Improvements in crop yields and nutritional value are urgently required to address food insecurity. Generating novel allelic combinations by exploiting genetic diversity available in landrace collections provides one way to advance towards this objective. However, identifying valuable alleles remains one of the biggest challenges faced by wheat breeders. In a pilot study, we used exome capture data from UK elite cultivars and found that they have, on average, three times less genetic variation than the Watkins landrace collection. This coding sequence-based data most likely underestimates the genetic variation found within promoter and intergenic regions, which are known to be important for agronomic traits. Recent developments in the wheat genomics, such as the wheat genome assembly and annotation (IWGSC, RefSeq v1.0), have opened up new possibilities for in-depth analysis of the genetic variation across germplasm sets. In this study, we used a promoter-exome capture to analyse 100 Watkins landraces and 113 elite UK cultivars to compare genetic diversity and assess the effect of breeding in elite germplasm during the last hundred years. We hypothesize that modern breeding has impacted on haplotype diversity in elite cultivars and we aim to determine haplotype blocks that have been selected in UK breeding. This will allow us to identify and mine putative functional variation within both coding and non-coding sequences. In addition, variation such as presence/absence polymorphism, copy number variation, and selective sweeps will be explored. We hope to be able to predict how breeding has shaped these haplotypes and use this knowledge to better target and find haplotypes from landraces with potential in wheat breeding.