In this study, we performed whole-genome deep resequencing of the wheat breeding line L43 and the Shaanxi landrace Shaanxi Baimal using the BGI MGI-2000/MGI-T7 sequencing platform. The objective was to systematically characterize genomic differences between the two accessions and to evaluate their potential impacts on agronomic traits, with a particular focus on disease resistance and yield-related characteristics. Using the Chinese Spring reference genome v2.1, we identified a total of 18,076,855 homozygous single nucleotide polymorphisms (SNPs), 1,282,111 insertions/deletions (InDels), 975 copy number variations (CNVs), and 28,477 structural variations (SVs) between the two materials.Subgenome-specific analysis revealed that more than 90% of the differential SNPs, InDels, and SVs were located in the A and B subgenomes, whereas 27.17% of the differential CNVs were distributed in the D subgenome. Genome coverage analysis indicated that the differential intervals associated with SNPs, InDels, SVs, and CNVs covered 25.66%, 27.24%, 26.58%, and 6.85% of the whole genome, respectively. Functional enrichment analysis demonstrated that these intervals were significantly overrepresented in genes involved in disease resistance and yield-related biological processes.Detailed functional variation analysis showed that Shaanxi Baimal specifically harbored all nonsynonymous mutations present in the powdery mildew resistance genes (Pm3,?Pm5, and?Pm24) and the stripe rust resistance gene (Yr10). In contrast, 83.33% of the nonsynonymous mutations identified in the leaf rust resistance gene (Lr10) and in multiple yield-related genes (including?AGL6,?TaABI5A,?TaCKX2,?TaCKX4, and others) were enriched in line L43. Only five nonsynonymous mutations, located in?TaAP2A,?TaARF12B, and?TaGS34A, were found exclusively in Shaanxi Baimal.Copy number variation analysis further revealed that L43 exhibited copy number losses in several disease resistance genes (e.g.,?LOC123140906?and?LOC123129130) as well as in genes involved in GTP metabolism, including?TOC101,?Rab5, and?XLG3. These copy number alterations may be associated with reduced disease resistance and altered grain development capacity in L43. Gene Ontology (GO) enrichment analysis allowed us to identify 13 previously uncharacterized putative disease resistance genes that carry premature stop codons. Among these, nine were present in L43 and four were found in Shaanxi Baimal.In summary, through comprehensive analysis of whole-genome resequencing data from L43 and Shaanxi Baimal, this study not only provides a systematic overview of genomic differences between the two wheat accessions but also establishes a theoretical basis for the utilization of these germplasms in breeding programs aimed at improving disease resistance and yield-related traits. The identified allelic variants and copy number variations represent valuable targets for marker-assisted selection and gene functional studies in wheat improvement.