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Mascher, M.* ; Richmond, T.A.* ; Gerhardt, D.J.* ; Himmelbach, A.* ; Clissold, L.* ; Sampath, D.* ; Ayling, S.* ; Steuernagel, B.* ; Pfeifer, M. ; D'Ascenzo, M.* ; Akhunov, E.D.* ; Hedley, P.E.* ; Gonzales, A.M.* ; Morrell, P.L.* ; Kilian, B.* ; Blattner, F.R.* ; Scholz, U.* ; Mayer, K.F.X. ; Flavell, A.J.* ; Muehlbauer, G.J.* ; Waugh, R.* ; Jeddeloh, J.A.* ; Stein, N.*

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

Plant J. 76, 494-505 (2013)
Publ. Version/Full Text Volltext DOI PMC
Open Access Gold (Paid Option)
Creative Commons Lizenzvertrag
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.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Hordeum bulbosum; Hordeum pubiflorum; Hordeum vulgare; Triticeae; barley; genetic diversity; genomics; targeted resequencing; Mutation Discovery ; Natural Variation ; Wild Barley ; Maize ; Diversity ; Poaceae ; Domestication ; Nucleotide ; Map
ISSN (print) / ISBN 0960-7412
e-ISSN 1365-313X
Journal Plant Journal, The
Quellenangaben Volume: 76, Issue: 3, Pages: 494-505 Article Number: , Supplement: ,
Publisher Wiley
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Bioinformatics and Systems Biology (IBIS)