An optimized workflow was developed to apply the Xenium in situ sequencing platform to formalin‑fixed paraffin‑embedded (FFPE) sections of Medicago truncatula roots and nodules, incorporating customized tissue preparation, probe design, and imaging to overcome plant‑specific challenges such as cell wall autofluorescence. The protocol was validated across nodule developmental stages using both a 50‑gene panel for mature cell identity and an expanded 480‑gene panel covering multiple cell types, providing a scalable high‑resolution spatial transcriptomics method adaptable to other plant systems.

The study identifies the transcription factor MdBRC1 as a key inhibitor of bud growth during the ecodormancy phase in apple (Malus domestica), directly regulating dormancy‑associated genes and interacting with the flowering promoter MdFT2 to modulate bud break. Comparative transcriptomic analysis and gain‑of‑function experiments in poplar demonstrate that MdFT2 physically binds MdBRC1, attenuating its repressive activity and acting as a molecular switch for the transition to active growth.

The study integrated genetic architecture derived from maize GWAS into phenotypic simulations of hybrid populations, using ≥200 top GWAS hits and adjusting marker effect sizes, which increased the correlation between simulated and empirical trait data across environments (r = 0.397–0.915). These informed simulations produced realistic trait distributions and genomic prediction results that closely matched empirical observations, demonstrating improved utility for digital breeding programs.

The study applied the STOmics spatial transcriptomics platform to map gene expression at subcellular resolution in developing wheat (Triticum aestivum) seeds during grain filling, analyzing over four million transcripts. Eight functional cellular groups were identified, including four distinct endosperm clusters with radial expression patterns and novel marker genes, and subgenome‑biased expression was observed among specific paralogs. These results highlight spatial transcriptomics as a powerful tool for uncovering tissue‑specific and polyploid‑specific gene regulation in seeds.

The study combined spatial transcriptomics and single-nuclei RNA sequencing to map soybean (Glycine max) responses to Asian soybean rust caused by Phakopsora pachyrhizi, revealing two distinct host cell states: pathogen‑occupied regions and adjacent non‑infected regions that show heightened defense gene expression. Gene co‑expression network analysis identified a key immune‑related module active in the stressed cells, highlighting a cell‑non‑autonomous defense mechanism.

The study introduced full-length SOC1 genes from maize and soybean, and a partial SOC1 gene from blueberry, into tomato plants under constitutive promoters. While VcSOC1K and ZmSOC1 accelerated flowering, all three transgenes increased fruit number per plant mainly by promoting branching, and transcriptomic profiling revealed alterations in flowering, growth, and stress‑response pathways.

The study uses an imputation strategy that integrates deep single-cell RNA sequencing with spatial gene expression data to map transcriptional dynamics across barley inflorescence development at cellular resolution. By leveraging the BARVISTA web interface, the authors identify key transcriptional events in meristem founder cells, characterize complex branching mutants, and reconstruct spatio‑temporal trajectories of flower organogenesis, offering insights for targeted trait manipulation.

The study examines how the SnRK1 catalytic subunit KIN10 integrates carbon availability with root growth regulation in Arabidopsis thaliana. Loss of KIN10 reduces glucose‑induced inhibition of root elongation and triggers widespread transcriptional reprogramming of metabolic and hormonal pathways, notably affecting auxin and jasmonate signaling under sucrose supplementation. These findings highlight KIN10 as a central hub linking energy status to developmental and environmental cues in roots.

The study compared physiological, ion‑balance, and metabolic responses of two maize inbred lines—salt‑sensitive C68 and salt‑tolerant NC326—under salinity stress. Untargeted metabolomics identified 56 metabolites and, together with genetic analysis, linked 10 candidate genes to key protective metabolites, revealing constitutive and inducible mechanisms of salt tolerance.

The study models maize flowering time plasticity using a physiological reaction norm derived from multi-environment trial data, revealing genotype-specific differences in temperature-driven development and photoperiod perception. It introduces an envirotyping metric that shows genotypes can experience markedly different photoperiods even within the same environment, and demonstrates distinct adaptive strategies between tropical and temperate germplasm.