Genetic dissection of plant architecture reveals haplotypes controlling sink-related traits in oilseed rape under limited nitrogen fertilization.

BACKGROUND: Plant architecture and primary yield components strongly influence the sink strength for nitrogen in winter oilseed rape (Brassica napus). Their optimization can contribute substantially to enhance nitrogen utilization efficiency, reduce the nitrogen balance surplus and thus reduce negative side effects of oilseed rape cultivation. However, the genetic architecture of individual yield components is not sufficiently understood, and enhanced knowledge could accelerate breeding of more efficient varieties. Here, we manually assessed yield components and plant architectural traits in 323 experimental F1 hybrids derived from crosses between 162 father lines from a winter oilseed rape nested association mapping population and two different maternal testers. RESULTS: We observed significant genetic effects and differences between the two mothers for all traits. Although the mean number of siliques on side branches showed comparatively little variation, the F1 hybrids from the two different maternal testers differed greatly in their distribution of siliques on the side branches. On the sixth-lowest side branches from the base of the stem (level 6) the number of siliques was correlated with grain yield (r >0.3) and showed the highest heritability (h(2) = 0.289), while heritability for grain yield was h(2) = 0.414. CONCLUSION: By dissecting the genetic architecture of relevant traits, we identified haplotype blocks associated with the regulation of silique number on individual side branches, explaining up to 8% of total phenotypic variation. For certain alleles of block b000301 on chromosome A10, we observed a strong influence on the number of siliques, which ranged from 10.5 to 43.69 for siliques on side branch levels 11–15 and from 56.36 to 107.24 for siliques on side branch levels 6–10. Important haplotype blocks affecting many subtraits simultaneously were found to overlap with QTL found in other studies, emphasizing their relevance for breeding. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-07035-2.