A Reduced Exome Capture Targeting Highly Informative Regions of the Wheat Genome Provides Greater Value for Variant Discovery and Enables Cost-Effective Mapping-by-Sequencing

Reduced-representation sequencing approaches such as genotyping-by-sequencing and exome capture resequencing allow cost-effective variant discovery and genotyping. Exome capture resequencing has provided a catalogue of diversity present in wheat genic regions with a myriad of applications (Jordan et al., 2015). Exome capture-based sequencing has also been used for mapping-by-sequencing in segregating populations (Gardiner et al., 2016). Targeting of all exonic regions is useful for identifying a large number of potential functional polymorphisms but the amount of sequencing necessary to cover the greater than 2% (321 Mb plus flanking and off-targets regions) of the wheat genome at acceptable depth is still substantial. Further, as haplotypes can be defined on the basis of a much smaller number of markers many applications do not require such exhaustive sequencing. We have designed and tested a reduced capture targeting exonic and flanking regions that provide the greatest information content on the basis of earlier exome capture sequence analysis. This capture targets an order of magnitude less sequence space allowing for greater sequencing depth in targeted regions as well as more cost effective deployment in populations or bulks.

Gardiner, L.-J., Bansept-Basler, P., Olohan, L., Joynson, R., Brenchley, R., Hall, N., O’Sullivan, D.M. and Hall, A. (2016) Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat. Plant J., 87, 403–419. Available at: http://doi.wiley.com/10.1111/tpj.13204.

Jordan, K.W., Wang, S., Lun, Y., et al. (2015) A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol., 16, 48. Available at: http://genomebiology.com/2015/16/1/48.