Climate-ready seaweeds: pangenomics, seascape genomics, and multi-omics for breeding and restoration

Marine macroalgae are vital for coastal biodiversity, fisheries, aquaculture, and ecosystem health; their survival is increasingly threatened by marine heatwaves, rising ocean temperatures, and other environmental stressors. Although genomic resources such as chromosome-scale reference genomes and stress-responsive transcriptomes have grown, single-genotype assemblies and basic gene expression studies do not fully capture the intraspecific variation essential for climate resilience. This review provides an integrated framework for discovering, validating, and responsibly applying climate-adaptive traits in brown, red, and green seaweeds. The evidence base itself is asymmetric, and the review treats that asymmetry as a finding rather than smoothing it over: kelps and other brown algae supply most of the case material, red and green seaweeds are drawn on wherever comparable data exist, and lineages without such data are named as gaps. It discusses moving from single-reference genomes to multi-accession assemblies and graph pangenomes, which enable detailed resolution of core and accessory genes, presence–absence variation, copy number changes, inversions, and structural variants. The review also provides insight into how seascape and temporal genomics can identify locally adapted populations, connectivity pathways, genomic vulnerabilities, and recent evolutionary responses to climate change. Complementary layers—transcriptomics, epigenomics, metabolomics, proteomics, and microbiome profiling—resolve heat-shock responses, antioxidant defenses, photoprotection, cell-wall remodeling, and stress memory, although proteomic and metabolomic coverage of macroalgae remains far thinner than transcriptomic coverage and is identified here as a priority gap. Molecular insights become practical for breeding or restoration only after rigorous validation through high-throughput gametophyte screening, chlorophyll fluorescence phenotyping, functional genomics, common-garden studies, heatwave mesocosms, and field trials. The translation of validated traits into genomic selection, climate-resilient cultivars, provenance-based restoration, and assisted gene flow is discussed. Ensuring genetic diversity, biosecurity, long-term genomic monitoring, and adaptive management are crucial for responsible deployment. Integrating these methods can advance seaweed genomics from resource development and stress-biology descriptions toward a predictive, translational pipeline that supports resilient aquaculture and marine forest restoration.