1. Introduction

Alpine ecosystems occur across nearly all major mountain systems worldwide, from the Andes and the Himalayas to the Rocky Mountains, the Alps, and the highlands of East Africa and New Guinea (Fig. 1). In a biogeographic sense, “alpine” generally refers to the vegetation zone above the climatic treeline (Fig. 1C), where mean growing-season temperatures are typically below ~6.7 ℃; although absolute elevation varies widely with latitude and local climate (Körner, 1999; Körner and Paulsen, 2004). On the Qinghai–Tibet Plateau (QTP), the highest and largest alpine system globally, the alpine zone typically begins at approximately 4000 m a.s.l., reflecting the plateau’s extreme elevation. Despite their fragmented and often harsh environments, these high-elevation regions harbor remarkable biodiversity, including high levels of endemism, rapid lineage diversification, and unique life-history strategies (Hughes and Atchison, 2015; Pérez-Escobar et al., 2022; Smith and Young, 1987; Sun et al., 2017; Willis et al., 2004; Wootton et al., 2025). Alpine floras contribute disproportionately to global plant diversity and offer important opportunities for studying adaptive evolution under extreme environmental pressures.

Alpine plants are exposed to a suite of abiotic stresses, including extremely low temperatures, intense ultraviolet (UV) radiation, short growing seasons, and low soil nutrition level (Körner, 1999; Nagy and Grabherr, 2009). These stressors have driven the evolution of diverse morphological, physiological, and life-history adaptations (Sun et al., 2014; Wootton et al., 2025). Accelerated climate change and increased anthropogenic disturbance have caused alpine ecosystems experience rapid shifts in temperature and species composition, posing significant threats to cold-adapted taxa and the ecological integrity of mountain habitats (Grabherr et al., 1994; Steinbauer et al., 2018). Understanding how alpine plants have adapted to their environments and how they might respond to ongoing environmental change has become an increasingly urgent goal in evolutionary biology and conservation science.

Recent advances in genomic technologies have opened new avenues for investigating the molecular and evolutionary mechanisms that underlie adaptation in alpine plants. High-quality genome assemblies, population resequencing data, and transcriptomic and epigenomic resources are now available for a growing number of alpine species (Chen et al., 2019; Wötzel et al., 2022; Yang et al., 2024; Zhang et al., 2024b). These resources have enabled researchers to explore how genetic variation at different levels, including single nucleotide polymorphisms (SNPs), structural variants (SVs), whole-genome duplications (WGD), and selfish element (e.g., transposable elements), contributes to adaptation to high-elevation environments.

Despite the recent accumulation of genomic research on alpine plants, few attempts have been made to synthesize the current state of our knowledge about how different types of genomic variation contribute to alpine adaptations (but see Zhang et al., 2024b). Existing studies are often taxon-specific or mechanism-focused, limiting our ability to draw general conclusions across taxa, environments, and genomic contexts. Here, we synthesize current knowledge on the genomic architecture of alpine plant adaptation. We focus on four major types of genomic variation: SNP/loci-based adaptation, structural variants, whole-genome duplication, and transposable elements. We then outline how each contributes to adaptation in alpine environments. We also discuss emerging challenges and future directions in the field, particularly in light of climate-driven shifts and conservation needs.

