Genome-Wide Analysis of KNOX Genes: Identification, Evolution, Comparative Genomics, Expression Dynamics, and Sub-Cellular Localization in Brassica napus

<i>KNOX</i> genes play crucial roles in cell-fate determination and body plan specification during early embryogenesis. However, the specific gene structure and functional differentiation of <i>KNOXs</i> in <i>Brassica napus</i> is still unclear. We investigated <i>KNOX</i> genes in <i>Brassica rapa</i> (<i>B. rapa</i>), <i>Brassica oleracea</i> (<i>B. oleracea</i>), and <i>Brassica napus</i> (<i>B. napus</i>), which are polyploidy models with genome triplication after <i>Arabidopsis</i>-<i>Brassiceae</i> divergence. In total, 15, 14, and 32 <i>KNOX</i> genes were identified in <i>B. rapa</i>, <i>B. oleracea</i>, and <i>B. napus</i>, respectively. Phylogenetic analysis classified <i>BnKNOXs</i> (<i>B. napus</i>) into three classes with conserved domain organization. Synteny analysis indicated that <i>BnKNOXs</i> family expansion during allopolyploidization was mainly due to whole-gene and segmental duplications. <i>Cis</i>-element, gene structure, and expression pattern analyses showed high conservation within the same group. RNA-seq and qRT-PCR results divided <i>BnKNOXs</i> 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 <i>BnKNOX</i> genes in <i>B. napus</i>.