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<jats:p>Cassava (<jats:italic>Manihot esculenta</jats:italic> Crantz) starch consists of amylopectin and amylose, with its properties determined by the proportion of these two polymers. Waxy starches contain at least 95% amylopectin. In the food industry, waxy starches are advantageous, with pastes that are more stable towards retrogradation, while high-amylose starches are used as resistant starches. This study aimed to associate near-infrared spectrophotometry (NIRS) spectra with the waxy phenotype in cassava seeds and develop an accurate classification model for indirect selection of plants. A total of 1127 F<jats:sub>2</jats:sub> seeds were obtained from controlled crosses performed between 77 F<jats:sub>1</jats:sub> genotypes (wild-type, <jats:italic>Wx</jats:italic>_). Seeds were individually identified, and spectral data were obtained <jats:italic>via</jats:italic> NIRS using a benchtop NIRFlex N-500 and a portable SCiO device spectrometer. Four classification models were assessed for waxy cassava genotype identification: k-nearest neighbor algorithm (KNN), C5.0 decision tree (CDT), parallel random forest (parRF), and eXtreme Gradient Boosting (XGB). Spectral data were divided between a training set (80%) and a testing set (20%). The accuracy, based on NIRFlex N-500 spectral data, ranged from 0.86 (parRF) to 0.92 (XGB). The Kappa index displayed a similar trend as the accuracy, considering the lowest value for the parRF method (0.39) and the highest value for XGB (0.71). For the SCiO device, the accuracy (0.88−0.89) was similar among the four models evaluated. However, the Kappa index was lower than that of the NIRFlex N-500, and this index ranged from 0 (parRF) to 0.16 (KNN and CDT). Therefore, despite the high accuracy these last models are incapable of correctly classifying waxy and non-waxy clones based on the SCiO device spectra. A confusion matrix was performed to demonstrate the classification model results in the testing set. For both NIRS, the models were efficient in classifying non-waxy clones, with values ranging from 96−100%. However, the NIRS differed in the potential to predict waxy genotype class. For the NIRFlex N-500, the percentage ranged from 30% (parRF) to 70% (XGB). In general, the models tended to classify waxy genotypes as non-waxy, mainly SCiO. Therefore, the use of NIRS can perform early selection of cassava seeds with a waxy phenotype.</jats:p>

<jats:p>Freshwater ecosystems are threatened by eutrophication, which causes persistent and harmful algal blooms. Filter-feeding bivalve mollusks and submerged macrophytes (SMs) alleviate the eutrophication effects by inhibiting phytoplankton biomass blooms. However, very little is known about whether and how the combined manipulation of filter-feeding bivalves and SMs control eutrophication and influence phytoplankton assemblages. Here, we performed a nutrient-enriched freshwater mesocosm experiment to assess the combined effects of the filter-feeding bivalve <jats:italic>Cristaria plicata</jats:italic>, a cockscomb pearl mussel, and the macrophyte <jats:italic>Hydrilla verticillate</jats:italic> on the biomass and composition of phytoplankton assemblages. We found that addition of <jats:italic>C. plicata</jats:italic> and <jats:italic>H. verticillate</jats:italic> decreased the water nutrient concentrations and suppressed overall phytoplankton biomass. Further, distinct differences in taxa between restoration and control treatments were observed and noticeably competitive exclusion of cyanobacteria in the restoration treatments occurred. An antagonistic interaction between filter-feeding bivalves and SMs was only detected for total cyanobacteria biomass demonstrating that a larger magnitude of SM restoration may override the effect of filter-feeding bivalves. Our results suggest that manipulation, through the addition of bivalves as grazers, associated with the restoration of SMs, is an efficient approach for reducing cyanobacterial blooms and alleviating eutrophication.</jats:p>

