Comprehensive Morphological and Molecular Insights into Drought Tolerance Variation at Germination Stage in Brassica napus Accessions

Drought constitutes a noteworthy abiotic stressor, detrimentally impacting seed germination, plant development, and agricultural yield. In response to the threats imposed by climate change and water paucity, this study examined the morphological divergence and genetic governance of drought resilience traits at the germination stage in 196 rapeseed (<i>Brassica napus</i> L.) lines under both normal (0 MPa) and drought-induced stress (-0.8 MPa) scenarios. Our study showed that the composite drought tolerance D value is a reliable index for identifying drought resilience. Through a genome-wide association study (GWAS), we uncovered 37 significant SNP loci and 136 putative genes linked to drought tolerance based on the D value. A key discovery included the gene BnaA01g29390D (<i>BnNCED3</i>), encoding 9-cis-epoxycarotenoid dioxygenase, which exhibited significantly heightened expression levels in drought-resistant accessions (<i>p</i> < 0.01), underscoring its potential as a positive drought stress regulator and a suitable candidate for genetically enhancing drought resilience. Moreover, we pinpointed four stress-reactive transcription factors (BnaA07g26740D, BnaA07g26870D, BnaA07g26910D, and BnaA07g26980D), two E3 ubiquitin-protein ligases (BnaA05g22900D and BnaC06g28950D), two enzymes (BnaA01g29390D and BnaA03g48550D), and two photosystem-associated proteins (BnaA05g22950D and BnaC06g28840D) as vital components in drought response mechanisms. The construction of a regulatory network reveals an ABA-dependent pathway (<i>NCED3/RGLG5/IDD14</i>) that contributes to drought tolerance in rapeseed seedlings, alongside the involvement of a drought avoidance strategy (<i>APRR6/PHYB</i>). The SNPs and genes unveiled in this study offer a substantial theoretical foundation for subsequent investigations targeting genetic improvement for drought resilience during seed germination in rapeseed.