An early-flowering nrpd1 mutant generated by stress-induced ONSEN mobilization

Abiotic stresses like heat, salinity, and drought profoundly influence plant development and flowering. Beyond altering gene networks, environmental stresses can activate transposable elements to generate genetic and epigenetic variation. For example, the heat-responsive retrotransposon AtCOPIA78 (ONSEN) mobilizes in RNA-directed DNA methylation (RdDM)-defective backgrounds. Although ONSEN mobilization generates heritable phenotypic variation, its role in flowering remains unclear. In this study, we examined the impact of stress-activated ONSEN mobilization on flowering-time regulation using nrpd1 mutant backgrounds. By screening ONSEN-mobilized nrpd1 populations, we identified an early-flowering mutant, designated YUNOHANA which flowered earlier than the parental nrpd1 mutant despite sharing the same RdDM defect. The early-flowering phenotype was associated with reduced expression of the floral repressor FLOWERING LOCUS C (FLC) and increased expression of the floral activator FLOWERING LOCUS T (FT). Genome-wide analysis identified multiple ONSEN insertion sites in yunohana (yuno), though none resided within known flowering-time regulatory genes. Segregation-based genotyping of early-flowering F2 plants prioritized a subset of candidate loci, including insertion sites near AT1G50130, AT1G07240, and AT3G22100, although no single tested insertion fully co-segregated with the phenotype. Transcriptome profiling revealed that yuno retained a global expression pattern largely like that of nrpd1, with differences restricted to few loci. Furthermore, ONSEN transcript and extrachromosomal DNA levels were reduced in yuno than nrpd1, indicating suppressed transposon activity following mobilization. Together, our findings suggest that stress-activated ONSEN mobilization can be associated with heritable developmental variation without widespread transcriptional disruption and identify candidate loci potentially linked to flowering-time regulation.