Probing the design principles of photosynthetic systems through fluorescence noise measurement

Elucidating the energetic processes which govern photosynthesis, the engine of life on earth, are an essential goal both for fundamental research and for cutting-edge biotechnological applications. Fluorescent signal of photosynthetic markers has long been utilised in this endeavour. In this research we demonstrate the use of fluorescent noise analysis to reveal further layers of intricacy in photosynthetic energy transfer. While noise is a common tool analysing dynamics in physics and engineering, its application in biology has thus far been limited. Here, a distinct behaviour in photosynthetic pigments across various chemical and biological environments is measured. These changes seem to elucidate quantum effects governing the generation of oxidative radicals. Although our method offers insights, it is important to note that the interpretation should be further validated expertly to support as conclusive theory. This innovative method is simple, non-invasive, and immediate, making it a promising tool to uncover further, more complex energetic events in photosynthesis, with potential uses in environmental monitoring, agriculture, and food-tech.

A century of studying plant secondary metabolism-From "what?" to "where, how, and why?"

Over the past century, early advances in understanding the identity of the chemicals that collectively form a living plant have led scientists to deeper investigations exploring where these molecules localize, how they are made, and why they are synthesized in the first place. Many small molecules are specific to the plant kingdom and have been termed plant secondary metabolites, despite the fact that they can play primary and essential roles in plant structure, development, and response to the environment. The past 100 yr have witnessed elucidation of the structure, function, localization, and biosynthesis of selected plant secondary metabolites. Nevertheless, many mysteries remain about the vast diversity of chemicals produced by plants and their roles in plant biology. From early work characterizing unpurified plant extracts, to modern integration of 'omics technology to discover genes in metabolite biosynthesis and perception, research in plant (bio)chemistry has produced knowledge with substantial benefits for society, including human medicine and agricultural biotechnology. Here, we review the history of this work and offer suggestions for future areas of exploration. We also highlight some of the recently developed technologies that are leading to ongoing research advances.

Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere

Nitrogen is the most limiting factor in crop production. Legumes establish a symbiotic relationship with rhizobia and enhance nitrogen fixation. We analyzed 1,624 rhizosphere 16S rRNA gene samples and 113 rhizosphere metagenomic samples from three typical legumes and three non-legumes. The rhizosphere microbial community of the legumes had low diversity and was enriched with nitrogen-cycling bacteria (Sphingomonadaceae, Xanthobacteraceae, Rhizobiaceae, and Bacillaceae). Furthermore, the rhizosphere microbiota of legumes exhibited a high abundance of nitrogen-fixing genes, reflecting a stronger nitrogen-fixing potential, and Streptomycetaceae and Nocardioidaceae were the predominant nitrogen-fixing bacteria. We also identified helper bacteria and confirmed through metadata analysis and a pot experiment that the synthesis of riboflavin by helper bacteria is the key factor in promoting nitrogen fixation. Our study emphasizes that the construction of synthetic communities of nitrogen-fixing bacteria and helper bacteria is crucial for the development of efficient nitrogen-fixing microbial fertilizers.

Low phosphorus impact on Moso bamboo (Phyllostachys edulis) root morphological polymorphism and expression pattern of the related genes

Moso bamboo typically grows in phosphorus (P)-deficient soil that limits its growth and development. In this study, 10 Moso bamboo genotypes (Ph-1 to Ph-10) were evaluated for their responses to P deficiency during the seedling stage by growing them in both P-sufficient and P-deficient conditions. Adaptive responses to low P (LP) conditions were observed in the majority of genotypes. Under P deficiency conditions, the total biomass decreased in several genotypes, but at the same time, the root-to-shoot ratio increased. Principal component analysis identified two main comprehensive traits (PC1 and PC2) related to the root volume and surface area and P concentration and accumulation. Based on the analysis, two genotypes (Ph-6 and Ph-10) were identified with significantly different levels of tolerance to P deficiency. The results revealed that the genotype Ph-10 responded to P deficiency by significantly increasing the root surface area and volume, while simultaneously reducing the number of root cortex cells when compared with the genotype Ph-6, which showed the lowest tolerance (intolerant). The genotype Ph-10 exhibited a robust response to external LP conditions, marked by elevated expression levels of PHOSPHATE TRANSPORTERs and SYG1/PHO81/XPR1s. In situ Polymerase Chain Reaction (PCR) analysis also revealed distinct tissue-specific expression patterns of the genes in the roots, particularly highlighting the differences between Ph-6 and Ph-10. The results provide a foundation for elucidating the mechanism of LP tolerance, thus potentially contributing to developing high P-use efficiency in Moso bamboo species.

Pseudomonas chlororaphis IRHB3 assemblies beneficial microbes and activates JA-mediated resistance to promote nutrient utilization and inhibit pathogen attack

Introduction

The rhizosphere microbiome is critical to plant health and resistance. PGPR are well known as plant-beneficial bacteria and generally regulate nutrient utilization as well as plant responses to environmental stimuli. In our previous work, one typical PGPR strain, Pseudomonas chlororaphis IRHB3, isolated from the soybean rhizosphere, had positive impacts on soil-borne disease suppression and growth promotion in the greenhouse, but its biocontrol mechanism and application in the field are not unclear.

Methods

In the current study, IRHB3 was introduced into field soil, and its effects on the local rhizosphere microbiome, disease resistance, and soybean growth were comprehensively analyzed through high-throughput sequencing and physiological and molecular methods.

Results and discussion

We found that IRHB3 significantly increased the richness of the bacterial community but not the structure of the soybean rhizosphere. Functional bacteria related to phosphorus solubilization and nitrogen fixation, such as Geobacter, Geomonas, Candidatus Solibacter, Occallatibacter, and Candidatus Koribacter, were recruited in rich abundance by IRHB3 to the soybean rhizosphere as compared to those without IRHB3. In addition, the IRHB3 supplement obviously maintained the homeostasis of the rhizosphere microbiome that was disturbed by F. oxysporum, resulting in a lower disease index of root rot when compared with F. oxysporum. Furthermore, JA-mediated induced resistance was rapidly activated by IRHB3 following PDF1.2 and LOX2 expression, and meanwhile, a set of nodulation genes, GmENOD40b, GmNIN-2b, and GmRIC1, were also considerably induced by IRHB3 to improve nitrogen fixation ability and promote soybean yield, even when plants were infected by F. oxysporum. Thus, IRHB3 tends to synergistically interact with local rhizosphere microbes to promote host growth and induce host resistance in the field.

