Recent advances in omics and next generation sequencing technologies are having great impact on the plant, livestocks and microorganisms breeding programs. These technologies have provided huge biological data which require fast and precise analysis using various bioinformatics tools. By creating, developing and using algorithms and bioinformatics software to simulate biological processes, systems biology systematically studies functions of genes, proteins and metabolic pathways, and integrates biological data in forms of mathematical models. Using systems biology approaches, we identify agriculturally important candidate genes and proteins in order to be incorporated in breeding programs.