2. Phylogenetic and biogeographic context of alpine plants

Comparative phylogenetic studies have revealed that alpine plant diversity arises through a complex interplay of in situ diversification, colonization from adjacent lowlands, and repeated range shifts driven by Quaternary climate fluctuations (Table 1; Hughes and Atchison 2015; Ding et al., 2020; Cao et al., 2025; Wootton et al., 2025). Biodiversity hotspots, such as the QTP and the Andes Mountains, exhibit strong signals of recent and rapid radiations, often triggered by mountain uplift, topographic complexity, and emerging ecological opportunities (Favre et al., 2015; Pérez-Escobar et al., 2022; Sun et al., 2017; Wen et al., 2014). In these systems, alpine species are frequently more closely related to each other than would be expected from their regional species pools, suggesting strong phylogenetic clustering and trait conservatism, particularly with respect to physiological traits like cold tolerance (Li et al., 2014; Niu et al., 2025; Padullés Cubino et al., 2022; Qian et al., 2021). This pattern is also pronounced in tropical and subtropical mountain regions (e.g., the Andes, East African highlands), where harsh environmental filters tend to favor lineages with conserved adaptive traits (Linder, 2014; Smith and Young, 1987). In the European Alps, diverse sky-island flora is dominated by young lineages that accumulated primarily during the Plio–Pleistocene through extensive lineage turnover, rather than by the persistence of ancient paleoendemics (Wootton et al., 2025). These findings suggest that, despite differences in geological history and biogeographic context, many alpine floras, whether in the QTP, Andes, or European Alps, share a common signature of rapid and recent lineage turnover, often linked to Plio-Pleistocene climatic oscillations (Ahmad et al., 2025; Rana et al., 2024).

Notably, phylogenetic studies increasingly reveal compelling patterns of convergent evolution among distantly related alpine taxa, reflected in repeated evolution of traits such as dwarfism, compact cushion-like growth forms, dense pubescences, and enhanced cold tolerance (Sun et al., 2014; Yang et al., 2025; Zhang et al., 2021a, 2022). Similar patterns of convergence have also been observed in Arctic plants (Birkeland et al., 2020; Cai et al., 2025; Körner, 1999), which face analogous abiotic stresses, suggesting a broader evolutionary parallel across cold-adapted floras (see Box 1). Such convergence is not confined to a single region or lineage, but recurs across multiple mountain systems worldwide (Nagy and Grabherr, 2009), suggesting that alpine environments act as predictable evolutionary filters that repeatedly shape organismal traits. These trends highlight the importance of comparative, multi-lineage, and cross-regional approaches to uncover the underlying genetic and developmental mechanisms of adaptation.

Together, these findings establish alpine plants not only as models for studying biodiversity under strong environmental constraint, but also as powerful systems for addressing fundamental questions in evolutionary biology, including the drivers and dynamics of rapid radiation, the role of geological and climatic processes in shaping biodiversity, and the repeatability of adaptive evolution across lineages and ecosystems.

3. Genomic signatures of alpine adaptation

Alpine plant genomes bear the imprint of multiple evolutionary forces acting at different levels of genetic organization. Here, we focus on four major sources of genomic variation that underpin adaptive evolution in alpine lineages (Fig. 2).

3.1. Adaptive SNPs and positively selected genes

Site-based evolutionary analyses (Fig. 2A), including both population-level polymorphisms (e.g., adaptive SNPs) and interspecific divergence (e.g., positively selected genes), have become a cornerstone for uncovering the molecular basis of local adaptation in alpine plants. Genomic studies across diverse high-mountain lineages demonstrate that adaptive changes can arise from both recent selection on standing variation and long-term divergence accumulated over millions of years. Such changes often involve similar functional categories, underscoring the multifaceted nature of high-elevation adaptation. Here, we summarize all available alpine plant genomic studies to date (Table 2), highlighting how both population-scale and phylogenetic-scale approaches have collectively advanced our understanding of the evolutionary processes shaping extreme-environment specialists.

Population genomic scans in alpine species often employ methods such as F_ST outlier detection and genotype–environment association (GEA; e.g., BayEnv, LFMM) to identify loci under differential selection along environmental gradients (Caye et al., 2019; de Villemereuil and Gaggiotti, 2015). A well-studied example comes from Arabis alpina in the French Alps, where pool-sequencing of ten populations across an elevational gradient revealed 19 genomic regions associated with elevation, including a locus containing an ANAC062 homolog, known to regulate freezing tolerance and pathogen defense in Arabidopsis thaliana (Lobréaux and Miquel, 2020). Similarly, whole-genome pooled sequencing of three Brassicaceae species (A. alpina, A. halleri, and Cardamine resedifolia) across the Swiss Alps identified a significantly higher number of shared candidate genes for local adaptation than expected by chance, suggesting parallel evolution across related lineages exposed to similar alpine environments (Rellstab et al., 2020).

