Genotype Theme of the WISP Consortium

The Genotyping Theme is coordinated by the Cereal Genomics Group at Bristol University. The technology for high throughput genotyping is based on the group's next generation sequencing (based on a wheat exome-specific NimbleGen capture array (NimbleGen array reference 100819_Wheat_Hall_cap_HX1)) of various wheat genomes, and numerous lines of wheat progenitors and alien species. This array has been used to enrich for exome sequences in over 50 wheat/alien/progenitor lines. The enriched libraries have been sequenced on Illumina GAIIx and HiSeq platforms to generate between 9.8 and 48.7 million 100 base pair reads per line. SNP discovery, using a series of custom Perl scripts, has identified over 95,266 putative varietal SNPs between 8 UK elite varieties in 26,551 distinct reference sequences (Winfield et al., 2012; see the results section of this web site to access the full dataset). It is important to note that our pipeline allows varietal SNPs to be distinguished from the more frequent homoeologous SNPs. As most SNPs in hexaploids act as dominant markers (Allen et al., 2011), we have used additional Perl scripts to enrich our dataset for co-dominant SNPs; using this procedure we have identified 10,251 putative varietal co-dominant SNPs contained within 5,308 contigs (Allen et al., 2012). Using the pipelines mentioned above, ~290,000 SNPs have so far been identified between elite hexaploid cultivars and 9 landraces derived from the Watkins collection. A further ~650,000 SNPs have been identified between hexaploid wheat and 10 wheat relatives including Rye, Thinopyrum sp., Aegilops sp. and Triticum uratu. These SNPs and further SNP develop for specific purposes are now being used in the WISP program to genotype the lines and crosses generated by the various partners. In most cases our genotyping is being carried out by either KASPar based technology or via the wheat 90K iSelect genotyping chip from Illumina. We continue to investigate further technologies, such as Affymetrix's Axiom arrays, as a possible route to delivering faster and cheaper genotyping to members of the WISP Consortium.