Predicting And Analysis Of Candidate Gene For Leaf Lobe Trait In Brassica Rapa

Lobed-leaf trait is not only an easily recognizable morphological trait,but also an important agronomic trait related to plant photosynthesis and stress resistance.In previous study,the construction of NIL-F2 population derived from the cross between the recurrent parent RcBr and lobed-leaf main effect QTL near iso-genic lines(NIL)were used for fine mapping and candidate gene prediction.Based on that,the candidate gene structure and expression characteristics were analyzed in this study.The results will lay the solid foundation for cloning and molecular mechanism of gene controlling leaf lobe trait in Brassica rapa.The main results are as follows:1.Morphological observation and measurement of photosynthetic characters between RcBr and NILRcBr with loed-leaf and their counterpart,NIL with smooth leaf margin were observed by scanning electron microscopy,which found that leaf margin was layered arrangement in RcBr samples with glossy in a magnification of 300 times and 2500 times,compared with the NIL samples,the performance is smooth.Measurement of photosynthetic characters revealed that RcBr affected the chlorophyll biosynthesis,which resuited in photosynthetic efficiency increased significantly.It has significant advantages in photosynthesis.2.Fine mapping and candidate gene predictionBased on the constructed NIL-F2 population,the phenotypic identification showed that the presence and absence for lobed-leaf in the NIL-F2 population fits to 3:1 very well,which indicated the leaf lobe was controlled by a single dominant gene in RcBr background.In previous studies,1060 homozygous recessive individuals were selceted for the fine mapping and the candidate intervals were narrowed down to 44.7kbp regions between two markers WXInDel-31 and BrID10909.Basing on gene annotation,Bra009489 was selected for candidate gene in this candidate interval.The predicted gene plays an important role in encoding of the dehydration response protein and this protein is expressed in the formation of the leaf lobes.3.Bioinformatics analysis of Bra009489The full-length of Bra009489 gene was 2284bp.It contains seven coding sequences(CDS)and encodes 590 amino acid sequences.The analysis showed that it may be a non-secreted protein and the protein does not exist in the N-terminal signal peptide.It includes a multiple of modification sites and exist one protein family database(Pfam)domain:Methyltransferase domain.The cluster analysis found that Bra009489 protein had a high homology with Arabidopsis dehydration response protein.4.The structure and polymorphic analysis of Bra009489Sequencing analysis between RcBr and NIL revealed that it exists many SNPs differences for Bra009489.The phenomenon of frameshift in RcBr coding region at the end of CDS5 leads to premature termination of protein translation in the process of protein translation.The Polymorphic analysis of Bra009489 gene showed the same results.5.Expression pattern analysis of Bra009489 geneExpression analysis of Bra009489 revealed that it has the same trends in different periods and tissues for RcBr and NIL and a high level in RcBr especially in the sixth leaf stage.It has a relatively lower level in young leaf stage,four leaf stage,eight leaf stage,roots and stems.The lowest expression level is in roots and stems of NIL.