Plant Biology Research Research Articles

Influence of previous drought exposure on the 3D microstructure of the cambium and developing xylem in Eucalyptus clones: An X-ray CT investigation

Summary In plant biology research, X-ray computed tomography (CT) has been demonstrated to be useful for studying the complex tissues of trees qualitatively and quantitatively. The cambium plays a very important role in plant growth and development. However, this tissue is relatively poorly studied due to its complex nature and its localization between layers of xylem and phloem cells. Antecedent environmental conditions may have a substantial impact on plant responses to drought and recovery dynamics. Therefore, this study aimed to investigate the impact of previous drought exposure on the 3D microstructure of two commercial Eucalyptus clones by monitoring the development of the cambium, in the same plant and same area of cambial tissue, during a 4-week trial consisting of well-watered, mild drought, severe drought, and rewatering phases. To track microstructural changes, the plants were imaged weekly with non-destructive X-ray micro-computed tomography (μCT). On the last day of the experiment, X-ray nano-CT was also performed. Our results indicate that trees subjected to earlier well-watered conditions were more affected by the severe drought, compared to those previously exposed to mild drought conditions. Thus, previous exposure to water deficit may provide the benefit of increased drought tolerance during future water deficit. Previous mild drought exposure can facilitate morphological adjustments, which potentially enhances drought tolerance during subsequent drought events.

Transcriptome-guided selection of stable reference genes for expression analysis in spinach.

Accurate measurement of gene expression levels is vital for advancing plant biology research. This study explores the identification and validation of stable reference genes (RGs) for gene expression analysis in Spinacia oleracea. Leveraging transcriptome data from various developmental stages, we employed rigorous statistical analyses to identify potential RGs. A total of 1196 candidate genes were initially screened based on expression variability, with subsequent refinement using criteria such as low variance and stability. Among 12 commonly used candidate RGs, EF1α and H3 emerged as the most stable across diverse experimental conditions, while GRP and PPR exhibited lower stability. These findings were further validated through qRT-PCR assays and comprehensive statistical analyses, including geNorm, NormFinder, BestKeeper, and RefFinder. Our study underscores the importance of systematic RG selection to ensure accurate normalization in gene expression studies, particularly in the context of S. oleracea developmental stages and physiological processes like flowering. These validated RGs provide a robust foundation for future gene expression analysis in S. oleracea and contribute to the advancement of molecular research in plant biology.

Current challenges for plant biology research in the Global South.

In an attempt to address the large inequities faced by the plant biology communities from the Global South (i.e. countries located around the tropics and the Southern Hemisphere) at international conferences, this Viewpoint is the reflexive thinking arising from the concurrent session titled 'Arabidopsis and its translational research in the Global South' organized at the International Conference of Arabidopsis Research 2023 (ICAR 2023) in Chiba, Japan in June 2023. Here, we highlight the main obstacles plant biology communities in the Global South face in terms of knowledge production, as measured by the unequal production and citation of publications, investigating and advancing local plant genomics and biodiversity, combating disparities in gender and diversity, and current initiatives to break isolation of scientists.

The need for a strict delimitation of early tree life stages in vegetation ecology

