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A user guide to the Brassica 60K Illumina Infinium™ SNP genotyping array

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Abstract

The Brassica napus 60K Illumina Infinium™ SNP array has had huge international uptake in the rapeseed community due to the revolutionary speed of acquisition and ease of analysis of this high-throughput genotyping data, particularly when coupled with the newly available reference genome sequence. However, further utilization of this valuable resource can be optimized by better understanding the promises and pitfalls of SNP arrays. We outline how best to analyze Brassica SNP marker array data for diverse applications, including linkage and association mapping, genetic diversity and genomic introgression studies. We present data on which SNPs are locus-specific in winter, semi-winter and spring B. napus germplasm pools, rather than amplifying both an A-genome and a C-genome locus or multiple loci. Common issues that arise when analyzing array data will be discussed, particularly those unique to SNP markers and how to deal with these for practical applications in Brassica breeding applications.

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Acknowledgements

ASM is supported by DFG Emmy Noether Grant MA6473/1–1.

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Authors and Affiliations

  1. Department of Plant Breeding, IFZ for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany

    Annaliese S. Mason, Rod J. Snowdon, Anna Stein & Christian Werner

  2. School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane, 4072, Australia

    Jacqueline Batley

  3. Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2, Canada

    Erin E. Higgins & Isobel A. P. Parkin

  4. School of Plant Biology and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Perth, Australia

    Jacqueline Batley

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  1. Annaliese S. Mason
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  2. Erin E. Higgins
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Correspondence to Annaliese S. Mason.

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Communicated by R. K. Varshney.

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Mason, A.S., Higgins, E.E., Snowdon, R.J. et al. A user guide to the Brassica 60K Illumina Infinium™ SNP genotyping array . Theor Appl Genet 130, 621–633 (2017). https://doi.org/10.1007/s00122-016-2849-1

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