The Construction Of Non-heading Chinsese Cabbage Genomic Database And Analysis Of Relative Transcription Factors Of Chinese Cabbage

In this study,the genomic and agronomic data of non-heading Chinese cabbage core germplasm resources have been obtained,documented and analyzed.The results have been integrated into the NHCCBase and website interface.This database employs MySQL database management software to store huge amount of genomic data,which accumulated to be around 327 million features,including 42.3 million SNPs.This database is entirely compatible to international rules,at the same time,is also a well-expandable database.In addition,two robust analysis tools have been developed and embedded into this platform.One is SSRFace,which serves to detect SSRs using EST sequences and design the corresponding primers automatically.The GeMint visualization system which based on the visualization technology can help build a bioinformatics platform as well as construct a database easily.In summary,NHCCBase is a useful resource for gene cloning,comparative genome analysis and accelerating good cultivars selection with interest in pre-breeding stage.The SQUAMOSA PROMOTER BINDING PROTEIN(SBP)-box gene family contains highly conserved plant-specific transcription factors that play an important role in plant development,especially in flowering.Chinese cabbage(Brassica rapa ssp.pekinensis)is a leafy vegetable grown worldwide,and is used as a model crop for research in genome duplication.The present study aimed to characterize the SBP-box transcription factor genes in Chinese cabbage.Twenty-nine SBP-box genes were identified in the Chinese cabbage genome and classified into six groups.We identified twenty-three orthologous and five co?orthologous SBP-box gene pairs between Chines cabbage and Arabidopsis,and constructed an interaction network among these genes.Sixteen SBP-box genes were found more abundant in flowers than in other tissues,suggesting their involvement in flowering.We show that the MiR156/157 family members may regulate the coding regions or 3'-UTR regions of Chinese cabbage SBP-box genes.As SBP-box genes were found to potentially participate in some plant development pathways,quantitative real-time PCR analysis was performed and showed that Chinese cabbage SBP-box genes were also sensitive to exogenous hormone methyl jasmonic acid and salicylic acid.The SBP-box genes have rundergone gene duplication and loss,evolving a more refined regulation for diverse stimulation in plant tissues.Our comprehensive genome-wide analysis provides insights into the SBP-box gene family of Chinese cabbage.Whirly transcription factors are plant-specific and highly-conserved single-strand DNA binding proteins.They play a vital role in plant resistance signal transduction,telomere structure and organelle structure.Using bioinformatics methods,we identified 196 Whirly transcription factors from 71 plant species across alga,mosses,lycophytes,gymnospenns,monocots and eudicots.In this study,these Whirly genes were classified into Group O,Group P and Group M.Members of Group O were identified from lower plants and gymnosperm plants,while most members in Group P and Group M were found associated with chloroplast and mitochondria,respectively.The number of members in Group M was larger than Group P,and the number of members from polyploidy plants was larger than diploid plants.Characterization motifs of Whirly family in the plant kingdom and inside Brassicaceae family were identified,which provided information for the further analysis of the characterization and expression profiles of Whirly transcription factors.