| As an important oil crop in the world,the seed yield and oil content of Brassica napus(AACC,2n=38)have always been the focus of people’s attention.The analyses of numerous quantitative trait loci were performed on seed yield of rapeseed using different statistical methods to analyze its genetic components.However,the understanding for the complex trait seed yield is still insufficient.In this study,QTL reanalysis was carried out for phenotypic traits of Brassica napus Bna TNDH population in 19 experimental environments.Considering interactions between related traits,complex genetic components of seed yield were studied combining with QTLs that directly or indirectly contribute to seed yield from multiple traits or multiple environments.The Bna TN reciprocal introgression populations derived from Bna TNDH population were also used for tracking and fine mapping of multiple major oil content QTLs in Brassica napus.Increasing oil production is an important goal of rapeseed breeding,and the aggregating favorable alleles by genetic recombination is the main method to increase oil production.Also,the recombination is vitally significance to population genetic diversity and species evolution.Therefore,in this study,the high-density genetic maps constructed by three Bna TN populations were used to analyze the genome-wide landscape of recombination.The main results are as follows:1.QTL re-analysis was carried out for 22 phenotypic traits(seed yield and yield related traits,seed quality traits and developmental traits and stress resistance traits)of Bna TNDH population under 19 experimental environments.Referring to previous studies,some QTLs whose peak value can be repeatedly detected above the P=0.5 level,although they do not reach the P=0.05 level,which could be overlapped with the significant QTLs that have reached the 0.05 level and 1000 permutation tests,as true micro QTLs.These QTLs and QTLs that have reached the P=0.05 significant level were named as identified QTLs.A total of 2,569 identified QTLs associated with 22 identified traits were detected in this study.Previously,the meta-analysis method was used to integrate the identified QTL for the same trait detected in different experimental environments,and the integrated QTL was named consensus QTL.Getting 1,904 consensus QTLs after meta-analysis,which contains 80 seed yield consensus QTLs and 97 seed oil content consensus QTLs.In this study,it was further proposed that both directly and indirectly related QTLs should be considered on the basis of the identified QTLs and consensus QTLs in the analysis of complex traits.For example,further integrated analysis of seed yield QTLs was carried out combining with QTLs directly or indirectly contributing to seed yield under multiple traits or environments,and the QTLs that contributed to seed yield after integration were named “essential QTLs”.A total of 525 seed yield essential QTLs were identified,among which 428 essential QTLs showed pleiotropic and environmental effects.2.The 97 oil content QTLs were detected in the Bna TNDH population,contained a total of seven major QTLs: q OC.A1-2,q OC.A1-9,q OC.A3-6,q OC.A8-2,q OC.A10-3,q OC.C3-5 and q OC.C3-7,which can explain up to 15.4% of the oil content phenotypic variation.Subsequently,six major oil content QTLs(q OC.A1-9,q OC.A1-2,q OC.A3-6,q OC.A8-2,q OC.A10-3 and q OC.C3-5)were used for fine mapping with the Bna TN reciprocal introgression populations derived from Bna TNDH population and their offspring.And the intervals were shorted to 316 Kb,183 Kb,174 Kb,330 Kb,116 Kb and 163 Kb,respectively,these could lay the foundation for gene cloning or genetic improvement of oil content.3.Three high-density genetic maps were constructed for Bna TNDH population and its derived reciprocal introgression populations Bna T-BC4F2 and Bna N-BC4F2,and positions of centromeres on the Ningyou7 genome were anchored.The genetic maps of the three populations showed high collinearity among the NY7 genome,but some inversions and HEs(homoeologous exchanges)were also detected.The high-density genetic maps of the three Bna TN populations were used to analyze the genome-wide landscape of recombination of the three populations,and found that the occurrence of recombination varied across different genetic background,subgenomes,chromosomes and genome regions,and were significantly affected by the genomic features such as the gene density,transposable elements and chromosome rearrangements.4.Undergone five generations,89% and 80% of A and C genome could be reconstructed with recombination compared with Bna TNDH population,respectively.A total of 134 recombination hotspots were identified in the three populations,and most genes located in the recombination hotspots and coldspots were separately involved with the positive and negative regulation on the process of DNA replication and meiosis;recombination hotspots are beneficial to the QTL detection,gene cloning,as well as the combination of favorable alleles to improve the traits of rapeseed(such as seed oil content).In summary,the detection of seed yield essential QTLs provides a method for analyzing the genetic basis of complex traits,and can be a reference for understanding complex traits in crops.Candidate materials and candidate genes were identified by fine mapping of multiple major oil content QTLs.And the candidate genes could be verified in subsequent work,also the molecular markers closely with oil content QTL can be applied to the breeding of high oil content rapeseed with marker-assisted selection.Investigating and understanding the recombination variation of allopolyploid Brassica napus will provide significant insights to the formation of important traits,genetic improvement and polyploid genome evolution. |
