Genetic variation of BnaA3.NIP5;1 expressing in the lateral root cap contributes to boron deficiency tolerance in Brassica napus

Boron (B) is essential for vascular plants. Rapeseed ( Brassica napus ) is the second leading crop source for vegetable oil worldwide, but its production is critically dependent on B supplies. BnaA3 . NIP5;1 was identified as a B-efficient candidate gene in B . napus in our previous QTL fine mapping. However, the molecular mechanism through which this gene improves low-B tolerance remains elusive. Here, we report genetic variation in BnaA3 . NIP5; 1 gene, which encodes a boric acid channel, is a key determinant of low-B tolerance in B . napus . Transgenic lines with increased BnaA3 . NIP5;1 expression exhibited improved low-B tolerance in both the seedling and maturity stages. BnaA3.NIP5;1 is preferentially polar-localized in the distal plasma membrane of lateral root cap (LRC) cells and transports B into the root tips to promote root growth under B-deficiency conditions. Further analysis revealed that a CTTTC tandem repeat in the 5’UTR of BnaA3 . NIP5;1 altered the expression level of the gene, which is tightly associated with plant growth and seed yield. Field tests with natural populations and near-isogenic lines (NILs) confirmed that the varieties carried BnaA3 . NIP5;1 Q allele significantly improved seed yield. Taken together, our results provide novel insights into the low-B tolerance of B . napus , and the elite allele of BnaA3 . NIP5;1 could serve as a direct target for breeding low-B-tolerant cultivars.