Legume-specific SnRK1 promotes malate supply to bacteroids for symbiotic nitrogen fixation

Nodulation is an energy-expensive behavior driven by legumes by providing carbon sources to bacteroids and obtaining nitrogen sources in return. The energy sensor sucrose nonfermenting 1-related protein kinase 1 (SnRK1) is the hub of energy regulation in eukaryotes. However, the molecular mechanism by which SnRK1 coordinates the allocation of energy and substances during symbiotic nitrogen fixation (SNF) remains unknown. In this study, we identified the novel legume-specific SnRK1α4, a member of the SnRK1 family that positively regulates SNF. Phenotypic analysis showed that nodule size and nitrogenase activity increased in SnRK1α4-overexpressing plants and decreased significantly in snrk1α4 mutants. We demonstrated that a key upstream kinase involved in nodulation, Does Not Make Infection 2 (DMI2), can phosphorylate SnRK1α4 at Thr175 to cause its activation. Further evidence clarified that SnRK1α4 phosphorylates the malate dehydrogenases MDH1/2 to promote malate production in the cytoplasm, supplying carbon sources to bacteroids. Therefore, our findings reveal an essential role of the DMI2-SnRK1α4-MDH pathway in supplying carbon sources to bacteroids for SNF and provide a new module for constructing cereal crops with SNF.

Home-based microbial solution to boost crop growth in low-fertility soil

Soil microbial inoculants are expected to boost crop productivity under climate change and soil degradation. However, the efficiency of native vs commercialized microbial inoculants in soils with different fertility and impacts on resident microbial communities remain unclear. We investigated the differential plant growth responses to native synthetic microbial community (SynCom) and commercial plant growth-promoting rhizobacteria (PGPR). We quantified the microbial colonization and dynamic of niche structure to emphasize the home-field advantages for native microbial inoculants. A native SynCom of 21 bacterial strains, originating from three typical agricultural soils, conferred a special advantage in promoting maize growth under low-fertility conditions. The root : shoot ratio of fresh weight increased by 78-121% with SynCom but only 23-86% with PGPRs. This phenotype correlated with the potential robust colonization of SynCom and positive interactions with the resident community. Niche breadth analysis revealed that SynCom inoculation induced a neutral disturbance to the niche structure. However, even PGPRs failed to colonize the natural soil, they decreased niche breadth and increased niche overlap by 59.2-62.4%, exacerbating competition. These results suggest that the home-field advantage of native microbes may serve as a basis for engineering crop microbiomes to support food production in widely distributed poor soils.

Understanding the plant-microbe interactions in environments exposed to abiotic stresses: An overview

Abiotic stress poses a severe danger to agriculture since it negatively impacts cellular homeostasis and eventually stunts plant growth and development. Abiotic stressors like drought and excessive heat are expected to occur more frequently in the future due to climate change, which would reduce the yields of important crops like maize, wheat, and rice which may jeopardize the food security of human populations. The plant microbiomes are a varied and taxonomically organized microbial community that is connected to plants. By supplying nutrients and water to plants, and regulating their physiology and metabolism, plant microbiota frequently helps plants develop and tolerate abiotic stresses, which can boost crop yield under abiotic stresses. In this present study, with emphasis on temperature, salt, and drought stress, we describe current findings on how abiotic stresses impact the plants, microbiomes, microbe-microbe interactions, and plant-microbe interactions as the way microorganisms affect the metabolism and physiology of the plant. We also explore crucial measures that must be taken in applying plant microbiomes in agriculture practices faced with abiotic stresses.

Functional Analysis of Bna-miR399c-PHO2 Regulatory Module Involved in Phosphorus Stress in Brassica napus

Phosphorus stress is one of the important factors restricting plant growth and development, and the microRNA (miRNA) family is involved in the regulation of the response to plant nutrient stress by repressing the expression of target genes at the post-transcriptional or translational level. miR399 is involved in the transportation of phosphate in multiple plants by improving tolerance to low Pi conditions. However, the effect of miR399 on the response of low Pi stress in rapeseed (Brassica napus L.) is unclear. The present study showed a significant increase in taproot length and lateral root number of plants overexpressing Bna-miR399c, while the biomass and Pi accumulation in shoots and roots increased, and the anthocyanin content decreased and chlorophyll content improved under low Pi stress. The results illustrate that Bna-miR399c could enhance the uptake and transportation of Pi in soil, thus making B. napus more tolerant to low Pi stress. Furthermore, we confirmed that BnPHO2 is one of the targets of Bna-miR399c, and the rejection of Pi in rapeseed seedlings increased due to the overexpression of BnPHO2. Hence, we suggest that miR399c-PHO2 module can effectively regulate the homeostasis of Pi in B. napus. Our study can also provide the theoretical basis for germplasm innovation and the design of intelligent crops with low nutrient input and high yield to achieve the dual objectives of income and yield increase and environmental protection in B. napus.

Maize-soybean relay strip intercropping reshapes the rhizosphere bacterial community and recruits beneficial bacteria to suppress Fusarium root rot of soybean

Rhizosphere microbes play a vital role in plant health and defense against soil-borne diseases. Previous studies showed that maize-soybean relay strip intercropping altered the diversity and composition of pathogenic Fusarium species and biocontrol fungal communities in the soybean rhizosphere, and significantly suppressed soybean root rot. However, whether the rhizosphere bacterial community participates in the regulation of this intercropping on soybean root rot is not clear. In this study, the rhizosphere soil of soybean healthy plants was collected in the continuous cropping of maize-soybean relay strip intercropping and soybean monoculture in the fields, and the integrated methods of microbial profiling, dual culture assays in vitro, and pot experiments were employed to systematically investigate the diversity, composition, and function of rhizosphere bacteria related to soybean root rot in two cropping patterns. We found that intercropping reshaped the rhizosphere bacterial community and increased microbial community diversity, and meanwhile, it also recruited much richer and more diverse species of Pseudomonas sp., Bacillus sp., Streptomyces sp., and Microbacterium sp. in soybean rhizosphere when compared with monoculture. From the intercropping, nine species of rhizosphere bacteria displayed good antagonism against the pathogen Fusarium oxysporum B3S1 of soybean root rot, and among them, IRHB3 (Pseudomonas chlororaphis), IRHB6 (Streptomyces), and IRHB9 (Bacillus) were the dominant bacteria and extraordinarily rich. In contrast, MRHB108 (Streptomyces virginiae) and MRHB205 (Bacillus subtilis) were the only antagonistic bacteria from monoculture, which were relatively poor in abundance. Interestingly, introducing IRHB3 into the cultured substrates not only significantly promoted the growth and development of soybean roots but also improved the survival rate of seedlings that suffered from F. oxysporum infection. Thus, this study proves that maize-soybean relay strip intercropping could help the host resist soil-borne Fusarium root rot by reshaping the rhizosphere bacterial community and driving more beneficial microorganisms to accumulate in the soybean rhizosphere.