AbstractAimFor practical and theoretical purposes, ecological studies commonly classify trees into five major life‐cycle stages: seed, seedling, sapling, juvenile and adult. Whereas the seed and adult stages are usually accurately delimited across studies, there are discrepancies and ambiguity in the categorization of seedlings, saplings and juveniles, which can significantly affect the conclusions of community ecology studies. Here we propose a standardized set of criteria intended for community‐level research for delimiting these three stages based on biological and ecological rationales.MethodsWe assessed the relevance of such standardization by conducting a meta‐analysis of the effects of two human‐caused disturbances (defaunation and logging) on each early tree life stage and examining differences in effect sizes and confidence intervals among: (1) studies that match our delimitation criteria, (2) studies that do not match these criteria, and (3) all studies grouped together regardless of the criteria they used.ResultsWe found stronger effects with narrower confidence intervals when considering only the studies that matched our standardized delimitation criteria. In fact, the proportion of significant effects was between 1.7 (defaunation) and 5.4 (logging) times higher in studies matching our delimitation criteria than in studies that do not match them, probably because confidence intervals were 2.3–3.1 times smaller in the former group than in the latter. For logging studies, the direction of the effects changed in 30%–50% of the cases when comparing the results from all data and studies not matching our criteria with the results of the studies matching our criteria, always from non‐significant to significant effects.ConclusionsThese findings underscore the need for an ecologically meaningful categorization of early tree life stages based on standardized measures to increase the confidence, accuracy, reproducibility and generalization in plant biology and community ecological research. Synthesis efforts will particularly benefit from this standardized protocol.

Analysis of plant pararetrovirus promoter sequence(s) for developing a useful synthetic promoter with enhanced activity in rice, pearl millet, and tobacco plants.

Promoters are one of the most important components for many gene-based research as they can fine-tune precise gene expression. Many unique plant promoters have been characterized, but strong promoters with dual expression in both monocot and dicot systems are still lacking. In this study, we attempted to make such a promoter by combining specific domains from monocot-infecting pararetroviral-based promoters sugarcane bacilliform virus (SCBV) and banana streak virus (BSV) to a strong dicot-infecting pararetroviral-based promoter mirabilis mosaic virus (MMV). The generated chimeric promoters, MS, SM, MB, and BM, were tested in monocot and dicot systems and further validated in transgenic tobacco plants. We found that the developed chimeric promoters were species-specific (monocot or dicot), which depended on their respective core promoter (CP) region. Furthermore, with this knowledge, deletion-hybrid promoters were developed and evaluated, which led to the development of a unique dual-expressing promoter, MSD3, with high gene expression efficiency (GUS and GFP reporter genes) in rice, pearl millet, and tobacco plants. We conclude that the MSD3 promoter can be an important genetic tool and will be valuable in plant biology research and application.

Small Peptides: Orchestrators of Plant Growth and Developmental Processes.

Small peptides (SPs), ranging from 5 to 100 amino acids, play integral roles in plants due to their diverse functions. Despite their low abundance and small molecular weight, SPs intricately regulate critical aspects of plant life, including cell division, growth, differentiation, flowering, fruiting, maturation, and stress responses. As vital mediators of intercellular signaling, SPs have garnered significant attention in plant biology research. This comprehensive review delves into SPs' structure, classification, and identification, providing a detailed understanding of their significance. Additionally, we summarize recent findings on the biological functions and signaling pathways of prominent SPs that regulate plant growth and development. This review also offers a perspective on future research directions in peptide signaling pathways.

Manipulating nature heatwaves in chambers: bridging controlled and field conditions for accurate warming study in plant and soil systems.

Abstract Understanding plant responses to climate variables such as heatwaves is crucial for plant biology research, necessitating growth environments that are highly controllable and reproducible. Traditional field methods lack control due to absent cooling systems and struggle to isolate field variables. Standard enclosures similarly fail to account for authentic environmental dynamics. To overcome these limitations, we developed AmbControl, a sunlit facility that bridges controlled environments with field conditions. AmbControl accurately captured the 2021 and 2022 heatwave fluctuations, allowing for the simulation of varying heat scenarios, including temperature scenarios ranging from +1.5°C to -4°C, and a stable 28.9°C. We observed differential temperature controls during night and day in the +1.5°C scenario, registering variations of ?1.0°C at night and ?1.8°C during the day. Temperature manipulations also inevitably altered relative humidity, highlighting its role as a confounding factor. The AmbControl system is essential for advanced climate impact studies, offering a platform for the next generation of agronomic experiments and climate resilience research.

Arabidopsis as a model for translational research.

