| The chromosome A9, about37Mbp in length, is the longest among A-genome chromosomes and carries genes for major agronomical traits, such as seed size, seed coat color, and glucosinolate and fat synthesis in Brassica species. Therefore, dissecting this chromosome is of great scientific and practical significance.In this study, the procedure of PCR walking was used to screen ZBjH BAC library with the markers A9-88and A9-32which was found to co-segregate with the yellow seed in A9chromosome of B. juncea by our laboratory.395of752BACs screened out were end sequenced, and resultant674BAC end sequences were used for further analysis.533primer pairs were developed from these end sequences for next-round screen. In addition,38SSR and15STS primer pairs were designed according to B. rapa sequence available in public data. The BAC contig was constructed around the yellow seed coat gene on A9chromosome in B. juncea.The contig begins at the marker124J24R and ends at the marker173J1L, covers up to2.2Mb including full length of Scaffolds000185,000059,0000169,000135and000102, and part of the Scaffolds000040and000066as revealed by BLAST against BRAD database. Comparison in scaffold order around this region between B. juncea, B. rapa and B. napus showed that Scaffolds0000169whose chromosomal position was previously unknown was located between the scaffolds000059and000135in B. juncea except the same insertion of the scaffolds as found in B. napus, indicating the chromosome A9has undergone different structural rearrangements during evolution of B. juncea and B. napus. These results lay the foundations for map-based cloning of genes and better understanding of evolution of the Brassica A9chromosome. |
