Construction Of BAC Physical Map On Chromosome A9 In Brassica Juncea And Comparative Genome Analysis

The three species of Brassica, i.e., B.rapa, B. juncea and B.napus possess common A genome. Among the 10 chromosomes of A genome, A9 is the longest. Researches on what happened to A9 chromosome in different genetic backgrounds are still remain to study. Brassica rapa and and Brassica napus genome sequences generated by next-generation sequencing technology provide the basis for this study. On the other hand, A9 chromosome carries genes for major agronomical traits, such as seed size, seed coat color, glucosinolate synthesis, lipid synthesis and so on. therefore, constructing a physical map of Brassica juncea chromosome A9 is of both theoretical and practical significance.To obtain a precise physical map of Brassica juncea chromosome A9.,we used markers located on the A9 chromosome to design primers as starting points to screen BAC library. Using homology B. rapa sequences, BAC end sequence, unigene sequence of Sichuan Yellow-seed acquired by RNA-seq technology and survey sequence of Brassica juncea Survey to design STS primer to extend contigs.In this study,1728 pairs of primers were designed and 3200 positive BAC were screened out. This physical map is composed of 16 contigs and 5 singletons. According to the principle of the minimum path,435 BACs were chosed as seed BACs to represent the whole physical map and then were subject to end sequencing. At last,862 qualified sequences were received. As the average insert size of BAC is 126 kb, the contigs accounted up to be 52.08 M, covering 1.37 times of chromosome A9. Using BLAST, we mapped the seed BAC end sequences to chromosome A9 of Brassica rapa and Brassica napus respectively, It is showed that the physical map covered 36.4 Mb and 31.0 Mb. Brassica juncea A9 chromosome have higher homology with Brassica rapa A9 chromosome than Brassica napus A9 chromosome. Compared with Brassica napus A9 chromosome and BAC end sequence of Brassica juncea A9 chromosome, there are two chromosome inversions about 1.4 Mb and 3.6 Mb in Brassica rapa A9 chromosome. While compared with BAC end sequence of Brassica juncea A9 chromosome, there is a Deletion mutation about 0.98 Mb in Brassica napus A9 chromosome, which lied in one of the two chromosome inversions and was consist with the predicted position of centromere of Brassica napus A9 chromosome not assembled yet.