Few studies have attempted to identify genotype–environment associations in alpine plants distributed on the QTP (Rana et al., 2025), instead relying on genome-wide selection scans. Nevertheless, several species show clear genomic signals of high-elevation adaptation. In Salix brachista (cushion willow), population resequencing detected candidate SNPs in genes involved in hypoxia response, UV protection, and cold tolerance (Chen et al., 2019). In Prunus mira (Tibetan wild peach), high-elevation-specific alleles were found to be enriched in genes linked to photoperiod regulation, DNA repair, and membrane stabilization (Wang et al., 2021). More recently, in Dasiphora fruticosa spanning elevational gradients on the QTP, genome scans not only revealed SNPs under positive selection but also noted the substantial role of purifying selection in maintaining the functional integrity of stress-responsive genes under persistent environmental pressure (Yang et al., 2024). These findings highlight that both adaptive and purifying forces shape SNP variation in alpine plants, and underscore the need for integrating environmental association analyses in QTP systems to better resolve genotype–environment relationships.

Genome-wide association study (GWAS) approaches, particularly metabolite-based GWAS (mGWAS), offer powerful opportunities to directly link genomic variation to ecologically and physiologically relevant traits. Such approaches have been successfully used to study high-elevation crop species. For example, in Tibetan hulless barley (Hordeum vulgare var. coeleste), mGWAS identified SNPs associated with key metabolites that may play roles in cold tolerance, UV protection, and other stress responses critical for high-elevation adaptation (Zeng et al., 2020). Similarly, in Prunus mira, integrated metabolomic and genomic analyses pinpointed loci associated with fruit pigment composition and other metabolite profiles potentially linked to high-elevation resilience (Wang et al., 2021). These mGWAS examples illustrate how combining population genomics with metabolomics can bridge the gap between genotype, phenotype, and environment, offering a promising avenue for future studies on wild alpine plants.

Comparative genomic analyses using codon-substitution models have also been used to reveal genome-wide patterns of historical adaptation. In Crucihimalaya himalaica, a close relative of Arabidopsis endemic to the QTP, chromosome-scale sequencing identified hundreds of genes under positive selection, enriched for functions such as DNA repair, UV response, ubiquitin-mediated proteolysis, and reproductive development (Zhang et al., 2019). Similarly, comparative transcriptomics of five Saussurea species (three alpine, two lowland) revealed Miocene diversification of alpine lineages and hundreds of positively selected genes involved in oxidoreductase activity, membrane stability, polysaccharide metabolism, UV-B response, DNA repair, and lipid transport, pointing to strong past selection on core adaptive traits (Zhang et al., 2021b).

While population genomic SNP-based scans detect allele-frequency shifts within species, codon-level selection models capture deeper, cross-species signatures of adaptive evolution. Despite temporal differences, both approaches frequently converge on similar functional categories, such as DNA repair, UV protection, membrane integrity, stress signaling, and reproductive timing, suggesting recurrent selection on conserved adaptive pathways. Across independent alpine systems, recurrent signatures in similar pathways highlight a degree of molecular predictability in adaptation to extreme environments (Birkeland et al., 2020). Our recent comparative genomic study of distantly related alpine plants on the QTP revealed extensive molecular convergence in genes and pathways underlying cold tolerance, UV protection, and hypoxia response, further supporting the idea that distinct lineages can independently recruit similar genetic solutions to cope with analogous environmental challenges (Zhang et al., 2023). These patterns underscore the combined importance of recent and ancient genetic changes, and recurrent molecular convergence in shaping high-altitude adaptation.

