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Development of SRAP, SNP and Multiplexed SCAR molecular markers for the major seed coat color gene in Brassica rapa L.

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Abstract

Seed coat color inheritance in B. rapa was studied in F1, F2, F3, and BC1 progenies from a cross of a Canadian brown-seeded variety ‘SPAN’ and a Bangladeshi yellow sarson variety ‘BARI-6’. A pollen effect was found when the yellow sarson line was used as the maternal parent. Seed coat color segregated into brown, yellow-brown and bright yellow classes. Segregation was under digenic control where the brown or yellow-brown color was dominant over bright yellow seed coat color. A sequence related amplified polymorphism (SRAP) marker linked closely to a major seed coat color gene (Br1/br1) was developed. This dominant SRAP molecular marker was successfully converted into single nucleotide polymorphism (SNP) markers and sequence characterized amplification region (SCAR) markers after the extended flanking sequence of the SRAP was obtained with chromosome walking. In total, 24 SNPs were identified with more than 2-kb sequence. A 12-bp deletion allowed the development of a SCAR marker linked closely to the Br1 gene. Using the five-fluorescence dye set supplied by ABI, four labeled M13 primers were integrated with different SCAR primers to increase the throughput of SCAR marker detection. Using multiplexed SCAR markers targeting insertions and deletions in a genome shows great potential for marker assisted selection in plant breeding.

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Acknowledgments

The research was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC), Bunge Canada and the Manitoba Canola Growers Association in an Industrial Research Chair (IRC) program and by Genome Canada/Genome Prairie/Genome Alberta. Mr. Rahman was supported by a University of Manitoba Graduate Fellowship, a Manitoba Graduate Scholarship and an NSERC Scholarship.

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Authors and Affiliations

  1. Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada, R3T 2N2

    Mukhlesur Rahman, Peter B. E. McVetty & Genyi Li

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  1. Mukhlesur Rahman
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  2. Peter B. E. McVetty
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  3. Genyi Li
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Correspondence to Genyi Li.

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Communicated by A. Bervillé.

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Rahman, M., McVetty, P.B.E. & Li, G. Development of SRAP, SNP and Multiplexed SCAR molecular markers for the major seed coat color gene in Brassica rapa L. . Theor Appl Genet 115, 1101–1107 (2007). https://doi.org/10.1007/s00122-007-0636-8

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  • DOI: https://doi.org/10.1007/s00122-007-0636-8

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