A high-throughput stereo-imaging system for quantifying rape leaf traits during the seedling stage

Xiong Xiong; Lejun Yu; Wanneng Yang; Meng Liu; Ni Jiang; Di Wu; Guoxing Chen; Lizhong Xiong; Kede Liu; Qian Liu

doi:10.1186/s13007-017-0157-7

A high-throughput stereo-imaging system for quantifying rape leaf traits during the seedling stage

Plant Methods. 2017 Jan 31:13:7. doi: 10.1186/s13007-017-0157-7. eCollection 2017.

Authors

Xiong Xiong^#¹, Lejun Yu^#¹, Wanneng Yang^{2

3}, Meng Liu², Ni Jiang¹, Di Wu³, Guoxing Chen⁴, Lizhong Xiong², Kede Liu², Qian Liu¹

Affiliations

¹ Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, 1037 Luoyu Rd., Wuhan, 430074 People's Republic of China.
² National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 People's Republic of China.
³ College of Engineering, Huazhong Agricultural University, Wuhan, 430070 People's Republic of China.
⁴ MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan, 430070 People's Republic of China.

^# Contributed equally.

Abstract

Background: The fitness of the rape leaf is closely related to its biomass and photosynthesis. The study of leaf traits is significant for improving rape leaf production and optimizing crop management. Canopy structure and individual leaf traits are the major indicators of quality during the rape seedling stage. Differences in canopy structure reflect the influence of environmental factors such as water, sunlight and nutrient supply. The traits of individual rape leaves traits indicate the growth period of the rape as well as its canopy shape.

Results: We established a high-throughput stereo-imaging system for the reconstruction of the three-dimensional canopy structure of rape seedlings from which leaf area and plant height can be extracted. To evaluate the measurement accuracy of leaf area and plant height, 66 rape seedlings were randomly selected for automatic and destructive measurements. Compared with the manual measurements, the mean absolute percentage error of automatic leaf area and plant height measurements was 3.68 and 6.18%, respectively, and the squares of the correlation coefficients (R²) were 0.984 and 0.845, respectively. Compared with the two-dimensional projective imaging method, the leaf area extracted using stereo-imaging was more accurate. In addition, a semi-automatic image analysis pipeline was developed to extract 19 individual leaf shape traits, including 11 scale-invariant traits, 3 inner cavity related traits, and 5 margin-related traits, from the images acquired by the stereo-imaging system. We used these quantified traits to classify rapes according to three different leaf shapes: mosaic-leaf, semi-mosaic-leaf, and round-leaf. Based on testing of 801 seedling rape samples, we found that the leave-one-out cross validation classification accuracy was 94.4, 95.6, and 94.8% for stepwise discriminant analysis, the support vector machine method and the random forest method, respectively.

Conclusions: In this study, a nondestructive and high-throughput stereo-imaging system was developed to quantify canopy three-dimensional structure and individual leaf shape traits with improved accuracy, with implications for rape phenotyping, functional genomics, and breeding.

Keywords: Canopy three-dimensional structure; Individual leaf traits; Morphological classification; Stereo-imaging system.