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Abstract BackgroundThe use of 3D imaging techniques, such as X-ray CT, in root phenotyping has become more widespread in recent years. However, due to the complexity of the root structure, analyzing the resulting 3D volumes to obtain detailed architectural root traits remains a challenging computational problem. When it comes to image-based phenotyping of excavated maize root crowns, two types of root features that are notably missing from existing methods are the whorls and soil line. Whorls refer to the distinct areas located at the base of each stem node from which roots sprout in a circular pattern (Liu S, Barrow CS, Hanlon M, Lynch JP, Bucksch A. Dirt/3D: 3D root phenotyping for field-grown maize (zea mays). Plant Physiol. 2021;187(2):739–57.https://doi.org/10.1093/plphys/kiab311.). The soil line is where the root stem meets the ground. Knowledge of these features would give biologists deeper insights into the root system architecture (RSA) and the below- and above-ground root properties. ResultsWe developed TopoRoot+, a computational pipeline that produces architectural traits from 3D X-ray CT volumes of excavated maize root crowns. Building upon the TopoRoot software (Zeng D, Li M, Jiang N, Ju Y, Schreiber H, Chambers E, et al. Toporoot: A method for computing hierarchy and fine-grained traits of maize roots from 3D imaging. Plant Methods. 2021;17(1).https://doi.org/10.1186/s13007-021-00829-z.) for computing fine-grained root traits, TopoRoot + adds the capability to detect whorls, identify nodal roots at each whorl, and compute the soil line location. The new algorithms in TopoRoot + offer an additional set of fine-grained traits beyond those provided by TopoRoot. The addition includes internode distances, root traits at every hierarchy level associated with a whorl, and root traits specific to above or below the ground. TopoRoot + is validated on a diverse collection of field-grown maize root crowns consisting of nine genotypes and spanning across three years. TopoRoot + runs in minutes for a typical volume size of$$\:40{0}^{3}$$on a desktop workstation. Our software and test dataset are freely distributed on Github. ConclusionsTopoRoot + advances the state-of-the-art in image-based phenotyping of excavated maize root crowns by offering more detailed architectural traits related to whorls and soil lines. The efficiency of TopoRoot + makes it well-suited for high-throughput image-based root phenotyping. 

Summary Mosses hold a unique position in plant evolution and are crucial for protecting natural, long‐term carbon storage systems such as permafrost and bogs. Due to small stature, mosses grow close to the soil surface and are exposed to high levels of CO₂, produced by soil respiration. However, the impact of elevated CO₂(eCO₂) levels on mosses remains underexplored.We determined the growth responses of the mossPhyscomitrium patensto eCO₂in combination with different nitrogen levels and characterized the underlying physiological and metabolic changes.Three distinct growth characteristics, an early transition to caulonema, the development of longer, highly pigmented rhizoids, and increased biomass, define the phenotypic responses ofP. patensto eCO₂. Elevated CO₂impacts growth by enhancing the level of a sugar signaling metabolite, T6P. The quantity and form of nitrogen source influences these metabolic and phenotypic changes. Under eCO₂,P. patensexhibits a diffused growth pattern in the presence of nitrate, but ammonium supplementation results in dense growth with tall gametophores, demonstrating high phenotypic plasticity under different environments.These results provide a framework for comparing the eCO₂responses ofP. patenswith other plant groups and provide crucial insights into moss growth that may benefit climate change models. 

SUMMARY The demand for agricultural production is becoming more challenging as climate change increases global temperature and the frequency of extreme weather events. This study examines the phenotypic variation of 149 accessions ofBrachypodium distachyonunder drought, heat, and the combination of stresses. Heat alone causes the largest amounts of tissue damage while the combination of stresses causes the largest decrease in biomass compared to other treatments. Notably, Bd21‐0, the reference line forB. distachyon, did not have robust growth under stress conditions, especially the heat and combined drought and heat treatments. The climate of origin was significantly associated withB. distachyonresponses to the assessed stress conditions. Additionally, a GWAS found loci associated with changes in plant height and the amount of damaged tissue under stress. Some of these SNPs were closely located to genes known to be involved in responses to abiotic stresses and point to potential causative loci in plant stress response. However, SNPs found to be significantly associated with a response to heat or drought individually are not also significantly associated with the combination of stresses. This, with the phenotypic data, suggests that the effects of these abiotic stresses are not simply additive, and the responses to the combined stresses differ from drought and heat alone. 

