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

Anthony Hall & Laura-Jayne Gardiner
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. We present 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. 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. We use a capture design employing an 'island strategy' to enable analysis of the large gene/promoter space of wheat with only 2x160 Mb NimbelGen 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. Here, we release the targeted sequence of the capture probe sets on the wheat RefSeqv1, the design space that was used to tile our capture probes across and finally the positions of the probes themselves across this design space for both the gene and promoter capture probe sets. This project was supported by the BBSRC via an ERA-CAPS grant BB/N005104/1, BB/N005155/1 and BBSRC Designing Future Wheat BB/P016855/1.
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      NameSizeDateProperties
      iRods Data ObjectCapture_design_space_GENE.fasta495MB2018-07-05 09:24
      iRods Data ObjectCapture_design_space_PROMOTER.fasta273MB2018-07-05 09:24
      iRods Data ObjectGene-capture-HC-targets.bed2.7MB2018-07-05 09:24
      iRods Data ObjectProm-capture-HC+5UTR-targets.bed2.7MB2018-07-05 09:24
      iRods Data ObjectProm-capture-HC-targets.bed2.7MB2018-07-05 09:24
      iRods Data ObjectREADME742 B2018-07-05 09:24
      iRods Data ObjectWheat_gene_capture_probes.bed190MB2018-07-05 09:24
      iRods Data ObjectWheat_prom2_capture_probes.bed189MB2018-07-05 09:24
      iRods Data ObjectWheat_prom_capture_probes.bed182MB2018-07-05 09:24