Abstract
Whether A-subgenome dominance in the allotetraploid Brassica napus (AACC, 2n = 38) is uniform across all chromosomes and ecotype backgrounds remains poorly characterized at the chromosome level. A subgenome-resolved, position-controlled pipeline was applied to 607 geographically and ecotypically diverse B. napus accessions (394 winter-type, 127 spring-type, and 86 semi-winter-type), characterizing SNP diversity within a conserved 20-kb syntenic window per chromosome (19 target regions; 1,510 high-quality biallelic SNPs; zero missing genotype calls). The A subgenome exhibited significantly higher mean minor allele frequency (MAF: 0.295 vs. 0.222; Welch’s t = 8.71, p = 7.99 × 10−18, Cohen’s d = 0.456), nucleotide diversity (pi: 0.0429 vs. 0.0335), and coding SNP proportion (16.4% vs. 11.2%; χ² = 8.33, p = 0.004). At the chromosome level, A-subgenome dominance dissolved into a mosaic of chromosome-specific patterns, with six of nine homoeologous pairs showing reversals or near-equivalence. Ecotype stratification confirmed the A > C difference was not confounded by panel composition (two-way ANOVA interaction: F = 0.12, p = 0.89). Bayesian inference yielded P(A > C) = 0.9998 (95% HDI: [0.0565, 0.0899]). Leave-one-out sensitivity analysis confirmed robustness across all chromosomes (ΔmMAF change < 0.1%). Subgenome dominance in B. napus operates as a chromosome-specific quantitative mosaic rather than a binary genome-wide dichotomy, with mechanistic support from functional annotation, and robustness confirmed by multiple independent validation frameworks. The targeted-region design covers approximately 0.05% of the B. napus genome and provides a methodologically rigorous foundation for genome-wide validation.