rice. Here, a genome-wide association analysis revealed that the QTL for SDW, qSDW-5, was stably detected in the three cultivation methods commonly used in production practice. Through gene-based haplotype analysis of the annotated genes within the putative region of qSDW-5, and validated by gene expression and knockout transgenic experiments, LOC_Os05g09520, which is identical to the reported GW5/GSE5 controlling grain width (GW) and thousand grain weight (TGW) was identified as the causal gene for qSDW-5. Five main haplotypes of LOC_Os05g09520 were identified in the diverse international rice collection used in this study and their effects on SDW, GW and TGW were analyzed. Phenotypic comparisons of the major haplotypes of LOC_Os05g09520 in the three subpopulations (indica, japonica and aus) revealed the same patterns of wider GW and higher TGW along with higher SDW. Furtherly, the haplotype analysis of 138 rice varieties/lines widely used in southern China showed that 97.8% of the cultivars/lines carry Hap2 LOC_Os05g09520 . These results not only provide a promising gene source for the molecular breeding of rice varieties with strong early growth vigor, but also elucidate the effect of the LOC_Os05g09520 haplotypes on SDW, GW, and TGW in rice. Importantly, this study provides direct genetic evidence that these three traits are significantly correlated, and suggests a breeding strategy for developing high-yielding and slender grain-shaped indica cultivars with strong early growth vigor.

Abstract Background Photoperiod sensitivity is among the most important agronomic traits of rice, as it determines local and seasonal adaptability and plays pivotal roles in determining yield and other key agronomic characteristics. By controlling the photoperiod, early-maturing rice can be cultivated to shorten the breeding cycle, thereby reducing the risk of yield losses due to unpredictable climate change. Furthermore, early-maturing and high-yielding rice needs to be developed to ensure food security for a rapidly growing population. Early-maturing and high-yielding rice should be developed to fulfill these requirements. OsCKq1 encodes the casein kinase1 protein in rice. OsCKq1 is a gene that is activated by photophosphorylation when Ghd7, which suppresses flowering under long-day conditions, is activated. Results This study investigates how OsCKq1 affects heading in rice. OsCKq1-GE rice was analyzed the function of OsCKq1 was investigated by comparing the expression levels of genes related to flowering regulation. The heading date of OsCKq1-GE lines was earlier (by about 3 to 5 days) than that of Ilmi (a rice cultivar, Oryza sativa spp. japonica), and the grain length, grain width, 1,000-grain weight, and yield increased compared to Ilmi. Furthermore, the culm and panicle lengths of OsCKq1-GE lines were either equal to or longer than those of Ilmi. Conclusions Our research demonstrates that OsCKq1 plays a pivotal role in regulating rice yield and photoperiod sensitivity. Specifically, under long-day conditions, OsCKq1-GE rice exhibited reduced OsCKq1 mRNA levels alongside increased mRNA levels of Hd3a, Ehd1, and RFT1, genes known for promoting flowering, leading to earlier heading compared to Ilmi. Moreover, we observed an increase in seed size. These findings underscore OsCKq1 as a promising target for developing early-maturing and high-yielding rice cultivars, highlighting the potential of CRISPR/Cas9 technology in enhancing crop traits.

Soil is limited resource with vital role in maintenance of variety ecosystems. One of the greatest treat for soils is soil erosion. This natural hazard is widely spread in the terrestrial world, and the territory of Bulgaria is also affected. Important role for soil protection has a forest vegetation and afforestation is widely used for erosion control activity. The main benefits of afforestation are reduction of water runoff, erosion and sedimentation year-round, which is important for the areas located around the reservoirs and their basins. They also decrease the migration of vital substances for soils and sedimentation yield. The main goal of the study is to establish the influence of erosion control afforestation to the main soil characteristics in the territory of two watershed situated in Southwest Bulgaria. Soil samples and dead leaf cover were analyzed as well as some characteristics of afforestation and topographic charac-teristics. It was established high water resistance of the soil aggregates under the planted forests and low resistance in the controls. The amounts of content of org. carbon and total nitrogen varying with slope and exposure. The differences between parameters of soils under afforestation and in control samples is established which shows an important influence of forest to the soil characteristics.

Morus sp. is a versatile resource with diverse benefits; however, its cultivation may entail negative environmental impacts. Environmental legislation imposes constraints to mitigate these effects. The current study presents a three-tier classification approach to assess the severity of constraints imposed by environmental legislation on Morus sp. cultivation. The approach is tested in a case study area located in BG0000254 Besaparski vazvishenita, Bratsigovo Municipality, Bulgaria. Approximately 23.6% of this area is under strict protection, thereby prohibiting cultivation. In about 21.3% of the area, Morus sp. cultivation is feasible but most probably an Appropriate Assessment procedure will be required to ensure nonsignificant negative impact. In the remaining 56.4% of the area, notification/screening is necessary, with the likelihood of not requiring a full Appropriate Assessment procedure. Thus, despite a significant portion being under strict protection, there remains potential for Morus sp. cultivation within the study area, albeit with varying procedural complexities. Thе proposed constraints classification approach can inform land use planning, facilitating informed decision-making in site selection not only for Morus sp. but for all types of permanent crops.

