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<jats:p><jats:italic>Miscanthus</jats:italic> is a promising crop for bioenergy and biorefining in Europe. The improvement of <jats:italic>Miscanthus</jats:italic> as a crop relies on the creation of new varieties through the hybridization of germplasm collected in the wild with genetic variation and suitable characteristics in terms of resilience, yield and quality of the biomass. Local adaptation has likely shaped genetic variation for these characteristics and is therefore important to quantify. A key biomass quality parameter for biorefining is the ease of conversion of cell wall polysaccharides to monomeric sugars. Thus far, the variability of cell wall related traits in <jats:italic>Miscanthus</jats:italic> has mostly been explored in accessions from limited genetic backgrounds. Here we analysed the soil and climatic conditions of the original collection sites of 592 <jats:italic>Miscanthus</jats:italic> genotypes, which form eight distinct genetic groups based on discriminant analysis of principal components of 25,014 single-nucleotide polymorphisms. Our results show that species of the genus <jats:italic>Miscanthus</jats:italic> grow naturally across a range of soil and climate conditions. Based on a detailed analysis of 49 representative genotypes, we report generally minor differences in cell wall characteristics between different genetic groups and high levels of genetic variation within groups, with less investigated species like <jats:italic>M. floridulus</jats:italic> showing lower recalcitrance compared to the other genetic groups. The results emphasize that both inter- and intra- specific variation in cell wall characteristics and biomass recalcitrance can be used effectively in <jats:italic>Miscanthus</jats:italic> breeding programmes, while also reinforcing the importance of considering biomass yield when quantifying overall conversion efficiency. Thus, in addition to reflecting the complexity of the interactions between compositional and structural cell wall features and cell wall recalcitrance to sugar release, our results point to traits that could potentially require attention in breeding programmes targeted at improving the <jats:italic>Miscanthus</jats:italic> biomass crop.</jats:p>

<jats:p>Tomato curly stunt virus (ToCSV) is a monopartite begomovirus infecting tomatoes in South Africa, with sequence similarity to tomato yellow leaf curl virus (TYLCV). While there are numerous reports on the mechanism of TYLCV resistance in tomato, the underlying mechanisms in the tomato-ToCSV pathosystem is still relatively unknown. The main aim of this study was to investigate and compare the global methylation profile of ToCSV in two near-isogenic tomato lines, one with a tolerant phenotype (T, NIL396) and one with a susceptible phenotype (S, NIL395). Bisulfite conversion and PCR amplification, coupled with a next-generation sequencing approach, were used to elucidate the global pattern of methylation of ToCSV cytosine residues in T and S leave tissue at 35 days post-infection (dpi). The extent of methylation was more pronounced in tolerant plants compared to susceptible plants in all sequence (CG, CHG and CHH) contexts, however, the overall methylation levels were relatively low (&amp;lt;3%). Notably, a significant interaction (p &amp;lt; 0.05) was observed between the viral genomic region and susceptible vs. tolerant status for CG methylated regions where it was observed that the 3’IR CG methylation was significantly (p &amp;lt; 0.05) higher than CG methylation of other genomic regions in tolerant and susceptible plants. Additionally, statistically significant (EdgeR p &amp;lt; 0.05) differentially methylated cytosines were located primarily in the genomic regions V2/V1 and C4/C1 of ToCSV. The relative expression, using RT-qPCR, was also employed in order to quantify the expression of various key methylation-related genes, <jats:italic>MET1, CMT2, KYP4/SUVH4, DML2, RDM1, AGO4</jats:italic> and <jats:italic>AGO6</jats:italic> in T vs. S plants at 35dpi. The differential expression between T and S was significant for <jats:italic>MET1, KYP4/SUVH4</jats:italic> and <jats:italic>RDM1</jats:italic> at p&amp;lt;0.05 which further supports more pronounced methylation observed in ToCSV from T plants vs. S plants. While this study provides new insights into the differences in methylation profiles of ToCSV in S vs. T tomato plants, further research is required to link tolerance and susceptibility to ToCSV.</jats:p>

