Rare Natural <scp>SNP</scp> Activates <i>SHOOT APICAL MERISTEM ENLARGER1</i> to Increase Branch Number and Silique Number on the Main Inflorescence in <i>Brassica napus</i>

Brassica napus is the second most important oil crop worldwide. Number of primary branches (Branch number, BN) and silique number on the main inflorescence (SMI) are key yield-related quantitative traits. Here, we cloned a major QTL, qDB.A09, which simultaneously influences BN and SMI. The causal gene, SHOOT APICAL MERISTEM ENLARGER1 (SAME1), encodes a mutator-like transposase-derived transcription factor and is functionally confirmed to positively regulate BN and SMI in B. napus. A rare C-to-A single nucleotide polymorphism (SNP1055), located 1.4 kb downstream of SAME1, is associated with its elevated expression in the boundary region between the organising centre and central zone of the shoot apical meristem (SAM). Functional analysis indicates that high SAME1 expression represses the expression of BnaC06.ARR15 and expands the BnaA09.WUS expression domain, resulting in enlarged SAM size and increased BN and SMI, with BN increased by 3.40 ± 0.45 and SMI increased by 32.67 ± 4.03. In addition, the seed yield per plant is increased by 22.05%. We further demonstrate that qDB.A09 significantly increases BN and SMI in the elite cultivar ZS11, with BN increased by 3.10 ± 0.67 and SMI increased by 27.35 ± 9.12. This study provides a new genetic locus that can be utilised for the genetic improvement of yield-related traits in B. napus.