SNP-based QTL mapping provided useful information for novel loci that can be used in breeding programs to control tillering and improve yield in wheat via marker-assisted selection. Tillering is one of the most important agronomic traits affecting biomass and grain yield potential in wheat. Wheat lines with very limited tillering capacity are more productive than free-tillering lines under severe drought conditions. In this study, three recombinant inbred line (RIL) populations were generated and used, having H461, a low-tillering genotype, as a common parent. A linkage map containing 7808 single nucleotide polymorphism loci was constructed on the basis of H461/CN16 RIL population. Three QTL controlling low tillering were identified on Chromosome (Chr.) 2D (Qltn.sicau-2D), Chr. 2B (Qltn.sicau-2B), and Chr. 5A (Qltn.sicau-5A). Qltn.sicau-2D, Qltn.sicau-2B, and Qltn.sicau-5A explained up to 19.1, 14.6, and 9.6 % of the phenotypic variance, respectively. Comparing with previous findings, Qltn.sicau-2D and Qltn.sicau-2B should thus be novel tillering QTL. The effects of these QTL were further validated in two additional RIL populations. Significant effects of Qltn.sicau-2D were detected across all growth stages in different genetic backgrounds, making it an ideal target for breeding programs as well as for further characterization of the gene(s) underlying this locus.