Premature seed shattering in canola causes massive losses in yield by up to 50% in adverse climatic conditions. In the model plant Arabidopsis thaliana, which belongs to the same family as canola, the Brassicaceae, eight genes participate in a shattering cascade. Phylogenetic reconstruction, syntenic relationships, genomics loci, promoter sequences, and identification of transcription factor-binding sites (TFBSs) faced shattering cascade genes’ analysis. Among these, three genes, SHATTERPROOF1, SHATTERPROOF2, and FRUITFUL (SHP1, SHP2, FUL), belonged to a MADS-box family implicated in fruit dehiscence zone and valve margin constitute a core regulatory module. But, in Brassica, the exact number of genes involved in shattering remained obscure. Grouping BnSHP1-N, BnSHP2-N, and BnFUL-N into their respective clades was according to phylogenetic reconstruction of core regulatory modules (SHP1, SHP2, and FUL) and from other species homologs. The eight shattering cascade genes showed no conservation, indicating their involvement in crushing through separate pathways. The increased number of homologs/paralogs in Brassica was due to occurrences of genome duplication or a triplication event during evolution. Exonization and intronization could be responsible for a variable number and size of the exons and introns in gene structures. Comparative genome synteny analysis of SHP1, SHP2, and FUL revealed correlation and evolutionary insights into gene region relationships in all Brassicaceae. Study results provided basic information on cloning, phylogenetic reconstruction, genomics loci, and identifying transcription factor-binding sites (TFBSs) of core regulatory module genes that might be helpful for developing shattering-resistant genome-edited plants to prevent future yield losses in canola.

Keywords: Brassica napus L, genome analysis, shattering genes, core regulatory module, homologs, exonization, intronization

Key findings: The phylogenetic reconstruction of SHP1, SHP2, and FUL genes and homologs from other species conglomerated BnSHP1-N, BnSHP2-N, and BnFUL-N into their respective clades. The rise in homologs in Brassica resulted from genome duplications or triplications that occurred during evolution. When analyzing gene structure, exons and introns may vary in size and number due to exonization and intronization. Comparative genome synteny analysis of SHP1/2 and FUL genes revealed correlation and evolutionary insights throughout the Brassicaceae. The promoter analysis unveiled that the expression divergence may correlate with their divergent promoters, where regulatory motifs, particularly CArG-boxes, might have played varying roles in the siliques of these plants.