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

Authors Organisations
  • Di Wu(Author)
    Huazhong Agricultural University
    School of Information Engineering, Wuhan Technology and Business University
  • Dan Wu(Author)
    Huazhong Agricultural University
  • Hui Feng(Author)
    Huazhong Agricultural University
  • Lingfeng Duan(Author)
    Huazhong Agricultural University
  • Guoxing Dai(Author)
    Huazhong Agricultural University
  • Xiao Liu(Author)
    Huazhong Agricultural University
  • Kang Wang(Author)
    Huazhong Agricultural University
  • Peng Yang(Author)
    Huazhong Agricultural University
  • Guoxing Chen(Author)
    Huazhong Agricultural University
  • Alan Gay(Author)
  • John Doonan(Author)
  • Zhiyou Niu(Author)
    Huazhong Agricultural University
  • Lizhong Xiong(Author)
    Huazhong Agricultural University
  • Wanneng Yang(Author)
    Huazhong Agricultural University
Type Article
Original languageEnglish
Article number100165
JournalPlant Communications
Issue number2
Early online date29 Jan 2021
Publication statusPublished - 08 Mar 2021
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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 R2 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 R2 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. This study reports a deep learning-integrated micro-CT image analysis pipeline to rapidly (4.6 min per plant) and accurately quantify 24 phenotypic traits of rice culms and to visualize the 3D bending stress distribution of the culms. This approach will enable future high-throughput screening of large rice populations for lodging resistance.


  • deep learning, high-throughput, lodging resistance, micro-CT, rice culm, SegNet, Plant Breeding/methods, X-Ray Microtomography/instrumentation, Oryza/genetics, Disease Resistance/genetics, Deep Learning, Phenotype, Plant Diseases/genetics