Background In the present study populations, representing different rounds of recombination were used for the analysis of phenotypic effects associated with the sdw1/denso locus. Other studies have mostly focused only on one type of population. Many different QTLs mapped at the same position as the sdw1/denso locus may indicate a pleiotropy of this gene or a tight linkage between genes conditioning quantitative traits. To date, results of studies have not unequivocally proven either of these two phenomena. Results Both breeding and molecular mapping experiments were undertaken to examine 200 single seed descent (SSD) and 60 doubled haploid (DH) lines obtained from the Maresi (with a semi-dwarfing gene) and Pomo cross combination. They were evaluated for the type of juvenile growth habit and certain agronomic traits were measured after harvesting. The estimates of mean values, standard errors and significance of effects were analyzed. In terms of the analyzed characteristics, the greatest variability was obtained for genotypes with the prostrate growth habit. Microsatellite markers (SSR) were also used to identify co-segregation with the sdw1/denso locus and Bmag0013, Bmag0877, Bmag0306b markers were linked the closest. A partial linkage map of chromosome 3H with the sdw1/denso semi-dwarfing gene was constructed and QTLs were identified. Conclusions Our experiments confirmed the impact of the semi-dwarfing gene on plant height, heading and flowering date both in SSD and DH populations, which may indicate pleiotropy. Moreover, a partial linkage between sdw1/denso locus and grain weight per spike and 1000-grain weight was found in the SSD population.