Crop plant signaling for real-time plant identification in smart farm: A systematic review and new concept in artificial intelligence for automated weed control

The continued emergence of herbicide-resistant weeds and the increasing labor costs are threatening the ability of growers to manage weeds and maintain profits.The smart farm with the advantage of non-invasive and high-efficiency operation plays an important role in increasing the sustainability of agricultural system as it can optimize crop inputs such as herbicides while preserving resources including soil and water.An automatic weed control system requires a sensing subsystem capable of detecting and distinguishing crop plants from weeds.The overlapping plants remain a challenge for successful detection of weeds.Crop plant signaling is a new robot-plant interaction technique that allows the visualization of exogenous fluorescent signals applied to crop plants for crop/weed identification.Based on all published articles in the leading edge of knowledge,a comprehensive review of the mushrooming crop plant signaling for discriminations of weeds and crops is highlighted.The discussion outlines the significant progress that has been made in developing new and more robust automated systems along with the current challenges and future prospects.This paper details the promise of crop plant signaling for accurate and automated plant recognitions in cropping systems.There is no doubt that this review is of great significance to scholars in related research field to study the solutions to real-time weed control.

Study on Plant Radiation Signal Transduction for Human Self-Healing

We selected 450 patients with chronic and difficult diseases as receptors, and selected edible and medicinal plant combinations as biological signal donors, and randomly participated in a new experiment. After adjusting the patient’s biological field, the compensating bio information energy (CBE) high-tech is applied to transmit the signal of plant radiation to the patient’s body. The physical therapy of this health care mode has the characteristics of no contact, no drugs, no intervention, no toxic side effects, no pain, and no electromagnetic radiation and so on. Before and after the experiment, the main function test, cell function, cell biochemistry and body temperature of each patient were used for the same body control and data statistical analysis, and then the comprehensive integration method was used to evaluate the effect. We found that after 1 - 4 courses of treatment (7 - 28 dx 2h), the potential disease risk of patients was significantly reduced, the relevant medical indicators improved rapidly, and the cell function and symptoms improved simultaneously. The effective rate was up to 90%, the significant efficiency was up to 57%. This experiment shows that this new physical therapy can treat both symptoms and root causes, make chronic and difficult diseases self-healing and rehabilitation, and has no ethical problems. It also shows that information on plant health can play an important role in reversing cell aging and restoring cell function. Therefore, it opens up a new field of natural therapy, which can be called cell information therapy.

Stress Knowledge Map:A knowledge graph resource for systems biology analysis of plant stress responses

Stress Knowledge Map(SKM;https://skm.nib.si)is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical,signaling,and regulatory molecular interactions in plants:a highly curated model of plant stress signaling(PSS;543 reactions)and a large comprehensive knowledge network(488390 interactions).Both were constructed by domain experts through systematic curation of diverse literature and database resources.SKM provides a single entry point for investigations of plant stress response and related growth trade-offs,as well as interactive explorations of current knowledge.PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin.Here,we describe the features of SKM and show,through two case studies,how it can be used for complex analyses,including systematic hypothesis generation and design of validation experiments,or to gain new insights into experimental observations in plant biology.

Integrative analysis of the transcriptome and metabolome reveals the response mechanism to tomato spotted wilt virus

Tomato spotted wilt virus(TSWV)is an important virus that has rapidly spread throughout the world.TSWV seriously hinders the production of tomato(Solanum lycopersicum)and other plants.In order to discover more new genes and metabolites related to TSWV resistance in tomato plants,the genes and metabolites related to the resistance of tomato plants inoculated with TSWV were identified and studied herein.The tomato TSWV-resistance line YNAU335(335)and TSWV-susceptible lines NO5 and 96172I(961)were used as the transcriptome and metabolome research materials.Transcriptomic and metabolomic techniques were used to analyze the gene and metabolite response mechanisms to TSWV inoculation.A total of 3566,2951,and 2674 differentially expressed genes(DEGs)were identified in lines 335,NO5,and961,respectively.Meanwhile,208,228,and 273 differentially accumulated metabolites(DAMs)were identified in lines 335,NO5,and 961,respectively.In line 335,the number of DEGs was the highest,but the number of DAMs was lowest.Furthermore,903 DEGs and 94 DAMs were common to the response to TSWV in the three inbred lines.The 903 DEGs and 94 DAMs were mainly enriched in the plant hormone signal transduction and flavonoid synthesis pathways.In addition,many nucleotide-binding site-leucine-rich repeat genes and transcription factors were found that might be involved in the TSWV response.These results provide new insights into TSWV resistance mechanisms.

