Glucosinolates are amino acid derived secondary metabolites found in the order Capparales. It is an important class of phytochemicals involved in plant-microbe, plant-insect, plant-animal and plant-human interactions. It is, therefore, important to understand genetic mechanism of glucosinolate biosynthesis in Brassica for efficient manipulation. In this study, QTL mapping of leaf and seed glucosinolates was performed in B. rapa using two RIL populations, SR-RILs and BU-RILs. QTL mapping was performed using SR-RILs developed from a cross of Chinese cabbage and turnip rapeseed and a genetic map in B.rapa. Genetic map was developed using a total 1,579 molecular markers including 9 markers specific to glucosinolate genes, GSL-ELONG, GSL-PRO, GSL-FMOOX1, and GSL-AOP/ALK. Several QTL for progoitrin, gluconapin, glucoalyssin, glucobrassicanapin, 2-methylpropyl and 4-hydoxyglucobrassicin glucosinolates were identified with phenotype variance between 6 and 54%. Interestingly, a major QTL for 5C aliphatic glucosinolates was co-localized with a candidate Br-GSL-ELONG locus on linkage group A3, displayed co-segregation with co-dominant SCAR marker BrMAM1-1. The Br-GSL-ELONG locus was identified to regulate 20 µmole/g seed 5C glucosinolate biosynthesis. BU-RILs derived from a cross of yellow sarson and USU9 was segregated for glucoerucin, gluconapin and progoitrin 4C aliphatic glucosinolates with 4-hydoxyglucobrassicin. Phenotyping was performed in controlled and field environments for seed glucosinolates and controlled environments for leaf glucosinolates. Genetic map was developed using SRAP markers and glucosinolate gene, GSL-ELONG and GSL-PRO specific 4 loci were integrated on map. Four and three QTL were identified for seed glucoerucin and gluconapin, respectively in both environments with phenotypic variance up to 49%. Additionally, genetic manipulation of glucosinolates was performed by backcross with MAS in B. rapa. Resynthesized B. napus line was backcrossed with B. rapa genotypes, RI16, BAR6 and USU9 for replacement or introgression of glucosinolate genes, GSL-ELONG- and GSL-PRO+. In RI16 genotype, 15 to 25 µmole/g seed 5C glucosinolates reduced in 15 BC3F2 lines those were positive with GSL-ELONG- marker and negative with the A-genome and gene specific marker BrMAM1-1. This suggests that the functional allele has replaced by non-functional from B. oleracea. GSL-PRO+ positive backcross lines in RI16 genotype displayed sinigrin 3C aliphatic glucosinolate in B. rapa. This suggests introgression of GSL-PRO+ in B. rapa.