Screening of mutants using chlorophyll fluorescence

Classification of tomato seedling chilling injury based on chlorophyll fluorescence imaging and DBO-BiLSTM

Introduction

Tomatoes are sensitive to low temperatures during their growth process, and low temperatures are one of the main environmental limitations affecting plant growth and development in Northeast China. Chlorophyll fluorescence imaging technology is a powerful tool for evaluating the efficiency of plant photosynthesis, which can detect and reflect the effects that plants are subjected to during the low temperature stress stage, including early chilling injury.

Methods

This article primarily utilizes the chlorophyll fluorescence image set of tomato seedlings, applying the dung beetle optimization (DBO) algorithm to enhance the deep learning bidirectional long short term memory (BiLSTM) model, thereby improving the accuracy of classification prediction for chilling injury in tomatoes. Firstly, the proportion of tomato chilling injury areas in chlorophyll fluorescence images was calculated using a threshold segmentation algorithm to classify tomato cold damage into four categories. Then, the features of each type of cold damage image were filtered using SRCC to extract the data with the highest correlation with cold damage. These data served as the training and testing sample set for the BiLSTM model. Finally, DBO algorithm was applied to enhance the deep learning BiLSTM model, and the DBO-BiLSTM model was proposed to improve the prediction performance of tomato seedling category labels.

Results

The results showed that the DBO-BiLSTM model optimized by DBO achieved an accuracy, precision, recall, and F1 score with an average of over 95%.

Discussion

Compared to the original BiLSTM model, these evaluation parameters improved by 9.09%, 7.02%, 9.16%, and 8.68%, respectively. When compared to the commonly used SVM classification model, the evaluation parameters showed an increase of 6.35%, 7.33%, 6.33%, and 6.5%, respectively. This study was expected to detect early chilling injury through chlorophyll fluorescence imaging, achieve automatic classification and labeling of cold damage data, and lay a research foundation for in-depth research on the cold damage resistance of plants themselves and exploring the application of deep learning classification methods in precision agriculture.

Comparative analysis of the effects of microplastics and nitrogen on maize and wheat: Growth, redox homeostasis, photosynthesis, and AsA-GSH cycle

Microplastics (MPs) pose a significant threat to the function of agro-ecosystems. At present, research on MPs has mainly focused on the effects of different concentrations or types of MPs on a crop, while ignoring other environmental factors. In agricultural production, the application of nitrogen (N) fertilizer is an important means to maintain the high yield of crops. The effects of MPs and N on growth parameters, photosynthetic system, active oxygen metabolism, nutrient content, and ascorbate-glutathione (AsA-GSH) cycle of maize and wheat were studied in order to explicit whether N addition could effectively alleviate the effects of MPs on maize and wheat. The results showed that MPs inhibited the plant height of both maize and wheat, and MPs effects on physiological traits of maize were more severe than those of wheat, reflecting in reactive oxygen metabolism and restriction of photosynthetic capacity. Under the condition of N supply, AsA-GSH cycle of two plants has different response strategies to MPs: Maize promoted enzyme activity and co-accumulation of AsA and GSH, while wheat tended to consume AsA and accumulate GSH. N application induced slight oxidative stress on maize, which was manifested as an increase in hydrogen peroxide and malonaldehyde contents, and activities of polyphenol oxidase and peroxidase. The antioxidant capacity of maize treated with the combination of MPs + N was better than that treated with N or MPs alone. N could effectively alleviate the adverse effects of MPs on wheat by improving the antioxidant capacity.

Zinc regulation of chlorophyll fluorescence and carbohydrate metabolism in saline-sodic stressed rice seedlings

Saline-sodic stress can limit the absorption of available zinc in rice, subsequently impacting the normal photosynthesis and carbohydrate metabolism of rice plants. To investigate the impact of exogenous zinc application on photosynthesis and carbohydrate metabolism in rice grown in saline-sodic soil, this study simulated saline-sodic stress conditions using two rice varieties, 'Changbai 9' and 'Tonghe 899', as experimental materials. Rice seedlings at 4 weeks of age underwent various treatments including control (CT), 2 μmol·L-1 zinc treatment alone (Z), 50 mmol·L-1 saline-sodic treatment (S), and 50 mmol·L-1 saline-sodic treatment with 2 μmol·L-1 zinc (Z + S). We utilized JIP-test to analyze the variations in excitation fluorescence and MR820 signal in rice leaves resulting from zinc supplementation under saline-sodic stress, and examined the impact of zinc supplementation on carbohydrate metabolism in both rice leaves and roots under saline-sodic stress. Research shows that zinc increased the chloroplast pigment content, specific energy flow, quantum yield, and performance of active PSII reaction centers (PIABS), as well as the oxidation (VOX) and reduction rate (Vred) of PSI in rice leaves under saline-sodic stress. Additionally, it decreased the relative variable fluorescence (WK and VJ) and quantum energy dissipation yield (φDO) of the rice. Meanwhile, zinc application can reduce the content of soluble sugars and starch in rice leaves and increasing the starch content in the roots. Therefore, the addition of zinc promotes electron and energy transfer in the rice photosystem under saline-sodic stress. It enhances rice carbohydrate metabolism, improving the rice plants' ability to withstand saline-sodic stress and ultimately promoting rice growth and development.

