Background: Human demand for wheat will continue to increase together with the continuous global population growth. Agronomic traits in wheat are susceptible to environmental conditions. Therefore, in breeding practice, priority is given to QTLs of agronomic traits that can be stably detected across multiple environments and over many years.

Results: In this study, QTL analysis was conducted for eight agronomic traits using an introgression line population across eight environments (drought stressed and well-watered) for five years. In total, 44 additive QTLs for the above agronomic traits were detected on 15 chromosomes. Among these, qPH-6A, qHD-1A, qSL-2A, qHD-2D and qSL-6A were detected across seven, six, five, five and four environments, respectively. The means in the phenotypic variation explained by these five QTLs were 12.26%, 9.51%, 7.77%, 7.23%, and 8.49%, respectively.

Conclusions: We identified five stable QTLs, which includes qPH-6A, qHD-1A, qSL-2A, qHD-2D and qSL-6A. They play a critical role in wheat agronomic traits. One of the dwarf genes Rht14, Rht16, Rht18 and Rht25 on chromosome 6A might be the candidate gene for qPH-6A. The qHD-1A and qHD-2D were novel stable QTLs for heading date and they differed from known vernalization genes, photoperiod genes and earliness per se genes.

Extraction of DNA was performed using the CTAB method. Following the principle of uniform distribution on the chromosome, 565 simple sequence repeat (SSR) markers covering the whole genome of wheat were selected based on the high-density microsatellite consensus map [34]. The selected SSR markers were screened for polymorphisms between the two parents, which yielded 187 polymorphic markers. The polymorphic SSR markers were then used to perform a genome-wide screen of the IL population.

Marker type: 2 for Shaanhan8675;  0 for Lumai14; -1 for missing markers