Construction Of An Oilseed Rape (Brassica Napus L.) Genetic Map With EST-derived SSR Markers

As genome and cDNA sequencing projects progress, tremendous sequence information can be exploited for marker development and gene discovery. SSR markers have been widely used for gene mapping and genetic diversity research, attributed to their abundance, high polymorphism, co-dominant inheritance, simplicity for analysis and etc. However, there are limited number of SSR markers available in Brassica crops, which can’t satisfy the requirement of current research. We developed 1000 SSR markers (designated as BnEMS) based on EST sequences of Brassica napus, and constructed a linkage map using these novel EST-SSRs markers and a double haploid population. In addition, we have analyzed orthologous nature of EST sequences of Brassica napus, by querying which to genome sequence of Arabidopsis thaliana and BAC sequences of Brassica rapa, respectively. The main results are as follows:1.216 SSR markers, being polymorphic between two Brassica napus cultivars (No.2127-17 and ZY821), were selected from 1000 designed EST-SSRs markers to construct genetic linkage map, in which 198 BnEMS markers with 237 loci were mapped. In addition, we have mapped 230 public SSRs of Brassica crops as anchored marker.2. Our linkage map contained 516 marker loci, covering 19 linkage group with total length of 1899.61cM, and average interval of 3.92cM between adjacent loci.31.6% marker loci were detected distorted in this genetic map, major of which clustered in specific regions and distorted to the same parent.3. All the 1000 EST sequences of B. napus were searched against the genome sequences of Arabidosis thaliana,751 showed homology with 721 genes of Arabidopsis thaliana. Furthermore,158 of the 198 mapped BnEMS markers, corresponding 181 marker loci, are homologous with Arabidopsis thaliana genome sequence. The distribution of homologous regions corresponding to these 181 marker loci in Arabidopsis thaliana genome were as follows:49 hits on AtCh1,28 hits on AtCh2,35 hits on AtCh3, 25 hits on AtCh4, and 44 hits on AtCh5, which accounted for 27.1%,15.5%,19.3%, 13.8% and 24.3%, respectively.4. We found that 48 BnEMS marker loci which mapped on A genome of Brassica napus are homologous with 42 mapped BAC sequences of Brassica rapa through alignment. Then comparing our map with the standard map JWF3 of Brassica rapa, the result showed the A1-A10 of B.napus were in good accordant with the A1-A10 of B.rapa.