Basic Plant Science Research Articles

The 33rd International Conference on Arabidopsis Research (ICAR2023).

The 33rd International Conference on Arabidopsis Research (ICAR2023) was held at Makuhari Messe International Conference Hall in Chiba prefecture from June 5 to 9, 2023. This annual conference, which rotates among hosts in North America, Asia-Oceania, and Europe, covers the full range of plant biology research involving Arabidopsis and other plant species. The conference hosted more than 1200 participants, including approximately 800 international attendees from 42 countries (or regions), and featured about 900 oral and poster presentations. Reflecting the conference theme, "Arabidopsis for Sustainable Development Goals (SDGs)," there were numerous exemplary presentations regarding basic plant science using Arabidopsis and translational research conducted to achieve SDGs by exploiting the knowledge gained from Arabidopsis to improve crop production. The conference concluded on a high note, with more than 99% of survey respondents expressing their general satisfaction with ICAR2023. This report aims to summarize the organization, objectives, and outcomes of the conference.

Cas9-Mediated Targeted Mutagenesis in Plants.

Genome engineering technologies enable targeted mutations to be induced at almost any location in plant genomes. In particular, Cas9 nucleases use easily recoded RNA guides to target user-defined sequences and generate double-stranded breaks (DSB) that are then repaired by the cell's endogenous repair mechanisms. Incorrect repair results in mutations at the target. When the targets are in coding sequences, this often results in loss-of-function mutations. In this chapter, we describe a method to rapidly design and assemble RNA-guided Cas9 constructs for plants and test their ability to induce mutations at their intended targets in rapid assays using both Agrobacterium-mediated transient expression and PEG-mediated DNA delivery to protoplasts, the latter of which can be adapted to a wide range of plant species. We describe a PCR-based method for detecting mutagenesis and outline the steps required to segregate the Cas9 transgene from the targeted mutation to enable the production of transgene-free mutated plants. These techniques are amenable to a range of plant species and should accelerate the application of Cas-9-mediated genome engineering for basic plant science as well as crop development.

Plant Bioelectronics and Biohybrids: The Growing Contribution of Organic Electronic and Carbon-Based Materials.

Life in our planet is highly dependent on plants as they are the primary source of food, regulators of the atmosphere, and providers of a variety of materials. In this work, we review the progress on bioelectronic devices for plants and biohybrid systems based on plants, therefore discussing advancements that view plants either from a biological or a technological perspective, respectively. We give an overview on wearable and implantable bioelectronic devices for monitoring and modulating plant physiology that can be used as tools in basic plant science or find application in agriculture. Furthermore, we discuss plant-wearable devices for monitoring a plant’s microenvironment that will enable optimization of growth conditions. The review then covers plant biohybrid systems where plants are an integral part of devices or are converted to devices upon functionalization with smart materials, including self-organized electronics, plant nanobionics, and energy applications. The review focuses on advancements based on organic electronic and carbon-based materials and discusses opportunities, challenges, as well as future steps.

The epigenetic mechanisms regulating floral hub genes and their potential for manipulation.

Gene regulatory networks formed by transcription factors play essential roles in the regulation of gene expression during plant reproductive development. These networks integrate endogenous, phytohormonal, and environmental cues. Molecular genetic, biochemical, and chemical analyses performed mainly in Arabidopsis have identified network hub genes and revealed the contributions of individual components to these networks. Here, I outline current understanding of key epigenetic regulatory circuits identified by research on plant reproduction, and highlight significant recent examples of genetic engineering and chemical applications to modulate the epigenetic regulation of gene expression. Furthermore, I discuss future prospects for applying basic plant science to engineer useful floral traits in a predictable manner as well as the potential side effects.

Gaining Acceptance of Novel Plant Breeding Technologies.

Ensuring the sustainability of agriculture under climate change has led to a surge in alternative strategies for crop improvement. Advances in integrated crop breeding, social acceptance, and farm-level adoption are crucial to address future challenges to food security. Societal acceptance can be slow when consumers do not see the need for innovation or immediate benefits. We consider how best to address the issue of social licence and harmonised governance for novel gene technologies in plant breeding. In addition, we highlight optimised breeding strategies that will enable long-term genetic gains to be achieved. Promoted by harmonised global policy change, innovative plant breeding can realise high and sustainable productivity together with enhanced nutritional traits.

