The study generated a dataset of 420 sgRNAs targeting promoters, exons, and introns of 137 tomato genes in protoplasts, linking editing efficiency to chromatin accessibility, genomic context, and sequence features. Open chromatin sites showed higher editing rates, while transcriptional activity had little effect, and a subset of guides produced near‑complete editing with microhomology‑mediated deletions. Human‑trained prediction models performed poorly, highlighting the need for plant‑specific guide design tools.

The study examined how DNA methylation influences cold stress priming in Arabidopsis thaliana, revealing that primed plants exhibit distinct gene expression and methylation patterns compared to non-primed plants. DNA methylation mutants, especially met1 lacking CG methylation, showed altered cold memory and misregulation of the CBF gene cluster, indicating that methylation ensures transcriptional precision during stress recall.

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.

A common garden experiment with six white spruce seed sources was conducted for seven years across two Quebec sites differing in latitude and climate to evaluate local adaptation. Bud set timing, frost tolerance, and non‑structural carbohydrate (NSC) profiles showed strong site, seed source, and interaction effects, with NSC concentrations correlating with cold hardiness and suggesting implications for assisted migration strategies.

Using genome‑wide association studies in Arabidopsis thaliana, the authors identified the chromatin‑associated protein CDCA7 as a trans‑regulator that specifically controls CG methylation (mCG) and TE silencing. CDCA7 and its paralog CDCA7β bind the remodeler DDM1, modulating its activity without broadly affecting non‑CG methylation or histone variant deposition, and natural variation in CDCA7 regulatory sequences correlates with local ecological adaptation.

The study integrates genome, transcriptome, and chromatin accessibility data from 380 soybean accessions to dissect the genetic and regulatory basis of symbiotic nitrogen fixation (SNF). Using GWAS, TWAS, eQTL mapping, and ATAC-seq, the authors identify key loci, co‑expression modules, and regulatory elements, and validate the circadian clock gene GmLHY1b as a negative regulator of nodulation via CRISPR and CUT&Tag. These resources illuminate SNF networks and provide a foundation for soybean improvement.

The study compares neutral genetic diversity and adaptive differentiation between old-growth and recently planted Norway spruce (Picea abies) stands in northern Sweden, finding similar overall genetic diversity but stronger local adaptation signals in natural forests. Planted stands exhibit weaker adaptive variation and higher vulnerability to future climate change, underscoring the need to conserve adaptive genetic variation in forest management.

A common garden experiment with 320 wild barley (Hordeum vulgare) accessions across two seasons quantified over 30 photophysiological traits, revealing heritable variation and strong genotype-by-environment interactions. Genome-wide association studies and population genetics identified signals of local adaptation, particularly involving stomatal conductance under water limitation, highlighting its role in maintaining photosynthesis and biomass.

A forward genetic screen in the negative photoblastic plant Aethionema arabicum identified a phytochrome A null mutant (koy2) that fails to inhibit seed germination under various light qualities, demonstrating that phytochrome A mediates light‑inhibited germination. The study links natural variation in phytochrome A signaling to local adaptation across the Irano‑Turanian region.

The study performed transcriptome profiling of Cryptomeria japonica individuals from different geographic origins grown in three common gardens across Japan, assembling 77,212 transcripts guided by the species' genome. Using SNP-based genetic clustering and weighted gene co‑expression network analysis, they identified gene modules whose expression correlated with genetic differentiation, revealing that defense‑related genes are up‑regulated in Pacific‑side populations while terpenoid metabolism genes are higher in Sea‑of‑Japan populations, indicating local adaptation via regulatory changes.