Transcriptome Analysis of Molecular Mechanisms Underlying Phenotypic Variation in Phaseolus vulgaris Mutant‘nts’

The phenotype of a common bean plant is often closely related to its yield,and the yield of plants with reduced height or poor stem development during growth is low.Mutants serve as an essential gene resource for common bean breeding genetic research.Although model plants and crops are studied to comprehend the molecular mechanisms and genetic basis of plant phenotypes,the molecular mechanism of phenotypic variation in common beans remains underexplored.We here used the mutant‘nts’as material for transcriptome sequencing analysis.This mutant was obtained through 60Co-γirradiation from the common bean variety‘A18’.Differentially expressed genes were mainly enriched in GO functional entries such as cell wall organization,auxin response and transcription factor activity.Metabolic pathways significantly enriched in KEGG analysis included plant hormone signal transduction pathways,phenylpropanoid biosynthesis pathways,and fructose and mannose metabolic pathways.AUX1(Phvul.001G241500),the gene responsible for auxin transport,may be the key gene for auxin content inhibition.In the plant hormone signal transduction pathway,AUX1 expression was downregulated and auxin transport across the membrane was blocked,resulting in stunted growth of the mutant‘nts’.The results provide important clues for revealing the molecular mechanism of‘nts’phenotype regulation in bean mutants and offer basic materials for breeding beneficial phenotypes of bean varieties.

Signal convergence through the lenses of MAP kinases： paradigms of stress and hormone signaling in plants

Common mechanisms plants use to translate the external stimuli into cellular responses are the activation of mitogen-activated protein kinase （MAPK） cascade. These MAPK cascades are highly conserved in eukaryotes and consist of three subsequently acting protein kinases, MAP kinase kinase kinase （MAPKKK）, MAP kinase kinase （MAPKK） and MAP kinase （MAPK） which are linked in various ways with upstream receptors and downstream targets. Plant MAPK cascades regulate numerous processes, including various environmental stresses, hormones, cell division and developmental processes. The number of MAPKKs in Arabidopsis and rice is almost half the number of MAPKs pointing important role of MAPKKs in integrating signals from several MAPKKKs and transducing signals to various MAPKs. The cross talks between different signal transduction pathways are concentrated at the level of MAPKK in the MAPK cascade. Here we discussed the insights into MAPKK mediated response to environmental stresses and in plant growth and development.

Unraveling salt stress signaling in plants

Salt stress is a maior environmental factor limiting plant growth and productivity. A better understanding of the mechanisms mediating salt resistance will help researchers design ways to improve crop performance under adverse environmental conditions. Salt stress can lead to ionic stress, osmotic stress and secondary stresses, particularly oxidative stress, in plants. Therefore, to adapt to salt stress, plants rely on signals and pathways that re-establish cellular ionic, osmotic, and reactive oxygen species （ROS） homeostasis. Over the past two decades, genetic and biochemical analyses have revealed several core stress signaling pathways that participate in salt resistance. The Salt Overly Sensitive signaling pathway plays a key role in maintaining ionic homeostasis, via extruding sodium ions into the apoplast. Mitogenactivated protein kinase cascades mediate ionic, osmotic, and ROS homeostasis. SnRK2 （sucrose nonfermenting l-related protein kinase 2） proteins are involved in maintaining osmotic homeostasis. In this review, we discuss recent progress in identifying the components and pathways involved in the plant＇s response to salt stress and their regulatory mechanisms. We also review progress in identifying sensors involved in salt-induced stress signaling in plants.

