The area for crop cultivation has been affected by abiotic stress, such as water deficit, high drought, heavy metals, salinity, and temperature. This has drastically reduced the yield strength of the field. Hence, it is crucial to identify the genes responsible and their pathways for the crops development that are resilient to abiotic stress. To identify genes responsible for abiotic stress, with the help of expressed sequence tags (ESTs), we can identify the potential genes. The remaining genes are used for reconstruction and repair of the fault genes. For this, the in-silico method is being used as it reduces the time taken for the reconstruction of new genes in crops, which helps in identifying the qualitative trait locus (QLT) on the crop genome. These analyses were made viable with the aid of functional genomics, where we computationally study the transcription process, protein production, and metabolites. The recent advancement in functional genomics has allowed us to explore genomics, gene expression microarrays, and gene expression profiling with the help of RNA-Seq. These omics studies provide a detailed report of the molecular mechanisms of how genes express under abiotic stress; the modification occurs due to the stress and tolerance mechanisms of crops and the stability and yield of crops. However abiotic stress is a complex trait where the process of identifying the gene associated with stress response is important as the genome analysis of mutants is dependent on the gene.