Unveiling mirtron-triggered gene silencing mechanisms in soybean seed coat pigmentation

Background The diversity of soybean seed coat colors is largely determined by anthocyanin accumulation, regulated by chalcone synthase (CHS) genes at the I locus. While RNA interference (RNAi) has been implicated in this process, the underlying mechanisms remain incompletely understood. This study investigates the role of mirtrons (miRNA precursor derived from intronic sequences) in gene silencing related to seed coat pigmentation in black and yellow soybean varieties. Results To validate the presence and function of these mirtrons, we conducted small RNA sequencing (sRNA-seq) for each allele at the I locus. Our analysis reveals a complex, multi-layered regulatory mechanism involving the genomic architecture the I locus, mRNA, and sRNA interactions. We identified mirtron-triggered miRNAs (MT-miRNAs) and their amplification into secondary miRNAs, which collectively mediate genome-wide silencing of CHS genes. Conclusion This study elucidates a cascade of mirtron-triggered gene silencing (MTGS) that regulates seed coat pigmentation soybeans. These findings provide novel insights into RNAi-mediated control of anthocyanin biosynthesis and highlight the significance of mirtrons in plant gene regulation.