Copper-sensitive OsSPL9 TF regulates expression of indica rice domestication-associated miRNAs and phenotypes

Domestication of indica rice facilitated better harvest and yield, however the molecular mechanisms that drove multitude of the associated phenotypes is poorly understood. A few genetic and epigenetic mechanisms have been attributed to indica rice domestication; however, upstream regulators of these variations are unknown. Here, we identified a copper (Cu)-dependent regulatory module, involved in the regulation of OsSPL9 TF and two classes of RNAs under its control. Differential accumulation of Cu-associated micro(mi)RNAs and Cu-associated protein-coding RNAs were a major portion of the differences between wild (Oryza nivara) and cultivated rice lines. We identified OsSPL9 as an upstream regulator of these changes through genetic and molecular analysis as well as by using Cu stressed conditions. OsSPL9 bound to the promoters of these genes through a conserved GTAC enriched motif. Although OsSPL9 might have Cu-independent roles, Cu-associated miRNAs and their targets acted as a regulatory loop with OsSPL9. Mis-expression of SPL9 alone, or any individual Cu-associated miRNA, also altered levels of other Cu-miRNAs and their cognate targets. OsSPL9-mediated regulation was closely linked to Cu accumulation and metabolism, indicating previously unappreciated roles of metal ions in mediating domestication-associated phenotypes. Our study facilitates a better understanding of the crosstalk between genetic and epigenetic regulation that contributed to indica rice domestication.