A user guide to the Brassica60K Illumina Infinium™ SNP genotyping array

Annaliese S. Mason, Erin E. Higgins, Rod J. Snowdon, Jacqueline Batley, Anna Stein, Christian Werner, Isobel A P Parkin

Research output: Contribution to journalReview articlepeer-review

47 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)621–633
Number of pages13
JournalTheoretical and Applied Genetics
Issue number4
Publication statusPublished - Apr 2017


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