Genome-Wide Identification of the Brx Gene Family in Foxtail Millet: Function, Evolution, and Expression

Foxtail millet (Setaria italica), domesticated from green foxtail (Setaria viridis), is a crucial cereal crop that plays a significant role in global food security. With the escalating environmental challenges, exploring novel stress - resistance mechanisms in foxtail millet has become a frontier in modern agricultural science and an urgent need for sustainable agriculture.In this study, we comprehensively investigated the BRX gene family in the foxtail millet genome by integrating advanced bioinformatics techniques with rigorous experimental validation. Using cutting - edge algorithms for phylogenetic analysis, we clarified the evolutionary relationships among BRX gene family members and identified previously unrecognized sub - clades and evolutionary trajectories unique to foxtail millet, rice, Arabidopsis thaliana, and green foxtail. This in - depth phylogenetic analysis provides new insights into the genetic divergence and convergence of the BRX family across different plant species.Through high - resolution motif and domain analyses, we discovered a new set of conserved elements and potential functional modules within the BRX family. These findings challenge the existing understanding of the family's functional conservation, suggesting novel regulatory mechanisms that could be utilized for crop improvement.Advanced statistical models were employed to assess the nonsynonymous to synonymous substitution ratio, enabling us to accurately quantify the evolutionary pressures on BRX gene family members in green foxtail and foxtail millet. Our results revealed unique selective forces that may have driven the adaptation of these species to diverse ecological niches.The latest genomic mapping strategies were applied in synteny analysis, offering a comprehensive view of the genomic architecture and evolutionary background of BRX family members in multiple plant species. We identified new syntenic blocks and chromosomal rearrangements, which contribute to understanding the dynamic evolution of BRX genes and their potential role in species - specific adaptation. Notably, this study innovatively carried out miRNA prediction, an aspect not covered in previous similar research. We found that four foxtail millet genes interact with four rice miRNAs, which are known to play important roles in rice development and metabolism. This discovery further validates the strong functionality of the foxtail millet BRX genes.Using the latest quantitative expression profiling techniques, we analyzed the tissue - specific expression patterns of SiBRXs under drought, salt stress, and cold conditions. Our results revealed previously unknown expression patterns and regulatory nodes, which are essential for understanding how foxtail millet responds to environmental stresses at the molecular level.Overall, this study breaks new ground in understanding the role of the BRX gene family in foxtail millet's growth and stress responses. These novel findings not only deepen our knowledge of plant genetics but also provide a solid foundation for targeted genetic improvement and breeding strategies aimed at enhancing stress resilience in foxtail millet and other related crop species.