TY - JOUR T1 - Integrating genomic resources to present full gene and promoter capture probe sets for bread wheat JF - bioRxiv DO - 10.1101/363663 SP - 363663 AU - Laura-jayne Gardiner AU - Thomas Brabbs AU - Alina Akhunova AU - Katherine Jordan AU - Hikmet Budak AU - Todd Richmond AU - Sukwinder Singh AU - Leah Catchpole AU - Eduard Akhunov AU - Anthony Hall Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/07/06/363663.abstract N2 - Background Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits.Results We present and validate two gold standard capture probe sets for hexaploid bread wheat, a gene and a promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high confidence genes and promoters that were identified in the genome alongside a large proportion of the low confidence genes and promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for SNP calling while significantly reducing cost per sample for gene and promoter capture.Conclusions We show that a capture design employing an ‘island strategy’ can enable analysis of the large gene/promoter space of wheat with only 2×160 Mb probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.List of abbreviationsCIMMYTInternational Maize and Wheat Improvement Center (Centro Internacional de Mejoramiento de Maíz y Trigo)IWGSCInternational Wheat Genome Sequencing ConsortiummiRNAMicro RNANRNon-redundantPCRPolymerase Chain ReactionqPCRQuantitative Polymerase Chain ReactionSNPSingle Nucleotide PolymorphismTGACThe Genome Analysis Centre (now known as the Earlham Institute)TSSTranscription Start SiteUTRUntranslated Region ER -