title: Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond.
abstract: Advanced resources for genome-assisted research in barley (Hordeum vulgare) including a whole-genome shotgun assembly and an integrated physical map have recently become available. These have made possible studies that aim to assess genetic diversity or to isolate single genes by whole-genome resequencing and in silico variant detection. However such an approach remains expensive given the 5 Gb size of the barley genome. Targeted sequencing of the mRNA-coding exome reduces barley genomic complexity more than 50-fold, thus dramatically reducing this heavy sequencing and analysis load. We have developed and employed an in-solution hybridization-based sequence capture platform to selectively enrich for a 61.6 megabase coding sequence target that includes predicted genes from the genome assembly of the cultivar Morex as well as publicly available full-length cDNAs and de novo assembled RNA-Seq consensus sequence contigs. The platform provides a highly specific capture with substantial and reproducible enrichment of targeted exons, both for cultivated barley and related species. We show that this exome capture platform provides a clear path towards a broader and deeper understanding of the natural variation residing in the mRNA-coding part of the barley genome and will thus constitute a valuable resource for applications such as mapping-by-sequencing and genetic diversity analyzes.
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Mascher
authors.forename: Todd A
authors.initials: TA
authors.lastname: Richmond
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Gerhardt
authors.forename: Axel
authors.initials: A
authors.lastname: Himmelbach
authors.forename: Leah
authors.initials: L
authors.lastname: Clissold
authors.forename: Dharanya
authors.initials: D
authors.lastname: Sampath
authors.forename: Sarah
authors.initials: S
authors.lastname: Ayling
authors.forename: Burkhard
authors.initials: B
authors.lastname: Steuernagel
authors.forename: Matthias
authors.initials: M
authors.lastname: Pfeifer
authors.forename: Mark
authors.initials: M
authors.lastname: D'Ascenzo
authors.forename: Eduard D
authors.initials: ED
authors.lastname: Akhunov
authors.forename: Pete E
authors.initials: PE
authors.lastname: Hedley
authors.forename: Ana M
authors.initials: AM
authors.lastname: Gonzales
authors.forename: Peter L
authors.initials: PL
authors.lastname: Morrell
authors.forename: Benjamin
authors.initials: B
authors.lastname: Kilian
authors.forename: Frank R
authors.initials: FR
authors.lastname: Blattner
authors.forename: Uwe
authors.initials: U
authors.lastname: Scholz
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Flavell
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Muehlbauer
authors.forename: Robbie
authors.initials: R
authors.lastname: Waugh
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Jeddeloh
authors.forename: Nils
authors.initials: N
authors.lastname: Stein
mesh_terms: D059472:Exome; D018745:Genome, Plant; D023281:Genomics / Q000379:methods* / Q000639:trends; D001467:Hordeum / Q000235:genetics*; D011003:Ploidies; D020641:Polymorphism, Single Nucleotide; D014908:Triticum / Q000235:genetics
keywords: Hordeum bulbosum; Hordeum pubiflorum; Hordeum vulgare; Triticeae; barley; genetic diversity; genomics; targeted resequencing
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