SNP Marker Identification and Validation for UK Wheat Improvement

Globally, wheat is the most widely grown crop and one of the three most important crops for human and livestock feed. With the world's population set to reach nine billion by 2050 wheat yields need to increase by at least 50% to avoid recurring food crises, and this must be achieved despite limitations on land, water and energy resources.  However, the current elite cultivars have a restricted pool of genetic diversity due to the domestication and inbreeding processes which have shaped the evolutionary history of wheat. The wheat improvement strategic program (WISP) is a BBSRC funded collaborative programme for wheat improvement in the UK. The objective of the WISP is to produce new and novel wheat germplasm which is characterised for traits relevant to academics and breeders and has genetic markers associated with these traits. However, the complex nature of the wheat genome has, until recently, hindered the development of markers of practical use to wheat breeders. To generate co-dominant SNP-based markers we have sequenced 56.5 Mb representing the exome of each of 42 wheat lines including elite and landrace varieties, synthetic diploid and tetraploid accessions and wheat relatives. These sequences have been used to identify 95,266 putative single nucleotide polymorphisms, subsets of which have been validated on a variety of genotyping platforms including KASPar (KBioscience), iSelect (Illumina and SNP developing group) and Axiom (Affymetrix).  These markers and related information have been made publically available on an interactive web-based database in order to facilitate their use on genotyping programs worldwide.