A Systematic Dissection Of The Mechanisms Underlying The Natural Variation Of Flowering Related Traits In Brassica Napus

Oilseed rape or rapeseed(Brassica napus L.)is one of the most important oil crops worldwide.Flowering time in rapeseed is an important agronomic trait,which strongly influences successful reproduction and life cycle adaptation.Thus,identifying functional markers for flowering time traits is crucial for successful rapeseed breeding.To date,the genetic architecture and molecular basis for the flowering time have been well described in Arabidopsis thaliana.However,the genetic mechanism of flowering time remains largely unknown in rapeseed.Therefore,in this study,we performed joint SNP-based GWAS(SNP-GWAS),haplotype-based GWAS(hap-GWAS)and transcriptomics analysis to uncover the genetic architecture and candidate genes of flowering time in rapeseed using a panel of 373 rapeseed accessions.The main results of this research are summarized as follows:First,in order to classify candidate genes controlling vegetative growth traits(budding and bolting)in B.napus,we conducted systematic research,including SNP-GWAS,hap-GWAS and transcriptomics analysis.In total,seven SNP QTLs and 26 hap.QTLs were reported as being linked to the budding and bolting.By combining SNP and hap-GWAS analysis across 373 diverse populations in four environments,we identified three precise integrated genomic regions for flowering time in rapeseed,with a novel region of FTC06.After combining these three interconnected regions with transcriptomics analysis,a total of 14 highly expressed candidate genes linked to flowering time were discovered.These results may be used to construct a genetic mechanism for early flowering time in rapeseed.Second,we conducted systematic research(including SNP-GWAS and hap-GWAS analysis)to identify candidate genes controlling days to flowering(DTF),days to full flowering(Full)and days to final flowering(Final)traits in B.napus.In total,ten SNP QTLs and 28 hap.QTLs were reported as being linked to the three flowering time traits.By SNP and hap-GWAS analysis across 373 diverse populations in all environments,we identified three specific and accurate co-localized regions for flowering time in rapeseed FT.A03,FT.A08 and FT.A10,which were overlapped by both SNP and hap-GWAS.After combining these three interconnected regions with transcriptomics analysis,30 highly expressed candidate genes linked to flowering time were discovered.A total of five highly expressed key pleiotropic candidate genes were detected by the integration of GWAS(SNP and haplotype),transcriptomics and network analysis.These results may be used to construct a genetic mechanism for flowering time in B.napus.Third,understanding the genetic determinants of flowering intervals is usually considered a prerequisite for a successful breeding program of rapeseed.In this part,we performed systematic research,including SNP-GWAS,hap-GWAS and transcriptomics analysis.We identified 104 flowering times(FT)candidate genes from nine integrated genomic regions of SNP and hap-GWAS influencing flowering interval traits using diverse populations across four environments.In total,52 FT-related genes were identified to be highly expressed.These genes,loci and haplotypes with different allele distributions across germplasm populations provide a resource for understanding genetic differences in the genome and improving the marker-trait association(MTA)of oilseed rape.Overall,in our study,we detected two integrated genomic regions in FT.A01(0.353-1.812 Mb)and FT.A10(13.003-15.578 Mb),simultaneously controlling DTF and FP.In which A01 harbored the gene most essential gene Bna A01g01640D(FD),and FT.A10(13.003-15.578 Mb),Bna A10g18430D(CO),Bna A10g22080D(FLC),which may be useful for shortening the flowering period and help to escape the SSR disease.Thus,a total of 15 key flowering time genes were found to control both DTF and FP simultaneously.Interestingly,integrated genomic regions FT.A10(13.003-15.578 Mb)were also responsible for controlling all the flowering traits used in this research except budding and possessed the central flowering repressor Flowering Locus C(Bna A10g22080D-FLC)as well as FT.A03(chr A03: 22.077-24.034Mb)controlled viz.Budding,Bolting,DTF,Full,Final,IDF,FP and possessed the gene Bna A03g43820D-AG,which plays a key role in the successful floral transition from vegetative to reproductive stages in B.napus.