Abstract Plants perceive a multitude of environmental signals and stresses, and integrate their response to them in ways that culminate in modified phenotypes, optimized for plant survival. This ability of plants, known as phenotypic plasticity, is found throughout evolution, in all plant lineages. For any given environment, the specifics of the response to a particular signal may vary depending on the plants’ unique physiology and ecological niche. The bryophyte lineage, including mosses, which diverged from the vascular plants ~450–430 million years ago, represent a unique ecological and phylogenetic group in plant evolution. Several aspects of the moss life cycle, their morphology including the presence of specialized tissue types and distinct anatomical features, gene repertoires and networks, as well as the habitat differ significantly from those of vascular plants. To evaluate the outcomes of these differences, we explore the phenotypic responses of mosses to environmental signals such as light, temperature, CO2, water, nutrients, and gravity, and compare those with what is known in vascular plants. We also outline knowledge gaps and formulate testable hypotheses based on the contribution of anatomical and molecular factors to specific phenotypic responses. 

Summary Plant responses to abiotic environmental challenges are known to have lasting effects on the plant beyond the initial stress exposure. Some of these lasting effects are transgenerational, affecting the next generation. The plant response to elevated carbon dioxide (CO₂) levels has been well studied. However, these investigations are typically limited to plants grown for a single generation in a high CO₂environment while transgenerational studies are rare.We aimed to determine transgenerational growth responses in plants after exposure to high CO₂by investigating the direct progeny when returned to baseline CO₂levels.We found that both the flowering plantArabidopsis thalianaand seedless nonvascular plantPhyscomitrium patenscontinue to display accelerated growth rates in the progeny of plants exposed to high CO₂. We used the model species Arabidopsis to dissect the molecular mechanism and found that DNA methylation pathways are necessary for heritability of this growth response.More specifically, the pathway of RNA‐directed DNA methylation is required to initiate methylation and the proteins CMT2 and CMT3 are needed for the transgenerational propagation of this DNA methylation to the progeny plants. Together, these two DNA methylation pathways establish and then maintain a cellular memory to high CO₂exposure. 

Abstract Heterotrimeric G-proteins modulate multiple signaling pathways in many eukaryotes. In plants, G-proteins have been characterized primarily from a few model angiosperms and a moss. Even within this small group, they seem to affect plant phenotypes differently: G-proteins are essential for survival in monocots, needed for adaptation but are nonessential in eudicots, and are required for life cycle completion and transition from the gametophytic to sporophytic phase in the moss Physcomitrium (Physcomitrella) patens. The classic G-protein heterotrimer consists of three subunits: one Gα, one Gβ and one Gγ. The Gα protein is a catalytically active GTPase and, in its active conformation, interacts with downstream effectors to transduce signals. Gα proteins across the plant evolutionary lineage show a high degree of sequence conservation. To explore the extent to which this sequence conservation translates to their function, we complemented the well-characterized Arabidopsis Gα protein mutant, gpa1, with Gα proteins from different plant lineages and with the yeast Gpa1 and evaluated the transgenic plants for different phenotypes controlled by AtGPA1. Our results show that the Gα protein from a eudicot or a monocot, represented by Arabidopsis and Brachypodium, respectively, can fully complement all gpa1 phenotypes. However, the basal plant Gα failed to complement the developmental phenotypes exhibited by gpa1 mutants, although the phenotypes that are exhibited in response to various exogenous signals were partially or fully complemented by all Gα proteins. Our results offer a unique perspective on the evolutionarily conserved functions of G-proteins in plants. 