Understanding Plant Hormones: Mechanisms and Functions in Growth and Development

Plant hormones, or phytohormones, are critical regulators of plant growth, development, and responses to environmental stimuli. These bioactive compounds, though present in minute quantities, orchestrate a wide array of physiological processes, including seed germination, root and shoot development, flowering, fruit ripening, and senescence. This review provides a comprehensive overview of the key plant hormones, including auxins, gibberellins, cytokinins, abscisic acid, ethylene, brassinosteroids, jasmonates, and salicylic acid. Each hormone’s biosynthesis, signaling mechanisms, and functional roles are discussed, highlighting their contributions to various aspects of plant life. Additionally, the review explores how these hormones interact with each other in complex networks to modulate plant responses to internal and external cues. By delving into the intricate hormonal regulatory systems, this review aims to enhance our understanding of how plants coordinate growth and adapt to changing environments. Insights into these hormonal mechanisms not only advance basic plant science but also offer practical applications in agriculture and horticulture, potentially leading to improved crop management, stress resistance, and yield enhancement.

Biotechnological Advances in Lycopene β-Cyclases.

Lycopene β-cyclase is one of the key enzymes in the biosynthesis of carotenoids, which catalyzes the β-cyclization of both ends of lycopene to produce β-carotene. Lycopene β-cyclases are found in a wide range of sources, mainly plants and microorganisms. Lycopene β-cyclases have been extensively studied for their important catalytic activity, including for use in genetic engineering to modify plants and microorganisms, as a blocking target for lycopene industrial production strains, and for their genetic and physiological effects related to microorganic and plant biological traits. This review of lycopene β-cyclases summarizes the major studies on their basic classification, functional activity, metabolic engineering, and plant science.

Gloxinia-An Open-Source Sensing Platform to Monitor the Dynamic Responses of Plants.

The study of the dynamic responses of plants to short-term environmental changes is becoming increasingly important in basic plant science, phenotyping, breeding, crop management, and modelling. These short-term variations are crucial in plant adaptation to new environments and, consequently, in plant fitness and productivity. Scalable, versatile, accurate, and low-cost data-logging solutions are necessary to advance these fields and complement existing sensing platforms such as high-throughput phenotyping. However, current data logging and sensing platforms do not meet the requirements to monitor these responses. Therefore, a new modular data logging platform was designed, named Gloxinia. Different sensor boards are interconnected depending upon the needs, with the potential to scale to hundreds of sensors in a distributed sensor system. To demonstrate the architecture, two sensor boards were designed—one for single-ended measurements and one for lock-in amplifier based measurements, named Sylvatica and Planalta, respectively. To evaluate the performance of the system in small setups, a small-scale trial was conducted in a growth chamber. Expected plant dynamics were successfully captured, indicating proper operation of the system. Though a large scale trial was not performed, we expect the system to scale very well to larger setups. Additionally, the platform is open-source, enabling other users to easily build upon our work and perform application-specific optimisations.

Super-Agrobacterium ver. 4: Improving the Transformation Frequencies and Genetic Engineering Possibilities for Crop Plants.

Agrobacterium tumefaciens has been utilized for both transient and stable transformations of plants. These transformation methods have been used in fields such as breeding GM crops, protein production in plant cells, and the functional analysis of genes. However, some plants have significantly lower transient gene transfer and stable transformation rates, creating a technical barrier that needs to be resolved. In this study, Super-Agrobacterium was updated to ver. 4 by introducing both the ACC deaminase (acdS) and GABA transaminase (gabT) genes, whose resultant enzymes degrade ACC, the ethylene precursor, and GABA, respectively. A. tumefaciens strain GV2260, which is similar to other major strains (EHA105, GV3101, LBA4404, and MP90), was used in this study. The abilities of the Super-Agrobacterium ver. 4 were evaluated in Erianthus ravennae, Solanum lycopersicum “Micro-Tom,” Nicotiana benthamiana, and S. torvum. Super-Agrobacterium ver. 4 showed the highest T-DNA transfer (transient transformation) frequencies in E. ravennae and S. lycopersicum, but not in N. benthamiana and S. torvum. In tomato, Super-Agrobacterium ver. 4 increased the stable transformation rate by 3.6-fold compared to the original GV2260 strain. Super-Agrobacterium ver. 4 enables reduction of the amount of time and labor required for transformations by approximately 72%, and is therefore a more effective and powerful tool for plant genetic engineering and functional analysis, than the previously developed strains. As our system has a plasmid containing the acdS and gabT genes, it could be used in combination with other major strains such as EHA105, EHA101, LBA4404, MP90, and AGL1. Super-Agrobacterium ver. 4, could thus possibly be a breakthrough application for improving basic plant science research methods.