<jats:p>Indole-3-acetic acid (IAA) production is a pathogenicity/virulence factor in the <jats:italic>Pseudomonas syringae</jats:italic> complex, including <jats:italic>Pseudomonas savastanoi</jats:italic>. <jats:italic>P. savastanoi</jats:italic> pathovars (pvs.) genomes contain the <jats:italic>iaaL</jats:italic> gene, encoding an enzyme that catalyzes the biosynthesis of the less biologically active compound 3-indole-acetyl-ϵ-L–lysine (IAA–Lys). Previous studies have reported the identification of IAA–Lys in culture filtrates of <jats:italic>P. savastanoi</jats:italic> strains isolated from oleander (pv. nerii), but the conversion of IAA into a conjugate was not detectable in olive strains (pv. savastanoi). In this paper, we show the distribution of <jats:italic>iaaL</jats:italic> alleles in all available <jats:italic>P. savastanoi</jats:italic> genomes of strains isolated from woody hosts. Most strains encode two different paralogs, except for those isolated from broom (pv. retacarpa), which contain a single allele. In addition to the three previously reported <jats:italic>iaaL</jats:italic> alleles (<jats:italic>iaaL</jats:italic><jats:sub>Psv</jats:sub>, <jats:italic>iaaL</jats:italic><jats:sub>Psn</jats:sub> and <jats:italic>iaaL</jats:italic><jats:sub>Pto</jats:sub>), we identified <jats:italic>iaaL</jats:italic><jats:sub>Psf</jats:sub>, an exclusive allele of strains isolated from ash (pv. fraxini). We also found that the production of IAA–Lys in <jats:italic>P. savastanoi</jats:italic> pv. savastanoi and pv. nerii depends on a functional <jats:italic>iaaL</jats:italic><jats:sub>Psn</jats:sub> allele, whereas in pv. fraxini depends on <jats:italic>iaaL</jats:italic><jats:sub>Psf</jats:sub>. The production of IAA–Lys was detected in cultures of an olive strain heterologously expressing IaaL<jats:sub>Psn-1</jats:sub>, IaaL<jats:sub>Psf-1</jats:sub> and IaaL<jats:sub>Psf-3</jats:sub>, but not when expressing IaaL<jats:sub>Psv-1</jats:sub>. In addition, <jats:italic>Arabidopsis</jats:italic> seedlings treated with the strains overproducing the conjugate, and thus reducing the free IAA content, alleviated the root elongation inhibitory effect of IAA. IAA–Lys synthase activity assays with purified allozymes confirmed the functionality and specificity of lysine as a substrate of IaaL<jats:sub>Psn-1</jats:sub> and IaaL<jats:sub>Psf-3</jats:sub>, with IaaL<jats:sub>Psf-3</jats:sub> showing the highest catalytic efficiency for both substrates. The IAA–Lys synthase activity of IaaL<jats:sub>Psn-1</jats:sub> was abolished by the insertion of two additional tyrosine residues encoded in the inactive allozyme IaaL<jats:sub>Psv-1</jats:sub>. These results highlight the relevance of allelic variation in a phytohormone-related gene for the modulation of auxin production in a bacterial phytopathogen.</jats:p>