Arabidopsis thaliana is currently the most-studied plant species on earth, with an unprecedented number of genetic, genomic, and molecular resources having been generated in this plant model. In the era of translating foundational discoveries to crops and beyond, we aimed to highlight the utility and challenges of using Arabidopsis as a reference for applied plant biology research, agricultural innovation, biotechnology, and medicine. We hope that this review will inspire the next generation of plant biologists to continue leveraging Arabidopsis as a robust and convenient experimental system to address fundamental and applied questions in biology. We aim to encourage lab and field scientists alike to take advantage of the vast Arabidopsis datasets, annotations, germplasm, constructs, methods, molecular and computational tools in our pursuit to advance understanding of plant biology and help feed the world's growing population. We envision that the power of Arabidopsis-inspired biotechnologies and foundational discoveries will continue to fuel the development of resilient, high-yielding, nutritious plants for the betterment of plant and animal health and greater environmental sustainability.

Non-thermal plasma enhances rice seed germination, seedling development, and root growth under low-temperature stress

Recently, non-thermal plasma (NTP) technologies have found widespread application across diverse fields, including plant growth, medical science, and biological and environmental research. Rice (Oryza sativa L.) is exceptionally sensitive to temperature changes. Notably, low-temperature stress primarily affects the germination and reproductive stages of rice, often leading to reduced crop yield. This study aimed to identify optimal conditions for enhancing rice seed germination and seedling growth under low temperatures using NTP technology. Our research indicated that NTP treatment at 15.0 kV for 30 s optimally promotes rice seed germination and growth under low-temperature stress. Furthermore, NTP treatment increases the activity and expression of antioxidant enzymes, such as superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD), under low-temperature conditions. Moreover, it downregulates the expression of β-ketoacyl-[acyl carrier protein] synthase I (KASI) and cis-epoxy carotenoid dioxygenase 3 (NCED3) and upregulates the expression of alternative oxidase (AOX1B), BREVIS RADIX-like homologous gene (BRXL2), WRKY transcription factor 29 (WRKY29), and EREBP transcription factor 2 (EREBP2) in roots after tandem 7 days low-temperature (16 ℃) and 7 days room-temperature (28 ℃) treatments. Transcriptomic analysis revealed the involvement of various key genes in phosphotransferase activity, phosphate-containing compound metabolic processes, and defense responses. These analyses provide comprehensive information on gene expression at the transcriptional level, offering new insights for a deeper understanding of candidate genes required for root growth in rice.

A large sequenced mutant library - valuable reverse genetic resource that covers 98% of sorghum genes.

Mutant populations are crucial for functional genomics and discovering novel traits for crop breeding. Sorghum, a drought and heat-tolerant C4 species, requires a vast, large-scale, annotated, and sequenced mutant resource to enhance crop improvement through functional genomics research. Here, we report a sorghum large-scale sequenced mutant population with 9.5 million ethyl methane sulfonate (EMS)-induced mutations that covered 98% of sorghum's annotated genes using inbred line BTx623. Remarkably, a total of 610 320 mutationswithin the promoter and enhancer regions of 18 000 and 11 790 genes, respectively, can be leveraged for novel research of cis-regulatory elements. A comparison of the distribution of mutations in the large-scale mutant library and sorghum association panel (SAP) provides insights into the influence of selection. EMS-induced mutations appeared to be random across different regions of the genome without significant enrichment in different sections of a gene, including the 5' UTR, gene body, and 3'-UTR. In contrast, there were low variation density in the coding and UTR regions in the SAP. Based on the Ka /Ks value, the mutant library (~1) experienced little selection, unlike the SAP (0.40), which has been strongly selected through breeding. All mutation data are publicly searchable through SorbMutDB (https://www.depts.ttu.edu/igcast/sorbmutdb.php) and SorghumBase (https://sorghumbase.org/). This current large-scale sequence-indexed sorghum mutant population is a crucial resource that enriched the sorghum gene pool with novel diversity and a highly valuable tool for the Poaceae family, that will advance plant biology research and crop breeding.

