Soybean genomics research community strategic plan: A vision for 2024-2028.

This strategic plan summarizes the major accomplishments achieved in the last quinquennial by the soybean [Glycine max (L.) Merr.] genetics and genomics research community and outlines key priorities for the next 5 years (2024-2028).

A multi-omics approach reveals a link between ribosomal protein alterations and proteome rebalancing in Arabidopsis thaliana seeds.

The ability of seeds to restore their amino acid content and composition after the elimination of the most abundant seed storage proteins (SSPs) is well-documented, yet the underlying mechanisms remain unclear. To better understand how seeds compensate for major proteomic disruptions, we conducted a comprehensive analysis on an Arabidopsis mutant lacking the three most abundant SSPs, the cruciferins. Our initial findings indicated that carbon, nitrogen, and sulfur levels, as well as total protein and oil content, remained unchanged in these mutants suggesting rebalanced seeds.

Comparative RNA profiling identifies stage-specific phasiRNAs and coexpressed Argonaute genes in Bambusoideae and Pooideae species.

Phased, small interfering RNAs (PhasiRNAs) play a crucial role in supporting male fertility in grasses. Earlier work in maize (Zea mays) and rice (Oryza sativa)-and subsequently many other plant species-identified premeiotic 21-nucleotide (nt) and meiotic 24-nt phasiRNAs. More recently, a group of premeiotic 24-nt phasiRNAs was discovered in the anthers of 2 Pooideae species, barley (Hordeum vulgare) and bread wheat (Triticum aestivum).

Mathematical model of RNA-directed DNA methylation predicts tuning of negative feedback required for stable maintenance.

RNA-directed DNA methylation (RdDM) is a plant-specific de novo methylation pathway that is responsible for maintenance of asymmetric methylation (CHH, H = A, T or G) in euchromatin. Loci with CHH methylation produce 24 nucleotide (nt) short interfering (si) RNAs. These siRNAs direct additional CHH methylation to the locus, maintaining methylation states through DNA replication.

Plant pattern recognition receptors: from evolutionary insight to engineering.

The plant immune system relies on germline-encoded pattern recognition receptors (PRRs) that sense foreign and plant-derived molecular patterns, and signal health threats. Genomic and pangenomic data sets provide valuable insights into the evolution of PRRs and their molecular triggers, which is furthering our understanding of plant-pathogen co-evolution and convergent evolution. Moreover, in silico and in vivo methods of PRR identification have accelerated the characterization of receptor-ligand complexes, and advances in protein structure prediction algorithms are revealing novel PRR sensor functions.

Targeted engineering of camelina and pennycress seeds for ultrahigh accumulation of acetyl-TAG.

Acetyl-TAG (3-acetyl-1,2-diacylglycerol), unique triacylglycerols (TAG) possessing an acetate group at the -3 position, exhibit valuable properties, such as reduced viscosity and freezing points. Previous attempts to engineer acetyl-TAG production in oilseed crops did not achieve the high levels found in naturally producing seeds. Here, we demonstrate the successful generation of camelina and pennycress transgenic lines accumulating nearly pure acetyl-TAG at 93 mol% and 98 mol%, respectively.

Small-sized starch nanoparticles for efficient penetration of plant cells.

Starch nanoparticles (sNPs) are considered ideal materials for applications in plant and agricultural sciences aiming at increasing crop yields, and improving resilience due to their non-toxicity, global availability, hydrophilicity, and biodegradability. However, the lack of research on the interaction between sNPs and plant cell walls has limited their application in these fields. Here, we designed Nile blue A-based sNPs (NB@G50-NPs) to investigate the penetration of small-sized sNPs (G50-NPs) through the plant cell wall.

Mechanism of maltogenic α-amylase modification on barley granular starches spanning the full range of amylose.

Amylopectin (AP)-only (APBS), normal (NBS), and amylose (AM) only (AOBS) barley starches were selected here to investigate catalysis pattern of maltogenic α-amylase (MA) on hydrolyzing AP and AM granular starches. MA shortened starch side chains with degree of polymerization (DP) 11-30. MA-treated APBS exhibited porous granular structures and dramatically increased degree of branching (DB, 17-20 %), and reduced ordered degrees, suggesting high hydrolysis and transglycosylation activities of MA.

Student reflections on emotional engagement reveal science fatigue during the COVID-19 online learning transition.

