3D Reconstruction Enables High-Throughput Phenotyping and Quantitative Genetic Analysis of Phyllotaxy

Abstract

Abstract Differences in canopy architecture play a role in determining both the light and water use efficiency. Canopy architecture is determined by several component traits, including leaf length, width, number, angle, and phyllotaxy. Phyllotaxy may be among the most difficult of the leaf canopy traits to measure accurately across large numbers of individual plants. As a result, in simulations of the leaf canopies of grain crops such as maize and sorghum, this trait is frequently approximated as alternating 180° angles between sequential leaves. We explore the feasibility of extracting direct measurements of the phyllotaxy of sequential leaves from 3D reconstructions of individual sorghum plants generated from 2D calibrated images and test the assumption of consistently alternating phyllotaxy across a diverse set of sorghum genotypes. Using a voxel-carving-based approach, we generate 3D reconstructions from multiple calibrated 2D images of 366 sorghum plants representing 236 sorghum genotypes from the sorghum association panel. The correlation between automated and manual measurements of phyllotaxy is only modestly lower than the correlation between manual measurements of phyllotaxy generated by two different individuals. Automated phyllotaxy measurements exhibited a repeatability of R 2 = 0.41 across imaging timepoints separated by a period of two days. A resampling based genome wide association study (GWAS) identified several putative genetic associations with lower-canopy phyllotaxy in sorghum. This study demonstrates the potential of 3D reconstruction to enable both quantitative genetic investigation and breeding for phyllotaxy in sorghum and other grain crops with similar plant architectures.

Plant phenotyping relevance

3D再構成とボクセル・カービングによりソルガムの葉序を自動抽出し、手動測定との比較および反復性を評価しており、表現型取得手法が研究の中心である。

Code and data availability

The paper's Data Availability section publicly deposits the raw sorghum images on Zenodo and the phenotypic data, GWAS result files, and analysis/figure code on GitHub (jdavis-132/phyllotaxy). The reconstruction/skeletonization code (cropsinsilico/SorghumVoxelCarving) is also mentioned but its URL has no exact match in