Insights into the regulation of C-repeat binding factors in plant cold signaling

Cold temperatures, a major abiotic stress, threaten the growth and development of plants, worldwide. To cope with this adverse environmental cue, plants from temperate climates have evolved an array of sophisticated mechanisms to acclimate to cold periods, increasing their ability to tolerate freezing stress. Over the last decade, significant progress has been made in determining the molecular mechanisms underpinning cold acclimation, including following the identification of several pivotal components, including candidates for cold sensors, protein kinases, and transcription factors. With these developments, we have a better understanding of the CBF-dependent cold-signaling pathway. In this review, we summarize recent progress made in elucidating the cold-signaling pathways, especially the C-repeat binding factor-dependent pathway, and describe the regulatory function of the crucial components of plant cold signaling. We also discuss the unsolved questions that should be the focus of future work.

Reactive oxygen species signaling and stomatal movement in plant responses to drought stress and pathogen attack

Stomata, the pores formed by a pair of guard cells, are the main gateways for water transpiration and photosynthetic CO2 exchange, as well as pathogen invasion in land plants. Guard cell movement is regulated by a combination of environmental factors, including water status, light, CO2 levels and pathogen attack, as well as endogenous signals, such as abscisic acid and apoplastic reactive oxygen species （ROS）. Under abiotic and biotic stress conditions, extracellular ROS are mainly produced by plasma membrane-localized NADPH oxidases, whereas intracellular ROS are produced in multiple organelles. These ROS form a sophisticated cellular signaling network, with the accumulation of apoplastic ROS an early hallmark of stomatal movement. Here, we review recent progress in understanding the molecular mechanisms of the ROS signaling network, primarily during drought stress and pathogen attack. We summarize the roles of apoplastic ROS in regulating stomatal movement, ABA and CO2 signaling, and immunity responses. Finally, we discuss ROS accumulation and communication between organelles and cells. This information provides a conceptual framework for understanding how ROS signaling is integrated with various signaling pathways during plant responses to abiotic and biotic stress stimuli.

The crossroads of receptor-mediated signaling and endocytosis in plants

Plants deploy numerous plasma membrane receptors to sense and rapidly react to environmental changes. Correct localization and adequate protein levels of the cell-surface receptors are critical for signaling activation and modulation of plant development and defense against pathogens. After ligand binding, receptors are internalized for degradation and signaling attenuation. However, one emerging notion is that the Iigand-induced endocytosis of reCeptor complexes is important for the signal duration, amplitude, and specificity. Recently, mutants of maior endocytosis players, including clathrin and dynamin, have been shown to display defects in activation of a subset of signal transduction pathways, implying that signaling in plants might not be solely restricted to the plasma membrane. Here, we summarize the up-to-date knowledge of receptor complex endocytosis and its effect on the signaling outcome, in the context of plant development and immunity.

Transcriptome Profiling Reveals Candidate Genes Involved in Stem Swelling of Tumorous Stem Mustard

Tumorous stem mustard is well known for its swollen stem from which pickled“Fuling Mustard”is made.The molecular mechanisms governing the formation of the modified swollen stems are still poorly understood.This paper aims to identify candidate genes involved in the developmental regulation of the swollen stems.We sought to map previously published transcriptome datasets for Brassica juncea,including those derived from swollen stems at four different developmental stages and a mutant variety without swollen stems.Using pairwise comparisons of the five datasets,we identified 31368 differentially expressed genes(DEGs).A total of 55 DEGs related to plant hormone signal transduction and 259 continuously up-or downregulated transcription factors were identified during stem development using Gene Ontology(GO)analysis.Quantitative real-time PCR(qRT-PCR)results showed that the expressions of 12 important candidate DEGs were consistent with RNA-seq results.Our study provided digital gene expression profiling and a dynamic view of the swollen stem development process.Furthermore,we identified candidate genes for further studies on mechanisms of modified stem development in non-model species.