<jats:sec><jats:title>Introduction</jats:title><jats:p>The discovery of RT-PCR-based pathogen detection and gene expression analysis has had a transformative impact on the field of plant protection. This study aims to analyze the global research conducted between 2001 and 2021, focusing on the utilization of RT-PCR techniques for diagnostic assays and gene expression level studies. By retrieving data from the 'Dimensions' database and employing bibliometric visualization software, this analysis provides insights into the major publishing journals, institutions involved, leading journals, influential authors, most cited articles, and common keywords.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>The 'Dimensions' database was utilized to retrieve relevant literature on RT-PCR-based pathogen detection. Fourteen distinct search queries were employed, and the resulting dataset was analyzed for trends in scholarly publications over time. The bibliometric visualization software facilitated the identification of major publishing journals, institutions, leading journals, influential authors, most cited articles, and common keywords. The study's search query was based on the conjunction 'AND', ensuring a comprehensive analysis of the literature.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>The analysis revealed a significant increase in the number of scholarly publications on RT-PCR-based pathogen detection over the years, indicating a growing interest and investment in research within the field. This finding emphasizes the importance of ongoing investigation and development, highlighting the potential for further advancements in knowledge and understanding. In terms of publishing journals, Plos One emerged as the leading journal, closely followed by BMC Genomics and Phytopathology. Among the highly cited journals were the European Journal of Plant Pathology, BMC Genomics, and Fungal Genetics and Biology. The publications with the highest number of citations and publications were associated with the United Nations and China. Furthermore, a network visualization map of co-authorship analysis provided intriguing insights into the collaborative nature of the research. Out of 2,636 authors analyzed, 50 surpassed the level threshold, suggesting active collaboration among researchers in the field.</jats:p></jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>Overall, this bibliometric analysis demonstrates that the research on RT-PCR-based pathogen detection is thriving. However, there is a need for further strengthening using modern diagnostic tools and promoting collaboration among well-equipped laboratories. The findings underscore the significance of RT-PCR-based pathogen detection in plant protection and highlight the potential for continued advancements in this field. Continued research and collaboration are vital for enhancing knowledge, developing innovative diagnostic tools, and effectively protecting plants from pathogens.</jats:p></jats:sec>

<jats:p>Olive trees (<jats:italic>Olea europaea</jats:italic> L.) are deeply interwoven with the past, present and future of Mediterranean civilizations, both as essential economical as well as cultural valuables. Olive horticulture constitutes one of the primary agroecosystems in the Mediterranean regions of today. Being inhabitant of ecological niches, <jats:italic>Olea europaea</jats:italic> is prone to a peculiar vulnerability towards climatic and socioeconomical transformations that are briskly reshaping regional and global agroecosystems. Because of climatic changes and the biosafety risks of global agricultural trades, olive plants are highly susceptible to newly emerging diseases and pests, and the traditional olive horticultural crop protection practices are under scrutiny towards reducing their ecological impact. Hence there is an eminent demand for a more nature-positive olive tree crop management. Recent innovations in precision agriculture are raising the prospect for innovative crop protection methods that may provide olive farmers the required agility to respond to present and future agricultural challenges. For instance, endo-therapy, which is the systemic delivery of active ingredients <jats:italic>via</jats:italic> trunk injection, is a technology that holds promise of a true step-change in sustainable olive crop management. Endo-therapy allows reaching vascular diseases inaccessible to foliar treatments and delivers active ingredients in a precise manner with no risks of off-target drifts. Similarly, progresses in biological precision delivery using controlled release of active ingredients based on innovative formulation technologies are showing an exciting potential for more targeted and sustainable crop protection solutions. This review summarizes the latest innovations on both physical and biological precision deliveries in the realm of olive arboriculture in the Mediterranean regions and gives an outlook how these technologies may help orchestrating innovative olive culture practices soon.</jats:p>