γ-Aminobutyric acid (GABA) improves pesticide detoxification in plants

It is important to ensure food safety to study the technology and mechanism of pesticide residues degradation in crops. Though γ-aminobutyric acid (GABA) has been widely reported to involve in plant stress resistance, whether exogenous application or endogenous regulation of GABA by gene-editing technology can promote the pesticide detoxification is not clear in plants. Using tomato and chlorothalonil (CHT) as research models, we discovered that exogenous application of GABA or endogenous elevation of GABA by knockout of pyruvate-dependent GABA transaminase promoted both CHT metabolism and plant stress tolerance to CHT. This is closely related to the active adaptation of GABA to CHT stress by regulating the plant GABA shunt pathway and polyamine pathway. The transcriptome data revealed 17 target genes that may be closely related to the involvement of GABA in CHT metabolism, including 4 peroxidases, 5 glycosyltransferases, 4 glutathione S-transferases, and 4 ABC transporters. In addition, the glutathione detoxification pathway and antioxidative enzyme also actively participated in the GABA-induced CHT detoxification process, which played an important role in relieving CHT stress. As a result, GABA significantly increased the photosynthetic capacity of tomato leaves under CHT stress. While studying photosynthesis, we unexpectedly found that GABA promotes stomatal closure in terms of decreased stomatal conductance and stomatal diameter. This result implies that GABA can reduce CHT absorption by regulating stomatal movement in leaves. Together, we provided a novel viewpoint that foliar application of GABA or metabolic engineering of GABA is an effective approach to reduce the risk of pesticide contamination in crop production.

Recent advances in methods for in situ root phenotyping

Roots assist plants in absorbing water and nutrients from soil. Thus, they are vital to the survival of nearly all land plants, considering that plants cannot move to seek optimal environmental conditions. Crop species with optimal root system are essential for future food security and key to improving agricultural productivity and sustainability. Root systems can be improved and bred to acquire soil resources efficiently and effectively. This can also reduce adverse environmental impacts by decreasing the need for fertilization and fresh water. Therefore, there is a need to improve and breed crop cultivars with favorable root system. However, the lack of high-throughput root phenotyping tools for characterizing root traits in situ is a barrier to breeding for root system improvement. In recent years, many breakthroughs in the measurement and analysis of roots in a root system have been made. Here, we describe the major advances in root image acquisition and analysis technologies and summarize the advantages and disadvantages of each method. Furthermore, we look forward to the future development direction and trend of root phenotyping methods. This review aims to aid researchers in choosing a more appropriate method for improving the root system.

Genomics-Assisted Improvement of Super High-Yield Hybrid Rice Variety "Super 1000" for Resistance to Bacterial Blight and Blast Diseases

The two-line rice hybrid "Super 1000" (GX24S × R900) represents a major landmark achievement of breeding for super-hybrid rice in China. However, both male parent R900 and hybrid "Super 1000" have an obvious defect of high susceptibility to rice bacterial blight (BB) and blast. Thus, improving disease resistance and maintaining the original high-yield capacity are essential for the sustainable application of "Super 1000." In this study, the application of closely linked single-nucleotide polymorphism (SNP) markers for foreground selection of dominant resistance gene loci together with genome-wide SNP markers for the background selection rapidly improved the disease resistance of R900 without disturbing its high-yield capacity. A series of improved R900 lines (iR900, in BC2Fn and BC3Fn generations) were developed to stack resistance genes (Xa23+Pi9, Xa23+Pi1+Pi2/9) by marker-assisted backcrossing and field selection for phenotypes, and further crossed with the female line GX24S to obtain improved hybrid variety Super 1000 (iS1000). The genetic backgrounds of iS1000 and "Super 1000" were profiled by using a 56 K SNP-Chip, and results showed that they shared 98.76% of similarity. Meanwhile, evaluation of the field disease resistance showed that the iR900 lines and iS1000 hybrids possess significantly enhanced resistance to both BB and rice blast. Resistance spectrum assays revealed that the iR900 lines and their derived hybrids exhibited high-level resistance to 28 Xoo strains tested, and enhanced resistance to leaf blast at the seedling stage when infected with 38 Magnaporthe oryzae isolates. Between 2019 and 2020, the multi-location field trials across the middle and lower reaches of the Yangtze River were launched and showed that the iS1000 slightly out-yielded than the original variety. In a large-scale demonstration site (6.73 ha, Yunnan, China), the iS1000 achieved 17.06 t/hm2 of yield in 2019. Moreover, the high similarity was observed in main agronomic traits and grain quality when comparing the improved lines/hybrids to original ones (iR900 vs. R900, iS1000 vs. S1000). This work presented a typical genomics-assisted breeding strategy and practice, which involves in directional introgression and rapid stack of multiple disease resistance genes, endowing the super-high-yield hybrid rice variety with holistic disease resistance but without yield penalty.

Effects of Rhizobia Isolated from Coffee Fields in the High Jungle Peruvian Region, Tested on Phaseolus vulgaris L. var. Red Kidney

Soils in the high jungle region of Peru continuously face erosion due to heavy rain, which leads to significant nutrient losses. Leguminous plants may provide a sustainable solution to this problem due to their ability to fix atmospheric nitrogen with the help of symbiotic rhizospheric microbes that reside in their root nodules and help restore soil fertility. The aim of this study was to isolate native rhizobial strains that can form functional nodules in red kidney beans to help improve their growth, development, and yield in field conditions. Rhizobium strains were isolated from soil samples collected from coffee fields using bean plants as trap hosts. The strain RZC12 was selected because it showed good root nodule promotion and a number of PGPR (plant-growth-promoting rhizobacteria) attributes. In the field, bean plants inoculated with the strain RZC12 and co-cultivated with coffee plants produced approximately 21 nodules per plant, whereas control plants produced an average of 1 nodule each. The inoculation with RZC12 significantly increased plant length (72.7%), number of leaves (58.8%), fresh shoot weight (85.5%), dry shoot weight (78%), fresh root weight (85.7%), and dry root weight (82.5%), compared with the control. The dry pod weight produced by the plants inoculated with RZC12 was 3.8 g, whereas the control plants produced 2.36 g of pods. In conclusion, RZC12 is a promising strain that can be used in field conditions to improve the overall productivity of red kidney beans.

Connecting primary and specialized metabolism: Amino acid conjugation of phytohormones by GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetases

GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetases catalyze the ATP-dependent conjugation of phytohormones with amino acids. Traditionally, GH3 proteins are associated with synthesis of the bioactive jasmonate hormone (+)-7- iso -jasmonoyl-l-isoleucine (JA-Ile) and conjugation of indole-3-acetic acid (IAA) with amino acids that tag the hormone for degradation and/or storage. Modifications of JA and IAA by GH3 acyl acid amido synthetases help maintain phytohormones homeostasis. Recent studies broaden the roles of GH3 proteins to include the regulation of JA biosynthesis; the modification of other auxins (i.e., phenylacetic acid and indole-3-butyric acid); the conjugation of auxinic herbicides, such as 4-dichlorophenoxyacetic acid, 4-(2,4-dichlorophenoxy)butyric acid, and dicamba; and the missing step in the isochorismate pathway for the biosynthesis of salicylic acid. The GH3 protein family joins the growing number of versatile enzyme families that blur the line between primary and specialized metabolism for an increasing range of biology functions.

