Genetic diversity analysis and core collection construction of tillering onion (Allium cepa L. var. aggregatum G. Don) based on phenotypic traits and SNP markers

Introduction Tillering onion ( Allium cepa L. var. aggregatum G. Don) is a specialty vegetable widely grown in China, yet its germplasm resources remain poorly characterized at the genetic level. The aim of this study was to characterize the phenotypic and molecular diversity of tillering onion germplasm and to construct a representative core collection. Methods We evaluated 87 tillering onion accessions collected from six Chinese provinces using 29 agronomic traits and single-nucleotide polymorphism (SNP) markers developed via specific-locus amplified fragment sequencing (SLAF-seq). Phenotypic diversity was assessed by coefficients of variation, genetic diversity indices, correlation analysis, principal component analysis (PCA), stepwise regression, and UPGMA clustering. Molecular diversity was characterized through population structure analysis and a high-quality SNP fingerprint. A core collection was constructed by integrating phenotype-based (QGA) and genotype-based (Core Hunter) approaches and was validated using mean difference percentage (MD%), coincidence rate of range (CR%), and variable rate of coefficient of variation (VR%). Results Phenotypic coefficients of variation ranged from 14.27% to 65.41%, and genetic diversity indices ranged from 0.514 to 2.234. Correlation analysis identified 137 significantly correlated trait pairs ( p < 0.05), including 100 at p < 0.01. PCA extracted 10 principal components accounting for 79. 31% of cumulative variance, and stepwise regression identified 14 representative traits (R² = 0.971). UPGMA clustering classified the accessions into eight groups. At the molecular level, SLAF-seq yielded 1,209,763 SNP loci, and population structure analysis divided the accessions into two subpopulations, with C1 showing slightly higher diversity (Nei's index = 0.281, PIC = 0.224) than C2. A fingerprint based on 335 high-quality SNP markers showed population-wide observed heterozygosity of 0.379–0.644 (mean 0.572), Nei's diversity index of 0.455–0.500 (mean 0.479), and PIC of 0.352–0.375 (mean 0.364). The core collection comprised nine accessions (M15, M24, M28, M37, M45, M47, M49, M62, M66), representing 10.34% of the total resources, with validation parameters of MD% = 10.0%, CR% = 83.6%, and VR% = 112.2%. Discussion These results provide a framework for germplasm conservation, elite accession identification, and parental selection in tillering onion breeding.