Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa. BMC genomics 11:594

National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
BMC Genomics (Impact Factor: 4.04). 10/2010; 11:594. DOI: 10.1186/1471-2164-11-594
Source: PubMed

ABSTRACT 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. 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).
In 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.
The 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.

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    • "S1–S4). PCr reactions were carried out following Panjabi et al. (2008) for IP markers, Kim et al. (2009), li et al. (2010), Xu et al. (2010) for SSr markers and Paritosh et al. (2013) for SnP markers. Total genetic lengths spanned by the maps ranged from 679.7 to 869.8 cM. "
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    • "The positions of the selected SSR markers on the chromosomes were determined based on previous genetic maps (Cheng et al. 2009, Fan et al. 2010, Li, H. et al. 2011, 2013, Wang et al. 2011, Xu et al. 2010). For markers that were not located on the existing genetic maps, their chromosome information was inferred by aligning their sequences with the genome sequences of B. rapa and B. oleracea by using BLASTn ( "
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    • " SSR, SSR : >6 , >4 , >3 , >2 Primer3 SSR , 113 , SSR, 66 EST-SSR , CcSSR001~CcSSR045 EST-SSR, CoSSR046~CoSSR066 EST-SSR 66 SSR 1.3 DNA CTAB DNA [14] 1.4 SSR PCR PCR 10 μL, 50 ng·μL –1 DNA 2.0 μL10 μmol·μL –1 0.5 μL0.5 U Taq 0.1 μL10 mmol·L –1 dNTPs 0.2 μL10×PCR buffer 1 μL50 mmol·L –1 Mg 2+ 0.8 μLdd H 2 O 5.4 μLPCR 94 3 min; 94 30 s, 60 30 s, 72 45 s, 10 , 0.5; 94 30 s, 55 30 s, 72 45 s, 35 ; 72 10 min, 10 10 minTaq dNTP , 1.5% 2 结果与分析 2.1 GenBank EST-SSR GenBank EST 113 SSR( 2), , 40 表 2 黄麻 EST 中 SSR 分布频率 Table 2 Number of SSR frequencies of EST in jute Repeat type SSR Number of SSR Total length (bp) Average length (bp) Dinucleotide 11 (9.7%) 159 14.5 Trinucleotide 79 (69.9%) 1426 18.1 Tetranucleotide 15 (13.3%) 197 13.1 Pentanucleotide 8 (7.1%) 145 18.1 Total 113 (100.0%) 1927 17.1 69.9%, , 13.3%, , 9.7% 7.1%, , 18.1 bp, , 13.1 bp 2.2 GenBank EST-SSR 113 EST-SSR 43 3 23 11 6 ( 3) (CT)n (AT)n , (ACC)n(CGA)n (AGA)n 2.4 GenBank EST-SSR [3-4,6] , , 66 EST-SSR 66 SSR 2 6 ( 4 1), 64 (97.0%) "
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