Analysis of Photosynthetic Characteristics and Screening High Light-Efficiency Germplasm in Sugarcane

Sugarcane is a globally significant crop for sugar and energy production, and developing high light-efficiency sugarcane varieties is crucial for enhancing yield and quality. However, limited research is available on the screening of sugarcane germplasm with high photosynthetic efficiency, especially with different leaf positions. The present study, conducted in Guangxi, China, aimed to analyze the photosynthetic characteristics of 258 sugarcane varieties at different leaf positions over three consecutive years in field experiments. The results showed significant differences in photosynthetic characteristics among genotypes, years, and leaf positions. Heritability estimates for various photosynthetic parameters ranged from 0.76 to 0.88. Principal component analysis revealed that the first three principal components accounted for over 99% of the cumulative variance. The first component represented photosynthetic efficiency and light utilization, the second focused on electron transfer and reaction center status, and the third was associated with chlorophyll content. Cluster and discriminant analysis classified sugarcane genotypes into three categories: high photosynthetic efficiency (HPE) with 86 genotypes, medium photosynthetic efficiency (MPE) with 60 genotypes, and low photosynthetic efficiency (LPE) with 112 genotypes. Multi-year trials confirmed that HPE sugarcane genotypes had higher single-stem weight and sucrose content. This study provides valuable insights into the photosynthetic physiological characteristics of different sugarcane varieties, which can contribute to further research regarding high yields and sugar breeding.

Sunlight-induced repair of photosystem II in moss Semibarbula orientalis under submergence stress

Lower plants such as bryophytes often encounter submergence stress, even in low precipitation conditions. Our study aimed to understand the mechanism of submergence tolerance to withstand this frequent stress in moss (Semibarbula orientalis ) during the day and at night. These findings emphasise that light plays a crucial role in photoreactivation of PSII in S. orientalis , which indicates that light not only fuels photosynthesis but also aids in repairing the photosynthetic machinery in plants. Submergence negatively affects photosynthesis parameters such as specific and phenomenological fluxes, density of functional PSII reaction centres (RC/CS), photochemical and non-photochemical quenching (Kp and Kn), quantum yields (ϕP0 , ϕE0 , ϕD0 ), primary and secondary photochemistry, performance indices (PIcs and PIabs), etc. Excessive antenna size caused photoinhibition at the PSII acceptor side, reducing the plastoquinone pool through the formation of PSII triplets and reactive oxygen species (ROS). This ROS-induced protein and PSII damage triggered the initiation of the repair cycle in presence of sunlight, eventually leading to the resumption of PSII activity. However, ROS production was regulated by antioxidants like superoxide dismutase (SOD) and catalase (CAT) activity. The rapid recovery of RS/CS observed specifically under sunlight conditions emphasises the vital role of light in enabling the assembly of essential units, such as the D1 protein of PSII, during stress in S. orientalis . Overall, light is instrumental in restoring the photosynthetic potential in S. orientalis growing under submergence stress. Additionally, it was observed that plants subjected to submergence stress during daylight hours rapidly recover their photosynthetic performance. However, submergence stress during the night requires a comparatively longer period for the restoration of photosynthesis in the moss S. orientalis .

Overexpression of the FERONIA receptor kinase MdMRLK2 enhances apple cold tolerance

Cold is one of the main abiotic stresses in temperate fruit crops, affecting the yield and fruit quality of apple in China and European countries. The plant receptor-like kinase FERONIA is widely reported to be involved in abiotic stresses. However, its function in apple cold resistance remains unknown. Modification of cell wall components and accumulation of soluble sugars and amino acids are important strategies by which plants cope with cold. In this study, expression of the apple FERONIA receptor-like kinase gene MdMRLK2 was rapidly induced by cold. Apple plants overexpressing MdMRLK2 (35S:MdMRLK2) showed enhanced cold resistance relative to the wild type. Under cold conditions, 35S:MdMRLK2 apple plants had higher amounts of water insoluble pectin, lignin, cellulose, and hemicellulose, which may have resulted from reduced activities of polygalacturonase, pectinate lyase, pectinesterase, and cellulase. More soluble sugars and free amino acids and less photosystem damage were also observed in 35S:MdMRLK2 apple plants. Intriguingly, MdMRLK2 interacted with the transcription factor MdMYBPA1 and promoted its binding to MdANS and MdUFGT promoters, leading to more anthocyanin biosynthesis, particularly under cold conditions. These findings complemented the function of apple FERONIA MdMRLK2 responding to cold resistance.