<jats:p>As the critical sensors and decoders of calcium signal, calcium-dependent protein kinase (CDPK) has become the focus of current research, especially in plants. However, few resources are available on the properties and functions of CDPK gene family in <jats:italic>Triticum aestivum</jats:italic> (TaCDPK). Here, a total of 79 <jats:italic>CDPK</jats:italic> genes were identified in the wheat genome. These <jats:italic>TaCDPKs</jats:italic> could be classified into four subgroups on phylogenesis, while they may be classified into two subgroups based on their tissue and organ-spatiotemporal expression profiles or three subgroups according to their induced expression patterns. The analysis on the signal network relationships and interactions of TaCDPKs and NADPH (reduced nicotinamide adenine dinucleotide phosphate oxidases, NOXs), the key producers for reactive oxygen species (ROS), showed that there are complicated cross-talks between these two family proteins. Further experiments demonstrate that, two members of TaCDPKs, TaCDPK2/4, can interact with TaNOX7, an important member of wheat NOXs, and enhanced the TaNOX7-mediated ROS production. All the results suggest that TaCDPKs are highly expressed in wheat with distinct tissue or organ-specificity and stress-inducible diversity, and play vital roles in plant development and response to biotic and abiotic stresses by directly interacting with TaNOXs for ROS production.</jats:p>

<jats:p>Mango (<jats:italic>Mangifera indica</jats:italic>) fruit is known for its taste, health benefits, and drought tolerance. Potassium (K<jats:sup>+</jats:sup>) is one of the most abundant ions in a plant cell. It is important for various biological functions related to plant growth, development, and flowering/fruiting. It significantly contributes to fruit yield, quality, and drought tolerance in plants. However, molecular mechanisms comprising K<jats:sup>+</jats:sup> transport in mango are least known. In the present study, 37 members of K<jats:sup>+</jats:sup> transport-related genes (PTGs) were identified in mango, which include 22 K<jats:sup>+</jats:sup> transporters (16 HAKs, 1 HKT, and 6 KEAs) and 15 K<jats:sup>+</jats:sup> channels (6 TPKs and 8 Shakers). All PTGs were predicted to be expressed at the plasma membrane and possess characteristic motifs and domains. Phylogenetic analysis identified a strong kinship of PTGs among <jats:italic>Oryza sativa</jats:italic>, <jats:italic>Arabidopsis thaliana</jats:italic>, <jats:italic>Cicer arietinum</jats:italic>, <jats:italic>Malus domestica</jats:italic>, and <jats:italic>M. indica</jats:italic>. The promoter analysis identified 60 types of <jats:italic>cis</jats:italic>-elements related to various biological processes. RNA-seq-based expression profiling identified that <jats:italic>MiTPK1.2</jats:italic>, <jats:italic>MiHAK1</jats:italic>, <jats:italic>MiHAK2.1</jats:italic>, <jats:italic>HAK6.1</jats:italic>, and <jats:italic>MiAKT1.1</jats:italic> were most upregulated in roots and that <jats:italic>MiKEA2</jats:italic>, <jats:italic>MiAKT2</jats:italic>, and <jats:italic>MiAKT1</jats:italic> were upregulated in leaves. Moreover, <jats:italic>MiAKT6</jats:italic>, <jats:italic>MiHAK1.1</jats:italic>, <jats:italic>MiKAT2</jats:italic>, <jats:italic>MiKAT2.1</jats:italic>, <jats:italic>MiHKT1</jats:italic>, <jats:italic>MiTPK1.1</jats:italic>, <jats:italic>MiHAK7</jats:italic>, and <jats:italic>MiHAK12</jats:italic> were highly expressed during the five growth stages of mango fruit. The current study is the first comprehensive report on K<jats:sup>+</jats:sup> transport system in tropical fruits. Therefore, it will provide the foundation knowledge for the functional characterization of K<jats:sup>+</jats:sup> genes in mango and related plants.</jats:p>

