Plant tissues exhibit a layered architecture that makes spatial context decisive for interpreting transcriptional changes. This review explains why the location of gene expression is as important as its magnitude and synthesizes advances uniting single-cell/nucleus RNA-seq with spatial transcriptomics in plants. Surveyed topics include platform selection and material preparation; plant-specific sample processing and quality control; integration with epigenomic assays such as single-nucleus Assay for Transposase-Accessible Chromatin using sequencing (ATAC) and Multiome; and computational workflows for label transfer, deconvolution, spatial embedding, and neighborhood-aware cell–cell communication. Protoplast-based single-cell RNA sequencing (scRNA-seq) enables high-resolution profiling but introduces dissociation artifacts and cell-type biases, whereas ingle-nucleus RNA sequencing (snRNA-seq) improves the representation of recalcitrant lineages and reduces stress signatures while remaining compatible with multiomics profiling. Practical guidance is provided for mitigating ambient RNA, interpreting organellar and intronic metrics, identifying doublets, and harmonizing batches across chemistries and studies. Spatial platforms (Visium HD, Stereo-seq, bead arrays) and targeted imaging (Single-molecule fluorescence in situ hybridization (smFISH), Hairpin-chain-reaction FISH (HCR-FISH), Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH)) are contrasted with plant-specific adaptations and integration pipelines that anchor dissociated profiles in anatomical coordinates. Recent atlases in Arabidopsis, soybean, and maize illustrate how cell identities, chromatin accessibility, and spatial niches reveal developmental trajectories and stress responses jointly. A roadmap is outlined for moving from atlases to interventions by deriving gene regulatory networks, prioritizing cis-regulatory targets, and validating perturbations with spatial readouts in crops. Together, these principles support a transition from descriptive maps to mechanism-informed, low-pleiotropy engineering of agronomic traits.

This review presents soybean responses to drought, heat, and salinity within a signal–transcript–chromatin framework. In this framework, calcium/reactive oxygen species and abscisic acid cues converge on abscisic acid-responsive element binding factor (ABF/AREB), dehydration-responsive element binding protein (DREB), NAC, and heat shock factor (HSF) families. These processes are modulated by locus-specific chromatin and non-coding RNA layers. Base-resolved methylomes reveal a high level of CG methylation in the gene body, strong CHG methylation in heterochromatin, and dynamic CHH ‘islands’ at the borders of transposable elements. CHH methylation increases over that of transposable elements during seed development, and GmDMEa editing is associated with seed size. Chromatin studies in soybean and model species implicate the reconfiguration of salt-responsive histone H3 lysine 27 trimethylation (H3K27me3) in G. max and heat-linked H2A.Z dynamics at thermoresponsive promoters characterized in Arabidopsis and other plants, suggesting that a conserved chromatin layer likely operates in soybean. miR169–NF-YA, miR398–Cu/Zn Superoxide Dismutases(CSD)/copper chaperone of CSD(CCS), miR393–transporter inhibitor response1/auxin signaling F-box (TIR1/AFB), and miR396–growth regulating factors (GRF) operate across leaves, roots, and nodules. Overexpression of lncRNA77580 enhances drought tolerance, but with context-dependent trade-offs under salinity. Single-nucleus and spatial atlases anchor these circuits in cell types and microenvironments relevant to stress and symbiosis. We present translational routes, sentinel epimarkers (bisulfite amplicons, CUT&Tag), haplotype-by-epigenotype prediction, and precise cis-regulatory editing to accelerate marker development, genomic prediction and the breeding of resilient soybean varieties with stable yields.

Zgodnie z ustawą z dnia 16 kwietnia 2004 r. o ochronie przyrody (Dz. U. Nr 92, poz. 880) ogród botaniczny jest miejscem uprawy roślin z różnych stref klimatycznych oraz roślin określonego rodzaju (kolekcje specjalistyczne), a także związanej z nimi działalności naukowo-badawczej, dydaktyczno-oświatowej, popularyzatorskiej i rekreacyjnej. Kolekcje roślin znajdujące się w Ogrodzie Botanicznym są ściśle związane z działalnością naukowo-badawczą, koordynowaną merytorycznie przez Krajowe Centrum Roślinnych Zasobów Genowych IHAR-PIB w Radzikowie k. Warszawy. Tematyka badawcza poświęcona jest głównie gromadzeniu i ocenie zasobów genowych traw, prowadzonej od 1971 roku. Prace związane z zachowaniem bioróżnorodności były stale rozszerzane i objęły również gatunki roślin dwuliściennych o walorach użytkowych, rośliny do użytkowania na gruntach zdegradowanych i ugorowanych (tzw. kolekcja rekultywacyjna) oraz gatunki związane z trwałymi użytkami zielonymi (TUZ). Ogród Botaniczny IHAR w Bydgoszczy prowadzi działalność dydaktyczną, edukacyjną, popularyzatorską i rekreacyjną dla mieszkańców Bydgoszczy.