Genome-Wide Analysis of KNOX Genes: Identification, Evolution, Comparative Genomics, Expression Dynamics, and...

KNOX genes play crucial roles in cell-fate determination and body plan specification during early embryogenesis. However, the specific gene structure and functional differentiation of KNOXs in Brassica napus is still unclear. We investigated KNOX genes in Brassica rapa (B. rapa), Brassica oleracea (B. oleracea), and Brassica napus (B. napus), which are polyploidy models with genome triplication after Arabidopsis-Brassiceae divergence. In total, 15, 14, and 32 KNOX genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis classified BnKNOXs (B. napus) into three classes with conserved domain organization. Synteny analysis indicated that BnKNOXs family expansion during allopolyploidization was mainly due to whole-gene and segmental duplications. Cis-element, gene structure, and expression pattern analyses showed high conservation within the same group. RNA-seq and qRT-PCR results divided BnKNOXs into three classes with distinct expression patterns: Class I exhibited moderate and specific expression in buds and inflorescence tips; Class III showed specific low expression in seeds and stamens; while the second class showed expression in most tissues. Sub-cellular localization results showed that the three candidate genes from the three classes exhibited distinct subcellular localizations, with BnSTM-C and BnKNAT3a-A predominantly in the nucleus and BnKNATM1-A in the cytoplasm indicating different expression patterns. Collectively, these findings provide a foundation for further functional studies of BnKNOX genes in B. napus.