Over the past two decades, advances in genomics have revolutionized crop breeding, providing affordable tools to enhance the development and validation of distinctness, uniformity, and stability (DUS) in new crop varieties. The InnoVar project set out to validate the potential of these genomic tools to complement existing DUS testing methods, starting with wheat and extending the findings to other crops. Specifically, the project utilized the 90K Illumina SNP data for both bread wheat and durum wheat. In addition to exploring how this genomic data could support DUS testing, we also investigated its potential as a cross-over tool between DUS and VCU (Value for Cultivation and Use) testing. Our study further evaluated the use of transcriptomics to complement these cross-over traits, particularly focusing on the potential of both genomic and transcriptomic data to predict resistance to key wheat diseases, such as Septoria tritici blotch and Fusarium head blight. This study delved into the genetic dissection of DUS-related traits in wheat through genome-wide association studies (GWAS). We identified multiple significant SNP markers and haplotype blocks associated with these traits, highlighting their polygenic nature.  These findings offer valuable insights for wheat breeding programs, as they demonstrate the power of integrating phenotypic and genotypic data to accelerate the development of superior cultivars. The identified markers and candidate genes represent promising targets for future research and breeding efforts aimed at enhancing wheat yield and quality.