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.
This data is made available under the
Toronto Agreement
All of the data listed here is available under the prepublication data sharing principle of the
Toronto agreement.
By using this data, you agree to:
- respect the rights of the data producers and contributors to analyze and publish the first
global
analyses and certain other reserved analyses of this data set in a peer-reviewed publication.
- not redistribute, release, or otherwise provide access to the data to anyone outside of the
group, until
the data has been published & submitted to the public data repositories.
- contact the authors to discuss any plans to publish data or analyses that utilize this data to
avoid the
overlap of any planned analyses.
- fully cite the prepublication data along with any applicable versioning details.
- understand that this data as accessed is precompetitive and is not patentable in its present
state.
This agreement does not expire by time but only upon publication of the first global analysis by the
data
producers and contributors.
