Unveiling shared genetic regulators of plant architectural and biomass yield traits in sorghum.

Sorghum is emerging as an ideal genetic model for designing high-biomass bioenergy crops. Biomass yield, a complex trait influenced by various plant architectural characteristics, is typically regulated by numerous genes. This study aimed to dissect the genetic regulators underlying fourteen plant architectural traits and ten biomass yield traits in the Sorghum Association Panel across two growing seasons.

Disentangling genotype and environment specific latent features for improved trait prediction using a compositional autoencoder.

In plant breeding and genetics, predictive models traditionally rely on compact representations of high-dimensional data, often using methods like Principal Component Analysis (PCA) and, more recently, Autoencoders (AE). However, these methods do not separate genotype-specific and environment-specific features, limiting their ability to accurately predict traits influenced by both genetic and environmental factors. We hypothesize that disentangling these representations into genotype-specific and environment-specific components can enhance predictive models.

Chilling- and dark-regulated photoprotection in Miscanthus, an economically important C grass.

Tolerance of chilling dictates the geographical distribution, establishment, and productivity of C crops. Chilling reduces enzyme rate, limiting the sink for the absorbed light energy leading to the need for quick energy dissipation via non-photochemical quenching (NPQ). Here, we characterize NPQ upon chilling in three Miscanthus accessions representing diverse chilling tolerance in C grasses.

Genome-wide identification and diversity of FAD2, FAD3 and FAE1 genes in terms of biotechnological importance in Camelina species.

Background: False flax, or gold-of-pleasure (Camelina sativa) is an oilseed that has received renewed research interest as a promising vegetable oil feedstock for liquid biofuel production and other non-food uses. This species has also emerged as a model for oilseed biotechnology research that aims to enhance seed oil content and fatty acid quality. To date, a number of genetic engineering and gene editing studies on C.

Resilient plants, sustainable future.

The accelerated pace of climate change over the past several years should serve as a wake-up call for all scientists, farmers, and decision makers, as it severely threatens our food supply and could result in famine, migration, war, and an overall destabilization of our society. Rapid and significant changes are therefore needed in the way we conduct research on plant resilience, develop new crop varieties, and cultivate those crops in our agricultural systems. Here, we describe the main bottlenecks for these processes and outline a set of key recommendations on how to accelerate research in this critical area for our society.

Development of vegetative oil sorghum: From lab-to-field.

Biomass crops engineered to accumulate energy-dense triacylglycerols (TAG or 'vegetable oils') in their vegetative tissues have emerged as potential feedstocks to meet the growing demand for renewable diesel and sustainable aviation fuel (SAF). Unlike oil palm and oilseed crops, the current commercial sources of TAG, vegetative tissues, such as leaves and stems, only transiently accumulate TAG. In this report, we used grain (Texas430 or TX430) and sugar-accumulating 'sweet' (Ramada) genotypes of sorghum, a high-yielding, environmentally resilient biomass crop, to accumulate TAG in leaves and stems.

Use of the Puccinia sorghi haustorial transcriptome to identify and characterize AvrRp1-D recognized by the maize Rp1-D resistance protein.

The common rust disease of maize is caused by the obligate biotrophic fungus Puccinia sorghi. The maize Rp1-D allele imparts resistance against the P. sorghi IN2 isolate by initiating a defense response that includes a rapid localized programmed cell death process, the hypersensitive response (HR).

SERRATE drives phase separation behaviours to regulate m6A modification and miRNA biogenesis.

The methyltransferase complex (MTC) deposits N6-adenosine (mA) onto RNA, whereas the microprocessor produces microRNA. Whether and how these two distinct complexes cross-regulate each other has been poorly studied. Here we report that the MTC subunit B tends to form insoluble condensates with poor activity, with its level monitored by the 20S proteasome.

THI1 Gene Evolutionary Trends: A Comprehensive Plant-Focused Assessment via Data Mining and Large-Scale Analysis.

Molecular evolution analysis typically involves identifying selection pressure and reconstructing evolutionary trends. This process usually requires access to specific data related to a target gene or gene family within a particular group of organisms. While recent advancements in high-throughput sequencing techniques have resulted in the rapid accumulation of extensive genomics and transcriptomics data and the creation of new databases in public repositories, extracting valuable insights from such vast data sets remains a significant challenge for researchers.

Dissecting the genetic architecture of sunflower disc diameter using genome-wide association study.

Sunflower ( L.) plays an essential role in meeting the demand for edible oil worldwide. The yield of sunflower seeds encompasses several component traits, including the disc diameter.

The genomics and physiology of abiotic stressors associated with global elevational gradients in Arabidopsis thaliana.

Phenotypic and genomic diversity in Arabidopsis thaliana may be associated with adaptation along its wide elevational range, but it is unclear whether elevational clines are consistent among different mountain ranges. We took a multi-regional view of selection associated with elevation. In a diverse panel of ecotypes, we measured plant traits under alpine stressors (low CO partial pressure, high light, and night freezing) and conducted genome-wide association studies.

