Genomic prediction of cereal crop architectural traits using models informed by gene regulatory circuitries from maize.

Plant architecture is a major determinant of planting density, which enhances productivity potential for crops per unit area. Genomic prediction is well positioned to expedite genetic gain of plant architectural traits since they are typically highly heritable. Additionally, the adaptation of genomic prediction models to query predictive abilities of markers tagging certain genomic regions could shed light on the genetic architecture of these traits.

Calling for Equity-focused Quantitative Methodology in Discipline-based Education Research: An Introduction to Latent Class Analysis.

Mixture modeling is a latent variable (i.e., a variable that cannot be measured directly) approach to quantitatively represent unobserved subpopulations within an overall population.

Optimized Methods for Applying and Assessing Heat, Drought, and Nutrient Stress of Maize Seedlings in Controlled Environment Experiments.

Maize (), also known as corn, is an important crop that plays a crucial role in global agriculture. The economic uses of maize are numerous, including for food, feed, fiber, and fuel. It has had a significant historical importance in research as well, with important discoveries made in maize regarding plant domestication, transposons, heterosis, genomics, and epigenetics.

Maize Abiotic Stress Treatments in Controlled Environments.

Maize () is one of the world's most important crops, providing food for humans and livestock and serving as a bioenergy source. Climate change and the resulting abiotic stressors in the field reduce crop yields, threatening food security and the global economy. Water deficit (i.

DNA cytosine methylation suppresses meiotic recombination at the sex-determining region.

Meiotic recombination between homologous chromosomes is vital for maximizing genetic variation among offspring. However, sex-determining regions are often rearranged and blocked from recombination. It remains unclear whether rearrangements or other mechanisms might be responsible for recombination suppression.

Small DNA elements that act as both insulators and silencers in plants.

Insulators are -regulatory elements that separate transcriptional units, whereas silencers are elements that repress transcription regardless of their position. In plants, these elements remain largely uncharacterized. Here, we use the massively parallel reporter assay Plant STARR-seq with short fragments of eight large insulators to identify more than 100 fragments that block enhancer activity.

Dynamic Membrane Lipid Changes in Reveal Developmental and Environmental Adaptations.

Membrane lipid composition is critical for an organism's growth, adaptation, and functionality. Mosses, as early non-vascular land colonizers, show significant adaptations and changes, but their dynamic membrane lipid alterations remain unexplored. Here, we investigated the temporal changes in membrane lipid composition of the moss during five developmental stages and analyzed the acyl content and composition of the lipids.

Population histories of variable reproductive success and low winter precipitation correlate with risk-averse seed germination in a mediterranean-climate winter annual.

Premise: Seed germination involves risk; post-germination conditions might not allow survival and reproduction. Variable, stressful environments favor seeds with germination that avoids risk (e.g.

CRISPR/Cas9-based editing of NF-YC4 promoters yields high-protein rice and soybean.

Genome editing is a revolution in biotechnology for crop improvement with the final product lacking transgenes. However, most derived traits have been generated through edits that create gene knockouts. Our study pioneers a novel approach, utilizing gene editing to enhance gene expression by eliminating transcriptional repressor binding motifs.

Teosinte populations exhibit weak local adaptation to their rhizosphere biota despite strong effects of biota source on teosinte fitness and traits.

While biotic interactions often impose selection, species and populations vary in whether they are locally adapted to biotic interactions. Evolutionary theory predicts that environmental conditions drive this variable local adaptation by altering the fitness impacts of species interactions. To investigate the influence of an environmental gradient on adaptation between a plant and its associated rhizosphere biota, we cross-combined teosinte (Zea mays ssp.

Non-specific Phospholipase C4 Improves Phosphorus Remobilization From Old to Young Leaves in Camelina.

Camelina sativa is regarded as a low-input oilseed crop for versatile food, biofuels and industrial applications with potential production on marginal lands, whereas phosphate (P) deficiency greatly reduces camelina seed production. To improve camelina resilience to low P conditions, here we overexpressed the P deficiency-induced non-specific phospholipase C4 (NPC4) to test its effect on camelina seed production under different levels of P availability. NPC4-overexpressing (OE) plants displayed increased seed yield and oil production, with a greater magnitude of increases under P-deficient than P-sufficient conditions.

Epigenetic therapy potentiates transposable element transcription to create tumor-enriched antigens in glioblastoma cells.

