The Genotyping Theme

Objectives (as stated in the original LOLA proposal)

  1. Collation of existing wheat SNPs within a public web-based SNP database
  2. Generation of new wheat SNPs from both diploid, tetraploid and hexaploid Triticeae species
  3. Generation of extremely high-density SNP-based wheat maps
  4. Establishment and use of low, medium and high throughput genotyping platforms to genotype the wheat lines generated in the four pillars
  5. Generation, in collaboration with the LOLA partners, of a comprehensive database relating SNP polymorphisms with genotype and phenotype

Progress towards meeting our objectives

  1. Within six months of the project starting we established a public web-based SNP database containing all of the project's validated SNP markers. This database will continue to be updated as and when new markers become available (for instance the iSelect markers).
  2. As of February 2013 the sequencing of various varieties of hexaploid wheat, its various progenitors and numerous alien species is almost complete with just a few remaining lines to be sequenced. This data is currently being analysed and the resulting SNPs tested out as and when required by the project partners. While it is difficult to be exact, we estimate that we can currently call upon ~250,000 SNPs that are polymorphic across the range of species being investigated.
  3. Our current genetic maps cover approximately 19,000 markers mapped on either the UK standard population Avalon x Cadenza or the Rialto x Savannah population generated by Limagrain. In addition, numerous markers have been placed on both maps to aid comparison. We are currently mapping our remaining markers on the ITMI population, a process which we hope will be completed soon and which should take the map to over 20,000 markers. Our aim is to have mapped ~100,000 markers before the end of the WISP program in 2017.
  4. Genotyping technologies are developing very quickly; however, all genotyping technologies are driven by the availability of SNPs and their flanking sequences. Currently, our genotyping platforms of choice are KASPar (developed by KBioscience) and Infinium iSelect developed by Illumina. Both of these platforms appear to be established as the standard platforms for both academics and breeders. That said, we are continuing to investigate new genotyping technologies which could reduce cost or increase throughput. One such technology is the Axiom platform from Affymetrix. This platform, while not as developed for wheat as the other two platforms, has significant potential to reduce costs and increase throughput. Stay tuned for further results in this area
  5. Our ability to generate large data sets requires that we also put into place the ability to present and analysis those same datasets. Towards this end, our first priority has to been to make our data accessible. Hence, what we have done is what you see; we aim to make our data freely available so that it can benefit the whole of mankind. We encourage other groups who hold such data sets to do the same.
  6. Having achieved our objective of making our data accessible we are now moving on to analyse the data. To do this requires that we integrate genotype and phenotype data in such a manner that makes sense to both biologists and bioinformaticians. Through co-ordinated collaboration within WISP, this integration of datasets has begun and we hope to have a working model that can be accessed by the wider community before the start of 2014.