Expanding plant model systems: Classical references, emerging species, and a trait‑centric framework for modern plant science

For decades, plant biology has relied on a narrow set of classical model organisms—such as Arabidopsis thaliana, Oryza sativa, and Zea mays —to uncover core physiological, developmental, and molecular pathways. These systems enabled foundational discoveries, yet their glycophytic, annual, and domesticated life histories limit their relevance for studying many adaptive traits found across global plant diversity. Key innovations—including CAM and C4 photosynthesis, extreme salinity and desiccation tolerance, perennial wood formation, specialized secondary metabolism, and parasitic interactions—remain largely inaccessible within classical frameworks. Recent advances in third‑generation long‑read sequencing (PacBio HiFi, ONT Duplex), telomere‑to‑telomere (T2T) phased assemblies, pangenomics, single‑cell and spatial transcriptomics, and multi‑omics integration are dismantling these historical barriers. Together, these technologies enable high‑resolution characterization of polyploid, structurally complex, and ecologically specialized genomes, allowing previously intractable species to be developed as functional models. This review outlines the shift from traditional model‑centric approaches toward a trait‑centric, multi‑model framework. We evaluate the limitations of homology‑based functional inference across divergent regulatory and metabolic networks, highlight structural genomic constraints that undermine automated annotation transfer, and examine genomic enablers that resolve polyploidy, structural variation, and pangenomic diversity. We further synthesize emerging model systems—including halophytes, extremophytes, resurrection plants, alkaloid‑producing taxa, perennial woody species, parasitic lineages, and early‑diverging clades—that provide direct access to traits absent from classical references. Finally, we discuss persistent bottlenecks in transformation recalcitrance and functional gene validation, emphasizing how morphogenic regulators, viral vectors, CRISPR platforms, and AI‑driven biological foundation models are enabling direct in planta functional genomics across diverse species. Collectively, these developments establish a modernized, trait‑centric, multi‑model landscape that expands biological discovery and strengthens applications in agriculture, biotechnology, medicine, and biodiversity conservation.