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 investigated whether wheat homoeologous genes actively compensate for each other when one copy acquires a premature termination codon (PTC) mutation. By analyzing mutagenised wheat lines, the authors found that only about 3% of cases exhibited upregulation of the unaffected homoeolog, indicating that widespread active transcriptional compensation is absent in wheat.

Overexpression of the wheat bHLH transcription factor TaPGS1 leads to increased flavonol accumulation in the seed coat, which disrupts polar auxin transport and causes localized auxin accumulation, delaying endosperm cellularization and increasing cell number, thereby enlarging grain size. Integrated metabolomic and transcriptomic analyses identified upregulated flavonol biosynthetic genes, revealing a regulatory module that links flavonol-mediated auxin distribution to seed development in wheat.

The study evaluated how alginate oligosaccharide (AOS) chain length influences the levels of seven key phytohormones in wheat seedlings challenged with Botrytis cinerea. Hormone profiling revealed that mid‑range oligomers (DP 4‑6) most strongly up‑regulate defense‑related hormones (JA, SA, ABA, CTK), whereas longer oligomers (DP 7) most effectively suppress ethylene. These findings suggest that tailoring AOS polymerization can optimize disease resistance and growth in cereal crops.

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 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 investigates the altered timing of the core circadian oscillator gene ELF3 in wheat compared to Arabidopsis, revealing that dawn-specific expression in wheat arises from repression by TOC1. An optimized computational model integrating experimental expression data and promoter architecture predicts that wheat’s circadian oscillator remains robust despite this shift, indicating flexibility in plant circadian network design.

The study used phospho‑proteomics to uncover rapid phosphorylation changes in Arabidopsis seedlings upon light or sucrose exposure, identifying RS41 as a hyperphosphorylated SR protein. By creating single and higher‑order mutants of four RS genes, the authors demonstrated that these RS proteins are essential for photomorphogenic development and regulate light‑dependent alternative splicing, with loss of all four causing sterility.