Effective imputation of missing genotypes in low coverage skim-sequencing or reduced-complexity sequencing projects is essential to identify potentially causal associations and to build robust genomic selection (GS) models. The newly developed Practical Haplotype Graph (PHG) tool presents this opportunity for wheat breeders to efficiently store sequence data and accurately impute genotypes across the wheat genome. A first-generation wheat PHG demonstrated over 92% imputation accuracy using very low (0.01x) exome sequencing coverage depth, and imputation accuracy of 89% using GBS sequencing technology. Our project builds on these results by creating a customized PHG database with wheat exome capture sequence of 200 FHB resistant and adapted wheat cultivars exhibiting different levels of resistance. These haplotypes will inform imputation of lower coverage sequenced breeding lines with high accuracy. By incorporating FHB resistant varieties in the database composition, FHB resistance-associated haplotypes are represented and will be used for developing a GS model for FHB resistance, identifying novel FHB resistant haplotypes/QTLs, and developing diagnostic markers for these QTLs. I will describe the progress of this new bioinformatics platform in wheat populations, and how it will be used to inform selection for FHB resistant germplasm in US breeding programs.