Pan-Genomic Identification and Analysis of the Maize BBX Family

BBX transcription factors play crucial roles in plant growth, development, and stress resistance. Utilizing maize whole-genome data, we identified 35 members of the maize BBX gene family, comprising 18 core genes, 14 near-core genes, 4 non-essential genes, and 150 private genes. The phylogenetic tree constructed using Arabidopsis thaliana revealed that the fourth subfamily contained the largest number of core genes, totaling eight, and exhibited significant diversity throughout the evolutionary process of maize. The Ka/Ks ratios of the BBX family members in the 26 genomes indicated that, except for ZmBBX20 and ZmBBX42 under positive selection, the remaining genes were subjected to purifying selection. Further analysis combining transcriptome data and RT-qPCR demonstrated that maize BBX family member expression levels changed significantly in response to cold stress after cold treatment, highlighting their important roles in abiotic stress responses. In summary, in this study, we utilized the maize pan-genome and bioinformatics approaches to investigate maize BBX family member evolutionary relationships and functional roles, providing a new theoretical framework for further research on this gene family.