The basic region/leucine zipper motif (bZIP) transcription factor family is one of the largest families of transcriptional regulators in plants. bZIP genes have been systematically characterized in some plants, but not in rapeseed (Brassica napus). In this study, we identified 247 BnbZIP genes in the rapeseed genome, which we classified into 10 subfamilies based on phylogenetic analysis of their deduced protein sequences. The BnbZIP genes were grouped into functional clades with Arabidopsis genes with similar putative functions, indicating functional conservation. Genome mapping analysis revealed that the BnbZIPs are distributed unevenly across all 19 chromosomes, and that some of these genes arose through whole-genome duplication and dispersed duplication events. All expression profiles of 247 bZIP genes were extracted from RNA-sequencing data obtained from 17 different B. napus ZS11 tissues with 42 various developmental stages. These genes exhibited different expression patterns in various tissues, revealing that these genes are differentially regulated. Our results provide a valuable foundation for functional dissection of the different BnbZIP homologs in B. napus and its parental lines and for molecular breeding studies of bZIP genes in B. napus.

Calmodulin-binding transcription activators (CAMTAs) are pivotal regulators decoding calcium signals, with crucial roles in plant development, hormone responses, and adaptation to abiotic stresses. Although extensive research has been conducted on CAMTAs in model plants such as Arabidopsis thaliana, a comprehensive genome-wide analysis of the CAMTA gene family across the economically important Brassica U-triangle species has not been performed. In this study, we systematically identified and characterized 64 CAMTA genes from the genomes of Brassica U-triangle species. Phylogenetic analysis classified these genes into four conserved groups, a finding corroborated by analyses of gene structure and conserved motifs. These analyses revealed strong evolutionary preservation of functional domains, especially the calmodulin-binding domain (CaMBD). Chromosomal distribution and collinearity assessment highlighted the significant impact of polyploidization on the expansion of the CAMTA family, with most orthologous pairs being under purifying selection. Cis-element analysis in promoters uncovered an abundance of stress- and hormone-related elements, suggesting diverse regulatory roles for these genes. Furthermore, RNA-Seq and RT-qPCR expression profiling demonstrated that BnaCAMTA genes exhibit tissue-specific expression and are dynamically responsive to various phytohormones (ABA, JA, and GA) and abiotic stresses (salt and drought), particularly in the root. Notably, BnaCAMTA5.2, which was prioritized among several validated candidates, mediates the antagonistic regulation of hypocotyl and root growth under GA and salt stress, indicating its key role in balancing growth promotion and stress adaptation. Additionally, we identified a set of stress-related miRNAs that potentially target BnaCAMTAs, suggesting a potential layer of post-transcriptional regulation. Our results provide valuable insights into the evolutionary and functional diversity of CAMTA genes in Brassica U-triangle species and lay a foundation for further research into their roles in enhancing stress resistance in B. napus.

Brassica napus L. is one of the most important oil crops in the world, and improving its nitrogen efficiency is a key strategy for enhancing low-nitrogen tolerance and increasing yield. Ammonium transporters (AMTs) play critical roles in NH₄⁺ transport in plants and significantly influence nitrogen use efficiency and yield. To identify promising candidate AMT genes for rapeseed improvement, this study systematically analyzed the evolution and expression of AMT genes across the Archaeplastida plants, especially in Brassica species of the U’s triangle. A total of 368 AMT genes were identified from 35 Archaeplastida species, including 180 AMT1 and 188 AMT2 homologs. Gene duplication analysis revealed that small-scale duplication (SSD) was the primary mechanism driving gene expansion from aquatic algae to angiosperms in both AMT1 and AMT2 families, which were under the influence of purifying selection. In the U’s triangle, allopolyploidization, particularly whole-genome duplication (WGD), was the primary mechanism for AMT expansion, accompanied by gene loss. Expression profiling indicated that most BnAMTs respond to hormonal and low-nitrogen signals and exhibit tissue-specific expression patterns. Notably, four candidate genes (BnAMT1;5, BnAMT1;12, BnAMT2;2, BnAMT2;4) exhibited high expression levels and responsiveness to low-nitrogen stress. Haplotype analysis further linked specific polymorphisms in BnAMT1;5 and BnAMT2;2 to variations in plant height and yield. Collectively, these findings elucidate the evolutionary processes and regulatory mechanisms of AMTs, laying a foundation for enhancing nitrogen utilization efficiency in B. napus and other crops.