Modern Applied Botany: Changes in the perception of applied botanists to themselves and others during the last century.

Subsequent to a short chronicle of the history of applied research in plant biology in Germany, the relevance of modern Applied Botany is illustrated by three relevant post-harvest processes. The metabolic reactions that play a key role in the determination of quality of the related plant-derived commodities from each are presented. Increased understanding of the processes involved in these processes has facilitated improvement of product quality in the resulting products. In each instance, it has been necessary to regard plant metabolism comprehensively and not to focus on a single physiological process. Moreover, the various interactions with the environment have to be considered. These illustrations demonstrate that transfer and application of basic plant knowledge into product-related research can provide significant information that is valuable for improvement of plant-derived products. In some instances, these correlations can even account for traditional and well-established processes, as illustrated for the malting process. However, interdisciplinary work and intensive cooperation with growers and producers must be an integral part of developing feasible and economically acceptable solutions that can be transferred into practice. Ultimately, the major challenge in Applied Botany today is the implementation of new concepts and ideas into product-related research. In consequence, modern Applied Botany acts as a mediator between basic plant science and industrial, product-related research.

Plant Phenotyping: Past, Present, and Future

A plant develops the dynamic phenotypes from the interaction of the plant with the environment. Understanding these processes that span plant’s lifetime in a permanently changing environment is essential for the advancement of basic plant science and its translation into application including breeding and crop management. The plant research community was thus confronted with the need to accurately measure diverse traits of an increasingly large number of plants to help plants to adapt to resource-limiting environment and low-input agriculture. In this overview, we outline the development of plant phenotyping as a multidisciplinary field. We sketch the technological advancement that laid the foundation for the development of phenotyping centers and evaluate the upcoming challenges for further advancement of plant phenotyping specifically with respect to standardization of data acquisition and reusability. Finally, we describe the development of the plant phenotyping community as an essential step to integrate the community and effectively use the emerging synergies.

Translational Research for Climate Resilient, Higher Yielding Crops

Investment in scientific research is generally asymmetrical: it depends on precedents, current trends in science and technology, and economic, political and social agendas. However, asymmetry occasionally leads to bottlenecks that limit delivery of valuable technologies. This review considers the case of translating plant research to crop genetic improvement. Considerable progress has been made in basic plant science in recent decades fueled largely by the revolution in genetics. Meanwhile, human population has continued to grow exponentially, the natural resource base upon which agriculture depends has diminished significantly, and the climate is becoming less conducive to agriculture in general, especially in already food insecure regions. However, although basic research has delivered promising outputs using model crop species, relatively few new ideas have been tested in a mainstream breeding context. Past successful translational research projects—including enhancing the vitamin A content of maize, increasing the ability of rice to tolerate flooding, approaches for improving the yield potential of spring wheat, and traits for increasing the climate resilience of maize and sorghum—required interdisciplinary and often international collaboration to deliver adequate proofs of concept. They were also driven by a visionary approach and the necessary time commitment from the research institutions and funding bodies involved. These attributes are prerequisite for capitalizing on basic plant research and harnessing it to food security.

Plant Phenotyping: Past, Present, and Future.

A plant develops the dynamic phenotypes from the interaction of the plant with the environment. Understanding these processes that span plant's lifetime in a permanently changing environment is essential for the advancement of basic plant science and its translation into application including breeding and crop management. The plant research community was thus confronted with the need to accurately measure diverse traits of an increasingly large number of plants to help plants to adapt to resource-limiting environment and low-input agriculture. In this overview, we outline the development of plant phenotyping as a multidisciplinary field. We sketch the technological advancement that laid the foundation for the development of phenotyping centers and evaluate the upcoming challenges for further advancement of plant phenotyping specifically with respect to standardization of data acquisition and reusability. Finally, we describe the development of the plant phenotyping community as an essential step to integrate the community and effectively use the emerging synergies.

