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 entering an era of greater precision and efficiency. In this context, three-dimensional (3D) phenotyping techniques-leveraging multidimensional spatial resolution capabilities-have overcome the limitations of two-dimensional (2D) phenotyping in breeding analyses, enabling precise characterization of crop spatial interactions, spatial distribution of plant architecture, 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, effective integration of extracted 3D phenotypic data with genotypic data serves as a powerful tool for future research on crop gene function and genomics-assisted breeding. This review systematically examines major advances in 3D phenotyping techniques and their representative applications, with particular emphasis on innovations in 3D phenotyping and analytical methodologies. In parallel, we describe the latest interdisciplinary advances in 3D phenotyping within crop functional genomics research and genomics-assisted breeding. We objectively evaluate the advantages and limitations of 3D phenotyping compared with 2D approaches to assist breeders in selecting appropriate technologies. Finally, we propose future perspectives to promote deeper integration of phenomics and breeding technologies. Despite existing conceptual and technical challenges, it is foreseeable that cross-disciplinary integration of phenomics and genomics will offer promising prospects for crop breeding.