Brassica rapa (2n=20, AA), contributing A genome to important oilseed crops Brassica juncea (2n=36, AABB) and Brassica napus (2n=38, AACC) in classical U’s triangle, is an important Brassica species. Wide variation for morphological traits exists in B. rapa, however, the genes governing most of the economically important traits are still unknown. In the present study, we used CRF2/3 population, derived from crossing between “Chiifu” and “Rapid cycling B. rapa” (RcBr) line, to map quantitative trait loci (QTL) for morphological and yield component traits. A total of 79 QTLs were detected in B. rapa genome for 12 morphological and yield component traits that were investigated for 3 years. Comparison of QTL location between B. rapa, B. juncea and B. napus chromosomes identified 5 key major conserved Brassica blocks (R, J, F, E, W) that contained QTL for morphological and yield component traits suggesting structural and functional conservation between the A, B, and C genomes of three Brassica species even though these genomes diverge many years ago. This might have resulted due to the selection of those few chromosomal regions in the A, B, C genomes containing genes for morphological and yield component traits that were derived from common ancestor. Searching of candidate genes in those QTL region using whole genome sequences of B. rapa revealed the presence of few genes of the same family governing same traits in different QTL region /chromosomal blocks. Further, single nucleotide polymorphism was identified for important genes between the B. rapa parental lines. The candidate gene(s) information from B. rapa could be used for isolation of orthologous gene(s) governing yield component traits in B. juncea and B. napus and could be used in marker assisted breeding program.