A rare dominant allele determines seed coat color and improves seed oil content in .

Yellow seed coat color (SCC) is a valuable trait in , which is significantly correlated to high seed oil content (SOC) and low seed lignocellulose content (SLC). However, no dominant yellow SCC genes were identified in . In this study, a dominant yellow SCC N53-2 was verified, and then 58,981 eQTLs and 25 trans-eQTL hotspots were identified in a double haploid population derived from N53-2 and black SCC material Ken-C8. A rare dominant allele () was subsequently cloned in a trans-eQTL hotspot that colocated with SCC, SOC, and SLC QTL hotspot on ChrA09 through QTL fine mapping and multi-omics analysis. Transgenic experiments revealed that the expression of produced yellow SCC seeds with significantly increased SOC and decreased SLC. Our result provides a rare dominant yellow SCC allele in , which has excellent potential for yellow SCC and high SOC rapeseed breeding.