Modern techniques like quantitative trait locus (QTL) sequencing (QTL-seq), genotyping by sequencing, and genome-wide association studies (GWAS) have expedited the identification of QTLs associated with complex traits in crop plants. GWAS capitalizes on the high recombination rates present in natural populations used for association studies. Carrot, radish, and beetroot are key vegetable root crops, globally significant for their contributions to balanced human diets. The economically valuable fleshy solid roots of these crops underscore the importance of understanding root complexities through genomic approaches to uncover QTLs governing root architecture. GWAS and QTL analysis have been effectively employed to understand root-related traits and pigmentation-related genes. Various mapping populations, such as doubled haploids (DHs), biparental mapping populations, and natural populations, have proven effective in QTL analysis studies and candidate gene identification. Despite their importance, limited research has focused on identifying QTLs and elucidating the genetic basis of quality traits, biotic and abiotic stress resistance in carrot, radish, and beetroot. In this regard, GWAS and QTL-seq hold promise for unraveling complex traits in these root crops. This chapter provides a summary of the latest advancements in GWAS and QTL mapping for different traits in root crops.