Drought alone and with associated abiotic stress such as heat and nutrient deficiency leads to significant agricultural crop loss. Thus, with changing climatic conditions, it is important to develop resilience measures in agricultural systems against drought stress. In this review, we discuss the modifications in plants while responding to drought giving special focus on roots as they are the primary sense organs in this context. Prospects of genomic crop improvement by pointing out the focus areas to engineer root system architecture and genomic regions involved in the related traits are also discussed. We have also listed instruments and software facilitating high throughput phenotyping of root system in field conditions as the phenotyping of root system architecture in the field is a challenge.