Copper-sensitive SPL9 TF regulates expression of indica rice domestication associated miRNAs and phenotypes [ChIP-seq]

ABSTRACT: Domestication of indica rice has facilitated better harvest and yield, however the molecular mechanisms that drove multitude of phenotypes is not fully understood. A few genetic mechanisms such as sequence variations as well as small (s)RNAs and epigenetics have been attributed to indica rice domestication, but upstream regulators of these variations are unknown. Here we identified a copper (Cu) dependent regulatory module involved in the regulation of a SPL family transcription factor (TF) as well as two classes of RNAs under its direct control. Differential accumulation of Cu-associated micro (mi)RNAs and Cu-associated protein-coding RNAs were a major portion of the differences between wild relative of indica rice (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 limited and excess conditions. OsSPL9 bound to the promoters of these genes through a conserved GTAC enriched motif. OsSPL9, Cu-associated miRNAs and their targets were in a regulatory loop, since mis-expression of SPL9 alone, or any individual Cu-associated miRNA also altered levels of other Cu-associated 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 has the potential to facilitate a better understanding of the crosstalk between genetic and epigenetic regulation that contributed to rice domestication connected to altered environment and growth conditions.

ORGANISM(S): Oryza sativa Indica Group

PROVIDER: GSE292471 | GEO | 2026/04/27

REPOSITORIES: GEO