The Research Topic has collated contributions from experts working in quantitative genomics with the integration of genetics, genomics, transcriptomics, metabolomics and phenomics. Thinking beyond conventional breeding approaches, this multi-omics approach helped gather information for enhancement of certain traits such as yield, disease resistance, secondary metabolite content, and mineral content, along with many others. This combined report comprises original research and review articles focusing improvement in Brassica, wheat, rice, soybean, and a medicinal plant. There is information on novel technologies for genotyping, genomic selection, expression, and metabolome analysis for identification and candidate gene validation through functional analysis.