Chlorophyll Fluorescence Imaging as a Tool for Evaluating Disease Resistance of Common Bean Lines in the Western Amazon Region of Colombia

The evaluation of disease resistance is considered an important aspect of phenotyping for crop improvement. Identification of advanced lines of the common bean with disease resistance contributes to improved grain yields. This study aimed to determine the response of the photosynthetic apparatus to natural pathogen infection by using chlorophyll (Chl_a) fluorescence parameters and their relationship to the agronomic performance of 59 common bean lines and comparing the photosynthetic responses of naturally infected vs. healthy leaves. The study was conducted over two seasons under acid soil and high temperature conditions in the western Amazon region of Colombia. A disease susceptibility index (DSI) was developed and validated using chlorophyll a (Chl_a) fluorescence as a tool to identify Mesoamerican and Andean lines of common bean (Phaseolus vulgaris L.) that are resistant to pathogens. A negative effect on the functional status of the photosynthetic apparatus was found with the presence of pathogen infection, a situation that allowed the identification of four typologies based on the DSI values ((i) moderately resistant; (ii) moderately susceptible; (iii) susceptible; and (iv) highly susceptible). Moderately resistant lines, five of them from the Mesoamerican gene pool (ALB 350, SMC 200, BFS 10, SER 16, SMN 27) and one from the Andean gene pool (DAB 295), allocated a higher proportion of energy to photochemical processes, which increased the rate of electron transfer resulting in a lower sensitivity to disease stress. This photosynthetic response was associated with lower values of DSI, which translated into an increase in the accumulation of dry matter accumulation in different plant organs (leaves, stem, pods and roots). Thus, DSI values based on chlorophyll fluorescence response to pathogen infection could serve as a phenotyping tool for evaluating advanced common bean lines. Six common bean lines (ALB 350, BFS 10, DAB 295, SER 16, SMC 200 and SMN 27) were identified as less sensitive to disease stress under field conditions in the western Amazon region of Colombia, and these could serve as useful parents for improving the common bean for multiple stress resistance.

Processing of D1 Protein: A Mysterious Process Carried Out in Thylakoid Lumen

In oxygenic photosynthetic organisms, D1 protein, a core subunit of photosystem II (PSII), displays a rapid turnover in the light, in which D1 proteins are distinctively damaged and immediately removed from the PSII. In parallel, as a repair process, D1 proteins are synthesized and simultaneously assembled into the PSII. On this flow, the D1 protein is synthesized as a precursor with a carboxyl-terminal extension, and the D1 processing is defined as a step for proteolytic removal of the extension by a specific protease, CtpA. The D1 processing plays a crucial role in appearance of water-oxidizing capacity of PSII, because the main chain carboxyl group at carboxyl-terminus of the D1 protein, exposed by the D1 processing, ligates a manganese and a calcium atom in the Mn4CaO5-cluster, a special equipment for water-oxidizing chemistry of PSII. This review focuses on the D1 processing and discusses it from four angles: (i) Discovery of the D1 processing and recognition of its importance: (ii) Enzyme involved in the D1 processing: (iii) Efforts for understanding significance of the D1 processing: (iv) Remaining mysteries in the D1 processing. Through the review, I summarize the current status of our knowledge on and around the D1 processing.

Physiological Characteristics of Cultivated Tepary Bean (Phaseolus acutifolius A. Gray) and Its Wild Relatives Grown at High Temperature and Acid Soil Stress Conditions in the Amazon Region of Colombia

Common bean (Phaseolus vulgaris L.) is sensitive to different types of abiotic stresses (drought, high temperature, low soil fertility, and acid soil), and this may limit its adaptation and consequently to its yield under stress. Because of this, a sister species, tepary bean (Phaseolus acutifolius A. Gray), has recently gained attention in breeding for improved abiotic stress tolerance in common bean. In this study, we evaluated the adaptation of 302 accessions of tepary bean (Phaseolus acutifolius A. Gray) and its wild relatives (grouped in four types of tepary bean genetic resource: cultivated, acutifolius regressive, acutifolius wild, tenuifolius wild) when grown under high temperature and acid soil conditions with aluminum toxicity in the Amazon region of Colombia. Our objective was to determine differences among four types of tepary bean genetic resource in their morpho-phenological, agronomic, and physiological responses to combined high temperature and acid soil stress conditions. We found that cultivated P. acutifolius var acutifolius presented a greater number of pods per plant, as well as larger seeds and a greater number of seeds per pod. Some traits, such as root biomass, days to flowering and physiological maturity, specific leaf area, and stomatal density, showed significant differences between types of tepary bean genetic resource, probably contributing to difference in adaptation to combined stress conditions of high temperature and acid soil conditions. The photochemical quenching (qP) was higher in cultivated P. acutifolius var. acutifolius, while energy dissipation by non-photochemical quenching (NPQ) in the form of heat and the coefficient of non-photochemical dissipation (qN) were higher in acutifolius regressive and tenuifolius wild accessions. We have identified 6 accessions of cultivated and 19 accessions of tenuifolius wild that exhibited grain yields above 1800 kg ha⁻¹. These accessions could be suitable to use as parents to improve dry seed production of tepary bean under combined stress conditions of high temperature and acid soil.

