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Development and evaluation of single-nucleotide polymorphism markers in allotetraploid rapeseed (Brassica napus L.)

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Abstract

Single-nucleotide polymorphisms (SNPs) and insertion–deletions (INDELs) are currently the important classes of genetic markers for major crop species. In this study, methods for developing SNP markers in rapeseed (Brassica napus L.) and their in silico mapping and use for genotyping are demonstrated. For the development of SNP and INDEL markers, 181 fragments from 121 different gene sequences spanning 86 kb were examined. A combination of different selection methods (genome-specific amplification, hetero-duplex analysis and sequence analysis) allowed the detection of 18 singular fragments that showed a total of 87 SNPs and 6 INDELs between 6 different rapeseed varieties. The average frequency of sequence polymorphism was estimated to be one SNP every 247 bp and one INDEL every 3,583 bp. Most SNPs and INDELs were found in non-coding regions. Polymorphism information content values for SNP markers ranged between 0.02 and 0.50 in a set of 86 varieties. Using comparative genetics data for B. napus and Arabidopsis thaliana, an allocation of SNP markers to linkage groups in rapeseed was achieved: a unique location was determined for seven gene sequences; two and three possible locations were found for six and four sequences, respectively. The results demonstrate the usefulness of existing genomic resources for SNP discovery in rapeseed.

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Acknowledgments

This study was funded by the Bavarian State Ministry of Environment, Public Health and Consumer Protection. The authors thank Friedrich Felsenstein from EpiGene GmbH for making the DHPLC instrument available for polymorphism screening.

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Author notes

  1. Gerhard Wenzel

    Present address: Dean’s Office, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Alte Akademie 8, 85350, Freising, Germany

  2. Volker Mohler

    Present address: Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture, Am Gereuth 8, 85354, Freising, Germany

Authors and Affiliations

  1. Plant Breeding, Department of Plant Sciences, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Am Hochanger 4, 85350, Freising, Germany

    Peter Westermeier, Gerhard Wenzel & Volker Mohler

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  1. Peter Westermeier
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  2. Gerhard Wenzel
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  3. Volker Mohler
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Correspondence to Peter Westermeier.

Additional information

Communicated by A. Schulman.

This study is dedicated to the memory of Gerhard Schwarz.

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Westermeier, P., Wenzel, G. & Mohler, V. Development and evaluation of single-nucleotide polymorphism markers in allotetraploid rapeseed (Brassica napus L.). Theor Appl Genet 119, 1301–1311 (2009). https://doi.org/10.1007/s00122-009-1135-x

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  • DOI: https://doi.org/10.1007/s00122-009-1135-x

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