Efficient infiltration of water through cell membranes is arbitrated by a family of transmembrane water channels called aquaporins (AQPs). Aquaporin belongs to a highly conserved group of membrane proteins called major intrinsic proteins that facilitate the transport of water and a variety of low molecular weight solutes across biological membranes,which is essential for plants to survive in stress conditions. This study identified 59 BrAQP genes from B. rapa database and Br135K microarray dataset, which was formed by applying low-temperature stresses to contrasting Chinese cabbage two inbreed lines, Chiifu and Kenshin. Based on phylogenetic analyses of BrAQPs revealed four distinct subfamilies, such as plasma membrane intrinsic proteins (PIP), tonoplast intrinsic proteins (TIP), NOD26-like intrinsic proteins (NIP), small basic intrinsic proteins (SIP) with aquaporin of Tomato and Arabidopsis thaliana. All BrAQP genes were firstly examined through homology study with existing biotic and abiotic stress resistance-related aquaporin genes of other plant species and found a high degree of homology. We selected PIP subfamily genes for expression analysis based on microarray data with high and differential transcript abundance levels and homology study with stress related aquaporin genes of other plant species. In our study, we characterized all B. rapa aquaporin genes and understanding the BrPIP subfamily gene function in plants under various environmental stimuli, the expressions of BrPIP genes under various abiotic stress conditions including cold, drought, salinity, water logging, ABA treatment and Fusarium oxysporum f. sp. Conglutinans infection were investigated by a quantitative real-time reverse transcription-PCR analysis. In our expression analysis, 4 BrPIP genes showed responsive expression against F. oxysporum f. sp. Conglutinans infection. The selected genes showed an organ-specific expression, and 12 out of 22 BrPIP genes were differentially expressed in Chiifu compared to Kenshin under cold stresses. Only 7 genes showed up regulation under drought stress and incase of salt stress 17 BrPIP genes were more responsiveness. Additionally, 18 BrPIP genes were up regulated by ABA treatment and all BrPIP genes showed down regulation under water logging stress. Together with expression and bioinformatic analyses, our results provides novel basis to allocate the stress-related biological function to each PIP gene.

The TIFY family is composed of a plant-specific group of genes with diversity of functions. This family represents four subfamily of proteins viz. ZML, TIFY, PPD and JASMONATE ZIM-domain (JAZ) proteins. TIFY proteins especially, JAZ proteins have been reported to perform different biological processes, such as developmental and stresses and hormone responses in Arabidopsis and rice. However, there is no information about this family genes in Brassicaceae. This study identifies 36 TIFY genes in Brassica rapa, an economically important crop species from this family. An extensive in silico analysis through phylogenetic grouping, protein motif organization and intron-exon distribution also confirmed 4 subfamilies of BrTIFY proteins. Out of 35 BrTIFY genes, we identified 21 under JAZ subfamily besides 7 TIFY, 6 ZML and 2 PPD. An extensive expression profiling of 21 BrTIFY JAZs both in tissues and organs of B. rapa revealed differential expression patterns. Almost all the BrTIFY JAZs predominantly expressed in leaves and flower buds. Besides, in a flower stage specific expression analysis we observed 14 BrTIFY JAZs with constitutive expression patterns. This indicates BrTIFY proteins have a strong involvement in the development of B. rapa flowers. Our protein interaction study also reveals the strong association of these proteins with the fertility and defense processes of B. rapa. To elucidate the stress responsiveness of BrTIFY genes, we analyzed the low temperature-treated whole-genome microarray data set and found almost all the BrTIFY JAZs were having variable transcript abundance in two contrasting inbred lines of B. rapa. Subsequently, all 21 BrTIFY JAZs were validated in response to cold stress in the same two lines via qPCR, where 9 genes were found to show up- regulation. And, a high and differential qPCR expression pattern of all the BrTIFY JAZs was also recorded against JA. Additionally, BrTIFY JAZs were tested against salt, drought, Fusarium, ABA and SA treatments and a considerable number of genes were found to be induced. The extensive annotation and transcriptome profiling reported in this study will be useful for understanding the involvement of TIFY genes in stress resistance and different developmental functions, which ultimately provides the basis for functional characterization and exploitation of the candidate genes for genetic engineering of B. rapa.

MADS-box transcription factor (TF), primarily involved in the floral organ specification with other several aspects of plant growth and development. Whole genome survey of B. rapa revealed 167 MADS-box genes and categorized into MIKCc, MIKC*, Mα, Mβ and Mγ groups based on phylogeny, protein motif structure and exon-intron organizations. MIKCc group belongs 89 genes, which is the highest in number than in any other crops till date. The MIKCc group has further classified into 13 sub-families. In case of chromosomal localization, remarkably 57 MIKCc type MADS-box genes were found in the duplicated segments of B. rapa genome, whereas only 4 M-type genes have resulted from tandem duplications. Besides floral and vegetative tissue expression we also identified MADS-box genes with their male and female gametophyte specific expression in different stages of flower bud development. Furthermore, from a low temperature treated whole genome microarray data set 19 BrMADS genes were found to show variable transcript abundance in two contrasting double haploid lines of B. rapa. Subsequently, the responsive genes were investigated under three abiotic stresses where they showed differential and corresponsive expression patterns. An extensive annotation and transcriptome profiling undertaken in this study might be useful for understanding the involvement of MADS-box genes in stress resistance besides their growth and developmental functions, which ultimately will provide the basis for functional characterization and exploitation of the candidate genes in the genetic engineering study of B. rapa