Construction Of BAC Contigs Around The Long Arm Of The Chromosome A09in Brassica Juncea

As an allotetraploidprogeny of Brassica rapa and Brassica nigra, Brassica juncea own a common A genome with Brassica rapa and Brassica napus, whose genome sequencing project has been completed. So, It is possible to discover the structural variations of B. juncea A09chromosome among the evolutionary progress by comparing the sequences and genes of B. rapa, B. napus and B. juncea A09chromosomes, based on the construction of physical map and sequencing of B. juncea A09chromosome.In this study, three molecular markers BnGMS351, S48-Ⅱ-2and DFR on A09were used to screen the ZBjuH BAC library by PCR walking.780BACs screened out and458were end sequenced, and resultant852BES were used for further analysis.423pairs of primer were developed from these BES for next-round screen. In addition,65SSR and122STS primer pairs were designed according to B. rapa sequence available in public data respectively. BAC contigs about6.6Mbp in length was constructed, giving useful new information for sequencing B. juncea A09chromosome, and comparative physical mapping and map-based cloning of key genes in B. juncea.The contig constructed in this study start at the marker061I04L and end at the marker049E02R, covers up to6.6Mb including full length of Scaffolds000066、000022、000056、000058. Comparison in scaffold order around this region between B. juncea,B. rapa and B. napus showed that a translocation events was foundin the area of Scaffolds000066-Scaffold000145. In addition,unanchored Scaffolds000344and000362, and the part of Scaffold000017that locating at B. rapa A07chromosome were inserted between Scaffolds000066and000102. Except for the differences, high colinearity and conservation were found between the three species at Scaffold000022,000056and000058. These results indicate that the A09chromosome has undergone structural rearrangements during evolution of B. juncea that similar to B. napus.