High-Resolution 3D Reconstruction of Individual Rice Tillers for Genetic Studies

The architecture of rice tillers plays a pivotal role in yield potential, yet conventional phenotyping methods have struggled to capture these intricate three-dimensional (3D) structures with high fidelity. In this study, a 3D model reconstruction method was developed specifically for rice tillers to overcome the challenges posed by their slender, feature-poor morphology in multi-view stereo-based 3D reconstruction. By applying strategically designed colorful reference markers, high-resolution 3D tiller models of 231 rice landraces were reconstructed. Accurate phenotyping was achieved by introducing ScaleCalculator, a software tool that integrated depth images from a depth camera to calibrate the physical sizes of the 3D models. The high efficiency of the 3D model-based phenotyping pipeline was demonstrated by extracting the following seven key agronomic traits: flag leaf length, panicle length, first internode length below the panicle, stem length, flag leaf angle, second leaf angle from the panicle, and third leaf angle. Genome-wide association studies (GWAS) performed with these 3D traits identified numerous candidate genes, nine of which had been previously confirmed in the literature. This work provides a 3D phenomics solution tailored for slender organs and offers novel insights into the genetic regulation of complex morphological traits in rice.