Integrated molecular and phenotypic analysis of onion (Allium cepa L.) germplasm reveals limited correspondence between genetic structure and phenotypic traits

The relationship between genetic structure and phenotypic variation in onion ( Allium cepa L.) germplasm remains poorly understood, especially in heterogeneous open-pollinated material. In this study, we examined this relationship in onion accessions from the Slovenian Plant Gene Bank (SRGB). We combined cytoplasmic markers, nuclear SSR and ILP markers, and phenotypic descriptors to evaluate the SRGB onion collection. A total of 243 genotypes were analyzed, including 240 individuals from 60 accessions and three reference cultivars. Cytoplasmic markers revealed limited polymorphism. Their profiles showed no clear correspondence with nuclear genetic clusters. In contrast, nuclear markers showed high diversity and significant population structure. Most nuclear variation occurred within accessions. Bayesian clustering and multivariate analyses consistently identified three nuclear genetic clusters. Phenotypic differences among these clusters were significant (PERMANOVA, R² = 0.274, p = 0.001), particularly for bulb size and morphology traits. However, genetic ancestry explained only a limited proportion of trait variation, with the strongest association observed for bulb diameter (R² = 0.207). Consistent with these results, Selection Index values varied widely among accessions, and high-ranking accessions were found across all genetic clusters. Together, these findings indicate that nuclear genetic structure reflects broad phenotypic tendencies, but it does not fully predict multi-trait breeding-oriented performance. The SRGB onion collection is therefore a structured germplasm resource with useful variation for future onion breeding. These results show that accession-level evaluation is needed when selecting gene bank material for onion breeding and hybrid development.