The effects of biochar soil amendment on rice growth may vary greatly with rice genotypes

While plant growth promotion with increased nutrient uptake had been well addressed for biochar soil amendment in agriculture, there was limited knowledge on the variation of such effects with crop genotypes. In a rice field experiment without and with biochar soil amendment at 20 t ha^-1, 19 mutants of a rice cultivar Wuyunjing 7 (Oryza sativa L.) were tested for plant growth in split plots respectively. At harvest, the biomass of grain, stem and leaves were measured and soil and plant samples were collected for measuring N, P and K nutrients. Across the 19 mutants, relative change with biochar soil amendment varied in a range of -41.6% to +35.6% for biomass production and agronomic traits, and -87.0% to +117% for nutrient accumulation. For the nutrients content, the relative change for N was seen in a narrow range of -29.4% to +16.6%, being similar among grain, leaf and shoot samples while that for P in a wide range of -109% to +105%. With factor analysis, variation of biomass and nutrient uptake was least explained with biochar effect (up to 7.0%) but largely by genotype effect (mostly by 40-70%). However, the genotype × biochar interaction effect could also explain 10-40% of the total variations though the interaction explained 40-70% of leaf P variation. Therefore, mutant and mutant × biochar interactions dominated the agronomic variation of rice production of the Wuyunjing 7 cultivar. Furthermore, across the traits analyzed, genotype effects were shown very significantly but negatively correlated to biochar effects. In other words, biochar soil amendment provided little growth or nutrient enhancement for those mutants bred for high efficiency. Hence, genotype selection should be considered in optimizing prioritizing biochar application in crop production. Of course, variation of biochar effect with crop genotypes deserved further plant physio-ecological studies.

Microbial Responses to the Reduction of Chemical Fertilizers in the Rhizosphere Soil of Flue-Cured Tobacco

The overuse of chemical fertilizers has resulted in the degradation of the physicochemical properties and negative changes in the microbial profiles of agricultural soil. These changes have disequilibrated the balance in agricultural ecology, which has resulted in overloaded land with low fertility and planting obstacles. To protect the agricultural soil from the effects of unsustainable fertilization strategies, experiments of the reduction of nitrogen fertilization at 10, 20, and 30% were implemented. In this study, the bacterial responses to the reduction of nitrogen fertilizer were investigated. The bacterial communities of the fertilizer-reducing treatments (D10F, D20F, and D30F) were different from those of the control group (CK). The alpha diversity was significantly increased in D20F compared to that of the CK. The analysis of beta diversity revealed variation of the bacterial communities between fertilizer-reducing treatments and CK, when the clusters of D10F, D20F, and D30F were separated. Chemical fertilizers played dominant roles in changing the bacterial community of D20F. Meanwhile, pH, soil organic matter, and six enzymes (soil sucrase, catalase, polyphenol oxidase, urease, acid phosphatase, and nitrite reductase) were responsible for the variation of the bacterial communities in fertilizer-reducing treatments. Moreover, four of the top 20 genera (unidentified JG30-KF-AS9, JG30-KF-CM45, Streptomyces, and Elsterales) were considered as key bacteria, which contributed to the variation of bacterial communities between fertilizer-reducing treatments and CK. These findings provide a theoretical basis for a fertilizer-reducing strategy in sustainable agriculture, and potentially contribute to the utilization of agricultural resources through screening plant beneficial bacteria from native low-fertility soil.

Envisioning Complex Futures: Collective Narratives and Reasoning in Deliberations over Gene Editing in the Wild

The development of technologies for gene editing in the wild has the potential to generate tremendous benefit, but also raises important concerns. Using some form of public deliberation to inform decisions about the use of these technologies is appealing, but public deliberation about them will tend to fall back on various forms of heuristics to account for limited personal experience with these technologies. Deliberations are likely to involve narrative reasoning-or reasoning embedded within stories. These are used to help people discuss risks, processes, and fears that are otherwise difficult to convey. In this article, we identify three forms of collective narrative that are particularly relevant to debates about modifying genes in the wild. Our purpose is not to privilege any particular narrative, but to encourage people involved in deliberations to make these narratives transparent. Doing so can help guard against the way some narratives-referred to here as "crafted narratives"-may be manipulated by powerful elites and concentrated economic interests for their own strategic ends.

Genetic Variation for Traits Related to Phosphorus Use Efficiency in Lens Species at the Seedling Stage

Phosphorus (P) is an essential, non-renewable resource critical for crop productivity across the world. P is immobile in nature and, therefore, the identification of novel genotypes with efficient P uptake and utilization under a low P environment is extremely important. This study was designed to characterize eighty genotypes of different Lens species for shoot and root traits at two contrasting levels of P. A significant reduction in primary root length (PRL), total surface area (TSA), total root tips (TRT), root forks (RF), total dry weight (TDW), root dry weight (RDW) and shoot dry weight (SDW) in response to P deficiency was recorded. A principal component analysis revealed that the TDW, SDW and RDW were significantly correlated to P uptake and utilization efficiency in lentils. Based on total dry weight (TDW) under low P, L4727, EC718309, EC714238, PL-97, EC718348, DPL15, PL06 and EC718332 were found promising. The characterization of different Lens species revealed species-specific variations for the studied traits. Cultivated lentils exhibited higher P uptake and utilization efficiency as compared to the wild forms. The study, based on four different techniques, identified EC714238 as the most P use-efficient genotype. The genotypes identified in this study can be utilized for developing mapping populations and deciphering the genetics for breeding lentil varieties suited for low P environments.

Cytochrome P450-catalyzed biosynthesis of furanoditerpenoids in the bioenergy crop switchgrass (Panicum virgatum L.)

Specialized diterpenoid metabolites are important mediators of plant-environment interactions in monocot crops. To understand metabolite functions in plant environmental adaptation that ultimately can enable crop improvement strategies, a deeper knowledge of the underlying species-specific biosynthetic pathways is required. Here, we report the genomics-enabled discovery of five cytochrome P450 monooxygenases (CYP71Z25-CYP71Z29) that form previously unknown furanoditerpenoids in the monocot bioenergy crop Panicum virgatum (switchgrass). Combinatorial pathway reconstruction showed that CYP71Z25-CYP71Z29 catalyze furan ring addition directly to primary diterpene alcohol intermediates derived from distinct class II diterpene synthase products. Transcriptional co-expression patterns and the presence of select diterpenoids in switchgrass roots support the occurrence of P450-derived furanoditerpenoids in planta. Integrating molecular dynamics, structural analysis and targeted mutagenesis identified active site determinants that contribute to the distinct catalytic specificities underlying the broad substrate promiscuity of CYP71Z25-CYP71Z29 for native and non-native diterpenoids.

