title: Affymetrix Axiom® Rye600k Genotyping Array
status: Public on Nov 23 2016
contact.city: Freising
contact.first: Eva
contact.last: Bauer
contact.email: e.bauer@tum.de
contact.address: Liesel-Beckmann-Str. 2
contact.department: Plant Breeding
contact.country: Germany
contact.institute: Technical University of Munich
contact.phone: ++49 8161 715243
organism: Secale cereale
description: We generated comprehensive whole-genome shotgun (WGS) sequence data from rye inbred line Lo7 to generate the first rye genome assembly (Lo7_v2) and resequenced a panel of ten diverse rye inbred lines and Secale vavilovii for exploring genome diversity. We discovered more than 90 million single nucleotide variants (SNVs) in the rye genome and developed a high-density genotyping array to experimentally validate more than 600k SNVs (SNPs and short indels). A high-density genetic map comprising ~88k markers enabled genetic anchoring of ~44k Lo7 WGS contigs along the rye genome. Detailed information is available in the associated publication.
  The original array contained 600,843 SNVs. 590,593 SNVs were developed from Lo7 WGS contigs. 2285 SNVs were taken from a previously developed custom Rye5k Illumina genotyping array based on a rye EST assembly Sce_Assembly02 (PMID: 21951788). 7,965 proprietary SNPs are omitted in this platform description.
  The development and applications of the array are described in more detail in the following publication:
  Bauer E, Schmutzer T, Barilar I, Mascher M, Gundlach H, Martis MM, Twardziok SO, Hackauf B, Gordillo A, Wilde P, Schmidt M, Korzun V, Mayer KFX, Schmid K, Schön C-C, Scholz U (2016) Towards a whole-genome sequence for rye (Secale cereale L.). Plant J (accepted)
manufacture_protocol: see manufacturer's web site