Access to large-scale omics datasets i.e. genomics, transcriptomics, proteomics, metabolomics, phenomics, etc. has revolutionized biology and led to the emergence of systems approaches to advance our understanding of biological processes. These omics approaches together they help to bring out the best of characters in plants. Breeding programs of the past century have relied on natural and mutant-induced genetic variations to select for favorable genetic combinations. The traditional breeding program that is conducted by mutagenesis using chemical compounds or irradiation, followed by screening for desired mutations, has several drawbacks. Therefore, transgenic breeding programs surfaced towards the end of the 20th century (1990) to overcome such problems. The 21st century is regarded as the post-genomic era and, the availability of genome sequence data for multiple crop plants has revolutionized plant breeding programs. Genomics is rapidly gaining importance in molecular breeding programs. Combinations of genomic tools with conventional breeding techniques have opened new doors in genome-based breeding programs. Among the genomic approaches commonly used are genomic selection, genome wide association studies, transgenic technology and CRISPR-CAS technologies are most promising. Transcriptomics is the study of the transcriptome the complete set of RNA transcripts that are produced by the genome, under specific circumstances or in a specific cell using high-throughput methods, such as microarray analysis. Comparison of transcriptomes allows the identification of genes that are differentially expressed in distinct cell populations, or in response to different treatments. Proteomics is the large scale of study of proteins, particularly their function and structure. Proteomics is an excellent approach for studying changes in metabolism in response to different stress conditions. Just as genomics is the study of DNA and genetic information within a cell, and transcriptomics is the study of RNA and differences in mRNA expression; metabolomics is the study of substrates and products of metabolism, which are influenced by both genetic and environmental factors, Metabolomics is a powerful approach because metabolites and their concentrations, unlike other “omics” measures, directly reflect the underlying biochemical activity and state of cells/tissues. Thus metabolomics best represents the molecular phenotype. With the rapid development in high-throughput phenotyping technologies, research in this area is entering a new era called ‘phenomics.’ The crop phenotyping community not only needs to build a multi-domain, multi-level and multi-scale crop phenotyping big database, but also to research technical systems for phenotypic traits identification and develop bioinformatics technologies for information extraction from the overwhelming amounts of omics data.