Due to the climate change that has become evident especially in the last ten years, ecosystems such as forests and pastures in the Mediterranean climate zone have become even more vulnerable to degradation. High erosive precipitation increases the amount of erosion in these soils with increasing their erodibility. The aim of this study was to determine to what extent some polymers, such as polyacrylamide and polyvinylalcohol, can prevent runoff and soil loss from erosion pans where a pasture soil was placed. For this purpose, aggregates of soil samples

The Chinese artichoke (Stachys affinis syn. S. sieboldii) is a widely cultivated crop, and its rhizome is used as a medicinal vegetable. To investigate the causes of viral diseases in Chinese artichokes, the infection rates of four virus species infecting Chinese artichoke were investigated. Since the Chinese artichoke propagates through its tuber, this study aimed to determine whether viral transmission to the progeny is possible through the tuber, by identifying the virus present in the tuber and investigating its accumulation. First, reverse transcription polymerase chain reaction analysis was performed to detect viruses using total RNA extracted from the flowers, leaves, and tubers of Chinese artichoke plants. Alfalfa mosaic virus (AMV) and Chinese artichoke mosaic virus (ChAMV) had high infectivity in Chinese artichoke and most plants were simultaneously infected with AMV and ChAMV. These viruses were present in all tissues, but their detection frequency and accumulation rates varied across different tissues of the Chinese artichoke. Also, we sequenced the coat protein (CP) genes of AMV and ChAMV to investigate genetic variations of virus between the leaf and tuber. It provides information on CP gene sequences and genetic diversity of isolates identified from new hosts of AMV and ChAMV. This study offers valuable insights into the distribution and spread of the ChAMV and AMV within Chinese artichoke plants, which have implications for the management and control of viral infections in crops.

Dieback disease in mango trees has been observed in Indonesia, particularly in Java Island, with the causal agent remaining unidentified. One of the important pathogens that are responsible for causing mango dieback is Colletotrichum. Field surveys were conducted in various mango cultivating areas in Java Island, Indonesia to assess prevalence of Colletotrichum as dieback disease pathogen. Eleven Colletotrichum isolates were recovered from symptomatic dieback twigs and morphologically characterized. Genetic diversity fingerprint analysis was carried out using rep-PCR. Phylogenetic analysis identified isolates as belonging to Colletotrichum asianum and Colletotrichum cairnsense using partial sequences of four gene regions, including ITS, ACT, GAPDH, and TUB2. Pathogenicity tests on mango seedlings cv. Arumanis showed that all fungal isolates were responsible for causing dieback symptoms. Subsequently, symptomatic tissue was reisolated to fulfill Koch’s Postulate. This study represented new funding for two species of Colletotrichum causing mango dieback in Indonesia.

Inoculation of Chinese cabbage leaves with high titer (107 cfu/ml) of the non-adapted bacteria Xanthomonas campestris pv. vesicatoria (Xcv) strain Bv5-4a.1 triggered rapid leaf tissue collapses and hypersensitive cell death (HCD) at 24 h. Electrolyte leakage and lipid peroxidation markedly increased in the Xcv-inoculated leaves. Defence-related gene expressions (BrPR1, BrPR4, BrChi1, BrGST1 and BrAPX1) were preferentially activated in the Xcv-inoculated leaves. The Xcv-triggered HCD was attenuated by continuous light but accelerated by a dark environment, and the prolonged high relative humidity also alleviated the HCD. Constant dark and increased relative humidity provided favorable conditions for the Xcv bacterial growth in the leaves. Pretreated fluridone (biosynthetic inhibitor of endogenous abscisic acid [ABA]) increased the HCD in the Xcv-inoculated leaves, but exogenous ABA attenuated the HCD. The pretreated ABA also reduced the Xcv bacterial growth in the leaves. These results highlight that the onset of HCD in Chinese cabbage leaves initiated by non-adapted pathogen Xcv Bv5-4a.1 and in planta bacterial growth was differently modulated by internal and external conditional changes.

The possibility of new viruses emerging in various regions worldwide has increased due to a combination of factors, including climate change and the expansion of international trading. Plant viruses spread through various transmission routes, encompassing well-known avenues such as pollen, seeds, and insects. However, research on potential transmission routes beyond these known mechanisms has remained limited. To address this gap, this study employed metatranscriptomic analysis to ascertain the presence of plant viruses in imported frozen fruits, specifically cherries and blueberries. This analysis aimed to identify pathways through which plant viruses may be introduced into countries. Virome analysis revealed the presence of six species of plant viruses in frozen cherries and blueberries: cherry virus A (CVA), prunus necrotic ringspot virus (PNRSV), prune dwarf virus (PDV), prunus virus F (PrVF), blueberry shock virus (BlShV), and blueberry latent virus (BlLV). Identifying these potential transmission routes is crucial for effectively managing and preventing the spread of plant viruses and crop protection. This study highlights the importance of robust quality control measures and monitoring systems for frozen fruits, emphasizing the need for proactive measures to mitigate the risk associated with the potential spread of plant viruses.

Soybean (Glycine max L.) is one of the most widely planted and used legumes in the world, being used for food, animal feed products, and industrial production. The soybean mosaic virus (SMV) is the most prevalent virus infecting soybean plants. This study developed a diagnostic method for the rapid and sensitive detection of SMV using a reverse transcription-recombinase polymerase amplification (RT-RPA) technique combined with a lateral flow strip (LFS). The RT-RPA and RT-RPA-LFS conditions to detect the SMV were optimized using the selected primer set that amplified part of the VPg protein gene. The optimized reaction temperature for the RT-RPA primer and RT-RPA-LFS primer used in this study was 38°C for both, and the minimum reaction time was 10 min and 5 min, respectively. The RT-RPA-LFS was as sensitive as RT-PCR to detect SMV with 10 pg/μl of total RNA. The reliability of the developed RT-RPA-LFS assay was evaluated using leaves collected from soybean fields. The RT-RPA-LFS diagnostic method developed in this study will be useful as a diagnostic method that can quickly and precisely detect SMV in the epidemiological investigation of SMV, in the selection process of SMV-resistant varieties, on local farms with limited resources.