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

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.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Developing SSR markers from ESTs will be important in dissecting of genetic base in jute. The aim of this study was to analyze the SSR distribution in ESTs of jute and develop new EST-derived SSR markers, and polymorphisms of EST-SSR markers in jute was also validated. All the 838 EST sequences of jute were downloaded from NCBI. Sixty-six pairs of primers were screened by the software SSRPrimer and designed by the software Primer3.0. The PCR products of these primers were detected by agarose gel electrophoresis. Polymorphism of six diverse accessions was tested. Among these primers, 42 (63.6%) successfully amplified at least one clear and stable fragment from the jute genome and showed polymorphism of at least two diverse accessions. The polymorphic SSRs contain repeat motifs with (AT)n or (GC-)n, which could be regarded as the dominant motifs in jute. The EST-SSR markers in jute developed effectively, which can not only enrich the number of molecular markers, but also illustrate dissecting genetic basis of important traits in jute.
    Acta Agronomica Sinica 04/2014; 40(6):1028-1034.
  • Source
    Breeding Science 08/2014; 64(4). DOI:10.1270/jsbbs.64.321 · 1.34 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: In Brassica napus, yellow petals had a much higher content of carotenoids than white petals present in a small number of lines, with violaxanthin identified as the major carotenoid compound in yellow petals of rapeseed lines. Using positional cloning we identified a carotenoid cleavage dioxygenase 4 gene, BnaC3.CCD4, responsible for the formation of flower colour, with preferential expression in petals of white-flowered B. napus lines. Insertion of a CACTA-like transposable element 1 (TE1) into the coding region of BnaC3.CCD4 had disrupted its expression in yellow-flowered rapeseed lines. α-Ionone was identified as the major volatile apocarotenoid released from white petals but not from yellow petals. We speculate that BnaC3.CCD4 may use δ- and/or α-carotene as substrates. Four variations, including two CACTA-like TEs (alleles M1 and M4) and two insertion/deletions (INDELs, alleles M2 and M3), were identified in yellow-flowered Brassica oleracea lines. The two CACTA-like TEs were also identified in the coding region of BcaC3.CCD4 in Brassica carinata. However, the two INDELs were not detected in B. napus and B. carinata. We demonstrate that the insertions of TEs in BolC3.CCD4 predated the formation of the two allotetraploids. © 2015 The Authors New Phytologist © 2015 New Phytologist Trust.
    New Phytologist 02/2015; DOI:10.1111/nph.13335 · 6.55 Impact Factor

Full-text (4 Sources)

Available from
Jun 10, 2014