Genome-wide regulatory and interaction landscape underlying functional divergence of rice AGAMOUS-like transcription factors

Angiosperm AGAMOUS-like (AG-like) genes are essential for flower formation. The molecular basis underlying the functions and divergence of rice four AG-like genes that belong to the AG lineage (OsMADS3 and OsMADS58) and AGL11 lineage (OsMADS13 and OsMADS21) has been poorly revealed. In this work, we created each AG-like in situ overexpressing (AGisOE) transgenic rice plant with AG-like fusion with GFP. The AG-like expression domains in AGisOE were found to be similar to those in the wild type, although their expression levels exhibited varying degree of elevation. In situ overexpression of OsMADS3, OsMADS13, and OsMADS21 differentially perturbed floral robustness and divergently affected flowering time, male fertility, seed-setting rate, and seed-borne fungal growth. Overall, the fitness of transgenic rice plants was reduced in these AGisOEs. Genome-wide characterizations of molecular interactions associated with these rice AG-like genes revealed that the phenotypic divergences observed in these AGisOEs were well supported by corresponding variations in their direct target genes, putative trans-acting factors, and protein-protein interaction partners. Our results provide new insights into the molecular basis underlying the functional divergence of rice AG-like duplicates in reproductive organs, and reveal the potential significance of expression dosage variation of a gene in plant evolution, new function display, and crop improvement.