The root system architecture is an important complex trait in rice and needs to be focused on account of its contribution to nutrient use efficiency in the current scenario of climate change. To understand the genomic regions associated with robust root length and root volume, a biparental F2 mapping population was developed using a stable ethyl methane sulphonate mutant of Samba Mahsuri viz. TI-128 having early seedling vigour and robust root system architecture with wild-type, Samba Mahsuri. The population was evaluated at the panicle initiation stage for root length (RL) and root volume (RV) and mutant-like (RL:3343cm; RV:80-100cm3) and wild type-like (RL:20-28 cm; RV:20-40 cm3) bulks consisting of 15 plants each were pooled. The two bulked pools and parents were subjected to whole genome resequencing on the Illumina HiSeqX10 platform emanating 10 GB of data per sample. The cleaned reads were subjected to the Mutation mapping (MutMap) pipeline for the SNP index followed by the QTL-plot pipeline for the delta SNP index for the identification of genomic regions, genes, and SNPs. Two major genomic regions on chromosome 12 (3.17 Mb to 3.74 Mb, 18.11 Mb to 20.79 Mb), and one on chromosome 2 (23.1 Mb to 23.2 Mb) were observed to be associated significantly with robust root length and volume. Validation in a panel of rice lines differing in root length and volume showed displayed association of three SNPs having SNP index near one viz., KASP_Chr12_S5 Loc_Os12g32420-expressed protein; KASP_Chr12_S4 Loc_Os12g06670-ACT domain-like protein kinases 6 (ACTPK6), KASP_Chr2_S6 Loc_Os2g38340-rapid alkalization factor conserved protein through Kompetitive Allele Specific PCR assays. The developed SNP markers have the potential in breeding programs for the selection of rice lines having better root-related traits for nutrient use efficiency.