Forward and reverse genetics approaches for combined stress tolerance in rice

Climate change impact on global agricultural food production has been evident in the past few decades. Abiotic factors such as heat, drought, and salinity share a major proportion of crop yield losses and posing a serious threat to global food security. Developing climate resilient crops has become a frontier area of basic plant science and agricultural research. Persistent efforts by scientists to understand crop responses under natural environment and progress in the field of genomics and phenomics has provided unprecedented pace to crop development programs. Rice is the most important cereal crop and staple food for more than 3 billion people worldwide. Heat, drought and salinity stress are the major constraints for global rice production. Hence, efforts are warranted to develop climate-resilient rice cultivars that can produce substantially under different abiotic stresses. Crop plants seldom face single stress in the natural environment. Indeed, heat and drought or drought and salinity are documented as very obvious combinations suggesting multiple stress tolerance as an important breeding target. Forward and reverse genetic tools could effectively contribute towards achieving the target food production to feed the future population despite limiting resources and unfavorable climatic conditions. Genetic approaches adopted for crop improvement programs categorized as forward and reverse genetics are discussed highlighting their potential benefits for tailoring stress tolerant cultivars.

Selectable marker independent transformation of recalcitrant maize inbred B73 and sorghum P898012 mediated by morphogenic regulators BABY BOOM and WUSCHEL2

Key messageDiscriminatory co-expression of maizeBBMandWUStranscriptional factor genes promoted somatic embryogenesis and efficientAgrobacterium-mediated transformation of recalcitrant maize inbred B73 and sorghum P898012 genotypes without use of a selectable marker gene.The use of morphogenic regulators to overcome barriers in plant transformation is a revolutionary breakthrough for basic plant science and crop applications. Current standard plant transformation systems are bottlenecks for genetic, genomic, and crop improvement studies. We investigated the differential use of co-expression of maize transcription factors BABY BOOM and WUSCHEL2 coupled with a desiccation inducible CRE/lox excision system to enable regeneration of stable transgenic recalcitrant maize inbred B73 and sorghum P898012 without a chemical selectable marker. The PHP78891 expression cassette contains CRE driven by the drought inducible maize RAB17M promoter with lox P sites which bracket the CRE, WUS, and BBM genes. A constitutive maize UBIM promoter directs a ZsGreen GFP expression cassette as a reporter outside of the excision sites and provides transient, transgenic, and developmental analysis. This was coupled with evidence for molecular integration and analysis of stable integration and desiccation inducible CRE-mediated excision. Agrobacterium-mediated transgenic introduction of this vector showed transient expression of GFP and induced somatic embryogenesis in maize B73 and sorghum P898012 explants. Subjection to desiccation stress in tissue culture enabled the excision of CRE, WUS, and BBM, leaving the UBIM::GFP cassette and allowing subsequent plant regeneration and GFP expression analysis. Stable GFP expression was observed in the early and late somatic embryos, young shoots, vegetative plant organs, and pollen. Transgene integration and expression of GFP positive T0 plants were also analyzed using PCR and Southern blots. Progeny segregation analysis of primary events confirmed correlation between functional GFP expression and presence of the GFP transgene in T1 plants generated from self pollinations, indicating good transgene inheritance. This study confirms and extends the use of morphogenic regulators to overcome transformation barriers.

Perturbation of H3K27me3-Associated Epigenetic Processes Increases Agrobacterium-Mediated Transformation.

Agrobacterium-mediated transformation is a core technology for basic plant science and agricultural biotechnology. Improving transformation frequency is a major goal for plant transgenesis. We previously showed that T-DNA insertions in some histone genes decreased transformation susceptibility, whereas overexpression of several Arabidopsis H2A and H4 isoforms increased transformation. Overexpression of several histone H2B and H3 isoforms had little effect on transformation frequency. However, overexpression of histone H3-11 (HTR11) enhanced transformation. HTR11 is a unique H3 variant that lacks lysine at positions 9 and 27. The modification status of these lysine residues in canonical H3 proteins plays a critical role in epigenetic determination of gene expression. We mutated histone H3-4 (HTR4), a canonical H3.3 protein that does not increase transformation when overexpressed, by replacing either or both K9 and K27 with the amino acids in HTR11 (either K9I, K27Q, or both). Overexpression of HTR4 with the K27Q but not the K9I substitution enhanced transformation. HTR4K27Q was incorporated into chromatin, and HTR4K27Q overexpression lines exhibited deregulated expression of H3K27me3-enriched genes. These results demonstrate that mutation of K27 in H3.3 is sufficient to perturb H3K27me3-dependent expression in plants as in animals and suggest a distinct epigenetic role for histone HTR11. Further, these observations implicate manipulation of H3K27me3-dependent gene expression as a novel strategy to increase transformation susceptibility.

