TY - JOUR
T1 - A user guide to the Brassica60K Illumina Infinium™ SNP genotyping array
AU - Mason, Annaliese S.
AU - Higgins, Erin E.
AU - Snowdon, Rod J.
AU - Batley, Jacqueline
AU - Stein, Anna
AU - Werner, Christian
AU - Parkin, Isobel A P
PY - 2017/4/1
Y1 - 2017/4/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85013224838&partnerID=8YFLogxK
U2 - 10.1007/s00122-016-2849-1
DO - 10.1007/s00122-016-2849-1
M3 - Review article
C2 - 28220206
AN - SCOPUS:85013224838
SN - 0040-5752
VL - 130
SP - 621
EP - 633
JO - Theoretical and Applied Genetics
JF - Theoretical and Applied Genetics
IS - 4
ER -