In addition to de novo mutation and segregating polymorphism within species, hybridization and adaptive introgression can serve as an important source of standing genetic variation for alpine adaptation. When low-elevation lineages expand upslope into habitats already occupied by well-adapted congeners, introgression can transfer “pre-tested” alleles associated with cold tolerance, UV protection, or hypoxia response. A well-documented example in plants is the introgression of genomic regions from Cupressus gigantea into C. duclouxiana, which facilitated the latter’s occupation of cooler and drier, higher-elevation habitats (Ma et al., 2019). Although introgressed alleles may manifest as SNPs, SVs, or regulatory variants rather than a separate genomic class, recognizing hybridization and introgression as mechanisms that supply adaptive variants across species boundaries provides a more complete view of the raw material shaping alpine adaptation.

3.2. Whole-genome duplication and gene family evolution

While whole-genome duplication (WGD) is a pervasive force in plant evolution and can create genetic raw material for rapid adaptation via duplicate retention and neofunctionalization (Fig. 2B), the incidence of polyploidy is heterogeneous across mountain systems. In particular, polyploid species do not dominate the Hengduan Mountains flora, only ~22% of infrageneric taxa are polyploid (Nie et al., 2005), and overall polyploid frequency on the QTP appears relatively low based on available compilations (Wen et al., 2014). These regional patterns caution against assuming universally elevated polyploidy in alpine floras, even though WGD can be pivotal in specific lineages.

Multiple alpine lineages nonetheless show lineage-specific WGD coincident with geological or ecological transitions. In Megacarpaea delavayi (Brassicaceae), a species-specific WGD after divergence from relatives is associated with expansions of gene families linked to DNA repair and UV-B response—processes central to survival at high elevation (Yang et al., 2020). Likewise, Rhododendron nivale subsp. boreale represents a high-elevation autotetraploid with a haplotype-resolved genome; comparative and expression analyses indicate expanded gene families tied to stress tolerance and signals of meiotic stabilization, with widespread allele-specific expression, together suggesting polyploidy facilitated both abiotic stress tolerance and stable reproduction in cold, UV-intense environments (Lyu et al., 2024). In the Andes, the octoploid Lepidium meyenii (maca) underwent two closely spaced WGDs (~6.7 Ma) temporally associated with rapid Andean uplift, followed by expansions in hormone signaling, secondary metabolism, and cold-response pathways that plausibly underpin its distinctive morphology and physiology at > 4000 m (Zhang et al., 2016).

Notably, alpine adaptation is not contingent on recent WGD. Even in lineages without evidence of a lineage-specific recent WGD, extensive gene family remodeling via tandem and segmental duplication is common. The cushion willow (Salix brachista) exemplifies this pattern: despite an absence of a newly inferred WGD, its genome shows expanded repertoires for DNA repair and flavonoid/UV-related biosynthesis, indicating alternative duplication routes to enhance stress tolerance (Chen et al., 2019). Complementing expansion patterns, emerging evidence also highlights convergent gene family contraction as a recurring feature in alpine plant genomes (Zhang et al., 2024c; Zhang et al., 2023), especially innate immune receptors (e.g., NLRs, RLPs, and RLKs) relative to lowland relatives (but also see Guo et al., 2018). This pattern of convergent contraction is interpreted as an energy-saving adaptation in pathogen-sparse alpine environments, allowing plants to reallocate resources from immune investment toward cold tolerance, UV protection, or other survival-critical pathways. Both expansions and contractions of gene families appear to be integral to alpine adaptation, with expansions often enhancing stress tolerance or metabolic capacity, and contractions potentially reflecting adaptive resource reallocation under reduced pathogen pressure in high-elevation environments.

Together, these findings indicate that WGD is one, but not the only, genomic route to high-elevation adaptation (Wen et al., 2014). Where polyploidy occurs, it can catalyze large-scale innovation; elsewhere, small-scale duplications and convergent gene family contraction reshape functional capacities to meet alpine challenges. Going forward, linking copy-number variation and duplicate gene expression to concrete ecological traits (e.g., freezing tolerance, photoprotection, hypoxia response) through functional assays and population-level analyses across multiple mountain systems will clarify when adaptation is driven by polyploidy versus other modes of gene family evolution, particularly in regions like the QTP, where polyploid incidence is comparatively low.

