A CACTA‐like transposable element in the upstream region of BnaA9.CYP78A9 acts as an enhancer to increase silique length and seed weight in rapeseed

Rapeseed (Brassica napus L.) is a model plant for polyploid crop research and the second‐leading source of vegetable oil worldwide. Silique length (SL) and seed weight (SW) are two important yield‐influencing traits in rapeseed. Using map‐based cloning, we isolated qSLWA9, which encodes a P450 monooxygenase (BnaA9.CYP78A9) and functions as a positive regulator of SL. The expression level of BnaA9.CYP78A9 in silique valves of long‐silique variety is much higher than that of regular‐silique variety, which results in elongated cells and a prolonged phase of silique elongation. Highly expressing BnaA9.CYP78A9 in long‐silique variety and transgenic plants had higher concentration of auxin in developing siliques, which induced a number of auxin ‐related genes but no genes in well‐known auxin biosynthesis pathways, suggesting that BnaA9.CYP78A9 may influence auxin concentration by affecting auxin metabolism or an unknown auxin biosynthesis pathway. A 3.7‐kb CACTA‐like transposable element (TE) inserted in the 3.9‐kb upstream regulatory sequence of BnaA9.CYP78A9 elevates the expression level, suggesting that the CACTA‐like TE acts as an enhancer to stimulate the high gene expression and silique elongation. Marker and sequence analysis revealed that the TE in B. napus had recently been introgressed from B. rapa by interspecific hybridization. The insertion of the TE is consistently associated with long‐siliques and large‐seeds in both B. napus and B. rapa collections. However, the frequency of the CACTA‐like TE in rapeseed varieties is still very low, suggesting that this allele has not been widely used in rapeseed breeding program and would be invaluable for yield improvement in rapeseed breeding.