Microbiome influence on host community dynamics: Conceptual integration of microbiome feedback with classical host-microbe theory

Microbiomes have profound effects on host fitness, yet we struggle to understand the implications for host ecology. Microbiome influence on host ecology has been investigated using two independent frameworks. Classical ecological theory powerfully represents mechanistic interactions predicting environmental dependence of microbiome effects on host ecology, but these models are notoriously difficult to evaluate empirically. Alternatively, host-microbiome feedback theory represents impacts of microbiome dynamics on host fitness as simple net effects that are easily amenable to experimental evaluation. The feedback framework enabled rapid progress in understanding microbiomes' impacts on plant ecology, and can also be applied to animal hosts. We conceptually integrate these two frameworks by deriving expressions for net feedback in terms of mechanistic model parameters. This generates a precise mapping between net feedback theory and classic population modelling, thereby merging mechanistic understanding with experimental tractability, a necessary step for building a predictive understanding of microbiome influence on host ecology.

Recomposition and storage of sunlight with intelligent phosphors for enhanced photosynthesis

This work presents a smart solar energy regulation strategy using photon tunable long persistent phosphors as solar energy harvesting antennas to enhance overall sunlight utilization by photosynthetic organisms in multiple modes.

Rapid Generation and Analysis of a Barley Doubled Haploid Line with Higher Nitrogen Use Efficiency Than Parental Lines by F1 Microspore Embryogenesis

Creating varieties with high nitrogen use efficiency (NUE) is crucial for sustainable agriculture development. In this study, a superior barley doubled haploid line (named DH45) with improved NUE was produced via F₁ microspore embryogenesis with three rounds of screening in different nitrogen levels by hydroponic and field experiments. The molecular mechanisms responsible for the NUE of DH45 surpassing that of its parents were investigated by RNA-seq analysis. A total of 1027 differentially expressed genes (DEGs) were identified that were up- or down-regulated in DH45 under low nitrogen conditions but showed no significant differences in the parents. GO analysis indicated that genes involved in nitrogen compound metabolic processes were significantly enriched in DH45 compared with the parents. KEGG analysis showed the MAPK signaling pathway plant to be highly enriched in DH45 relative to its parents, as well as genes involved in alanine, aspartate and glutamate metabolism, and arginine biosynthesis. In conclusion, our study revealed the potential to fix trait superiority in a line by combining crossing with F₁ microspore culture technologies in future crop breeding and also identified several candidate genes that are expressed in shoots and may enable barley to cope with low-nitrogen stress.

Identification of Plant Growth Promoting Rhizobacteria That Improve the Performance of Greenhouse-Grown Petunias under Low Fertility Conditions

The production of greenhouse ornamentals relies on high fertilizer inputs to meet scheduling deadlines and quality standards, but overfertilization has negative environmental impacts. The goals of this study were to identify plant-growth-promoting rhizobacteria (PGPR) that can improve greenhouse ornamental crop performance with reduced fertilizer inputs, and to identify the best measurements of plant performance for assessing the beneficial impact of PGPR on ornamentals. A high-throughput greenhouse trial was used to identify 14 PGPR isolates that improved the flower/bud number and shoot dry weight of Petunia × hybrida ‘Picobella Blue’ grown under low fertility conditions in peat-based media. These 14 PGPR were then applied to petunias grown under low fertility conditions (25 mg L⁻¹ N). PGPR-treated plants were compared to negative (untreated at 25 mg L⁻¹ N) and positive (untreated at 50, 75, 100, and 150 mg L⁻¹ N) controls. Multiple parameters were measured in the categories of flowering, vegetative growth, and vegetative quality to determine the best measurements to assess improvements in ornamental plant performance. Caballeronia zhejiangensis C7B12-treated plants performed better in almost all parameters and were comparable to untreated plants fertilized with 50 mg L⁻¹ N. Genomic analysis identified genes that were potentially involved in plant growth promotion. Our study identified potential PGPR that can be used as biostimulants to produce high-quality greenhouse ornamentals with lower fertilizer inputs.

Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics

Recent studies have demonstrated that drought leads to dramatic, highly conserved shifts in the root microbiome. At present, the molecular mechanisms underlying these responses remain largely uncharacterized. Here we employ genome-resolved metagenomics and comparative genomics to demonstrate that carbohydrate and secondary metabolite transport functionalities are overrepresented within drought-enriched taxa. These data also reveal that bacterial iron transport and metabolism functionality is highly correlated with drought enrichment. Using time-series root RNA-Seq data, we demonstrate that iron homeostasis within the root is impacted by drought stress, and that loss of a plant phytosiderophore iron transporter impacts microbial community composition, leading to significant increases in the drought-enriched lineage, Actinobacteria. Finally, we show that exogenous application of iron disrupts the drought-induced enrichment of Actinobacteria, as well as their improvement in host phenotype during drought stress. Collectively, our findings implicate iron metabolism in the root microbiome's response to drought and may inform efforts to improve plant drought tolerance to increase food security.

Introduction to emerging technologies in plant science

In recent years, an array of new technologies is propelling plant science in exciting directions and facilitating the integration of data across multiple scales. These tools come at a critical time. With an expanding global population and the need to provide food in sustainable ways, we as a civilization will be asking more of plants and plant biologists than ever before. This special issue on emerging technologies in plant science brings together a set of reviews that spotlight a range of approaches that are changing how we ask questions and allow scientific inquiry from macromolecular to ecosystem scales.

High Resistance of a Sludge Enriched with Nitrogen-Fixing Bacteria to Ammonium Salts and Its Potential as a Biofertilizer

The increasing use of chemical fertilizers causes the loss of natural biological nitrogen fixation in soils, water eutrophication and emits more than 300 Mton CO₂ per year. It also limits the success of external bacterial inoculation in the soil. Nitrogen fixing bacteria can be inhibited by the presence of ammonia as its presence can inhibit biological nitrogen fixation. Two aerobic sludges from wastewater treatment plants (WWTP) were exposed to high ammonium salts concentrations (>450 mg L⁻¹ and >2 dS m⁻¹). Microbial analysis after treatment through 16S pyrosequencing showed the presence of Fluviicola sp. (17.70%), a genus of the Clostridiaceae family (11.17%), and Azospirillum sp. (10.42%), which were present at the beginning with lower abundance. Denaturing gradient gel electrophoresis (DGGE) analysis based on nifH genes did not show changes in the nitrogen-fixing population. Nitrogen-Fixing Bacteria (NFB) were identified and associated with other microorganisms involved in the nitrogen cycle, presumably for survival at extreme conditions. The potential use of aerobic sludges enriched with NFB is proposed as an alternative to chemical fertilizer as this bacteria could supplement nitrogen to the plant showing competitive results with chemical fertilization.