3.3. Structural variants

Structural variants (SVs), including insertions, deletions, inversions, and large-scale chromosomal rearrangements (Fig. 2C), represent a major source of genomic variation with the potential to cause substantial phenotypic changes by altering gene dosage, disrupting coding regions, or modifying regulatory landscapes (Yuan et al., 2021). Their role in environmental adaptation is increasingly recognized in evolutionary genomics, particularly in contexts where rapid shifts in phenotype can confer survival advantages (Todesco et al., 2020). While transposable element (TE) insertions fall within the SV category, we consider TEs independently because their activity represents a dynamic and stress-responsive regulatory mechanism, particularly in alpine environments (Bennetzen and Wang, 2014).

Compelling examples of SV-mediated high-elevation adaptation come from vertebrates and humans. Large-scale long-read surveys in Tibetan highlanders and domestic ungulates have discovered SVs that are enriched in highland populations and that influence hypoxia-related genes and regulatory elements, e.g., multiple Tibetan-specific SVs affecting hypoxia and metabolic pathways (Shi et al., 2023) and a ~13 kb upstream duplication near EPAS1 in high-elevation sheep that alters regulation of this key hypoxia gene (Liang et al., 2024). These studies show that SVs can be direct targets of selection in hypoxic environments and provide a methodological and conceptual template for plant studies.

In plants, SV research in alpine systems is still rare, and direct links to high-elevation adaptation are limited. Classic cytogenetic and post-polyploidy mapping identified extensive chromosome reshuffling and intergenomic rearrangements in allo- and autopolyploids (e.g., Kengyilia thoroldiana), suggesting that structural reorganization often follows genome doubling and may be modulated by environment, but direct links to adaptive phenotypes remain tentative (Wang et al., 2012). Chromosome-scale comparisons in cushion willow reveal high overall synteny with Populus but lineage-specific fission–fusion events and rearrangements (including regions harboring the sex-determination locus), illustrating that large-scale architectural changes accompany divergence in mountain lineages even when adaptive function is not yet demonstrated (Chen et al., 2019). A graph-based pangenome of 32 Arabidopsis thaliana ecotypes uncovered ~61,000 SVs overlapping ~18,900 genes and showed that the Tibet-0 ecotype (a high-elevation form) carries the largest number of private SVs (Kang et al., 2023).

Taken together, the empirical landscape is clear: SVs are proven, potent agents of adaptation in animals and humans; in alpine plants evidence is emerging from a few high-quality studies but remains limited in taxonomic and geographic scope. Structural rearrangements such as inversions or large indels that suppress recombination may contribute to the maintenance of locally adapted haplotypes (Huang and Rieseberg, 2020; Todesco et al., 2020), a hypothesis that remains largely untested in high-elevation plant systems. Future alpine plant research should prioritize a) generation of chromosome-level assemblies across environmental transects and construction of graph-based pan-genomes to comprehensively catalogue SVs; b) population-scale genotyping of SVs to test frequency shifts and GEAs; c) integration with transcriptomics, epigenomics and physiological assays to link SVs to gene regulation and phenotypes; and d) functional validation (e.g., reporter assays, CRISPR perturbations, allele-swap or transgenic tests) to establish causality. These steps are necessary to reveal whether SVs, alone or in concert with SNPs are a common route to rapid alpine adaptation.

3.4. Selfish genetic element evolution

TEs often act as selfish genetic elements and are ubiquitous and dynamic components of plant genomes with the capacity to reshape genome size, structure and regulation (Fig. 2D; Bennetzen and Wang, 2014). By generating insertion polymorphisms, creating novel regulatory sequences, or altering local chromatin states, TEs can produce large-effect variants that selection can act upon (Chuong et al., 2017), a property that makes them plausible contributors to rapid environmental adaptation in alpine systems. In addition, DNA methylation (especially CHH/CHG contexts in plants) is a major host mechanism for TE silencing and can modulate the regulatory impact of nearby TEs.

