Theoretical and Applied Genetics

, Volume 130, Issue 4, pp 621–633 | Cite as

A user guide to the Brassica 60K Illumina InfiniumSNP genotyping array

  • Annaliese S. MasonEmail author
  • Erin E. Higgins
  • Rod J. Snowdon
  • Jacqueline Batley
  • Anna Stein
  • Christian Werner
  • Isobel A. P. Parkin


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.


Linkage Disequilibrium Decay Cluster File Genomic Introgression Seed Glucosinolate GenTrain Score 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



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

Compliance with ethical standards

Conflict of interest

The authors declare no conflicts of interest.

Supplementary material

122_2016_2849_MOESM1_ESM.pptx (390 kb)
Supplementary material 1 (PPTX 389 KB)
122_2016_2849_MOESM2_ESM.pptx (85 kb)
Supplementary material 2 (PPTX 84 KB)
122_2016_2849_MOESM3_ESM.xlsx (2.3 mb)
Supplementary material 3 (XLSX 2307 KB)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Annaliese S. Mason
    • 1
    Email author
  • Erin E. Higgins
    • 3
  • Rod J. Snowdon
    • 1
  • Jacqueline Batley
    • 2
    • 4
  • Anna Stein
    • 1
  • Christian Werner
    • 1
  • Isobel A. P. Parkin
    • 3
  1. 1.Department of Plant Breeding, IFZ for Biosystems, Land Use and NutritionJustus Liebig University GiessenGiessenGermany
  2. 2.School of Agriculture and Food Sciences and Centre for Integrative Legume ResearchThe University of QueenslandBrisbaneAustralia
  3. 3.Agriculture and Agri-Food CanadaSaskatoonCanada
  4. 4.School of Plant Biology and The UWA Institute of AgricultureThe University of Western AustraliaPerthAustralia

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