Natural Variation in the Promoter of GmSPL9d Affects Branch Number in Soybean

The branch number is a crucial factor that influences density tolerance and is closely associated with the yield of soybean. However, its molecular regulation mechanisms remain poorly understood. This study cloned a candidate gene for regulating the soybean branch number based on the rice homologous gene. Meanwhile, the genetic diversity of the was analyzed using 3599 resequencing data and identified 55 SNP/InDel variations, which were categorized into seven haplotypes. Evolutionary analysis classified these haplotypes into two groups: and . Soybean varieties carrying the haplotype exhibited a significantly lower branch number compared with those carrying the haplotype. Association analysis between the variation sites and branch number phenotypes revealed a significant correlation between the promoter variations and the branch number. Promoter activity assays demonstrated that the promoter displayed significantly higher activity than the promoter. Transgenic experiments confirmed that the plants that carried the promoter exhibited a significantly lower branch number compared with those that carried the promoter. These findings indicate that the variation in the promoter affected its transcription level, leading to differences in the soybean branch number. This study provides valuable molecular targets for improving the soybean plant structure.