Abstract Heterotrimeric G-protein complexes comprising Gα-, Gβ-, and Gγ-subunits and the regulator of G-protein signaling (RGS) are conserved across most eukaryotic lineages. Signaling pathways mediated by these proteins influence overall growth, development, and physiology. In plants, this protein complex has been characterized primarily from angiosperms with the exception of spreading-leaved earth moss (Physcomitrium patens) and Chara braunii (charophytic algae). Even within angiosperms, specific G-protein components are missing in certain species, whereas unique plant-specific variants—the extra-large Gα (XLGα) and the cysteine-rich Gγ proteins—also exist. The distribution and evolutionary history of G-proteins and their function in nonangiosperm lineages remain mostly unknown. We explored this using the wealth of available sequence data spanning algae to angiosperms representing extant species that diverged approximately 1,500 million years ago, using BLAST, synteny analysis, and custom-built Hidden Markov Model profile searches. We show that a minimal set of components forming the XLGαβγ trimer exists in the entire land plant lineage, but their presence is sporadic in algae. Additionally, individual components have distinct evolutionary histories. The XLGα exhibits many lineage-specific gene duplications, whereas Gα and RGS show several instances of gene loss. Similarly, Gβ remained constant in both number and structure, but Gγ diverged before the emergence of land plants and underwent changes in protein domains, which led to three distinct subtypes. These results highlight the evolutionary oddities and summarize the phyletic patterns of this conserved signaling pathway in plants. They also provide a framework to formulate pertinent questions on plant G-protein signaling within an evolutionary context. 

Abstract High‐throughput phenotyping (HTP) has emerged as one of the most exciting and rapidly evolving spaces within plant science. The successful application of phenotyping technologies will facilitate increases in agricultural productivity. High‐throughput phenotyping research is interdisciplinary and may involve biologists, engineers, mathematicians, physicists, and computer scientists. Here we describe the need for additional interest in HTP and offer a primer for those looking to engage with the HTP community. This is a high‐level overview of HTP technologies and analysis methodologies, which highlights recent progress in applying HTP to foundational research, identification of biotic and abiotic stress, breeding and crop improvement, and commercial and production processes. We also point to the opportunities and challenges associated with incorporating HTP across food production to sustainably meet the current and future global food supply requirements. 

Heterotrimeric G-protein-mediated signaling is a key mechanism to transduce a multitude of endogenous and environmental signals in diverse organisms. The scope and expectations of plant G-protein research were set by pioneering work in metazoans. Given the similarity of the core constituents, G-protein-signaling mechanisms were presumed to be universally conserved. However, because of the enormous diversity of survival strategies and endless forms among eukaryotes, the signal, its interpretation, and responses vary even among different plant groups. Earlier G-protein research in arabidopsis (Arabidopsis thaliana) has emphasized its divergence from Metazoa. Here, we compare recent evidence from diverse plant lineages with the available arabidopsis G-protein model and discuss the conserved and novel protein components, signaling mechanisms, and response regulation. 

Globally, most human caloric intake is from crops that belong to the grass family (Poaceae), including sugarcane (Saccharum spp.), rice (Oryza sativa), maize (or corn, Zea mays), and wheat (Triticum aestivum). The grasses have a unique morphology and inflorescence architecture, and some have also evolved an uncommon photosynthesis pathway that confers drought and heat tolerance, the C4 pathway. Most secondary-level students are unaware of the global value of these crops and are unfamiliar with plant science fundamentals such as grass architecture and the genetic concepts of genotype and phenotype. Green foxtail millet (Setaria viridis) is a model organism for C4 plants and a close relative of globally important grasses, including sugarcane. It is ideal for teaching about grass morphology, the economic value of grasses, and the C4 photosynthetic pathway. This article details a teaching module that uses S. viridis to engage entire classrooms of students in authentic research through a laboratory investigation of grass morphology, growth cycle, and genetics. This module includes protocols and assignments to guide students through the process of growing one generation of S. viridis mutants and reference wild-type plants from seed to seed, taking measurements, making critical observations of mutant phenotypes, and discussing their physiological implications.