The study is aimed at the investigation of the genetic diversity of spring bread wheat by loci determining agronomic important traits such as heading date, resistance to fungal diseases, grain weight per spike, thousand-grain weight, and grain quality. The collection of wheat varieties and breeding lines was evaluated during 2016-2020 at two locations of west Siberian region of Russia. Evaluation of resistance to the main fungal pathogens specific to the Siberian region (leaf rust, stem rust and powdery mildew) showed that 15% of the varieties were immune or highly resistant to diseases. The grain protein content of the varieties varied from 12.9% to 17.5% while gluten content changed from 21.3% to 39.3%. The obtained results evidenced that 62% of the wheat varieties belong to “strong” or “valuable” classes. Analysis of wheat collection with molecular markers specific for loci encoding high molecular weight glutenins indicated that 30% of them contain combinations of Ax2, Dx5 and Dy10 subunits positively influence on baking qualities. To identify quantitative trait loci responsible for the agronomic traits the wheat collection was genotyped with 9,500 polymorphic SNP markers. Genome-wide association study performed by MLM model revealed SNP markers on 6A chromosome in the region of localization of the NAM-1 locus. The collection of wheat varieties was examined on allelic composition at the Ppd-D1, Vrn-A1, Vrn-B1, Vrn-D1, and Vrn-B3 loci. Two novel alleles of the Vrn-B3 gene associated with a delay of heading date were found. Based on comparative analysis of the chromosomal localization of the known Lr, Sr, and Pm resistance genes and loci mapped in this study, an assumption was made that the QTLs on chromosomes 1DS, 2BL, 5AS, 6DL are new, not previously described resistance loci. The obtained results provide researchers with valuable data for the use of target loci in breeding programs.