Liquid metal-based plant electronic tattoos for in-situ monitoring of plant physiology

Flexible plant sensors,as a noninvasive and real-time monitoring method for plant physiology,are becoming crucial for precision agriculture.However,integrating flexible devices with plants are challenging due to their fragility and complex surfaces.In this study,we introduce a liquid metal-based plant electronic tattoo(LM-PET)that can harmlessly and continuously monitor the loss of water content and plant electrical signals,which are critical parameters for analyzing plant physiological status.The LM-PET achieves double-sided conductivity through soluble electrostatic spinning films and transferring technology,effectively addressing the issue of mismatch between the rigid interface of electronic devices and the surface of delicate plants.The fabricated tattoo electrode can adhere tightly to the leaf surface for a long time and can significantly broaden the scope of moisture monitoring,even in cases of severe wrinkling caused by water loss.At the optimum operating frequency of 100 kHz,the sensitivity of LM-PET can reach 25.4 kΩ%^(-1).Thus,LM-PETs can record the electrical signals generated when abiotic stresses threaten plants.They are also significant in providing a deeper understanding of the drought adaptation mechanisms of plants and developing drought-resistant varieties.They offer data-driven crop management and decision-making guidance,which is imperative for advancing precision agriculture.Overall,our findings provide valuable insights into the performance of agricultural inputs and facilitate real-time monitoring of plant growth and development.

New insights into plant nutrient signaling and adaptation to fluctuating environments

Over the past 50 years, the Green Revolution and exploitation of heterosis have allowed cereal grain yield to keep pace with world- wide population growth. Unfortunately, plant growth and crop productivity are heavily dependent on the application of synthetic fertilizers.

Plant mineral nutrient sensing and signaling

As terrestrial plants are sessile organisms and therefore must directly deal with an often complex and changing environment, they have had to develop complex and elegant strategies to survive and thrive in the face of environmental stress. This is particularly true for plant adaptation to the soil environment, where essential mineral nutrients often are found at sub- optimal levels and their concentrations can vary significantly, both spatially and temporally. Furthermore, plants also at times have to respond to excessively high and potentially toxic levels of essential nutrients, as well as toxic levels of non- essential metals and metalloids in the soil. Although plant mineral nutrition as a bona ~ide research discipline has a history of over 15o years, beginning with the pioneering work of Justus Von Liebieg and others in the mid-1800＇s, it is only very recently that researchers have begun to truly appreciate how sophisticated plants are with regards to the sensing of their mineral status and the maintaining of mineral homeostasis in the plant.

Evolutionary Lineages and Functional Diversification of Plant Hexokinases

Sequencing data from 10 species show that a plant hexokinase （HXK） family contains 5-11 genes. Functionally, a given family can include metabolic catalysts, glucose signaling proteins, and non-catalytic, apparent regulatory enzyme homologs. This study has two goals. The first aim is to develop a predictive method to determine which HXK proteins within a species have which type of function. The second aim is to determine whether HXK-dependent glucose signaling proteins occur among more primitive plants, as well as among angiosperms. Using a molecular phylogeny ap- proach, combined with selective experimental testing, we found that non-catalytic HXK homologs might occur in all plants, including the relatively primitive Selaginella moellendorffi. We also found that different lineages of angiosperm HXKs have apparent conserved features for catalytic activity and for sub-cellular targeting. Most higher-plant HXKs are expressed predominantly at mitochondria, with HXKs of one lineage occurring in the plastid, and HXKs of one monocot lineage occurring in the cytosol. Using protoplast transient expression assays, we found that HXK glucose signaling pro- teins occur likely in all higher plants and in S. moellendorffi as well. Thus, the use of glucose by plant HXK isoforms in metabolism and/or as a regulatory metabolite occurs as widespread, conserved processes.