<jats:p><jats:italic>Pseudomonas syringae</jats:italic> and <jats:italic>Botrytis cinerea</jats:italic> cause destructive bacterial speck and grey mold diseases in many plant species, leading to substantial economic losses in agricultural production. Our study discovered that the application of <jats:italic>Bacillus proteolyticus</jats:italic> strain OSUB18 as a root-drench enhanced the resistance of <jats:italic>Arabidopsis</jats:italic> plants against <jats:italic>P. syringae</jats:italic> and <jats:italic>B. cinerea</jats:italic> through activating Induced Systemic Resistance (ISR). The underlying mechanisms by which OSUB18 activates ISR were studied. Our results revealed that the <jats:italic>Arabidopsis</jats:italic> plants with OSUB18 root-drench showed the enhanced callose deposition and ROS production when inoculated with <jats:italic>Pseudomonas syringae</jats:italic> and <jats:italic>Botrytis cinerea</jats:italic> pathogens, respectively. Also, the increased salicylic acid (SA) levels were detected in the OSUB18 root-drenched plants compared with the water root-drenched plants after the <jats:italic>P. syringae</jats:italic> infection. In contrast, the OSUB18 root-drenched plants produced significantly higher levels of jasmonyl isoleucine (JA-Ile) than the water root-drenched control after the <jats:italic>B. cinerea</jats:italic> infection. The qRT-PCR analyses indicated that the ISR-responsive gene <jats:italic>MYC2</jats:italic> and the ROS-responsive gene <jats:italic>RBOHD</jats:italic> were significantly upregulated in OSUB18 root-drenched plants upon both pathogen infections compared with the controls. Also, twenty-four hours after the bacterial or fungal inoculation, the OSUB18 root-drenched plants showed the upregulated expression levels of SA-related genes (<jats:italic>PR1, PR2, PR5, EDS5</jats:italic>, and <jats:italic>SID2</jats:italic>) or JA-related genes (<jats:italic>PDF1.2, LOX3, JAR1</jats:italic> and <jats:italic>COI1</jats:italic>), respectively, which were consistent with the related hormone levels upon these two different pathogen infections. Moreover, OSUB18 can trigger ISR in <jats:italic>jar1</jats:italic> or <jats:italic>sid2</jats:italic> mutants but not in <jats:italic>myc2</jats:italic> or <jats:italic>npr1</jats:italic> mutants, depending on the pathogen’s lifestyles. In addition, OSUB18 prompted the production of acetoin, which was reported as a novel rhizobacterial ISR elicitor. In summary, our studies discover that OSUB18 is a novel ISR inducer that primes plants’ resistance against bacterial and fungal pathogens by enhancing the callose deposition and ROS accumulation, increasing the production of specific phytohormones and other metabolites involved in plant defense, and elevating the expression levels of multiple defense genes.</jats:p>

<jats:sec><jats:title>Background</jats:title><jats:p>The sustainability of crop production is impacted by climate change and land degradation, and the advanced application of nanotechnology is of paramount importance to overcome this challenge. The development of nanomaterials based on essential nutrients like zinc could serve as a basis for nanofertilizers and nanocomposite synthesis for broader agricultural applications and quality human nutrition. Therefore, this study aimed to synthesize zinc oxide nanoparticles (ZnO NPs) using pecan (Carya illinoinensis) leaf extract and investigate their effect on the growth, physiology, nutrient content, and antioxidant properties of mustard (Brassica juncea).</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>The ZnO NPs were characterized by UV-Vis spectrophotometry, Dynamic Light Scattering (DLS), X-ray diffractometer (XRD), Scanning Electron Microscopy (SEM), and Fourier Transform Infra-Red Spectroscopy (FTIR). Mustard plants were subjected to different concentrations of ZnONPs (0, 20, 40, 60, 80, 100 and 200 mg L-1) during the vegetative growth stage.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>The UV-Vis spectra of ZnO NPs revealed the absorption maxima at 362 nm and FTIR identified numerous functional groups that are responsible for capping and stabilizing ZnO NPs. DLS analysis presented monodispersed ZnO NPs of 84.5 nm size and highly negative zeta potential (-22.4 mV). Overall, the application of ZnO NPs enhanced the growth, chlorophyll content (by 53 %), relative water content (by 46 %), shoot biomass, membrane stability (by 54 %) and net photosynthesis significantly in a dose-dependent manner. In addition, the supplement of the ZnO NPs augmented K, Fe, Zn and flavonoid contents as well as overcome the effect of reactive oxygen species by increasing antioxidant capacity in mustard leaves up to 97 %.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>In conclusion, ZnO NPs can be potentially used as a plant growth stimulant and as a novel soil amendment for enhancing crop yields. Besides, the biofortification of B. juncea plants with ZnO NPs helps to improve the nutritional quality of the crop and perhaps potentiates its pharmaceutical effects.</jats:p></jats:sec>