4D surface shape measurement system with high spectral resolution and great depth accuracy

A 4D surface shape measurement system that combines spectral detection and 3D surface morphology measurements is proposed, which can realize high spectral resolution and great depth accuracy (HSDA system). A starring hyperspectral imager system based on a grating generates precise spectral data, while a structured light stereovision system reconstructs target morphology as a 3D point cloud. The systems are coupled using a double light path module, which realize point-to-point correspondence of the systems' image planes. The spectral and 3D coordinate data are fused and transformed into a 4D data set. The HSDA system has excellent performance with a spectral resolution of 3 nm and depth accuracy of 27.5 μm. A range of 4D imaging experiments are presented to demonstrate the capabilities and versatility of the HSDA system, which show that it can be used in broad range of application areas, such as fluorescence detection, face anti-spoofing, physical health state assessment and green plant growth condition monitoring.

Potential of indigenous crop microbiomes for sustainable agriculture

The intimate interactions of indigenous crops with their associated microbiomes during long-term co-evolution strengthen the capacity and flexibility of crops to cope with biotic and abiotic stresses. This represents a promising untapped field for searching novel tools to sustainably increase crop productivity. However, the current capability of harnessing the power of indigenous crop microbiomes for sustainable crop production is limited due to low efficiency of separating the targeted functional microbes. Here, we highlight the potential benefits and existing challenges of utilizing indigenous crop microbiomes to reduce agrochemical inputs and increase crop resistance to biotic and abiotic stresses. We propose a framework using Raman-spectroscopy-based single-cell-sorting technology combined with a synthetic community approach to design and optimize a functionally reliable 'beneficial biome' under controlled conditions. This framework will offer opportunities for sustainable agriculture and provide a new direction for future studies.

Recycling of sugar crop disposal to boost the adaptation of canola (Brassica napus L.) to abiotic stress through different climate zones

We need to produce higher foods even under declining natural resources to feed the projected population of 9 billion by 2050 and to sustain food security and nutrition. Abiotic stress has adversely affected canola crop and oil quality especially in sandy soils. To combat this stress, adaptation at the farm level using new and cost-effective amendments are required. Field trials were conducted in two different climatic zones to determine the efficacy of cane molasses, bagasse ash, sugar beet factory lime, and their compost mixtures to improve soil quality and heat stress-adapting canola. The results showed a significant improvement in bulk density, hydraulic conductivity, organic matter content, and available macronutrients of sandy soil and subsequent canola growth, yield, quality and water productivity due to the application of the tested soil amendments, particularly those mixed with compost. Despite the estimated reduction of yield by 18.5% due to heat stress, application of sugar beet lime and compost mixture not only compensated for this reduction but also increased the seed yield by 27.0%. These findings highlight the value of recycling compost-based sugar crop disposal as a cost-effective technology to boost crop tolerance to abiotic stress, ensuring sustainable agriculture and food security in arid environments.

Environmental and genetic regulation of plant height in soybean

BACKGROUND

Shoot architecture is fundamentally crucial to crop growth and productivity. As a key component of shoot architecture, plant height is known to be controlled by both genetic and environmental factors, though specific details remain scarce.

RESULTS

In this study, 308 representative soybean lines from a core collection and 168 F9 soybean progeny were planted at distinct field sites. The results demonstrated the presence of significant genotype × environment interaction (G × E) effects on traits associated with plant height in a natural soybean population. In total, 19 loci containing 51 QTLs (quantitative trait locus) for plant height were identified across four environments, with 23, 13 and 15 being QTLs for SH (shoot height), SNN (stem node number) and AIL (average internode length), respectively. Significant LOD ranging from 2.50 to 16.46 explained 2.80-26.10% of phenotypic variation. Intriguingly, only two loci, Loc11 and Loc19-1, containing 20 QTLs, were simultaneously detected across all environments. Results from Pearson correlation analysis and PCA (principal component analysis) revealed that each of the five agro-meteorological factors and four soil properties significantly affected soybean plant height traits, and that the corresponding QTLs had additive effects. Among significant environmental factors, AD (average day-length), AMaT (average maximum temperature), pH, and AN (available nitrogen) had the largest impacts on soybean plant height. Therefore, in spite of uncontrollable agro-meteorological factors, soybean shoot architecture might be remolded through combined efforts to produce superior soybean genetic materials while also optimizing soil properties.

CONCLUSIONS

Overall, the comprehensive set of relationships outlined herein among environment factors, soybean genotypes and QTLs in effects on plant height opens new avenues to explore in work aiming to increase soybean yield through improvements in shoot architecture.

Overexpression of NtSOS2 From Halophyte Plant N. tangutorum Enhances Tolerance to Salt Stress in Arabidopsis

The Salt Overly Sensitive (SOS) signaling pathway is key in responding to salt stress in plants. SOS2, a central factor in this pathway, has been studied in non-halophytes such as Arabidopsis and rice, but has so far not been reported in the halophyte Nitraria tangutorum. In order to better understand how Nitraria tangutorum acquires its tolerance for a high salt environment, here, the NtSOS2 was cloned from Nitraria tangutorum, phylogenetic analyses showed that NtSOS2 is homologous to the SOS2 of Arabidopsis and rice. Gene expression profile analysis showed that NtSOS2 localizes to the cytoplasm and cell membrane and it can be induced by salt stress. Transgenesis experiments showed that exogenous expression of NtSOS2 reduces leaf mortality and improves the germination rate, biomass and root growth of Arabidopsis under salt stress. Also, exogenous expression of NtSOS2 affected the expression of ion transporter-related genes and can rescue the phenotype of sos2-1 under salt stress. All these results revealed that NtSOS2 plays an important role in plant salt stress tolerance. Our findings will be of great significance to further understand the mechanism of salt tolerance and to develop and utilize molecular knowledge gained from halophytes to improve the ecological environment.

Microbiomes for All

Microbiome research projects are often interdisciplinary, involving fields such as microbiology, genetics, ecology, evolution, bioinformatics, and statistics. These research projects can be an excellent fit for undergraduate courses ranging from introductory biology labs to upper-level capstone courses. Microbiome research projects can attract the interest of students majoring in health and medical sciences, environmental sciences, and agriculture, and there are meaningful ties to real-world issues relating to human health, climate change, and environmental sustainability and resilience in pristine, fragile ecosystems to bustling urban centers. In this review, we will discuss the potential of microbiome research integrated into classes using a number of different modalities. Our experience scaling-up and implementing microbiome projects at a range of institutions across the US has provided us with insight and strategies for what works well and how to diminish common hurdles that are encountered when implementing undergraduate microbiome research projects. We will discuss how course-based microbiome research can be leveraged to help faculty make advances in their own research and professional development and the resources that are available to support faculty interested in integrating microbiome research into their courses.

Plants in the real world: An introduction to the JBC Reviews thematic series

The deep relationship between plants and humans predates civilization, and our reliance on plants as sources of food, feed, fiber, fuels, and pharmaceuticals continues to increase. Understanding how plants grow and overcome challenges to their survival is critical for using these organisms to meet current and future demands for food and other plant-derived materials. This thematic review series on "plants in the real world" presents a set of eight reviews that highlight advances in understanding plant health, including the role of thiamine (vitamin B₁), iron, and the plant immune system; how plants use ethylene and ubiquitin systems to control growth and development; and how new gene-editing approaches, the redesign of plant cell walls, and deciphering herbicide resistance evolution can lead to the next generation of crops.

