Deep rooting is an important trait in rice drought resistance. Genetic resources of deep-rooting varieties are valuable in breeding of water-saving and drought-resistant rice. In the present study, 234 BC2F7 backcross introgression lines were derived from a cross of Dongye 80 (an accession of Dongxiang wild rice as the donor parent) and R974 (an indica restorer line as the recurrent parent). A genetic linkage map containing 1977 bin markers was constructed by ddRADSeq for QTL analysis. Thirty-one QTLs for four root traits (the number of deep roots, the number of shallow roots, the total number of deep roots and the ratio of deep roots) were assessed on six rice chromosomes in two environments (2020 Shanghai and 2021 Hainan). Two of the QTLs, qDR5.1 and qTR5.2, were located on chromosome 5 in a 70-kb interval. They were detected in both environments. qDR5.1 explained 13.35％ of the phenotypic variance in 2020 Shanghai and 12.01％ of the phenotypic variance in 2021 Hainan. qTR5.2 accounted for 10.88％ and 10.93％ of the phenotypic variance, respectively. One QTL (qRDR2.2) for the ratio of deep roots was detected on chromosome 2 in a 210-kb interval and accounted for 6.72％ of the phenotypic variance in 2020. The positive effects of these three QTLs were all from Dongxiang wild rice. Furthermore, nine and four putative candidate genes were identified in qRDR2.2 and qDR5.1/qTR5.2, respectively. These findings added to our knowledge of the genetic control of root traits in rice. In addition, this study will facilitate the future isolation of candidate genes of the deep-rooting trait and the utilization of Dongxiang wild rice in the improvement of rice drought resistance.