Numerous quantitative studies in science education found that student engagement declined after the onset of the COVID-19 pandemic, but analyses to identify the factors that drove emotional engagement down are lacking. Emotional engagement is a multidimensional construct composed of interest in an academic discipline, value in an academic course, and anxiety. Here, we use qualitative analysis to examine how and why the emergency shift from face-to-face to online classes during and after the pandemic-induced emergency remote transition impacted student emotional engagement.

A strategy for identification and characterization of genic mutations using a temperature-sensitive chlorotic soybean mutant as an example.

Screening a transposon-mutagenized soybean population led to the discovery of a recessively inherited chlorotic phenotype. This "y24" phenotype results in smaller stature, weaker stems, and a smaller root system. Genome sequencing identified 15 candidate genes with mutations likely to result in a loss of function.

Metabolic Flux Analysis to Increase Oil in Seeds.

Ensuring an adequate food supply and enough energy to sustainably support future global populations will require enhanced productivity from plants. Oilseeds can help address these needs; but the fatty acid composition of seed oils is not always optimal, and higher yields are required to meet growing demands. Quantitative approaches including metabolic flux analysis can provide insights on unexpected metabolism (i.

The mA-YTH regulatory system in plants: A status.

Plants use mRNA methylation to regulate gene expression. As in other eukaryotes, the only abundant methylated nucleotide in plant mRNA bodies is N6-methyladenosine (mA). The conserved core components of mA-based genetic control are a multi-subunit nuclear methyltransferase, and a set of nuclear and cytoplasmic RNA-binding proteins consisting of an mA recognition module, the YT521-B homology (YTH) domain, and long intrinsically disordered regions (IDRs).

A MYB transcription factor underlying plant height in sorghum qHT7.1 and maize Brachytic 1 loci.

Manipulating plant height is an essential component of crop improvement. Plant height was generally reduced through breeding in wheat, rice, and sorghum to resist lodging and increase grain yield but kept high for bioenergy crops. Here, we positionally cloned a plant height quantitative trait locus (QTL) qHT7.

A peptide-receptor module links cell wall integrity sensing to pattern-triggered immunity.

Plants employ cell-surface receptors to perceive non- or altered-self, including the integrity of their cell wall. Here we identify a specific ligand-receptor module responsive to cell wall damage that potentiates immunity in Arabidopsis. Disruption of cell wall integrity by inhibition of cellulose biosynthesis promotes pattern-triggered immunity transcriptionally in a manner dependent on the receptor kinase MALE DISCOVERER 1-INTERACTING RECEPTOR-LIKE KINASE 2 (MIK2).

A 23-million-year record of morphological evolution within Neotropical grass pollen.

Grass-dominated biomes in South America comprise c. 20 million years of history, yet their evolution and underlying drivers remain poorly understood. Here we apply a novel approach that combines scanning electron microscopy imaging with computational analysis to quantify the morphometrics of grass (Poaceae) pollen micro-ornamentation from the Neotropics since the Early Miocene (23 million years ago).

Subfamily C7 Raf-like kinases MRK1, RAF26, and RAF39 regulate immune homeostasis and stomatal opening in Arabidopsis thaliana.

The calcium-dependent protein kinase CPK28 regulates several stress pathways in multiple plant species. Here, we aimed to discover CPK28-associated proteins in Arabidopsis thaliana. We used affinity-based proteomics and identified several potential CPK28 binding partners, including the C7 Raf-like kinases MRK1, RAF26, and RAF39.

Ribosome binding of phasiRNA precursors accelerates the 24-nt phasiRNA burst in meiotic maize anthers.

Reproductive phasiRNAs (phased, secondary, small interfering RNAs), produced from numerous PHAS loci, are essential for plant anther development. PHAS transcripts are enriched on endoplasmic reticulum-bound ribosomes in maize (Zea mays), but the impact of ribosome binding on phasiRNA biogenesis remains elusive. Through ribosome profiling of maize anthers at 10 developmental stages, we demonstrated that 24-PHAS transcripts are bound by ribosomes, with patterns corresponding to the timing and abundance of 24-PHAS transcripts.

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.

Identification of potential auxin response candidate genes for soybean rapid canopy coverage through comparative evolution and expression analysis.

Introduction: Throughout domestication, crop plants have gone through strong genetic bottlenecks, dramatically reducing the genetic diversity in today's available germplasm. This has also reduced the diversity in traits necessary for breeders to develop improved varieties. Many strategies have been developed to improve both genetic and trait diversity in crops, from backcrossing with wild relatives, to chemical/radiation mutagenesis, to genetic engineering.

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.