Molecular dissection of hemizygote-dependent dominance of super-early flowering in soybean

Abstract: In plants, numerous non-Mendelian inherited dominant effects, including over-, incomplete-, and codominance, are frequently observed, yet they remain insufficiently understood. A novel phenotype has been identified in specific soybean transformants overexpressing a single 35S::GmFT2a copy: super-early flowering dominance is exclusively observed in hemizygotes, not in homozygotes. Homozygous individual exhibits siRNA mediated DNA methylation, causing epigenetic transcriptional silencing, whereas no such effect occurs in hemizygotes. Intriguingly, two distinct rounds of DNA methylation establishment occur, each mediated by a different mechanism. The homozygotes that derived from the hemizygous mother plants carrying 35S::GmFT2a locus was associated with the initiation of CHH-context DNA methylation at 35S promoters mediated by 21 and 22 nucleotide (nt) siRNAs. Subsequently, 24 nt siRNAs contribute to additional CHG- and CG-context DNA methylation at 35S promoters during the homozygosity of genes in plants already homozygous in maternal lineage. Reducing DNA methylation levels can be achieved by generating a hemizygous genotype through a crossing experiment with a recessive genotype. This research has unveiled a phenomenon: hemizygote-dependent dominance resulting from transcriptional silencing in homozygote offsprings. It provides new insights into the molecular mechanism underlying dominant effects. All raw small RNA and Bisulfite sequencing data have been submitted to NCBI as BioProject PRJNA1027591, PRJNA1027571, and PRJNA1079524.