Cryopreservation is a crucial technique for the long-term ex situ conservation of plant genetic resources, particularly in the context of global biodiversity decline. This process entails freezing biological material at ultra-low temperatures using liquid nitrogen, which effectively halts metabolic activities and preserves plant tissues over extended periods. Over the past seven decades, a plethora of techniques for cryopreserving plant materials have been developed. These include slow freezing, vitrification, encapsulation dehydration, encapsulation–vitrification, droplet vitrification, cryo-plates, and cryo-mesh techniques. A key challenge in the advancement of cryopreservation lies in our ability to understand the molecular processes underlying plant freezing tolerance. These mechanisms include cold acclimatization, the activation of cold-responsive genes through pathways such as the ICE–CBF–COR cascade, and the protective roles of transcription factors, non-coding RNAs, and epigenetic modifications. Furthermore, specialized proteins, such as antifreeze proteins (AFPs) and late embryogenesis abundant (LEA) proteins, play crucial roles in protecting plant cells during freezing and thawing. Despite its potential, cryopreservation faces significant challenges, particularly in standardizing protocols for a wide range of plant species, especially those from tropical and subtropical regions. This review highlights the importance of ongoing research and the integration of omics technologies to improve cryopreservation techniques, ensuring their effectiveness across diverse plant species and contributing to global efforts regarding biodiversity conservation.

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.

To date, the use of liquid nitrogen (LN) in plant gene banks is relatively limited. Globally, in 2021, approximately 10,000 accessions were cryopreserved, and their explants were derived from in vitro plants. In Europe, out of 500 banks, only 20 use cryogenic temperatures to store plant germplasms. The implementation of seven conservation projects in Poland starting in the 1990s meant that the gene banking system in this country began to gradually develop. Plant gene bank is mainly based on the collection of seeds and makes little use of plant tissues, including those from in vitro culture. From the point of view of systematics, plant material belonging to spermatophytes dominates in Polish gene banks, while spore plants are rarely represented. This review represents the first summary of gene cryobank activities and resources in Poland. It contains a brief overview of the ex situ plant protection programs aimed at the use of LN and presents the characteristics of four existing gene cryobanks in this country. Special attention is devoted to the presentation of studies on the cryopreservation of seeds, as well as of plant tissues, such as embryonic axes and plumules of trees, and fern gametophytes, that make a permanent contribution to gene bank resources.

Cold stress reduces horticultural crop yield and postharvest quality by disrupting membrane fluidity, redox equilibrium, and the cell wall structure. This results in chilling injury, tissue softening, and loss of color. Long noncoding RNAs (lncRNAs) have emerged as key integrators of plant cold signaling pathways. LncRNAs mediate the interaction between calcium signaling systems and transcriptional cascades while coordinating hormone signaling networks, including those involving abscisic acid, jasmonic acid, ethylene, salicylic acid, and brassinosteroids. LncRNAs influence gene regulation through chromatin-based guidance, sequestration of repressive complexes, natural antisense transcriptional interference, microRNA-centered competing endogenous RNA networks, and control of RNA splicing, stability, localization, and translation. Studies in horticultural species revealed that cold-responsive lncRNAs regulate processes essential for fruit firmness, antioxidant levels, and shelf-life, including lipid modification, reactive oxygen species balance, and cell wall or cuticle remodeling. This review aims to summarize tissue- and developmental stage-specific expression patterns and highlight experimental approaches to validate RNA function, including gene editing, transcript recovery, advanced sequencing, and analysis of protein-RNA interactions. Integrating these results will facilitate the development of precise molecular markers and nodes of regulatory networks that increase cold tolerance, and improve the quality of horticultural crops.

Rye (Secale cereale L.) is one of the most important cereal crops cultivated in the world due to its ability to produce high yields even when grown under environmental stress conditions. About 27,000 Secale accessions have been collected and preserved in 70 gene banks worldwide. Although the germplasm represents a great source of genetic diversity, the molecular characteristics refers only to the part of them. Here, we present data obtained by the Simple Sequence Repeat markers (SSR) analysis of 100 rye accessions preserved in the gene bank of the Polish Academy of Sciences Botanical Garden – Center for Biological Diversity Conservation in Powsin. Additionally, the data presented in this article refers to evaluation of agronomoic traits and weather conditions measured for 14 years. The data was used in the research article “Investigation of obsolete diversity of rye (Secale cereale L.) using multiplexed SSR fingerprinting and evaluation of agronomic traits” [1].

W związku z nieustanną utratą siedlisk wielu gatunków i zmianami środowiska naturalnego spowodowanymi zmianami klimatycznymi, kolekcje ex situ w ostatnim czasie stały się bardzo cenioną formą zachowania różnorodności roślin. Szacuje się, że trzecia część wszystkich poznanych gatunków roślin na świecie oraz ponad 40% gatunków zagrożonych, reprezentowane są w ogrodach botanicznych na świecie. Różnorodność gatunków roślin zagrożonych w Europie została zabezpieczona w 62.7% jako efekt współpracy banków nasion flory naturalnej. Ogrody botaniczne z całym swoim zapleczem i zasobami w nich zgromadzonymi w bankach nasion, herbariach, szklarniach, szkółkach, laboratoriach i kolekcjach żywych roślin, mają znaczący wkład w ochronę różnorodności roślin na świecie i dlatego określane są jako Arka Noego dla roślin. W kolekcjach ex situ PAN Ogrodu Botanicznego CZRB dotychczas zabezpieczono około 30% rodzimej flory Polski oraz 58% gatunków o zagrożonych pulach genowych. Niniejsze opracowanie przedstawia stan zabezpieczenia różnorodności flory naturalnej na przykładzie pracy jednej instytucji zaangażowanej wraz z rekomendacjami do wdrożenia zintegrowanej ochrony świata roślin.