Finding Signals for Plant Promoters

The strongest signal of plant promoter is searched with the model of single motif with two types. It turns out that the dominant type is the TATA-box. The other type may be called TATA-less signal, and may be used in gene finders for promoter recognition. While the TATA signals are very close for the monocot and the dicot, their TATA-less signals are significantly different. A general and flexible multi-motif model is also proposed for promoter analysis based on dynamic programming. By extending the Gibbs sampler to the dynamic programming and introducing temperature, an efficient algorithm is developed for searching signals in plant promoters.

Structure-Function Analysis of Arabidopsis thaliana Histidine Kinase AHK5 Bound to Its Cognate Phosphotransfer Protein AHP1

The multi-step phosphorelay （MSP） system defines a key signal transduction pathway in plants and many eukaryotes. In this system, external stimuli first lead to the activation of a histidine kinase, followed by transfer of a phosphoryl group from the receiver domain of the kinase （HKRD） to downstream, cytosolic phosphotransfer proteins （HPs）. In order to establish the determinants of specificity for this signaling relay system, we have solved the first crystal structure of a plant HKRD, AHK5RD, in complex with one of its cognate HPs, AHP1. AHP1 binds AHK5RD via a prominent hydrogen bond docking ridge and a hydrophobic patch. These features are conserved among all AHP proteins, but differ significantly from other structurally characterized prokaryotic and eukaryotic HPs. Surface plasmon resonance experiments show that AHK5RD binds to AHP1-3 with similar, micromolar affinity, consistent with the transient nature of this signaling complex. Our correlation of structural and functional data provide the first insight, at the atomic level as well as with quantitative affinity data, into the molecular recognition events governing the MSP in plants.

Regulation Mechanisms of Stomatal Oscillation

Stomata function as the gates between the plant and the atmospheric environment. Stomatal movement, including stomatal opening and closing, controls CO2 absorption as the raw material for photosynthesis and water loss through transpiration. How to reduce water loss and maintain enough CO2 absorption has been an interesting research topic for some time. Simple stomatal opening may elevate CO2 absorption, but, in the meantime, promote the water loss, whereas simple closing of stomatal pores may reduce both water loss and CO2 absorption, resulting in impairment of plant photosynthesis. Both processes are not economical to the plant. As a special rhythmic stomatal movement that usually occurs at smaller stomatal apertures, stomatal oscillation can keep CO2 absorption at a sufficient level and reduce water loss at the same time, suggesting a potential improvement in water use efficiency. Stomatal oscillation is usually found after a sudden change in one environmental factor in relatively constant environments. Many environmental stimuli can induce stomatal oscillation. It appears that, at the physiological level, feedback controls are involved in stomatal oscillation. At the cellular level, possibly two different patterns exist： （i） a quicker responsive pattern; and （ii） a slower response. Both involve water potential changes and water channel regulation, but the mechanisms of regulation of the two patterns are different. Some evidence suggests that the regulation of water channels may play a vital and primary role in stomatal oscillation. The present review summarizes studies on stomatal oscillation and concludes with some discussion regarding the mechanisms of regulation of stomatal oscillation.

Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis

Temperature influences the distribution, range, and phenology of plants. The key transcriptional activators of heat shock response in eukaryotes, the heat shock factors （HSFs）, have undergone large-scale gene amplification in plants. While HSFs are central in heat stress responses, their role in the response to ambient temperature changes is less well understood. We show here that the warm ambient temperature transcriptome is dependent upon the HSFA1 clade ofArabidopsis HSFs, which cause a rapid and dynamic eviction of H2A.Z nucleosomes at target genes. A transcriptional cascade results in the activation of multiple downstream stress-responsive transcription factors, triggering large-scale changes to the transcriptome in response to elevated temperature. H2A.Z nucleosomes are enriched at temperature-responsive genes at non-inducible temperature, and thus likely confer inducibility of gene expression and higher responsive dynamics. We propose that the antagonistic effects of H2A.Z and HSF1 provide a mechanism to activate gene expression rapidly and precisely in response to temperature, while preventing leaky transcription in the absence of an activation signal.