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

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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          NameSizeDateMD5Properties
          iRods Data ObjectCapture_design_space_GENE.fasta495MB2020-07-31 16:061e4e53abb6f59f143e350a14b74fef33
          iRods Data ObjectCapture_design_space_PROMOTER.fasta273MB2020-07-31 16:07f81abad5137e7eb18ae62c48eb32844f
          iRods Data ObjectGene-capture-HC-targets.bed2.7MB2020-07-31 16:077adf6ae0601c083110956cc4d0d8291e
          iRods Data ObjectProm-capture-HC+5UTR-targets.bed2.7MB2020-07-31 16:06890bfc242be097d269f23b8d228d5a5f
          iRods Data ObjectProm-capture-HC-targets.bed2.7MB2020-07-31 16:07e026969709c0320c5aabb9bfd03ccda9
          iRods Data ObjectREADME742 B2020-07-31 16:06c2aaf696ffdee8fdc185283ab41c1ec0
          iRods Data ObjectWheat_gene_capture_probes.bed190MB2020-07-31 16:07de4d9e206de297e0ca4f89720e124e0a
          iRods Data ObjectWheat_prom2_capture_probes.bed189MB2020-07-31 16:0776e2f91d819b3b15c10a08269172b7a4
          iRods Data ObjectWheat_prom_capture_probes.bed182MB2020-07-31 16:062c7c875a892c34d51455e44dfdc7d459
          iRods Data Objectdatapackage.json3.7KB2020-09-21 11:32bd53f7a4c5677d2726a3125122b5e9a6