Inhibiting epigenetic modulators can transcriptionally reactivate transposable elements (TEs). These TE transcripts often generate unique peptides that can serve as immunogenic antigens for immunotherapy. Here, we ask whether TEs activated by epigenetic therapy could appreciably increase the antigen repertoire in glioblastoma, an aggressive brain cancer with low mutation and neoantigen burden.

pyMS-Vis, an Open-Source Python Application for Visualizing and Investigating Deconvoluted Top-Down Mass Spectrometric Experiments: A Histone Proteoform Case Study.

We report the development of an open-source Python application that provides quantitative and qualitative information from deconvoluted liquid-chromatography top-down mass spectrometry (LC-TDMS) data sets. This simple-to-use program allows users to search masses-of-interest across multiple LC-TDMS runs and provides visualization of their ion intensities and elution characteristics while quantifying their abundances relative to one another. Focusing on proteoform-rich histone proteins from the green microalga , we were able to quantify proteoform abundances across different growth conditions and replicates in minutes instead of hours typically needed for manual spreadsheet-based analysis.

SymRK Regulates G-Protein Signaling During Nodulation in Soybean () by Modifying RGS Phosphorylation and Activity.

Molecular interspecies dialogue between leguminous plants and nitrogen-fixing rhizobia results in the development of symbiotic root nodules. This is initiated by several nodulation-related receptors present on the surface of root hair epidermal cells. We have shown previously that specific subunits of heterotrimeric G-proteins and their associated regulator of G-protein signaling (RGS) proteins act as molecular links between the receptors and downstream components during nodule formation in soybeans.

Immunolocalization and Ultrastructure Show Ingestion of Cry Protein Expressed in by and Its Mode of Action.

Great interest exists in developing a transgenic trait that controls the economically important soybean () pest, soybean cyst nematode (SCN, ), due to its adaptation to native resistance. Soybean plants expressing the delta-endotoxin, Cry14Ab, were recently demonstrated to control SCN in both growth chamber and field testing. In that communication, ingestion of the Cry14Ab toxin by SCN second stage juveniles (J2s) was demonstrated using fluorescently labeled Cry14Ab in an in vitro assay.

FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants.

FatPlants, an open-access, web-based database, consolidates data, annotations, analysis results, and visualizations of lipid-related genes, proteins, and metabolic pathways in plants. Serving as a minable resource, FatPlants offers a user-friendly interface for facilitating studies into the regulation of plant lipid metabolism and supporting breeding efforts aimed at increasing crop oil content. This web resource, developed using data derived from our own research, curated from public resources, and gleaned from academic literature, comprises information on known fatty-acid-related proteins, genes, and pathways in multiple plants, with an emphasis on Glycine max, Arabidopsis thaliana, and Camelina sativa.

A sharp discovery.

Plant prickles are controlled by genes involved in the final step of cytokinin biosynthesis.

Phospholipase-mediated phosphate recycling during plant leaf senescence.

Background: Phosphorus is a macronutrient necessary for plant growth and development and its availability and efficient use affect crop yields. Leaves are the largest tissue that uses phosphorus in plants, and membrane phospholipids are the main source of cellular phosphorus usage.

Results: Here we identify a key process for plant cellular phosphorus recycling mediated by membrane phospholipid hydrolysis during leaf senescence.

Ectopic enhancer-enhancer interactions as causal forces driving RNA-directed DNA methylation in gene regulatory regions.

Cis-regulatory elements (CREs) are integral to the spatiotemporal and quantitative expression dynamics of target genes, thus directly influencing phenotypic variation and evolution. However, many of these CREs become highly susceptible to transcriptional silencing when in a transgenic state, particularly when organised as tandem repeats. We investigated the mechanism of this phenomenon and found that three of the six selected flower-specific CREs were prone to transcriptional silencing when in a transgenic context.

Manipulation of photosensory and circadian signaling restricts phenotypic plasticity in response to changing environmental conditions in Arabidopsis.

Plants exploit phenotypic plasticity to adapt their growth and development to prevailing environmental conditions. Interpretation of light and temperature signals is aided by the circadian system, which provides a temporal context. Phenotypic plasticity provides a selective and competitive advantage in nature but is obstructive during large-scale, intensive agricultural practices since economically important traits (including vegetative growth and flowering time) can vary widely depending on local environmental conditions.

The receptor-like kinase ARK controls symbiotic balance across land plants.

The mutualistic arbuscular mycorrhizal (AM) symbiosis arose in land plants more than 450 million years ago and is still widely found in all major land plant lineages. Despite its broad taxonomic distribution, little is known about the molecular components underpinning symbiosis outside of flowering plants. The ARBUSCULAR RECEPTOR-LIKE KINASE (ARK) is required for sustaining AM symbiosis in distantly related angiosperms.