<jats:p>Volumetric soil water content is commonly used for irrigation management in fruit trees. By integrating direct information on tree water status into measurements of soil water content, we can improve detection of water stress and irrigation scheduling. Thermal-based indicators can be an alternative to traditional measurements of midday stem water potential and stomatal conductance for irrigation management of pear trees (<jats:italic>Pyrus communis</jats:italic> L.). These indicators are easy, quick, and cost-effective. The soil and tree water status of two cultivars of pear trees ‘D’Anjou’ and ‘Bartlett’ submitted to regulated deficit irrigation was measured regularly in a pear orchard in Rock Island, WA (USA) for two seasons, 2021 and 2022. These assessments were compared to the canopy temperature (Tc), the difference between the canopy and air temperature (Tc-Ta) and the crop water stress index (CWSI). Trees under deficit irrigation had lower midday stem water potential and stomatal conductance but higher Tc, Tc-Ta, and CWSI. Tc was not a robust method to assess tree water status since it was strongly related to air temperature (R = 0.99). However, Tc-Ta and CWSI were greater than 0°C or 0.5, respectively, and were less dependent on the environmental conditions when trees were under water deficits (midday stem water potential values&amp;lt; -1.2 MPa). Moreover, values of Tc-Ta = 2°C and CWSI = 0.8 occurred when midday stem water potential was close to -1.5 MPa and stomatal conductance was lower than 200 mmol m<jats:sup>-2</jats:sup>s<jats:sup>-1</jats:sup>. Soil water content (SWC) was the first indicator in detecting the deficit irrigation applied, however, it was not as strongly related to the tree water status as the thermal-based indicators. Thus, the relation between the indicators studied with the stem water potential followed the order: CWSI &amp;gt; Tc-Ta &amp;gt; SWC = Tc. A multiple regression analysis is proposed that combines both soil water content and thermal-based indices to overcome limitations of individual use of each indicator.</jats:p>

<jats:p>During the high grazing of epiphytic zooplankton in submerged macrophyte beds, the changes in crustacean zooplankton functional groups are crucial for stabilizing a clear water state in shallow lakes. However, submerged macrophytes often experience low-light stress due to many ecological processes. It is unclear whether submerged macrophytes alter the zooplankton functional group and their resource use efficiency in the low-light environment. We conducted two mesocosm experiments involving the treatments of low-light and submerged macrophyte species (<jats:italic>Vallisneria natans</jats:italic> and <jats:italic>Potamogeton maackianus</jats:italic>). The results show that abiotic factors (e.g., light) were the most important variables in explaining the change in the zooplankton community. Specifically, zooplankton functional group (i.e., pelagic species, plant-associated species, and substrate scrapers) richness and zooplankton species diversity decreased with the decreasing light intensity, especially for low substrate scraper abundance. In addition, structural equation models showed that low-light stress reduced zooplankton resource use efficiency by reducing zooplankton functional group richness and species diversity. Compared to species diversity, zooplankton functional group richness had a greater influence on their resource use efficiency (Zp/Chl-<jats:italic>a</jats:italic>) in the low-light environment. Our results suggest that the low-light stress reduced zooplankton resource use efficiency by changing their functional group richness. Moreover, the abundance of substrate scrapers shaken from <jats:italic>V. natans</jats:italic> was higher than that from <jats:italic>P. maackianus</jats:italic>. Therefore, submerged macrophyte species influence crustacean zooplankton functional group richness and their resource use efficiency in the low-light environment. Selecting appropriate aquatic plant species to assure the high diversity of zooplankton should be considered when conducting lake restoration using submerged macrophytes.</jats:p>

<jats:p>Research on ecosystem services and residents’ well-being in old revolutionary base areas is an important task for China’s ecological civilization construction and rural revitalization. Taking Jinzhai County, the core area of Dabie Mountains, China, as an example, based on InVEST model, the methods of spatial autocorrelation and coupling coordinated development degree, the spatiotemporal evolution, spatial heterogeneity and coupling association patterns of ecosystem services and multidimensional well-being in the study area from 2005 to 2020 were discussed. The major results are: In the past 15 years, in the core area of the Dabie Mountains, ecosystem services such as food supply, soil retention and water yield showed an upward trend, carbon sequestration and biodiversity maintenance showed a downward trend. The comprehensive index of multidimensional well-being in the core area of Dabie Mountain increased by 27.23% and the spatial difference in multidimensional well-being is gradually narrowing. By the analysis of coupling coordination, the number of units with the type of coupling disharmony between ecosystem services and multidimensional well-being in the study area decreased significantly from 56.85% in 2005 to 26.81% in 2020, respectively. The analysis of geographical detection showed that the habitat quality factor was the dominant controlling factor of coupling coordination spatial difference. By bivariate spatial autocorrelation analysis, in the past 15 years, the number of units with the “high ecology-high well-being” synergy type increased from 5.44% to 13.31%. The results can provide a reference for accurate identification, optimal regulation and synergistic improvement between ecosystem services and relative poverty in the Dabie Mountain area.</jats:p>

