Evolution of the arbuscular mycorrhizal regulatory network through differential GRAS gene retention and protein interaction in land plants

Plants rely on an ancient genetic "toolkit" to establish arbuscular mycorrhizal symbiosis (AMS) with fungal partners. However, the symbiotic outcomes vary among AMS hosts, indicating divergence in downstream transcriptional reprogramming after the perception of symbiotic signals. To uncover the cross-species variation of the AMS regulatory network, we traced the evolutionary trajectory of the GRAS gene family, which encodes the major group of transcription factors in AMS regulation. Phylogenetic analysis of the GRAS family across land plants placed known symbiotic GRAS members within 12 anciently diverged lineages, with multiple lineages showing pronounced gene loss in nonmycorrhizal plants. This pattern pointed to three additional GRAS lineages as candidates for AMS regulation. Given that tomato harbors single-copy, AMS-induced genes in these lineages, we selected it for functional validation. CRISPR-Cas9 mutagenesis, combined with detailed phenotyping of fungal colonization and arbuscule morphology, and transcriptome profiling of mutant roots, confirmed that all three tomato genes are individually required for AMS development, designated Symbiosis-Required GRAS (SRG) 1 to 3. Large-scale phylogenomic analysis and protein interaction assays (by yeast two-hybrid and bimolecular fluorescence complementation) further showed that both the repertoire and interaction networks of symbiotic GRAS members vary among AMS hosts. In summary, together with 12 previously characterized lineages, the three SRGs identified in this study bring the total number of GRAS lineages with known symbiotic members across land plants to fifteen. Furthermore, our findings demonstrate that the symbiotic GRAS network has been dynamically reshaped by gene loss and rewiring of protein interactions during land plant evolution.