Three-dimensional phenotyping: Technological advances and applications in genomics-assisted crop breeding.

With rapid advancements in breeding technologies, phenomics, and artificial intelligence, crop breeding is progressively advancing toward an era of greater precision and efficiency. In this context, three-dimensional (3D) phenotyping techniques, leveraging their multi-dimensional spatial resolution capabilities, have overcome the limitations of two-dimensional (2D) phenotyping in breeding analysis, enabling precise characterization of crop spatial interactions, plant architecture spatial distribution, and complex 3D structural traits. Recent breakthroughs in computer technology for 3D reconstruction and 3D segmentation have provided robust technical support for crop 3D phenotypic analysis. Furthermore, the effective integration of extracted 3D phenotypic data with genotypic data serves as a powerful tool for future research in crop gene function and genomics-assisted breeding. This review systematically examines the major advances in 3D phenotyping techniques and their representative applications, with particular emphasis on innovations in 3D phenotyping and analysis techniques. Simultaneously, we describe the latest interdisciplinary advances in 3D phenotyping within crop gene function and genomics-assisted breeding research. We objectively evaluate the advantages and limitations of 3D phenotyping compared to 2D approaches to assist breeders in selecting appropriate technologies. Finally, addressing the conceptual challenges in current research, we propose future perspectives for promoting the deep integration of phenomics and breeding technologies. Despite facing technical challenges, it is foreseeable that the cross-disciplinary integration of phenomics and genomics will offer promising prospects for crop breeding.