Vol. 9, Special Issue 7, Part B (2025)

The escalating global population, coupled with the profound impacts of climate change, presents unprecedented challenges to global food security. Traditional plant breeding methods, while foundational to agricultural development, are often slow and labor-intensive, limiting the rate of genetic gain required to meet future demands. The advent of the genomics era has catalyzed a paradigm shift in crop improvement, offering a suite of powerful tools to accelerate the development of high-yielding, climate-resilient, and nutritious crop varieties. This comprehensive review focuses on the synergistic integration of three transformative technologies at the forefront of modern plant breeding: Genomic Selection (GS), High-Throughput Phenotyping (HTP), and Gene Editing, with a primary focus on the CRISPR/Cas9 system. Genomic Selection utilizes whole-genome marker data to predict the genetic merit of individuals, enabling breeders to select superior lines early in the breeding cycle, thereby increasing selection intensity and reducing cycle length. High-Throughput Phenotyping provides the capacity to rapidly and accurately measure complex plant traits on a large scale, offering unprecedented resolution for dissecting the genetic basis of quantitative traits and providing the critical phenotypic data required to build robust GS models. Gene editing, particularly CRISPR/Cas9, offers the ultimate precision, allowing for the direct and targeted modification of genes to create novel alleles, validate gene function, and introduce desirable traits with unparalleled efficiency. We delve into the theoretical foundations, methodologies, and practical applications of each technology individually. More importantly, we explore the profound synergies that emerge from their integration. HTP-derived phenotypes enhance the accuracy of GS predictions; GS identifies elite genetic backgrounds and candidate genes for targeted improvement via gene editing; and gene editing provides the means to validate causal variants and introduce novel diversity that can be efficiently managed and selected through GS and HTP. We also discuss the significant challenges that remain, including the management and analysis of massive datasets ("big data"), the development of cost-effective HTP platforms, the navigation of regulatory landscapes for gene-edited crops, and the need for enhanced interdisciplinary expertise. This review synthesizes the current state of the art, presents successful case studies, and provides a forward-looking perspective on how the continued convergence of GS, HTP, and gene editing will shape the future of plant breeding, driving the development of the next generation of crops to sustainably feed the world.