Area-ratio Fraunhofer line depth (aFLD) method approach to estimate solar-induced chlorophyll fluorescence in low spectral resolution spectra in a cool-temperate deciduous broadleaf forest

Solar-induced chlorophyll fluorescence (SIF) emissions were estimated by the "area-ratio Fraunhofer line depth (aFLD) method", a new retrieval methodology in spectra from a low spectral resolution (SR) spectroradiometer (MS-700: full width half maximum (FWHM) of 10 nm and spectral sampling interval of 3.3 nm), assisted with a scaling to reference SIF detected from high SR spectrum. The sparse pixels of a spectrum of low SR misses detecting the minimum of the O₂A absorption band around at 760 nm, which makes the SIF detection by conventional FLD methods lose accuracy considerably. To overcome this, the aFLD method uses the definite integral of spectra over a wide interval between 750 and 780 nm. The integration of the spectrum is insusceptible to the change in shape of the depression curve, leading to higher accuracy of the aFLD method. Daily SIF, calculated by the aFLD method using the spectra obtained with MS-700, was scaled to reference daily SIF calculated by the spectral fitting method using the spectra obtained from August to December 2019 with an ultrafine SR spectroradiometer (QE Pro, FWHM = 0.24 nm). As a result, SIF calculated from MS-700 spectra by aFLD method was strongly correlated with the reference SIF from QE Pro spectra (r² = 0.81) and was successfully scaled. Then, the scaled 11-year SIF from MS-700 at a deciduous broadleaf forest showed the correlation with GPP at multiple time steps: daily, monthly, and yearly, consistently during 2008-2018. The comparison of aFLD-derived SIF with the global Orbiting Carbon Observatory-2 (OCO-2) SIF data set (GOSIF) showed high correlation on monthly values during 2008-2017 (r² = 0.85). The combining approach of the aFLD method with a scaling to reference SIF successfully detected long-term canopy SIF emissions, which has great potential to provide essential information on ecosystem-level photosynthesis.

Linking remote sensing parameters to CO2 assimilation rates at a leaf scale

Solar-induced chlorophyll fluorescence (SIF) and photochemical reflectance index (PRI) are expected to be useful for remote sensing of photosynthetic activity at various spatial scales. This review discusses how chlorophyll fluorescence and PRI are related to the CO₂ assimilation rate at a leaf scale. Light energy absorbed by photosystem II chlorophylls is allocated to photochemistry, fluorescence, and heat dissipation evaluated as non-photochemical quenching (NPQ). PRI is correlated with NPQ because it reflects the composition of xanthophylls, which are involved in heat dissipation. Assuming that NPQ is uniquely related to the photochemical efficiency (quantum yield of photochemistry), photochemical efficiencies can be assessed from either chlorophyll fluorescence or PRI. However, this assumption may not be held under some conditions such as low temperatures and photoinhibitory environments. Even in such cases, photosynthesis may be estimated more accurately if both chlorophyll fluorescence and PRI are determined simultaneously. To convert from photochemical efficiency to CO₂ assimilation, environmental responses in stomatal conductance also need to be considered. Models linking chlorophyll fluorescence and PRI with CO₂ assimilation rates will contribute to understanding and future prediction of the global carbon cycle.

Photosynthesis: a multiscopic view

A recurring analogy for photosynthesis research is the fable of the blind men and the elephant. Photosynthesis has many complex working parts, which has driven the need to study each of them individually, with an inherent understanding that a more complete picture will require systematic integration of these views. However, unlike the blind men, who are limited to using their hands, researchers have developed over the past decades a repertoire of methods for studying these components, many of which capitalize on unique features intrinsic to each. More recent concerns about food security and clean, renewable energy have increased support for applied photosynthesis research, with the idea of either improving photosynthetic performance as a desired trait in select species or using photosynthetic measurements as a phenotyping tool in breeding efforts or for high precision crop management. In this review, we spotlight the migration of approaches for studying photosynthesis from the laboratory into field environments, highlight some recent advances and speculate on areas where further development would be fruitful, with an eye towards how applied photosynthesis research can have impacts at local and global scales.