Characterization of the CYP90 Gene Family and Its Expression Patterns Under Abiotic Stress and Developmental Stages in Brassica napus

The cytochrome P450 superfamily is vital for plant growth and stress responses, yet the CYP90 gene family in Brassica napus remains poorly characterized. In this study, we systematically identified 25 BnCYP90 genes across 16 chromosomes, classifying them into CYP90A, CYP90B, CYP90C, and CYP90D phylogenetic groups. Synteny and evolutionary analyses were consistent with purifying selection acting on this gene family. Promoter analysis identified diverse stress- and hormone-responsive elements, while network analyses predicted BnCYP90_4, BnCYP90_6, and BnCYP90_11 as highly connected nodes in candidate protein–protein interaction and miRNA-mediated regulatory networks. Furthermore, single nucleotide polymorphism (SNP) analysis of a natural population demonstrated that a missense variant (C09:66,297,283) in BnCYP90_25 was significantly associated with seed germination rate and aboveground biomass under salt stress. Transcriptome and RT-qPCR analyses highlighted distinct spatiotemporal expression profiles under abiotic stresses: BnCYP90_25 showed sustained activation under salt stress, BnCYP90_9 and BnCYP90_20 exhibited mid-stage responses to osmotic stress, and BnCYP90_21 and BnCYP90_25 rapidly responded to alkaline stress. Finally, weighted gene co-expression network analysis (WGCNA) identified BnCYP90_13 as a hub gene in the T1 developmental stage. Overall, this study comprehensively characterizes the BnCYP90 family, providing valuable candidate genes for future functional validation in breeding stress-tolerant B. napus.