Potential for Applying Continuous Directed Evolution to Plant Enzymes: An Exploratory Study

Plant evolution has produced enzymes that may not be optimal for maximizing yield and quality in today's agricultural environments and plant biotechnology applications. By improving enzyme performance, it should be possible to alleviate constraints on yield and quality currently imposed by kinetic properties or enzyme instability. Enzymes can be optimized more quickly than naturally possible by applying directed evolution, which entails mutating a target gene in vitro and screening or selecting the mutated gene products for the desired characteristics. Continuous directed evolution is a more efficient and scalable version that accomplishes the mutagenesis and selection steps simultaneously in vivo via error-prone replication of the target gene and coupling of the host cell's growth rate to the target gene's function. However, published continuous systems require custom plasmid assembly, and convenient multipurpose platforms are not available. We discuss two systems suitable for continuous directed evolution of enzymes, OrthoRep in Saccharomyces cerevisiae and EvolvR in Escherichia coli, and our pilot efforts to adapt each system for high-throughput plant enzyme engineering. To test our modified systems, we used the thiamin synthesis enzyme THI4, previously identified as a prime candidate for improvement. Our adapted OrthoRep system shows promise for efficient plant enzyme engineering.

Genomics-enabled analysis of specialized metabolism in bioenergy crops: current progress and challenges

Plants produce a staggering diversity of specialized small molecule metabolites that play vital roles in mediating environmental interactions and stress adaptation. This chemical diversity derives from dynamic biosynthetic pathway networks that are often species-specific and operate under tight spatiotemporal and environmental control. A growing divide between demand and environmental challenges in food and bioenergy crop production has intensified research on these complex metabolite networks and their contribution to crop fitness. High-throughput omics technologies provide access to ever-increasing data resources for investigating plant metabolism. However, the efficiency of using such system-wide data to decode the gene and enzyme functions controlling specialized metabolism has remained limited; due largely to the recalcitrance of many plants to genetic approaches and the lack of 'user-friendly' biochemical tools for studying the diverse enzyme classes involved in specialized metabolism. With emphasis on terpenoid metabolism in the bioenergy crop switchgrass as an example, this review aims to illustrate current advances and challenges in the application of DNA synthesis and synthetic biology tools for accelerating the functional discovery of genes, enzymes and pathways in plant specialized metabolism. These technologies have accelerated knowledge development on the biosynthesis and physiological roles of diverse metabolite networks across many ecologically and economically important plant species and can provide resources for application to precision breeding and natural product metabolic engineering.

Nuclear-encoded synthesis of the D1 subunit of photosystem II increases photosynthetic efficiency and crop yield

In photosynthetic organisms, the photosystem II (PSII) complex is the primary target of thermal damage. Plants have evolved a repair process to prevent the accumulation of damaged PSII. The repair of PSII largely involves de novo synthesis of proteins, particularly the D1 subunit protein encoded by the chloroplast gene psbA. Here we report that the allotropic expression of the psbA complementary DNA driven by a heat-responsive promoter in the nuclear genome sufficiently protects PSII from severe loss of D1 protein and dramatically enhances survival rates of the transgenic plants of Arabidopsis, tobacco and rice under heat stress. Unexpectedly, we found that the nuclear origin supplementation of the D1 protein significantly stimulates transgenic plant growth by enhancing net CO2 assimilation rates with increases in biomass and grain yield. These findings represent a breakthrough in bioengineering plants to achieve efficient photosynthesis and increase crop productivity under normal and heat-stress conditions.

Rethinking sources of nitrogen to cereal crops

Understanding how to manage N inputs to identify the practices that maximize N recovery has been an organizing principle of agronomic research. Because growth in N fertilizer inputs is expected to continue in an ongoing effort to boost crop production over coming decades, understanding how to efficiently manage recovery of fertilizer N will be important going forward. Yet synthesis of published data that has traced the fate of ¹⁵ N-labeled fertilizer shows that less than half of the N taken up by crops is derived from current-year N fertilizer. The source of the majority of N in crops is something other than current-year fertilizer and the sources are not really known. This is true for maize (only 41% of N in crops was from current-year N fertilizer), rice (32%), and small grains (37%). Recovery of organic fertilizer N (manure, green manure, compost, etc.) in crops is low (27%), though N recovery in subsequent years (10%) was greater than that for mineral fertilizers. Thus, while research on efficiency of N fertilizer use through improved rate, type, location, and timing is important, this research fails to directly address management of the majority of the N supplied to crops. It seems likely that the majority of non-fertilizer N found in crops comes from turnover of soil and crop residue N. We encourage the research community to revisit the mental model that fertilizer is a replacement for N supply from turnover of soil organic N (SON) and consider a model in which N fertilizer augments ongoing SON turnover and makes an important longer term contribution to SON maintenance and turnover. Research focused on the efficient recovery of N current-year fertilizer inputs neglects this potential role for building soil N and managing soil N turnover, which seems likely to be the most important source of crop N.

Transcriptome analysis in roots and leaves of wheat seedlings in response to low-phosphorus stress

Low phosphorus availability is a major abiotic factor constraining wheat growth. The molecular mechanisms of the wheat whole genome under low-phosphorus stress are still unclear. To obtain information on gene expression in wheat seedlings under low-phosphorus stress, transcriptome sequencing was performed on roots and leaves. The results showed that 2,318 (1,646 upregulated and 672 downregulated) transcripts were differentially expressed in the leaves, and 2,018 (1,310 upregulated and 708 downregulated) were differentially expressed in the roots. Further analysis showed that these differentially expressed genes (DEGs) were mainly enriched in carbon fixation in photosynthetic organs and in carbon metabolism, photosynthesis, glyoxylate and dicarboxylate metabolism and plant-pathogen interaction in both leaves and roots. These pathways were mainly associated with environmental adaptation, energy metabolism and carbohydrate metabolism, suggesting that the metabolic processes were strengthened in wheat seedlings under low-phosphorus stress and that more energy and substances were produced to resist or adapt to this unfavourable environment. This research might provide potential directions and valuable resources to further study wheat under low-phosphorus stress.

