AnatomyArray: A high-throughput platform for anatomical phenotyping in plants

Abstract The anatomy or the arrangement of cells often determines the organization and function of plant tissues. However, current methods in large-scale imaging and accurate quantification of anatomical traits face major limitations. To address these challenges, we introduce the AnatomyArray system, an integrated platform for multiplexed tissue sectioning and anatomical phenotyping in plants. This system includes a highly adaptable device for high-throughput paraffin sectioning and multichannel slide imaging of various plant tissues, along with AnatomyNet, a deep learning tool for analyzing tissue-scale patterns of cell arrangement and morphology. AnatomyNet delivers accurate, automated quantification of anatomical traits at both the tissue and cellular levels, outperforming existing tools in image analysis. Using the AnatomyArray system, we dissected the genetic basis of root anatomy in a diverse wheat (Triticum aestivum L.) population through anatomics-based genome-wide association studies. Among the candidate genes identified, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 14 (TaSPL14) was associated with stele and pericycle size in roots. Analysis of Taspl14 mutants confirmed that TaSPL14 plays a critical role in regulating root growth and tissue size by influencing phytohormone pathways. The AnatomyArray platform enables high-throughput characterization of cellular-level features and provides insights into the mechanisms shaping anatomical structure in plants.