Biotechnological strategies for studying actinorhizal symbiosis in Casuarinaceae: transgenesis and beyond

Since the recovery of the first transgenic plant in the early 1980s, plant transformation technologies have enabled advances in many aspects of basic plant science, including nitrogen-fixing root endosymbioses. Using the biological vectors Agrobacterium tumefaciens and A. rhizogenes, gene constructs have been successfully introduced in the actinorhizal tree species Casuarina glauca, thereby paving the way for functional analysis of the key genes involved in the symbiotic process with the actinobacterium Frankia. In recent years, not only studies of gene promoters in transgenic Casuarinaceae, but also the use of RNA interference to down-regulate genes of interest, have provided new insights into the early stages of the interaction between the root system and the actinobacterium. Opportunities offered by recent developments in genome editing technologies based on the engineered nucleases ZFNs (zinc-finger nucleases), TALENs (transcription activator-like effector nucleases) and RNA-guided CRISPR-Cas (clustered regularly interspaced short palindromic repeats-associated protein/Cas) will be briefly presented.

Seed vigour and crop establishment: extending performance beyond adaptation.

Seeds are central to crop production, human nutrition, and food security. A key component of the performance of crop seeds is the complex trait of seed vigour. Crop yield and resource use efficiency depend on successful plant establishment in the field, and it is the vigour of seeds that defines their ability to germinate and establish seedlings rapidly, uniformly, and robustly across diverse environmental conditions. Improving vigour to enhance the critical and yield-defining stage of crop establishment remains a primary objective of the agricultural industry and the seed/breeding companies that support it. Our knowledge of the regulation of seed germination has developed greatly in recent times, yet understanding of the basis of variation in vigour and therefore seed performance during the establishment of crops remains limited. Here we consider seed vigour at an ecophysiological, molecular, and biomechanical level. We discuss how some seed characteristics that serve as adaptive responses to the natural environment are not suitable for agriculture. Past domestication has provided incremental improvements, but further actively directed change is required to produce seeds with the characteristics required both now and in the future. We discuss ways in which basic plant science could be applied to enhance seed performance in crop production.

Precision genome editing in plants via gene targeting and piggyBac-mediated marker excision.

Precise genome engineering via homologous recombination (HR)-mediated gene targeting (GT) has become an essential tool in molecular breeding as well as in basic plant science. As HR-mediated GT is an extremely rare event, positive–negative selection has been used extensively in flowering plants to isolate cells in which GT has occurred. In order to utilize GT as a methodology for precision mutagenesis, the positive selectable marker gene should be completely eliminated from the GT locus. Here, we introduce targeted point mutations conferring resistance to herbicide into the rice acetolactate synthase (ALS) gene via GT with subsequent marker excision by piggyBac transposition. Almost all regenerated plants expressing piggyBac transposase contained exclusively targeted point mutations without concomitant re-integration of the transposon, resulting in these progeny showing a herbicide bispyribac sodium (BS)-tolerant phenotype. This approach was also applied successfully to the editing of a microRNA targeting site in the rice cleistogamy 1 gene. Therefore, our approach provides a general strategy for the targeted modification of endogenous genes in plants.

Speaking of food: connecting basic and applied plant science.

The Food and Agriculture Organization (FAO) predicts that food production must rise 70% over the next 40 years to meet the demands of a growing population that is expected to reach nine billion by the year 2050. Many facets of basic plant science promoted by the Botanical Society of America are important for agriculture; however, more explicit connections are needed to bridge the gap between basic and applied plant research. This special issue, Speaking of Food: Connecting Basic and Applied Plant Science, was conceived to showcase productive overlaps of basic and applied research to address the challenges posed by feeding billions of people and to stimulate more research, fresh connections, and new paradigms. Contributions to this special issue thus illustrate some interactive areas of study in plant science-historical and modern plant-human interaction, crop and weed origins and evolution, and the effects of natural and artificial selection on crops and their wild relatives. These papers provide examples of how research integrating the basic and applied aspects of plant science benefits the pursuit of knowledge and the translation of that knowledge into actions toward sustainable production of crops and conservation of diversity in a changing climate.