Pangenome studies of Arabidopsis thaliana have revealed extensive TE-insertion polymorphism among ecotypes and provided functional evidence for TE-mediated adaptation (Kang et al., 2023). For example, in the high-elevation Tibet-0 accession, a 332-bp TE insertion has been identified in the promoter of HPCA1 and found to enhance HPCA1 expression and improve drought resistance, offering a direct link between TE activity and an ecologically relevant adaptive phenotype. In A. arenosa, RNA-seq surveys document elevation-associated shifts in TE transcription, with particular TE families showing up- or down-regulation along elevational transects (Wos et al., 2021), implying environmental control of TE activity. The A. thaliana mobilome showed that accessions from different elevations and climates exhibit distinct patterns of CHH methylation, particularly near TEs, and these methylation changes are associated with differential expression of nearby genes (Quadrana et al., 2016). This suggests a potential mechanism by which plants adjust their epigenomes in response to abiotic stressors like temperature (Dubin et al., 2015; Kawakatsu et al., 2016).

In non-model taxa, genomic evidence is accumulating that show TE dynamics are relevant to high-elevation evolution. For example, the glasshouse plant Rheum nobile exhibits lineage-specific LTR retrotransposon expansion temporally associated with plateau uplift, and multi-omics analyses report links between TE insertions and expression of stress-relevant genes (Feng et al., 2023). Population genomic work on high-elevation Prunus mira (Tibetan wild peach) documents cases where TE presence/absence associates with altered expression of candidate adaptive genes, supporting a role for TEs in modulating trait-relevant gene expression in extreme environments (Wang et al., 2021). Furthermore, TE-mediated SVs have been detected in Corydalis hemidicentra, where a 254-bp TE insertion upstream of bHLH35 underlies an adaptive leaf color polymorphism in alpine habitats (Zhang et al., 2025).

Despite this progress, TE studies in alpine plants remain largely correlative. Most analyses identify TE insertions or expression changes and associate them with gene function or environmental variables, yet few directly test for adaptive value or selective constraint. Moreover, methylation profiling is still a research gap in alpine plants, and functional validation, e.g., through CRISPR/dCas9 epigenetic editing or TE knockout lines, has not yet been applied in alpine contexts. Comparative studies across independent alpine lineages could reveal whether similar TE families or regulatory mechanisms are repeatedly recruited in parallel high-elevation evolution.

3.5. Integrated synthesis of genomic mechanisms underlying alpine adaptation

Current evidence suggests that no single form of genomic variation universally dominates alpine adaptation across plant lineages; instead, different types of variation likely operate over distinct temporal and functional scales. SNP-level variation has thus far received the strongest empirical support due to the availability of large population datasets and mature statistical frameworks, and multiple studies have revealed convergent functional enrichment in cold response, membrane stability, flowering regulation, and DNA-damage repair pathways (Zhang et al., 2024c; Zhang et al., 2023). SVs, including inversions and large indels, may exert larger phenotypic effects by altering gene dosage, linkage relationships, or regulatory architectures, yet plant-based functional validation remains limited due to the requirement of high-quality assemblies and long-read sequencing (Kang et al., 2023). Whole-genome duplication and gene family evolution appear to act over macro-evolutionary timescales and may explain lineage-specific innovation, especially in taxa experiencing rapid radiations in mountain systems (Lyu et al., 2024; Xia et al., 2024). Finally, TEs represent a mechanistically distinct source of adaptive variation by modifying regulatory networks and chromatin states, with emerging evidence linking TE-mediated epigenomic changes to stress tolerance in high-elevation taxa (Quadrana et al., 2016).

Overall, these mechanisms are not mutually exclusive and may form a hierarchical cascade, where TE-mediated regulatory rewiring and SV-induced genomic rearrangements generate large-effect variants that subsequently undergo SNP-level fine-tuning during local adaptation.

