Mapping QTLs with main, epistatic, and QTL × environment effects for secondary seed dormancy using backcross...

A major QTL cluster on chromosome A09, represented by qSSD.A09, controlling secondary seed dormancy (SSD) was identified across four environments and BLUP using a high‑density SNP map, which contributed to the development of a KASP marker for MAS of low‑SSD germplasm. After winter oilseed rape cultivation, volunteer oilseed rape plants can appear in later crops. The genetic reduction of secondary seed dormancy (SSD) in oilseed rape can lower the number of volunteer plants. However, our understanding of the genetic basis of SSD in crops remains limited, making it challenging to select rapeseed cultivars with reduced SSD. Quantitative trait locus (QTL) mapping for SSD may explain this bottleneck and accelerate precision breeding for oilseed rape with low SSD via marker-assisted selection (MAS). To dissect the genetic architecture underlying SSD, we scanned for QTLs in 178 backcross recombinant inbred lines (BILs) derived from Huaiyou-SSD-V1 (high SSD) × Huaiyou-WSD-H2 (low SSD). The BILs were genotyped using a 90 K SNP array, yielding a total of 5738 high-quality polymorphic SNPs and consolidated into 723 bin markers, which were used to construct a high-density genetic linkage map covering all 19 chromosomes. Phenotyping was conducted across five environments, and best linear unbiased prediction (BLUP) value was employed for QTL mapping. In total, 3 additive QTLs were detected by single-environment analysis; 28 additive QTLs and 17 epistatic interaction pairs, involving 31 loci, were detected for SSD using joint analysis in multiple environments based on this map. A major QTL cluster on chromosome A09, designated as qSSD.A09, was consistently identified across four environments and BLUP, collectively explaining 7.83-12.18% of the phenotypic variance. Based on the flanking SNPs of these stable QTLs, a kompetitive allele-specific PCR (KASP) marker was developed to facilitate (MAS for breeding oilseed rape varieties with reduced SSD.