Role of the genomics-phenomics-agronomy paradigm in plant breeding

Plant breeding primarily focuses on improving agronomy traits, e.g. yield, quality, host plant resistance to pathogens and pests, and abiotic stress tolerance; however, the methods for their genetic improvement are being rapidly enhanced through genomics and phenomics. In the Genomics-Phenomics- Agronomy (G-P- A) paradigm, diverse research approaches have been conducted to bridge any two of these elements, and recently, all of them together. This review first highlights the progress to link (1) genomics to agronomy, (2) genomics to phenomics, and (3) phenomics to agronomy. Secondly, the G-P-A domain is dissected into different layers, each addressing the three elements simultaneously. These layers include genetic dissection through gene mapping using genome-wide association studies and genomic selection using best linear unbiased prediction, Bayesian approaches, and machine learning. The objective of the review is to help readers to grasp the core developments among the exponentially growing literature in each of these fields. Through this review, the connections among the three elements of the G-P- A paradigm are coherently integrated toward the prospect of sustainable development of agronomy traits through both genomics and phenomics.