Deciphering sphingolipid biosynthesis dynamics in cell cultures: Quantitative analysis amid data variability.

Sphingolipids are pivotal for plant development and stress responses. Growing interest has been directed toward fully comprehending the regulatory mechanisms of the sphingolipid pathway. We explore its biosynthesis and homeostasis in cell cultures, shedding light on fundamental metabolic mechanisms.

Trait-Mediated Variation in Seedling Performance in Costa Rican Successional Forests: Comparing Above-Ground, Below-Ground, and Allocation-Based Traits.

The interspecific relationship between functional traits and tree seedling performance can be inconsistent, potentially due to site-to-site or microsite variation in environmental conditions. Studies of seedling traits and performance often focus on above-ground traits, despite the importance of below-ground resource acquisition and biomass allocation to above versus below-ground functions. Here we investigate how varying environmental conditions across sites induce intraspecific variation in organ-level (above-ground, below-ground) and biomass allocation traits, affecting interspecific relationships between these traits and seedling performance.

Trait association and prediction through integrative k-mer analysis.

Genome-wide association study (GWAS) with single nucleotide polymorphisms (SNPs) has been widely used to explore genetic controls of phenotypic traits. Alternatively, GWAS can use counts of substrings of length k from longer sequencing reads, k-mers, as genotyping data. Using maize cob and kernel color traits, we demonstrated that k-mer GWAS can effectively identify associated k-mers.

Defining the Secondary Metabolites in the PBL3 Secretome with Antagonistic Activity Against .

Rice production worldwide is threatened by the disease bacterial panicle blight (BPB) caused by . Despite the threat, resources to control this disease, such as completely resistant cultivars or effective chemical methods, are still lacking. However, the need to control this disease has paved the way to explore biologically based approaches harnessing the antimicrobial activities of environmental bacteria.

Sphingolipid homeostasis: How do cells know when enough is enough? Implications for plant pathogen responses.

Sphingolipid homeostatic regulation is important for balancing plant life and death. Plant cells finely tune sphingolipid biosynthesis to ensure sufficient levels to support growth through their basal functions as major components of endomembranes and the plasma membrane. Conversely, accumulation of sphingolipid biosynthetic intermediates, long-chain bases (LCBs) and ceramides, is associated with programmed cell death.

Phenotypic and transcriptomic responses of diverse rice accessions to transient heat stress during early grain development.

Heat stress (HS) occurring during the grain-filling period has a detrimental effect on grain yield and quality in rice (). The development of heat-resilient cultivars could partly solve this issue if tolerant alleles can be identified and incorporated into the germplasm. In this study, we posit that some of the phenotypic variations for heat resilience during grain development could be due to variations in gene expression among accessions.

Accumulation of Large Lineage-Specific Repeats Coincides with Sequence Acceleration and Structural Rearrangement in Plantago Plastomes.

Repeats can mediate rearrangements and recombination in plant mitochondrial genomes and plastid genomes. While repeat accumulations are linked to heightened evolutionary rates and complex structures in specific lineages, debates persist regarding the extent of their influence on sequence and structural evolution. In this study, 75 Plantago plastomes were analyzed to investigate the relationships between repeats, nucleotide substitution rates, and structural variations.

The primate-specific presence of interferon regulatory factor-5 pseudogene 1.

Interferon regulatory factor 5 (IRF5) is a key transcription factor in inflammatory and immune responses, with its dysregulation linked to autoimmune diseases. Using bioinformatic approaches, including Basic Local Alignment Search Tool (BLAST) for sequence similarity searches, BLAST-Like Alignment Tool (BLAT) for genome-wide alignments, and several phylogenetics software, such as Multiple Alignment using Fast Fourier Transform (MAFFT), for phylogenetic analyses, we characterized the structure, origin, and evolutionary history of the human IRF5 pseudogene 1 (IRF5P1). Our analyses reveal that IRF5P1 is a chimeric processed pseudogene containing sequences derived from multiple sources, including IRF5-like sequences from disparate organisms.

Nonphotochemical quenching kinetics GWAS in sorghum identifies genes that may play conserved roles in maize and Arabidopsis thaliana photoprotection.

Photosynthetic organisms must cope with rapid fluctuations in light intensity. Nonphotochemical quenching (NPQ) enables the dissipation of excess light energy as heat under high light conditions, whereas its relaxation under low light maximizes photosynthetic productivity. We quantified variation in NPQ kinetics across a large sorghum (Sorghum bicolor) association panel in four environments, uncovering significant genetic control for NPQ.

Nitrogen starvation leads to TOR kinase-mediated downregulation of fatty acid synthesis in the algae Chlorella sorokiniana and Chlamydomonas reinhardtii.

Background: When subject to stress conditions such as nutrient limitation microalgae accumulate triacylglycerol (TAG). Fatty acid, a substrate for TAG synthesis is derived from de novo synthesis or by membrane remodeling. The model industrial alga Chlorellasorokiniana accumulates TAG and other storage compounds under nitrogen (N)-limited growth.

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.