<jats:sec><jats:title>Background</jats:title><jats:p>RAPID ALKALINIZATION FACTOR (RALFs) are cysteine-rich peptides that regulate multiple physiological processes in plants. This peptide family has considerably expanded during land plant evolution, but the role of ancient RALFs in modulating stress responses is unknown.Results: Here, we used the moss Physcomitrium patens as a model to gain insight into the role of RALF peptides in the coordination of plant growth and stress response in non-vascular plants. The quantitative proteomic analysis revealed concerted downregulation of M6 metalloprotease and some membrane proteins, including those involved in stress response, in PpRALF1, 2 and 3 knockout (KO) lines. The subsequent analysis revealed the role of PpRALF3 in growth regulation under abiotic and biotic stress conditions, implying the importance of RALFs in responding to various adverse conditions in bryophytes. We found that knockout of the PpRALF2 and PpRALF3 genes resulted in increased resistance to bacterial and fungal phytopathogens, Pectobacterium carotovorum and Fusarium solani, suggesting the role of these peptides in negative regulation of the immune response in P. patens. Comparing the transcriptomes of PpRALF3 KO and wild-type plants infected by F. solani showed that the regulation of genes in the phenylpropanoid pathway and those involved in cell wall modification and biogenesis was different in these two genotypes.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>Thus, our study sheds light on the function of the previously uncharacterized PpRALF3 peptide and gives a clue to the ancestral functions of RALF peptides in plant stress response.</jats:p></jats:sec>

<jats:p>Short term experiments have identified heat shock and cold response elements in many biological systems. However, the effect of long-term low or high temperatures is not well documented. To address this gap, we grew <jats:italic>Antirrhinum majus</jats:italic> plants from two-weeks old until maturity under control (normal) (22/16°C), cold (15/5°C), and hot (30/23°C) conditions for a period of two years. Flower size, petal anthocyanin content and pollen viability obtained higher values in cold conditions, decreasing in middle and high temperatures. Leaf chlorophyll content was higher in cold conditions and stable in control and hot temperatures, while pedicel length increased under hot conditions. The control conditions were optimal for scent emission and seed production. Scent complexity was low in cold temperatures. The transcriptomic analysis of mature flowers, followed by gene enrichment analysis and CNET plot visualization, showed two groups of genes. One group comprised genes controlling the affected traits, and a second group appeared as long-term adaptation to non-optimal temperatures. These included hypoxia, unsaturated fatty acid metabolism, ribosomal proteins, carboxylic acid, sugar and organic ion transport, or protein folding. We found a differential expression of floral organ identity functions, supporting the flower size data. Pollinator-related traits such as scent and color followed opposite trends, indicating an equilibrium for rendering the organs for pollination attractive under changing climate conditions. Prolonged heat or cold cause structural adaptations in protein synthesis and folding, membrane composition, and transport. Thus, adaptations to cope with non-optimal temperatures occur in basic cellular processes.</jats:p>

<jats:p>Sucrose controls various developmental and metabolic processes in plants. It also functions as a signaling molecule in the synthesis of carbohydrates, storage proteins, and anthocyanins, as well as in floral induction and defense response. We found that sucrose preferentially induced <jats:italic>OsWRKY7</jats:italic>, whereas other sugars (such as mannitol, glucose, fructose, galactose, and maltose) did not have the same effect. A hexokinase inhibitor mannoheptulose did not block the effect of sucrose, which is consequently thought to function directly. MG132 inhibited sucrose induction, suggesting that a repressor upstream of <jats:italic>OsWRKY7</jats:italic> is degraded by the 26S proteasome pathway. The 3-kb promoter sequence of <jats:italic>OsWRKY7</jats:italic> was preferentially induced by sucrose in the luciferase system. Knockout mutants of <jats:italic>OsWRKY7</jats:italic> were more sensitive to the rice blast fungus <jats:italic>Magnaporthe oryzae</jats:italic>, whereas the overexpression of <jats:italic>OsWRKY7</jats:italic> enhanced the resistance, indicating that this gene is a positive regulator in the plant defense against this pathogen. The luciferase activity driven by the <jats:italic>OsPR10a</jats:italic> promoter was induced by OsWRKY7 and this transcription factor bound to the promoter region of <jats:italic>OsPR10a</jats:italic>, suggesting that OsWRKY7 directly controls the expression of <jats:italic>OsPR10a</jats:italic>. We conclude that sucrose promotes the transcript level of <jats:italic>OsWRKY7</jats:italic>, thereby increasing the expression of <jats:italic>OsPR10a</jats:italic> for the defense response in rice.</jats:p>