A Sequence-based Reference Genetic Linkage Map Of Brassica Rapa

Brassica rapa is an economically important crop and a model plant for studies concerning polyploidization and the evolution of extreme morphology. The multinational B. rapa Genome Sequencing Project (BrGSP) was launched in 2003. In 2008, next generation sequencing technology was used to sequence the B. rapa genome. InDel polymorphism is the second most frequent type of sequence polymorphism in the genome, and can be developed as PCR-based markers which can be easily genotyped using simple procedures. With the recent completion of the sequencing of the B. rapa genome, the development of whole genome-wide InDel markers based on re-sequencing has become feasible. Several maps concerning B. rapa pseudochromosome assembly have been published but their coverage of the genome is incomplete, anchoring approximately 73.6% of the scaffolds on to chromosomes. Therefore, a new genetic map to aid pseudochromosome assembly is required.This study concerns the construction of a reference genetic linkage map for B. rapa, forming the backbone for anchoring sequence scaffolds of the B. rapa genome resulting from recent sequencing efforts. The development of this linkage map is vital for the integration of genome sequences and genetic information, and provides a useful resource for the international Brassica research community. The results we got are listed as follows:1. An optimized genotyping procedure of InDel markers was set up for B. rapa including the PCR reaction and detection systems, using six representative accessions of B. rapa .2. The map comprises a total of 507 sequence-based markers including 415 InDels and 92 SSRs with a total length of 1234.2 cM. The map defined herein represents average genetic and physical intervals of 2.43 cM and 559.8 Kbp per marker, respectively. Therefore, it is currently the most saturated linkage map for B. rapa. In the final linkage map, 90% of the covered genome had a marker within 5 cM. However, there were still two gaps (>15 cM) on A06 and A04, respectively.3. The high-resolution RCZ16_DH genetic linkage map with 507 sequence-based markers was successfully used to anchor and orientate scaffolds for the genome assembly of B. rapa together with the three publicly available B. rapa genetic maps, VCS_DH, JWF3P and CKDH. Using the developed linkage map, 152 scaffolds (235 Mb) were anchored on to the chromosomes, encompassing more than 82.9% of the B. rapa genome. Taken together with the previously available linkage maps, 183 scaffolds were anchored on to the chromosomes and the total coverage of the genome was 88.9%.