Molecular Mapping And Candidate Genes For Main Inflorescences Length And Stem Height In Brassica Napus L.

Main inflorescence length and stem height are important traits to plant type and yield of rapeseed.To identify candidate genes of main inflorescence length and stem height,we use quantitative traits locus(QTL)mapping with the high density SNP genetic map which is constructed with 60 k Brassica Illumina SNP of recombinant inbred lines(RIL)population,and do Genome-wide association study(GWAS)using the natural population constituted by Resequencing material.After that,we do RNA-seq to determine the different expression genes and conduct quantitative real-time PCR(qRT-PCR)as the identification.The main results display as follows.1.Phenotypic analysis of traits in RIL population and natural population.There are extremely significant differences of plant-type traits and yield traits in RIL population and natural population,which are including main inflorescence length and stem height.The phenotypes,consistent with normal distribution and genetic characteristics of quantitative traits,can be used for subsequent analysis.2.Correlation and path analysis of the traits in RIL population and natural population cultivated at different years.Main inflorescence length and stem height are highly significant correlation with plant height in RIL population and natural population of different years,and these two traits are also correlation with other plant-type traits and yield trait.A few traits exist differences in different populations and different years.The main inflorescence length and stem height are significant negative correlation,what proves that there is an interaction between the two traits.Path analysis in these two population show that there are differences between main inflorescence length and stem height and economic yield,what shows that main inflorescence length and stem height have influence on economic yield but influenced by environment.3.QTL mapping for main inflorescence length and stem height in RIL population.There are 15 QTLs of main inflorescence length and stem height in different years with interval mapping method by using the constructed map.The explanatory phenotypic variation of a single marker was between 8.88% and 19.61%.There are 4 QTLs of main inflorescence length,and the explanatory phenotypic variation of a single marker was between 13.05% and 17.99%.There are 11 QTLs of stem height,and the explanatory phenotypic variation of a single marker was between 8.88% and 19.61%.4.Genome-wide association study for main inflorescence length and stem height in natural population.There are 14 significant SNPs of main inflorescence length and stem height in the analysis of Naive model,Q model,PCA model,K model,Q+K model and PCA+K model after comparison(P<1/385691 or P<0.05/385691).There are 9 SNPs of main inflorescence length,and they were distributed in A02,A05,A07,A08,C02 and C06.The explanatory phenotypic variation of a single marker was between 6.84% and 25.99%.There are 5 SNPs of stem height,and they were distributed in A08,A10,C02 and C06.The explanatory phenotypic variation of a single marker was between 6.86% and 15.90%.5.Transcriptome analysis of extreme phenotype.There are 5788 different expression genes(DEGs)in stem top of the extremely accessions.There are 2846 significant up-regulated expression genes and 2942 significant down-regulated expression genes in stem top of SWU71.6.The prediction of candidate genes.According to the results of the QTL mapping,GWAS and RNA-seq,we get the candidate genes of main inflorescence length and stem height.There are 4 homologous candidate genes of Arabidopsis thaliana about main inflorescences length,and they are PHR2、CP12-1、ARF1A1C and PRPL11,what are involved in the function of chloroplast,photosynthesis,cell division and growth.There are 4 homologous candidate genes of Arabidopsis thaliana about stem height,and they are KRP3、J11、HYD1 and ALL1,what are involved in physiological activity of shoot apical meristem,cell division,synthesis and signal transduction of auxin and cytokinins.7.The detection of the candidate gene expression.In the result of qRT-PCR,the candidate genes of main inflorescences length,BnaA05gMIL-01 、 BnaA05gMIL-02 、 BnaA05gMIL-03 and BnaA08gMIL-04,are expressed higher in long inflorescence materials than short inflorescence materials.The candidate genes of stem height,BnaA08gSH-01、BnaA08gSH-02 and BnaC01gSH-04,are expressed higher in high stem materials.However,BnaA06gSH-03 are expressed higher in low stem materials.The research about these genes can facilitate marker-assisted breeding and lay the foundation for cloning genes related to main inflorescence length and stem height of Brassica napus L.