Journal
PLANT JOURNAL
Volume 76, Issue 3, Pages 494-505Publisher
WILEY
DOI: 10.1111/tpj.12294
Keywords
barley; genomics; genetic diversity; Hordeum bulbosum; Hordeum pubiflorum; Hordeum vulgare; targeted resequencing; Triticeae
Categories
Funding
- German Ministry of Education and Research (BMBF) [FKZ 0314000, FKZ 0315954]
- German Research Foundation (DFG) [SPP1530 (KI 1465/6-1)]
- Biotechnology and Biological Science Research Council (BBSRC) [BB/I00663X/1, BB/I008357/1]
- BBSRC [BB/I022899/1]
- USDA-NIFA [2011-68002-30029]
- BBSRC [BBS/E/T/000PR5885, BB/I00663X/1, BBS/E/T/000PR6193, BB/I008357/1, BB/I022899/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/I022899/1, BB/I008357/1, BBS/E/T/000PR5885, BBS/E/T/000PR6193, BB/I00663X/1] Funding Source: researchfish
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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 5Gb 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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