The study investigates the gene regulatory network (GRN) controlling flowering time in the allotetraploid crop Brassica napus by comparing its transcriptome to that of Arabidopsis thaliana. While most orthologous gene pairs show conserved expression dynamics, several flowering‑time genes display regulatory divergence, especially under cold conditions, indicating subfunctionalisation among paralogues. Despite these differences, the overall GRN topology remains similar to Arabidopsis, likely due to retention of multiple paralogues.

The study utilizes a large collection of fluorescently marked Ds-GFP insertional mutations in haploid maize pollen to link gene disruptions with quantitative fitness effects measured as transmission deviations. By integrating genome-derived features (e.g., codon usage) and expression profiling into interpretable machine learning models, they achieve high predictive performance (auROC >90%) for genes influencing pollen fitness, highlighting expression specificity as a key predictor.

The authors used a bottom‑up thermodynamic modelling framework to investigate how plants decode calcium signals, starting from Ca2+ binding to EF‑hand proteins and extending to higher‑order decoding modules. They identified six universal Ca2+-decoding modules that can explain variations in calcium sensitivity among kinases and provide a theoretical basis for interpreting calcium signal amplitude and frequency in plant cells.

Four barley genotypes were examined under simultaneous Fusarium culmorum infection and drought, revealing genotype-dependent Fusarium Head Blight severity and largely additive transcriptomic responses dominated by drought. Co‑expression and hormone profiling linked ABA and auxin to stress‑specific gene modules, and a multiple linear regression model accurately predicted combined‑stress gene expression from single‑stress data, suggesting modular regulation.

The study examined nitrogen use strategies in the model alga Chlamydomonas reinhardtii by comparing growth on ammonium, nitrate, and urea, finding similar molar nitrogen utilization efficiency under saturating conditions. Rapid nitrogen uptake and storage were demonstrated through pulse experiments, and source‑specific transcriptome analysis revealed distinct regulation of assimilation pathways and transporters, supporting a model of flexible nitrogen acquisition and storage.

The study investigates how maternal environmental conditions, specifically temperature and light intensity, influence seed longevity in eight Arabidopsis thaliana natural accessions. Seeds developed under higher temperature (27 °C) and high light showed increased longevity, with transcriptome analysis of the Bor-4 accession revealing dynamic changes in stored mRNAs, including upregulation of antioxidant defenses and raffinose family oligosaccharides. These findings highlight the genotype‑dependent modulation of seed traits by the maternal environment.

The study benchmarked over 20 web‑based gRNA on‑target efficiency prediction tools against an experimental plant CRISPR editing dataset, finding several machine‑learning based tools whose scores strongly correlated with observed InDel frequencies. Additionally, the performance of popular platforms such as CRISPOR and CRISPR‑P was assessed, offering guidance for improved gRNA design in plant genome editing.

The study evaluates the use of single-cell RNA sequencing (scRNA-seq) data to predict plant metabolic pathway genes (MPGs) in Arabidopsis thaliana, comparing five multi-label machine‑learning algorithms against traditional bulk RNA‑seq approaches. scRNA‑seq generated co‑expression networks that, while different, yielded significantly higher MPG classification accuracy, especially when data were split by genetic background or tissue type, and deep learning outperformed classical methods. The authors conclude that scRNA‑seq offers superior predictive power and should be incorporated into future MPG discovery pipelines.

The study integrated weekly morphophysiological measurements with high-density genotyping-by-sequencing data and a machine‑learning pipeline to dissect flowering time variation in diverse Cannabis sativa landraces. By applying mutual information, recursive feature elimination, random forest, and support vector machine classifiers to over 234,000 combined genetic, phenotypic, and environmental features, the authors identified 53 key markers that classify early, medium, and late flowering types with 96.6% accuracy. Notable loci, including CsFT3 and CsCFL1, were highlighted as promising targets for breeding and smart‑crop strategies.

The study investigates the evolutionary shift from archegonial to embryo‑sac reproduction by analyzing transcriptomes of Ginkgo reproductive organs and related species. It reveals that the angiosperm pollen‑tube guidance module MYB98‑CRP‑ECS is active in mature Ginkgo archegonia and that, while egg cell transcription is conserved, changes in the fate of other female gametophyte cells drove the transition, providing a molecular framework for this major reproductive evolution.