Soybean leaf siRNA and bisulfite sequencing

In plants, many dominant effects, such as overdominance, incomplete dominance, or codominance, are commonly observed and utilized, but poorly understood. Here, we report an identical phenotype of super-early flowering dominance only in heterozygotes but not in homozygotes in soybean, and reveal the molecular mechanism of this new phenomenon. We found that the homozygous gene triggers siRNA-mediated DNA methylation, causing transcriptional gene silencing, while the heterozygous gene does not. Interestingly, two rounds of DNA methylation establishment occur, each mediated by a distinct mechanism. The 21-22 nucleotide (nt) siRNAs are responsible for initiating DNA methylation in the CHH-context during the initial homozygosity of genes when the mother plants were heterozygous. In contrast, the 24 nt siRNAs play a role in the additional CHG- and CG-context DNA methylation during successive homozygosity of genes when the mother plants were already homozygous. Additionally, generating heterozygous genotype through a crossing experiment with recessive genotype can reduce the DNA methylation level and resume dominant phenotype. Our study provides a new insight into the molecular mechanism of the novel dominant effects and enriches the genetic theory of plants.