Uncovering a stable QTL qSRI.A06 and candidate gene for rapeseed pod shatter resistance

Rapeseed pods are prone to dehiscence, resulting in yield loss at maturity. In the present study, we investigated the shatter resistance index (SRI) of 280 doubled haploid (DH) lines derived from a cross between ZS11 (susceptible line) and R11 (resistant line). Based on the phenotypic data obtained from four environments and a high-density genetic map, a significant QTL (qSRI.A06) for shatter resistance on A06 chromosome were stably detected. This locus explained 4.80% - 15.00% of the phenotypic variation and the peak position covered a 664 Kb region. The effect of qSRI.A06 was verified in BC₃F₂ and BC₃F₃ populations and delimited in a 90.8 Kb region comprising 11 genes. Out of these genes, a differencially expressed gene, BnaA06g27900D, was identified to be involved in cell wall development by comparative transcriptome analysis. Regional association revealed four SNP/Indel variations in the promoter associated with pod shattering resistance. The highest Indels A06-41975887 showed suggestive association with SRI (p = 8.80E-06) with a TG allele variation. The stable locus qSRI.A06 and the candidate gene BnaA06g27900D will be helpful for understanding the resistance mechanism and improving shatter resistance in rapeseed.

The online version contains supplementary material available at 10.1007/s11032-025-01590-0.