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Plant J. 2013 Nov;76(3):494-505. doi: 10.1111/tpj.12294. Epub 2013 Aug 24.

Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond.

Author information

1
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany.

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.

KEYWORDS:

Hordeum bulbosum; Hordeum pubiflorum; Hordeum vulgare; Triticeae; barley; genetic diversity; genomics; targeted resequencing

PMID:
23889683
PMCID:
PMC4241023
DOI:
10.1111/tpj.12294
[Indexed for MEDLINE]
Free PMC Article

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