Biotechnological strategies for improved photosynthesis in a future of elevated atmospheric CO2

The improvement of photosynthesis using biotechnological approaches has been the focus of much research. It is now vital that these strategies be assessed under future atmospheric conditions. The demand for crop products is expanding at an alarming rate due to population growth, enhanced affluence, increased per capita calorie consumption, and an escalating need for plant-based bioproducts. While solving this issue will undoubtedly involve a multifaceted approach, improving crop productivity will almost certainly provide one piece of the puzzle. The improvement of photosynthetic efficiency has been a long-standing goal of plant biotechnologists as possibly one of the last remaining means of achieving higher yielding crops. However, the vast majority of these studies have not taken into consideration possible outcomes when these plants are grown long-term under the elevated CO₂ concentrations (e[CO₂]) that will be evident in the not too distant future. Due to the considerable effect that CO₂ levels have on the photosynthetic process, these assessments should become commonplace as a means of ensuring that research in this field focuses on the most effective approaches for our future climate scenarios. In this review, we discuss the main biotechnological research strategies that are currently underway with the aim of improving photosynthetic efficiency and biomass production/yields in the context of a future of e[CO₂], as well as alternative approaches that may provide further photosynthetic benefits under these conditions.

A Roadmap for Lowering Crop Nitrogen Requirement

Increasing nitrogen fertilizer applications have sustained a growing world population in the 20th century. However, to avoid any further associated environmental damage, new sustainable agronomic practices together with new cultivars must be developed. To date the concept of nitrogen use efficiency (NUE) has been useful in quantifying the processes of nitrogen uptake and utilization, but we propose a shift in focus to consider nitrogen responsiveness as a more appropriate trait to select varieties with lower nitrogen requirements. We provide a roadmap to integrate the regulation of nitrogen uptake and assimilation into varietal selection and crop breeding programs. The overall goal is to reduce nitrogen inputs by farmers growing crops in contrasting cropping systems around the world, while sustaining yields and reducing greenhouse gas (GHG) emissions.

The role of synthetic biology in climate change mitigation

There is growing agreement that the aim of United Nations Framework Convention on Climate Change, which is to avoid dangerous anthropogenic interference with the climate system, is not likely to be met without inclusion of methods to physically remove atmospheric carbon. A number of approaches have been suggested, but the community appears to be silent on the potential of one of the most revolutionary technologies of the current century, systems and synthetic biology (SSB). The potential of SSB to modulate the fast carbon cycle, and thereby mitigate climate change is in itself enormous, but if the history of genomics is any measure, it is also reasonable to expect sizeable economic returns on any investment. More generally, the approach to climate control has been badly unbalanced. The last three decades have seen intense international attention to emission control, with no parallel plan to test, scale and implement carbon removal technologies, including attention to their economic, legal and ethical implications. REVIEWERS: This article was reviewed by Richard Roberts, Aristides Patrinos, and Eugene Koonin, all of whom were nominated by Itai Yanai. For the full reviews, please go to the Reviewers' comments section.

Structural biology of plant sulfur metabolism: from sulfate to glutathione

Sulfur is an essential element for all organisms. Plants must assimilate this nutrient from the environment and convert it into metabolically useful forms for the biosynthesis of a wide range of compounds, including cysteine and glutathione. This review summarizes structural biology studies on the enzymes involved in plant sulfur assimilation [ATP sulfurylase, adenosine-5'-phosphate (APS) reductase, and sulfite reductase], cysteine biosynthesis (serine acetyltransferase and O-acetylserine sulfhydrylase), and glutathione biosynthesis (glutamate-cysteine ligase and glutathione synthetase) pathways. Overall, X-ray crystal structures of enzymes in these core pathways provide molecular-level information on the chemical events that allow plants to incorporate sulfur into essential metabolites and revealed new biochemical regulatory mechanisms, such as structural rearrangements, protein-protein interactions, and thiol-based redox switches, for controlling different steps in these pathways.

Effect of drought stress on the genetic architecture of photosynthate allocation and remobilization in pods of common bean (Phaseolus vulgaris L.), a key species for food security

BACKGROUND

Common bean is the most important staple grain legume for direct human consumption and nutrition. It complements major sources of carbohydrates, including cereals, root crop, or plantain, as a source of dietary proteins. It is also a significant source of vitamins and minerals like iron and zinc. To fully play its nutritional role, however, its robustness against stresses needs to be strengthened. Foremost among these is drought, which commonly affects its productivity and seed quality. Previous studies have shown that photosynthate remobilization and partitioning is one of the main mechanisms of drought tolerance and overall productivity in common bean.

RESULTS

In this study, we sought to determine the inheritance of pod harvest index (PHI), a measure of the partitioning of pod biomass to seed biomass, relative to that of grain yield. We evaluated a recombinant inbred population of the cross of ICA Bunsi and SXB405, both from the Mesoamerican gene pool, to determine the effects of intermittent and terminal drought stresses on the genetic architecture of photosynthate allocation and remobilization in pods of common bean. The population was grown for two seasons, under well-watered conditions and terminal and intermittent drought stress in one year, and well-watered conditions and terminal drought stress in the second year. There was a significant effect of the water regime and year on all the traits, at both the phenotypic and QTL levels. We found nine QTLs for pod harvest index, including a major (17% of variation explained), stable QTL on linkage group Pv07. We also found eight QTLs for yield, three of which clustered with PHI QTLs, underscoring the importance of photosynthate remobilization in productivity. We also found evidence for substantial epistasis, explaining a considerable part of the variation for yield and PHI.

CONCLUSION

Our results highlight the genetic relationship between PHI and yield and confirm the role of PHI in selection of both additive and epistatic effects controlling drought tolerance. These results are a key component to strengthen the robustness of common bean against drought stresses.

Genetic Analysis and Mapping of QTLs for Soybean Biological Nitrogen Fixation Traits Under Varied Field Conditions

Soybean is an important economic and green manure crop that is widely used in intercropping and rotation systems due to its high biological nitrogen fixation (BNF) capacity and the resulting reduction in N fertilization. However, the genetic mechanisms underlying soybean BNF are largely unknown. Here, two soybean parent genotypes contrasting in BNF traits and 168 F_9:11 recombinant inbred lines (RILs) were evaluated under four conditions in the field. The parent FC1 always produced more big nodules, yet fewer nodules in total than the parent FC2 in the field. Furthermore, nodulation in FC1 was more responsive to environmental changes than that in FC2. Broad-sense heritability (h² _b ) for all BNF traits varied from 0.48 to 0.87, which suggests that variation in the observed BNF traits was primarily determined by genotype. Moreover, two new QTLs for BNF traits, qBNF-16 and qBNF-17, were identified in this study. The qBNF-16 locus was detected under all of the four tested conditions, where it explained 15.9-59.0% of phenotypic variation with LOD values of 6.31-32.5. Meanwhile qBNF-17 explained 12.6-18.6% of observed variation with LOD values of 4.93-7.51. Genotype group analysis indicated that the FC1 genotype of qBNF-16 primarily affected nodule size (NS), while the FC2 genotype of qBNF-16 promoted nodule number (NN). On the other hand, the FC1 genotype of qBNF-17 influenced NN and the FC2 genotype of qBNF-17 impacted NS. The results on the whole suggest that these two QTLs might be valuable markers for breeding elite soybean varieties with high BNF capacities.