Multiomics dissection of the gibberellin-mediated runner inhibition in a tufted wild strawberry (Fragaria nilgerrensis)

This study integrates phenotypic, metabolomic, transcriptomic, and genomic approaches to compare asexual reproduction in the normal (FNG) and a tufted variant (FNGt) of wild strawberry Fragaria nilgerrensis. FNGt exhibited a “high-tillering, low-runnering” phenotype, producing significantly fewer daughter plants (9.0 vs. 87.2) but more branch crowns (7.6 vs. 0.6) than FNG at 250 days after transplanting. Metabolomic analysis revealed distinct gibberellin (GA) accumulation patterns, with higher GA20 and GA3 levels in FNGt during runner initiation. Exogenous GA treatment significantly increased runner number and decreased branch crown number in FNGt. Transcriptomic data showed upregulation of GA20ox alongside sustained high expression of the repressor DELLA, explaining the suppressed runnering phenotype. Co-expression network analysis indicated dynamic rewiring between transcriptional modules and GA metabolism across development. A chromosome-level genome of FNGt (264.97 Mb, 97.78% anchored) and comparative genomics confirmed close relatedness to FNG (∼1.9 Mya divergence). Together, these results demonstrate that runner inhibition in the tufted variant is initiated by persistent DELLA expression and executed through a reprogrammed, multi-layered transcriptional network.