PEO: Plant Expression Omnibus - a comparative transcriptomic database for 103 Archaeplastida.

The Plant Expression Omnibus (PEO) is a web application that provides biologists with access to gene expression insights across over 100 plant species, ~60 000 manually annotated RNA-seq samples, and more than 4 million genes. The tool allows users to explore the expression patterns of genes across different organs, identify organ-specific genes, and discover top co-expressed genes for any gene of interest. PEO also provides functional annotations for each gene, allowing for the identification of genetic modules and pathways. PEO is designed to facilitate comparative kingdom-wide gene expression analysis and provide a valuable resource for plant biology research. We provide two case studies to demonstrate the utility of PEO in identifying candidate genes in pollen coat biosynthesis in Arabidopsis and investigating the biosynthetic pathway components of capsaicin in Capsicum annuum. The database is freely available at https://expression.plant.tools/.

State-of-the-Art Molecular Plant Biology Research in Spain

Molecular plant biology is the study of the molecular basis of plant life [...]

Regularized multi-trait multi-locus linear mixed models for genome-wide association studies and genomic selection in crops

BackgroundWe consider two key problems in genomics involving multiple traits: multi-trait genome wide association studies (GWAS), where the goal is to detect genetic variants associated with the traits; and multi-trait genomic selection (GS), where the emphasis is on accurately predicting trait values. Multi-trait linear mixed models build on the linear mixed model to jointly model multiple traits. Existing estimation methods, however, are limited to the joint analysis of a small number of genotypes; in fact, most approaches consider one SNP at a time. Estimating multi-dimensional genetic and environment effects also results in considerable computational burden. Efficient approaches that incorporate regularization into multi-trait linear models (no random effects) have been recently proposed to identify genomic loci associated with multiple traits (Yu et al. in Multitask learning using task clustering with applications to predictive modeling and GWAS of plant varieties. arXiv:1710.01788, 2017; Yu et al in Front Big Data 2:27, 2019), but these ignore population structure and familial relatedness (Yu et al in Nat Genet 38:203–208, 2006).ResultsThis work addresses this gap by proposing a novel class of regularized multi-trait linear mixed models along with scalable approaches for estimation in the presence of high-dimensional genotypes and a large number of traits. We evaluate the effectiveness of the proposed methods using datasets in maize and sorghum diversity panels, and demonstrate benefits in both achieving high prediction accuracy in GS and in identifying relevant marker-trait associations.ConclusionsThe proposed regularized multivariate linear mixed models are relevant for both GWAS and GS. We hope that they will facilitate agronomy-related research in plant biology and crop breeding endeavors.

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.

Registration of HA‐R20 and HA‐R21 confection sunflower germplasms resistant to rust and downy mildew

AbstractRust and downy mildew (DM) are detrimental diseases in global sunflower (Helianthus annuus L.) production. Disease often results in yield loss and reduced seed quality. Host resistance to DM and rust is mediated by single dominant genes in sunflower. To better utilize genetic resistance, gene pyramiding is a common practice in crop breeding to extend the durability and longevity of resistance. Two confection sunflower germplasm lines, HA‐R20 (Reg. no. GP‐387, PI 702361) and HA‐R21 (Reg. no. GP‐388, PI 702362), were developed using the pedigree breeding method and DNA marker‐assisted selection and released by the USDA‐ARS Sunflower and Plant Biology Research Unit in collaboration with the North Dakota Agricultural Experiment Station in September 2022. HA‐R20 is an F3‐derived F4 confection restorer selection from the cross of HA‐DM2 and HA‐R8, carrying rust resistance genes R12 and R15 and DM resistance gene PlArg. HA‐R21 is an F3‐derived F4 confection maintainer selection from the cross of HA‐DM3 and HA‐R8, carrying rust resistance genes R13a and R15 and DM resistance gene Pl17. Disease reaction and marker testing for DM and rust confirmed that both germplasms harbor DM and rust R genes in the homozygous condition and are resistant to all DM and rust races identified in North America to date. These multiple disease‐resistant lines will provide the sunflower industry with durable disease‐resistant sources for the continued improvement of the crop.