4. Challenges and future directions 4.1. Research challenges

Although genomic studies have increasingly begun to reveal diverse mechanisms of alpine adaptation across taxa, our current understanding remains fragmented and largely correlational. The integrative synthesis above highlights that no single genomic pathway predominates across clades; however, this heterogeneity itself poses a major challenge, as it complicates the identification of generalizable principles and hinders predictive understanding of adaptive evolution. This variability is reflected in contrasting patterns in genome size evolution, WGD incidence, and TE activity among alpine lineages (Sklenář et al., 2022). For instance, lineage-specific WGD (e.g., Megacarpaea delavayi) and species-level fine-scale adaptations (e.g., Crucihimalaya) co-occur in different systems (Feng et al., 2022; Yang et al., 2020; Zhang et al., 2019), whereas small genomes have been associated with ecological flexibility in other clades (Xiao et al., 2025a). Such heterogeneity underscores the difficulty of inferring universal genomic predictors of alpine adaptation. Additionally, the role of hybridization and adaptive introgression remains underexplored in alpine plants, despite increasing evidence that upslope colonization is often accompanied by gene flow from locally adapted congeners (Ma et al., 2019).

Ecological constraints of high mountains compound these challenges. Alpine habitats are remote, fragmented, and environmentally extreme (Nagy and Grabherr, 2009; Sun et al., 2014); short growing seasons constrain field collections, common-garden work, and temporal replication. As a result, population-level sampling often lacks the spatial and environmental breadth needed to resolve adaptive variation along elevation, temperature, and moisture gradients, hampering inference about selection and local adaptation (Manel et al., 2012).

Beyond data acquisition, functional validation remains a major bottleneck. Most alpine taxa are slow-growing, recalcitrant to cultivation, and lack efficient transformation systems (Song et al., 2020), which constrains the use of gene editing and transgenic assays. Although arctic–alpine Arabis alpina has emerged as a useful model (Pyhäjärvi and Mattila, 2021), it remains an exception rather than the rule; for most alpine lineages, mechanistic assays linking genomic variants, regulatory elements, or SVs to fitness in vivo are still rare. Consequently, many conclusions rest on correlative genomic signatures rather than causal demonstrations. Finally, comparative power is weakened by taxonomic and geographic bias as well as heterogeneous analytical pipelines. Disentangling convergence from lineage-specific responses requires coordinated sampling across mountain systems and standardized workflows; current evidence suggests that even where parallel alpine adaptation occurs, its genomic basis depends on the depth of divergence among lineages, arguing for broader, integrative study designs (Bohutínská et al., 2021).

4.2. Future prospects

Overcoming these limitations will require coordinated methodological innovation, resource development, and cross-disciplinary collaboration (Fig. 3). Advances in long-read sequencing, haplotype-resolved assembly, and chromatin conformation capture now make it feasible to generate gold-standard, telomere-to-telomere (T2T) reference genomes even for polyploid and repeat-rich alpine species (Garg et al., 2024; Li and Durbin, 2024; Liu et al., 2025). When coupled with dense resequencing efforts and the reconstruction of pangenomes, such resources will enable fine-scale detection of SNPs, SVs, and repeat dynamics underlying adaptation (Kang et al., 2023; Shi et al., 2023). In addition to genome generation, the establishment of centralized databases that integrate sequence data with phenotypic, ecological, and climatic metadata will be crucial for bridging current geographic and environmental gaps in alpine genomic datasets, particularly if paired with high-resolution microclimate monitoring and remote sensing (Xiao et al., 2025b).

On the functional side, the development of tractable alpine model systems, species amenable to transformation, genome editing, and controlled-environment cultivation will be essential for experimentally testing candidate adaptive loci (Pyhäjärvi and Mattila, 2021). Comparative frameworks that span multiple lineages and regions, ideally using standardized analytical pipelines, will in turn allow robust evaluation of the balance between convergent and lineage-specific adaptive responses (Birkeland et al., 2020; Zhang et al., 2023). Finally, integration of genomics with transcriptomics, metabolomics, and epigenomics promises to deliver a multidimensional view of alpine adaptation, linking variation in DNA sequence and gene regulation to physiological function and ecological performance (Feng et al., 2023; Wang et al., 2021; Xu et al., 2025; Zeng et al., 2020). Such a synthesis will not only clarify the mechanisms of adaptation but also inform predictive frameworks for understanding how alpine biodiversity may respond to accelerating climate change.

