Genomic insights into alpine plant adaptation

Alpine plants persist in some of the harshest terrestrial environments, where low temperatures, high ultraviolet radiation, and short growing seasons impose strong selective pressures. Recent advances in genome sequencing and comparative genomics are unraveling the multifaceted mechanisms that enable their adaptation and diversification under these conditions. In this review, we synthesize current progress on how genetic variation at different levels, including single nucleotide polymorphisms (SNPs), structural variants, whole-genome duplication, gene family evolution, and transposable elements, contribute to high-elevation adaptations in alpine plants. SNP-based studies have provided critical insights into adaptive differentiation along environmental gradients as well as molecular convergence underlying high-elevation adaptation, while analyses of structural variations and transposable elements reveal their potential roles in shaping phenotypic diversity and environmental responsiveness. Despite these advances, major challenges remain in linking genomic variation to functional adaptation, reflecting limitations in sampling, comparative frameworks, and functional validation. This review emphasizes the promise of integrative multi-omics, pangenome reconstruction, and functional assays to bridge these gaps, and highlights how genomic insights can guide the conservation of alpine biodiversity under accelerating climate change. • Genomic studies are transforming our understanding of diverse mechanisms by which alpine plants adapt to high-elevation environments. • Structural variants, whole-genome duplication, and gene family evolution underpin lineage-specific and convergent adaptations. • Transposable element dynamics contribute to genomic plasticity and stress responsiveness in alpine environments. • Integrative multi-omics and pangenomes offer new opportunities to link genomic variation with ecological function and conservation.