Design and Implementation of a Measuring Device to Determine the Content of Pigments in Plant Leaves

The design and implementation of a measuring device for the determination of pigment content in plant leaves is a topic of essential importance in plant biology, agriculture, and environmental research. The timely and sufficiently accurate determination of the content of these molecules provides valuable insight into the health, photosynthetic activity, and physiological state of plants. This paper presents the key aspects and results of the development and implementation of such a measuring device. It makes it possible to measure a larger number of pigments per type compared with the devices for commercial use that are currently known to us, and the accuracy of measurements depends mostly on the specific type of plant that is being tracked. The developed device presents a measurement accuracy ranging between 72% and 97% compared with a reference method and between 87% and 90% compared with a reference technique. Also, by using the device, a significant reduction in time and required resources can be achieved in measuring the content of pigments and nitrogen in plant leaves. This is a prerequisite for the more effective monitoring of the growth and health of plants, as well as optimizing the process of growing and caring for them. The work will be continued with the focus of the research aimed at generalizing the models for determining pigments and nitrogen in plants.

ScPlant: A versatile framework for single-cell transcriptomic data analysis in plants

Single-cell transcriptomics has been fully embraced in plant biological research and is revolutionizing our understanding of plant growth, development, and responses to external stimuli. However, single-cell transcriptomic data analysis in plants is not trivial, given that there is currently no end-to-end solution and that integration of various bioinformatics tools involves a large number of required dependencies. Here, we present scPlant, a versatile framework for exploring plant single-cell atlases with minimum input data provided by users. The scPlant pipeline is implemented with numerous functions for diverse analytical tasks, ranging from basic data processing to advanced demands such as cell-type annotation and deconvolution, trajectory inference, cross-species data integration, and cell-type-specific gene regulatory network construction. In addition, a variety of visualization tools are bundled in a built-in Shiny application, enabling exploration of single-cell transcriptomic data on the fly.

Evaluation of Cell Biology and Genetics using VIKOR Method

Cell biology and genetics are fields of heredity research. They enable experts to examine indigenous people's genetic data to identify their current state of health. By taking necessary precautions, one can protect their health using this technology. Cell biology has quickly expanded in the medical field and has emerged as the only treatment for issues with human reproduction. Genetics, or the science of genes and heredity, is all about the study of features that are passed down from one generation to the next. The subject of cell biology is the smallest units of life, cells, and their structures and functions. Understanding the structure and physiological functioning of single cells, and how cells interact and work together in great numbers to generate tissues and organisms, is a goal of cell biology. Cell biology is based on the notion that a cell is the basic unit of all life. Understanding the tissues and organisms that make up cells in great detail is made possible by concentrating on the cell. If you want to teach in a classroom, you can look into botany or zoology. If you're interested in biological or industrial sciences or medical research, you can choose from genetics, microbiology, or biotechnology. Cell biology encompasses both eukaryotic and prokaryotic cells and has a wide range of subtopics, including the research of cellular metabolism, cell communication, cell cycle, chemistry, and cell composition. Cells can be examined using a variety of microscopy techniques, cell culturing, and cell fractionation. There are two different cell types: prokaryotic and eukaryotic ones. Despite having differing morphologies (see Prokaryote, Eukaryote), eukaryotic organisms are remarkably comparable in terms of underlying molecular make-up and functions. Over the past 50 years, cell biology has seen remarkable expansion as a key area of basic science (1). Medicine makes use of information from basic science domains such as cell biology for the benefit of patients (2-4). A subfield of biology known as cell biology focuses on the cell, including its different types, structures, functions, and interactions with other cells. The subfields of cell biology include cell composition, cell cycle, cell communication, and cell metabolism. Research in several domains, including genetics, biochemistry, neuroscience, plant biology, molecular biology, microbiology, and immunology, is tied to those in cell biology. The VIKOR (VIšekriterijumsko Compromising Rangiranje) Optimal Replacement Select method is used in the evaluation of Epidermal Growth Factor Receptor, Fibroblast Growth Factor Receptors, Discoidin Domain Receptor, Mitogen-Activated Protein Kinase, and Nuclear Receptor-Binding SET Domain Protein alternatives for skin, lung, head/neck, and cervical cancer. Fibroblast Growth Factor Receptors have the highest rank, whereas Nuclear Receptor-Binding SET Domain Protein has the lowest rank.

