Deficiency of available phosphorus (P) in soil limits wheat production and creates a need to develop P-deficiency-tolerant cultivars. Plant roots, important organs for absorbing nutrients and synthesizing growth regulators, are good candidates for P-efficiency screening. In this study, we evaluated five root traits under hydroponic culture conditions either with (AP) or without (NP) applied P in a recombinant inbred line population H461/CM107 of <i>Triticum aestivum </i>L. at the seedling stage. Four significant quantitative trait loci (QTL) were detected, on chromosomes 1D, 2D, 3D, and 7D in NP-treated plants, explaining up to 13.0, 11.0, 14.4, and 12.8% of the phenotypic variance, respectively. Among these QTL, <i>Qrt.sicau-3D </i>and <i>Qrt.sicau-7D </i>showed pleiotropic and additive effects. All QTL were found to be novel. The diversity array technology markers flanking the QTL were converted to simple sequence repeat markers that can be deployed in future genetic studies of P-deficiency. These QTL lead to an increase in root biomass and respond to P-deficiency stress; these characteristics are crucial to improve root traits for breeding or further investigation of the gene(s) involved in P-deficiency tolerance.