Integrating genomic resources to present full gene and promoter capture probe sets for bread wheat

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.