Alternative splicing and duplication of PI-like genes in maize

Alternative splicing and duplication provide possibility of functional divergence of MADS-box genes. Compared with its Arabidopsis counterpart PI gene, Zmm16 in maize recruit a new role in carpel abortion and floral asymmetry, whereas, the other two duplicated genes, Zmm18/29 have not yet been attributed to any function in flower development as a typical B class gene does. Here, alternatively spliced transcripts of three PIL genes were analyzed, among which we described the candidate functional isoforms and analyzed the potential effects of alternative splicing (AS) on protein-protein interactions (PPIs) as well, then their phylogenetic relationship with orthologs in typical grasses were further analyzed. Furthermore, we compared the cis-acting elements specific for three maize PIL genes, especially the elements related to jasmonic acid (JA) and gibberellic acid (GA), both hormones involved in sex-determination process in maize. Together with the results from the obvious different co-expression networks at kernel stage, we speculated that, due to duplication and alternative splicing, Zmm18/29 may play a role in kernel development, which is different from Zmm16. These results provide novel clues for experimental validation of evolutional meaning of maize PIL genes.