Quantitative trait loci (QTL) of agriculturally valuable traits of soft spring wheat (Triticum aestivum L.) were mapped in two simultaneous and independent experiments that were carried out in different agronomical backgrounds with respect to nitrogen availability (i.e., with and without introduction of a mineral nitrogen fertilizer) in order to reveal the effects of physiological and genetic interaction between the genotype and the environment. In total, 94 QTLs, which determine 31 physiologically and agriculturally important traits, have been identified. The connection between the trait expression and introduction of the fertilizer has been confirmed by both correlation analysis and the single-factor analysis of variance. The analyses of QTL and correlation, as well as the single-factor analysis of variance, showed that 15 of 31 traits varied confidently. This shows that the expression of these traits depends on the presence of nitrogen nutrition. In the course of two other experiments, differing from each other only by temperature and illumination regimes and providing the strict control and invariability of other growing parameters, 99 QTLs determining 30 different agronomically important traits have been identified. According to the results of the QTL mapping and an ANOVA analysis, changes in the temperature and illumination regimes did not influence 21 of 30 studied traits, which remained stable in their manifestation; only 9 traits varied under these conditions, which indicates that their manifestation is dependent on changes in these environmental factors. The connection between the loci identified and polymorphism by certain traits has been proven. Both statistical approaches used in this study demonstrated complementary results; for each of them, the maximum likelihood criterion was used, statistical significance was determined, and significance of results was evaluated. QTL analysis allowed a block structure of the T. aestivum genome to be revealed, the percentage of a phenotypic variability determined by each of the identified QTLs to be calculated, and the determination of which of the parents donated individual QTL alleles. Additionally it was carried out molecular-genetic analysis by PCR of mapping lines and accessions of T. aestivum with molecular genetic markers, which linked with revealed QTLs. PCR results shown good correlation with QTL and ANOVA analysis as well as with hybridological analysis of evaluated F1, F2 and parent forms. This study was funded by RFBR according to the research project № 16-04-00311.