Beyond advancing our understanding of adaptation to extreme environments, alpine plant genomics holds significant promise for conservation biology and sustainable agriculture (Hu et al., 2025; Sun et al., 2017). High-elevation ecosystems are among the most vulnerable to ongoing climate change, with even modest shifts in temperature and precipitation potentially leading to rapid habitat loss, species range contractions, and community restructuring (Jing et al., 2025). Genomic tools offer powerful avenues to anticipate and mitigate these risks. For example, the emerging landscape genomic approaches can pinpoint adaptive genetic variants associated with specific environmental parameters, providing markers to guide in situ conservation and habitat restoration (Aitken et al., 2024; Feng and Du, 2022). Predictive modeling, informed by genotype–environment associations and demographic simulations, can help identify populations at greatest risk as well as those harboring unique adaptive alleles that may be critical for future resilience (Sang et al., 2022).

It should be noted that these genomic insights are not limited to conservation per se. Alpine plants often possess traits of agronomic interest, such as tolerance to cold, drought, or intense solar radiation that could be leveraged in crop improvement programs (Wang et al., 2021). Integrating adaptive alleles or regulatory variants from alpine species into domesticated relatives through molecular breeding or genome editing could enhance resilience in agricultural systems facing increasingly variable climates (Wang et al., 2021; Zeng et al., 2018). Thus, genomic research on alpine plants bridges fundamental evolutionary biology with applied outcomes, reinforcing the value of preserving these unique genetic resources not only for biodiversity conservation but also for sustaining human livelihoods in a changing world.

5. Conclusions

Genomic research is transforming our understanding of how alpine plants evolve, adapt, and persist in some of the world’s most extreme and dynamic environments. Advances in high-throughput sequencing, population genomics, and integrative multi-omics approaches are revealing the intricate interplay between genetic variation, genome architecture, and environmental pressures that shape alpine plant evolution (Kang et al., 2023). By synthesizing recent findings across multiple layers of genomic organization, including SNPs, structural variants, transposable elements, epigenetic modifications, and gene family evolution, emerging patterns of both adaptation and divergence are coming into focus. These patterns highlight the roles of both conserved and lineage-specific genomic features in mediating physiological, morphological, and developmental responses to alpine conditions.

Yet, many fundamental questions remain. How predictable are the genomic routes to alpine adaptation across independent lineages? What roles do large-scale structural features, such as inversions or repeat expansions, play in long-term resilience to climatic fluctuations? To what extent do epigenetic mechanisms buffer phenotypic plasticity versus canalize adaptive traits? Addressing these questions will require coordinated efforts that integrate comparative genomics and multi-omics, functional assays, ecological context, and long-term monitoring.

Alpine plant genomics now sits at a rich intersection of evolutionary biology, ecology, and conservation science. As global climate change accelerates, insights from this field will be critical for identifying populations with high adaptive potential, guiding assisted migration, and informing habitat restoration. Understanding the genomic basis of alpine plant adaptation thus offers not only a window into evolutionary innovation under extreme selection, but also a scientific foundation for conserving biodiversity and sustaining ecosystem function in rapidly changing mountain systems.

Acknowledgments

This research was funded by the National Key R&D Program of China (2024YFF1306700), the Second Tibetan Plateau Scientific Expedition and Research (STEP) program (2024QZKK0200), the National Natural Science Foundation of China (Nos. 32300201, 32322006, 32471692), and the Science and Technology Major Project of Xizang (XZ202501ZY0151).

CRediT authorship contribution statement

Xu Zhang: Conceptualization; Investigation; Visualization; Writing - original draft; and Writing - review & editing. Tao Deng: Investigation; Funding acquisition; Writing - review & editing. Hengchang Wang: Investigation; Funding acquisition; Project administration; Writing - review & editing. Hang Sun: Conceptualization; Funding acquisition; Project administration; Supervision; Writing - review & editing.

Data availability

The data presented in this study are included within the article. Additional datasets used for visualizations are available from the corresponding author upon reasonable request.

Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.