The Phytochrome Interacting Factor 3 (PIF3) mediates low accumulated temperature (LAT) response in Brassica napus

Late-sowing of rapeseed is an effective strategy to fill the post-harvest window after late-season rice and align with the winter growing period. However, this cultivation practice is severely limited by reduced accumulated temperature (AT), which leads to inadequate vegetative growth before winter. Although AT has been implicated in restricting plant growth under late-sowing conditions, its precise regulatory mechanisms and underlying networks remain unclear. In this study, 482 rapeseed accessions were evaluated under normal and late-sowing dates. Four pairs of late-sowing sensitive and insensitive lines were selected, in which AT responsiveness and late-sowing performance showed high correlation. Two extreme lines, S0090 and S1258, were selected for further analysis. Integrated RNA sequencing (RNA-seq) and genome-wide association study (GWAS) analyses based on these extreme lines and a natural population of 135 germplasm identified the overlapping gene BnaPIF3 (PHYTOCHROME-INTERACTING FACTOR 3). Functional validation using CRISPR-Cas9 knockout mutants confirmed that BnaPIF3 regulates photosynthetic acclimation and growth under AT stress. This study provides a key target gene and molecular markers for breeding rapeseed varieties with improved AT sensitive, offering practical value for expanding rapeseed cultivation northward and utilizing winter-fallow fields in southern China.