Polygenic discrimination of leaf morphotypes in alpine Heldreichia bupleurifolia (Brassicaceae) across its natural range

Background and Aims Leaf morphology is a critical adaptive trait in plants, yet its genetic basis and environmental drivers remain poorly resolved in natural populations. Heldreichia bupleurifolia, a polymorphic alpine species in Turkey, exhibits three distinct leaf morphotypes (entire, mixed, lobed/dissected) across a west-to-east geographical gradient. This study aims to investigate genome-wide patterns of genetic variation associated with these morphotypes, identify candidate loci and pathways involved in phenotypic differentiation, and examine potential environmental correlates/drivers.Methods Using RADseq, we generated 61 286 high-confidence single nucleotide polymorphisms from 131 individuals across 20 populations. Genetic structure was analysed via principal components analysis, while morphotype differentiation was assessed using discriminant analysis of principal components (DAPC) and random forest (RF) classification. Gene Ontology enrichment analysis identified biological pathways linked to candidate loci. Field observations correlated morphotypes with substrate type.Results Three genetic clusters aligned with a west-to-east geographical gradient, with limited congruence to traditional subspecies classifications. DAPC and RF achieved perfect discrimination among morphotypes, identifying 167 loci (90 from DAPC, 83 from RF; five shared) localized to protein-coding regions. Enriched pathways included ion homeostasis and transmembrane transport, critical for nutrient-poor alpine soils. Lobed/dissected-leaved populations exclusively occupied volcanic substrates, while entire/mixed-leaved groups occurred on limestone, highlighting substrate-driven selection.Conclusion Our findings suggest that genetic differentiation among morphotypes may involve stress-related processes, particularly ion transport and homeostasis. The enrichment of these functions among candidate loci, alongside observed correlations between morphotypes and substrate types, also hints at a possible contribution of edaphic conditions. While these associations are correlative and require further validation, they underscore potential links between genotype, phenotype and environment, and highlight the value of integrating genomic and ecological data in alpine plant conservation.