Registration of HA‐DM9, HA‐DM10, and HA‐DM11 oilseed sunflower germplasms with dual resistance to sunflower downy mildew

AbstractDowny mildew (DM), caused by the obligate pathogen Plasmopara halstedii (Farl.) Berl. & de Toni, is a worldwide yield‐limiting disease of sunflower (Helianthus annuus L.). To obtain durable DM resistance in sunflower hybrids, there is a need to stack new resistance genes into the best available germplasm. The DM resistance genes Pl8, Pl17, and Pl18 were recently fine mapped to sunflower chromosomes 13, 4, and 2, respectively. The current study pyramided these genes into a single genotype by marker‐assisted selection. Three oilseed sunflower germplasms, HA‐DM9 (Reg. no. GP‐381, PI 700009), HA‐DM10 (Reg. no. GP‐379, PI 700004), and HA‐DM11 (Reg. no. GP‐380, PI 700005), are dual DM‐resistant germplasm lines developed and have been released by the USDA‐ARS, Sunflower and Plant Biology Research Unit in collaboration with the North Dakota Agricultural Experiment Station in 2021. The three lines, HA‐DM9 (Pl8Pl8/Pl17Pl17), HA‐DM10 (Pl8Pl8/Pl18Pl18), and HA‐DM11 (Pl17Pl17/Pl18Pl18), each stacked two different DM genes, providing broad resistance to all P. halstedii races identified in North America and Europe so far, and can be used in sunflower breeding programs to enhance DM resistance.

The ethylene-responsive transcription factor PpERF9 represses PpRAP2.4 and PpMYB114 via histone deacetylation to inhibit anthocyanin biosynthesis in pear.

Ethylene induces anthocyanin biosynthesis in most fruits, including apple (Malus domestica) and plum (Prunus spp.). By contrast, ethylene inhibits anthocyanin biosynthesis in pear (Pyrus spp.), but the underlying molecular mechanism remains unclear. In this study, we identified and characterized an ethylene-induced ETHYLENE RESPONSE FACTOR (ERF) transcription factor, PpETHYLENE RESPONSE FACTOR9 (PpERF9), which functions as a transcriptional repressor. Our analyses indicated PpERF9 can directly inhibit expression of the MYB transcription factor gene PpMYB114 by binding to its promoter. Additionally, PpERF9 inhibits the expression of the transcription factor gene PpRELATED TO APETALA2.4 (PpRAP2.4), which activates PpMYB114 expression, by binding to its promoter, thus forming a PpERF9-PpRAP2.4-PpMYB114 regulatory circuit. Furthermore, PpERF9 interacts with the co-repressor PpTOPLESS1 (PpTPL1) via EAR motifs to form a complex that removes the acetyl group on histone H3 and maintains low levels of acetylated H3 in the PpMYB114 and PpRAP2.4 promoter regions. The resulting suppressed expression of these 2 genes leads to decreased anthocyanin biosynthesis in pear. Collectively, these results indicate that ethylene inhibits anthocyanin biosynthesis by a mechanism that involves PpERF9-PpTPL1 complex-mediated histone deacetylation of PpMYB114 and PpRAP2.4. The data presented herein will be useful for clarifying the relationship between chromatin status and hormone signaling, with implications for plant biology research.