The allohexaploid bread wheat (Triticum aestivum L.), evolved through a recent polyploidization event between tetraploid Triticum turgidum L. (AABB) and diploid Aegilops tauschii Coss. (DD), ~8,000 years ago. Contribution of only a subpopulation of Ae. tauschii to hexaploid evolution, followed by domestication and extensive breeding with the objective of higher yield gain and strict end-use quality determining the market classes of wheat, have created a genetic bottleneck. Synthetic hexaploid wheat (SHW) lines are generated to restore the diversity and exploit the genetic resource in the primary gene pool of wheat. However, there are challenges with recovering the phenotypes observed in the parental background in the hexaploid bread wheat in pre-breeding programs. To understand and characterize the barriers in utilizing the progenitor genetic diversity, the transcriptome of four SHW lines and their corresponding tetraploid and diploid parents across ten tissues, totalling to 240 samples, was analysed. The comparison of expression bias of homoeologues present as >18,000 triads (1:1:1) between parental in-silico SHW-like scenarios and SHWs, indicated a large-scale suppression of D subgenome homoeoalleles in SHWs. Tissue-specificity was not observed in the homoeologues of a large proportion of the triads. The next largest fractions were triads where all homoeologues displayed the same tissue-specific expression followed by those where only one of the homoeologues was tissue-specific. Several SHW-tissues showed moderate relationship between tissue-specificity of the homoeologues and expression bias of the corresponding triad. The repression of the genes of the D subgenome was also validated in the differential expression analysis using the entire high-confidence gene set of hexaploid wheat. Qualitative analysis of the transcripts revealed all five splicing events with predominance of retained introns, and more differentially-spliced transcripts were associated with the D homoeoalleles in most SHW-tissue contexts. The introgression patterns of the SHW-C66 into the elite bread wheat cultivar Carberry was analysed using a BC1F5 population. Large introgression of SHW-C66 were found closer to centromeric regions while smaller fragments were present towards the ends of the chromosomes. Correspondingly, the majority of the chromosomes showed higher recombination rates away from the centromere. The donor allele frequency was higher than the expected 25% for BC1F5 population in multiple regions of the A and B subgenomes but not in the D subgenome. In comparison, a preliminary analysis using an elite wheat × elite wheat doubled haploid population showed no subgenome-level variation in recombination rates or donor allele frequencies. In this thesis work, both functional genomic and structural genomic investigations using a set of SHW parents and their derivative population with elite wheat cultivars have unearthed some key patterns that add to the collective knowledge needed to fully exploit genetic resources in broadening the genetic diversity in wheat improvement programs.