Agronomy, Vol. 15, Pages 1803: High-Resolution 3D Reconstruction of Individual Rice Tillers for Genetic Studies

Agronomy doi: 10.3390/agronomy15081803

Authors:
Jiexiong Xu
Jiyoung Lee
Gang Jiang
Xiangchao Gan

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.

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Jiexiong Xu www.mdpi.com