Towards premium rapeseed oil: leveraging allelic variation in BnaFAD2.A5, BnaFAD3.A4 and BnaFAD3.C4 for molecular design breeding

Background Improving the quality and frying stability of rapeseed oil has long been an important goal in rapeseed quality breeding. This goal can be achieved through molecular marker-assisted selection (MAS) combined with speed breeding strategies. In this study, genomic data from the high-oleic-acid, low-linolenic-acid material L3 and the recessive genic male sterile (RGMS) line RG430A were used to identify functional variation sites underlying key quality traits: one governing oleic acid content and two controlling linolenic acid content. Additionally, Kompetitive Allele-Specific PCR markers were developed to efficiently genotype these oleic and linolenic acid-related variants. Results By integrating speed breeding with MAS and phenotypic screening, a new RGMS line was developed with high oleic acid, low linolenic acid content, and favorable agronomic performance. Compared with the original RG430A, the new line shows an approximately 15.0% increase in oleic acid content (reaching 78.0%) and an approximately 52.6% reduction in linolenic acid content (decreasing to 3.6%), with no significant alterations in major agronomic traits. Conclusions Our study offers strategic insights for rapeseed quality breeding, and the developed RGMS line represents a promising germplasm resource for future high-quality hybrid breeding.