A deep learning-integrated micro-CT image analysis pipeline for quantifying rice lodging resistance-related traits.

Abstract

Lodging is a common problem in rice, reducing its yield and mechanical harvesting efficiency. Rice architecture is a key aspect of its domestication and a major factor that limits its high productivity. The ideal rice culm structure, including major_axis_culm, minor axis_culm, and wall thickness_culm, is critical for improving lodging resistance. However, the traditional method of measuring rice culms is destructive, time consuming, and labor intensive. In this study, we used a high-throughput micro-CT-RGB imaging system and deep learning (SegNet) to develop a high-throughput micro-CT image analysis pipeline that can extract 24 rice culm morphological traits and lodging resistance-related traits. When manual and automatic measurements were compared at the mature stage, the mean absolute percentage errors for major_axis_culm, minor_axis_culm, and wall_thickness_culm in 104 indica rice accessions were 6.03%, 5.60%, and 9.85%, respectively, and the R 2 values were 0.799, 0.818, and 0.623. We also built models of bending stress using culm traits at the mature and tillering stages, and the R 2 values were 0.722 and 0.544, respectively. The modeling results indicated that this method can quantify lodging resistance nondestructively, even at an early growth stage. In addition, we also evaluated the relationships of bending stress to shoot dry weight, culm density, and drought-related traits and found that plants with greater resistance to bending stress had slightly higher biomass, culm density, and culm area but poorer drought resistance. In conclusion, we developed a deep learning-integrated micro-CT image analysis pipeline to accurately quantify the phenotypic traits of rice culms in ∼4.6 min per plant; this pipeline will assist in future high-throughput screening of large rice populations for lodging resistance.

Plant phenotyping relevance

深層学習統合micro-CT画像解析パイプラインを開発し、イネ茎の形態・倒伏抵抗性関連形質を非破壊かつ高スループットに抽出・検証しており、植物フェノタイピング手法が研究の中心である。

Code and data availability

The paper's micro-CT rice culm phenotyping pipeline source code is explicitly stated to be publicly available on the authors' GitHub repository and their Crop Phenomics Group website; phenotypic data are in Supplemental Data 1 (not directly linked here).