Abstract
BackgroundThe Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola).ResultsIn this study, we identified over 23,000 simple sequence repeats (SSRs) from 536 sequenced BACs. 890 SSR markers (designated as BrGMS) were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH). Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs), 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus.ConclusionThe genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species.
Highlights
The Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa
Characterization of microsatellites in sequenced BACs of B. rapa As this study started, a total of 536 seed BACs had been sequenced to phase II or phase III by the BrGSP and deposited into NCBI-GenBank http://www.brassica.info/ resource/sequencing/status.php
More BACs had been sequenced for chromosomes A3 and A9 (153 and 85 respectively), which had been allocated to the Korea Brassica Genome Project (KBGP)
Summary
The Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. Of the six cultivated Brassica species, B. napus, B. rapa, B. juncea, and B. carinata provide about 12% of worldwide edible vegetable oil supplies [1]. They provide many of the vegetables in our daily diet such as cauliflower, broccoli, cabbage, kohlrabi, kale (B. oleracea) and turnip, Pakchoi and Chinese cabbage (B. rapa) [2]. Subsequent chromosomal rearrangements including segmental duplications or deletions and extensive interspersed gene loss or gain events since divergence from the common ancestor have resulted in the present diploid Brassica species [6,8], B. rapa (2n = 20, AA), B. nigra (2n = 16, BB) and B. oleracea (2n = 18, CC). The genome relationships between these Brassica species is commonly known as the triangle of U [10]
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