MADS-box Family Genes: Genome-Wide Identification, Characterization and Expression Profiling Under Stresses in Brassica

The MADS-box transcription factors have mainly been reported to be involved in floral organ specification and several other aspects of plant growth and development. Previously, there have been copious reports on genomics study of the MADS-box gene family in Arabidopsis, rice, tomato and soybean, while very few studies have been reported in other members of the Brassicaceae family and stress related functions as well. In this study, we identified 167 MADS-box genes through an extensive genome-wide survey of the Brassica rapa database and investigated gene structures, genome localizations, protein motif structures, phylogenetic relationships etc. Consequently, all the identified genes were further categorized into two classes, type I (further grouped into Mα, Mβ and Mγ) and type II (MIKC^c and MIKC*) based on phylogeny, protein motif structure and exon-intron organizations. Enchantingly, the B. rapa type II group acquires 100 members which is more than double than that of Arabidopsis, which indicates a higher frequencies of duplication and/or a lower rate of gene loss after duplication. In addition, we analyzed expression profiles for specific MIKC^c subfamilies in vegetative and reproductive organs and found 25 MIKC^c out of 89 exclusively accumulated their transcripts only in flower buds and the rest 64 genes showed differential expressions in both vegetative and reproductive parts of B. rapa.  Subsequently, we selected 19 BrMADS-box genes with differential expression from a low temperature treated whole genome microarray dataset and analyzed their expression in cold, salt and drought stress treated B. rapa plants at certain time courses. Several genes among them showed differential expression under all these stresses treated. Thus, the BrMADS-box genes might be useful breeding material for stress resistance Brassica crop development along with reproductive organ development.