Genotyping Identification of Maize Based on Three-Dimensional Structural Phenotyping and Gaussian Fuzzy Clustering

Abstract

The maize tassel represents one of the most pivotal organs dictating maize yield and quality. Investigating its phenotypic information constitutes an exceedingly crucial task within the realm of breeding work, given that an optimal tassel structure is fundamental for attaining high maize yields. High-throughput phenotyping technologies furnish significant tools to augment the efficiency of analyzing maize tassel phenotypic information. Towards this end, we engineered a fully automated multi-angle digital imaging apparatus dedicated to maize tassels. This device was employed to capture images of tassels from 1227 inbred maize lines falling under three genotype classifications (NSS, TST, and SS). By leveraging the 3D reconstruction algorithm SFM (Structure from Motion), we promptly obtained point clouds of the maize tassels. Subsequently, we harnessed the TreeQSM algorithm, which is custom-designed for extracting tree topological structures, to extract 11 archetypal structural phenotypic parameters of the maize tassels. These encompassed main spike diameter, crown height, main spike length, stem length, stem diameter, the number of branches, total branch length, average crown diameter, maximum crown diameter, convex hull volume, and crown area. Finally, we compared the GFC (Gaussian Fuzzy Clustering algorithm) used in this study with commonly used algorithms, such as RF (Random Forest), SVM (Support Vector Machine), and BPNN (BP Neural Network), as well as k-Means, HCM (Hierarchical), and FCM (Fuzzy C-Means). We then conducted a correlation analysis between the extracted phenotypic parameters of the maize tassel structure and the genotypes of the maize materials. The research results showed that the Gaussian Fuzzy Clustering algorithm was the optimal choice for clustering maize genotypes. Specifically, its classification accuracies for the Non-Stiff Stalk (NSS) genotype and the Tropical and Subtropical (TST) genotype reached 67.7% and 78.5%, respectively. Moreover, among the materials with different maize genotypes, the number of branches, the total branch length, and the main spike length were the three indicators with the highest variability, while the crown volume, the average crown diameter, and the crown area were the three indicators with the lowest variability. This not only provided an important reference for the in-depth exploration of the variability of the phenotypic parameters of maize tassels but also opened up a new approach for screening breeding materials.

Plant phenotyping relevance

トウモロコシ雄穂の3D画像取得、再構成、構造形質抽出を行う自動フェノタイピング装置と解析ワークフローが研究の中心であるため。

Code and data availability

The paper's 1227 maize tassel images/point clouds and phenotypic measurements are not publicly deposited; the Data Availability Statement says they are available only on request from the corresponding author. No author code or dataset URL is provided.

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