Flowers are one of the most important organs in plants. Their development serves as a key indicator of the transition from vegetative to reproductive growth and is regulated by various internal signals and environmental factors. NAC (NAM, ATAF, CUC) transcription factors (TFs) play a crucial regulatory role in floral organ development; however, research on the analysis and identification of the NAC TF family in Chinese cabbage (Brassica rapa L.) remains limited. In this study, we performed a comprehensive genome-wide analysis of NACs in B. rapa and identified 279 members of the BrNAC gene family. Their physicochemical properties, domain structure, collinearity relation, and cis-regulatory elements were evaluated. Phylogenetic analysis indicates that NAC proteins from Arabidopsis, B. rapa, B. oleracea, and B. nigra can be classified into seven distinct clades. BrNACs exhibit a tissue-specific expression, and nine BrNACs being specifically expressed in the inflorescence. Furthermore, nine flower-related BrNACs were selected for RT-qPCR analysis to validate their expression profiles. BrNAC2s has been cloned to investigate their subcellular localization, and examine the expression patterns of their promoters in Arabidopsis inflorescences. BrNAC2a and BrNAC2c are highly expressed in stamens while BrNAC2b exhibits elevated expression in pistils and pedicel. Collectively, our findings enhance the understanding of the BrNAC family and provide a foundation for future studies on the molecular mechanisms of BrNACs in floral development.

MADS-box is a vital transcription factor family that functions in plant growth and development. Apart from APETALA2, all genes in the ABCDE model that explain the molecular mechanism of floral organ development belong to the MADS-box family. Carpel and ovule numbers in plants are essential agronomic traits that determine seed yield, and multilocular siliques have great potential for the development of high-yield varieties of Brassica. In this study, ABCDE genes in the MADS-box family from Brassica rapa were identified and characterized. Their tissue-specific expression patterns in floral organs and their differential expression in different pistil types of B. rapa were revealed by qRT-PCR. A total of 26 ABCDE genes were found to belong to the MADS-box family. Our proposed ABCDE model of B. rapa is consistent with that of Arabidopsis thaliana, indicating that ABCDE genes are functionally conserved. These results of qRT-PCR showed that the expression levels of class C and D genes were significantly different between the wild-type (wt) and tetracarpel (tetrac) mutant of B. rapa. Interestingly, the expression of the homologs of class E genes was imbalanced. Therefore, it is speculated that class C, D, and E genes are involved in developing the carpel and ovule of B. rapa. Our findings reveal the potential for the selection of candidate genes to improve yield traits in Brassica crops.

The AP2/ERF transcription factor family is one of the largest transcription factor families in plants and plays essential roles in growth and development. Chili pepper, as a representative member of the Solanaceae family, is an important vegetable crop with enormous economic value. In this study, using the recently released gap-free telomere-to-telomere genome assembly of pepper, we re-annotated the AP2/ERF transcription factor family and identified 155 high-confidence members. Phylogenetic analysis classified these genes into five subfamilies: AP2 (19), ERF (82), DREB (51), RAV (1), and Soloist (2). Comprehensive analyses of gene structure, conserved motifs, chromosomal distribution, collinearity, cis-elements, and expression profiles revealed substantial structural conservation and functional diversification within the family. Expression profiling highlighted CaBBM, a key member of the AP2 subfamily, as a candidate developmental regulator, prompting further functional characterization. Expression analyses using qRT-PCR and promoter–GUS assays showed that CaBBM was preferentially expressed in stamens, while subcellular localization assays confirmed its nuclear localization. Preliminary analysis of biological functions suggests that heterologous expression of CaBBM in Arabidopsis can lead to phenotypes such as shorter primary roots, smaller leaves and floral organs, and decreased pollen number. In addition, yeast two-hybrid screening identified 12 candidate interacting proteins. These results provide a comprehensive framework for understanding the AP2/ERF family in chili pepper and lay a foundation for elucidating the function and regulatory mechanisms of CaBBM.