<jats:p>The sulfur-containing essential amino acid, methionine, is a key metabolite in plant cells since it is used as a precursor for the synthesis of vital metabolites. The transcript level of methionine’s catabolic enzyme, methionine γ-lyase (MGL), accumulates in the seeds to a high level compared to other organs. The aim of this study was to reveal the role of MGL during seed development and germination. Using [<jats:sup>13</jats:sup>C]<jats:italic>S</jats:italic>-methylmethionine (SMM), the mobile form of methionine that is used to feed flower stalks of wild-type (WT) plants, revealed that the contents of [<jats:sup>13</jats:sup>C]methionine in seeds were significantly reduced when the plants underwent heat and osmotic stresses. Moreover, the levels of [<jats:sup>13</jats:sup>C]isoleucine, a product of MGL, significantly increased. Also, using the MGL promoter and gene fused to the GUS reporter gene, it was demonstrated that the heat stress significantly increased the protein level in the seeds. Therefore, we can conclude that MGL became active under stresses apparently to produce isoleucine, which is used as an osmoprotectant and an energy source. Transgenic <jats:italic>Arabidopsis thaliana</jats:italic> RNAi seeds with targeted repression of <jats:italic>AtMGL</jats:italic> during the late developmental stages of seeds show that the seeds did not accumulate methionine when they were grown under standard growth conditions, unlike the <jats:italic>mgl</jats:italic>-2, a knockout mutant, which showed a three-fold higher level of methionine. Also, when the RNAi plants developed under mid-heat stress, the level of methionine significantly increased while the content of isoleucine decreased compared to the control seeds, which strengthened the assumption that MGL is active under stress. The germination efficiency of the RNAi lines and <jats:italic>mgl</jats:italic> seeds were similar to their controls. However, the seeds that developed during heat or salt stress showed significantly lower germination efficiency compared to the control seeds. This implies that MGL is important to maintain the ability of the seeds to germinate. The RNAi lines and <jats:italic>mgl</jats:italic> seeds that developed under regular conditions, but germinated during salt or osmotic stress, exhibited a lower germination rate, suggesting an essential role of MGL also during this process. The results of this study show the important role of AtMGL in seeds under stresses.</jats:p>

<jats:p>To address the problem of accurate recognition and localization of multiple clusters of green persimmons with similar color to the background under natural environment, this study proposes a multi-cluster green persimmon identification method based on improved Faster RCNN was proposed by using the self-built green persimmon dataset. The feature extractor DetNet is used as the backbone feature extraction network, and the model detection attention is focused on the target object itself by adding the weighted ECA channel attention mechanism to the three effective feature layers in the backbone, and the detection accuracy of the algorithm is improved. By maximizing the pooling of the lower layer features with the added attention mechanism, the high and low dimensions and magnitudes are made the same. The processed feature layers are combined with multi-scale features using a serial layer-hopping connection structure to enhance the robustness of feature information, effectively copes with the problem of target detection of objects with obscured near scenery in complex environments and accelerates the detection speed through feature complementarity between different feature layers. In this study, the K-means clustering algorithm is used to group and anchor the bounding boxes so that they converge to the actual bounding boxes, The average mean accuracy (mAP) of the improved Faster RCNN model reaches 98.4%, which was 11.8% higher than that of traditional Faster RCNN model, which also increases the accuracy of object detection during regression prediction. and the average detection time of a single image is improved by 0.54s. The algorithm is significantly improved in terms of accuracy and speed, which provides a basis for green fruit growth state monitoring and intelligent yield estimation in real scenarios.</jats:p>