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

Mason, Annaliese S., Higgins, Erin E., Snowdon, Rod J. , Batley, Jacqueline , Stein, Anna, Werner, Christian and Parkin, Isobel A. P.  (2017) A user guide to the Brassica 60K Illumina Infinium™ SNP genotyping array. TAG Theoretical and Applied Genetics, 1-13. doi:10.1007/s00122-016-2849-1


Author Mason, Annaliese S.
Higgins, Erin E.
Snowdon, Rod J. 
Batley, Jacqueline 
Stein, Anna
Werner, Christian
Parkin, Isobel A. P. 
Title A user guide to the Brassica 60K Illumina Infinium™ SNP genotyping array
Formatted title
A user guide to the Brassica 60K Illumina Infinium™ SNP genotyping array
Journal name TAG Theoretical and Applied Genetics   Check publisher's open access policy
ISSN 0040-5752
1432-2242
Publication date 2017-02-20
Sub-type Article (original research)
DOI 10.1007/s00122-016-2849-1
Open Access Status Not yet assessed
Start page 1
End page 13
Total pages 13
Place of publication Heidelberg, Germany
Publisher Springer
Collection year 2018
Language eng
Formatted 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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
School of Agriculture and Food Sciences
 
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