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Type: Journal article
Title: Development and evaluation of a barley 50k iSelect SNP array
Author: Bayer, M.
Rapazote-Flores, P.
Ganal, M.
Hedley, P.
Macaulay, M.
Plieske, J.
Ramsay, L.
Russell, J.
Shaw, P.
Thomas, W.
Waugh, R.
Citation: Frontiers in Plant Science, 2017; 8:1792-1-1792-10
Publisher: Frontiers Media
Issue Date: 2017
ISSN: 1664-462X
Statement of
Micha M. Bayer, Paulo Rapazote-Flores, Martin Ganal, Pete E. Hedley, Malcolm Macaulay, Jörg Plieske, Luke Ramsay, Joanne Russell, Paul D. Shaw, William Thomas, and Robbie Waugh
Abstract: High-throughput genotyping arrays continue to be an attractive, cost-effective alternative to sequencing based approaches. We have developed a new 50k Illumina Infinium iSelect genotyping array for barley, a cereal crop species of major international importance. The majority of SNPs on the array have been extracted from variants called in exome capture data of a wide range of European barley germplasm. We used the recently published barley pseudomolecule assembly to map the exome capture data, which allowed us to generate markers with accurate physical positions and detailed gene annotation. Markers from an existing and widely used barley 9k Infinium iSelect array were carried over onto the 50k chip for backward compatibility. The array design featured 49,267 SNP markers that converted into 44,040 working assays, of which 43,461 were scorable in GenomeStudio. Of the working assays, 6,251 are from the 9k iSelect platform. We validated the SNPs by comparing the genotype calls from the new array to legacy datasets. Rates of agreement averaged 98.1 and 93.9% respectively for the legacy 9k iSelect SNP set (Comadran et al., 2012) and the exome capture SNPs. To test the utility of the 50k chip for genetic mapping, we genotyped a segregating population derived from a Golden Promise × Morex cross (Liu et al., 2014) and mapped over 14,000 SNPs to genetic positions which showed a near exact correspondence to their known physical positions. Manual adjustment of the cluster files used by the interpreting software for genotype scoring improved results substantially, but migration of cluster files between sites led to a deterioration of results, suggesting that local adjustment of cluster files is required on a site-per-site basis. Information relating to the markers on the chip is available online at
Keywords: Barley; SNP; genotyping chip; iSelect; exome capture
Rights: Copyright © 2017 Bayer, Rapazote-Flores, Ganal, Hedley, Macaulay, Plieske, Ramsay, Russell, Shaw, Thomas and Waugh. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
RMID: 0030116361
DOI: 10.3389/fpls.2017.01792
Appears in Collections:Agriculture, Food and Wine publications

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