Research Article | Open Access

Volume 2025 |Article ID 100017 | https://doi.org/10.1016/j.plaphe.2025.100017

Genetic resolution of multi-level plant height in common wheat using the 3D canopy model from ultra-low altitude unmanned aerial vehicle imagery

Shuaipeng Fei,^1,2,6 Yidan Jia,^2,3,6 Lei Li,² Shunfu Xiao,¹ Jie Song,⁵ Shurong Yang,² Duoxia Wang,² Guangyao Sun,¹ Bohan Zhang,² Keyi Wang,⁴ Junjie Ma,⁴ Jindong Liu,² Yonggui Xiao ,² and Yuntao Ma ¹

¹College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
²National Wheat Improvement Centre, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
³College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
⁴Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
⁵College of Agriculture, Henan Key Laboratory of Hybrid Wheat, Henan Institute of Science and Technology, Xinxiang, 453003, China
⁶Shuaipeng Fei and Yidan Jia contributed equally to this work

Abstract

In quantitative genomic analysis of wheat plant height (PH), the average height of a few representative plants is typically used to represent the PH of the entire plot, which overlooks the variation in height among other plants. Extracting different height quantiles from canopy point clouds can address this limitation. For this purpose, low-cost UAV cross-circling oblique (CCO) imaging, combined with structure-from-motion (SfM) and multi-view stereopsis (MVS), was employed to generate precise canopy point clouds for 262 F5 recombinant inbred lines (Zhongmai 578 × Jimai 22) across seven environments. Multi-level 3D-PH measurements were extracted from six height quantiles, revealing a strong correlation (mean r = 0.95) between 3D-PH and field-measured PH (FM-PH) across environments. The 90 % and 92 % height quantiles showed the closest agreement with FM-PH compared to other quantiles. Eleven stable quantitative trait loci (QTLs) associated with multi-level 3D-PH were identified using a 50K single nucleotide polymorphism array. Among these, QPhzj.caas-3A.2 (detected by 3D-PH) and QPhzj.caas-7A.1 (detected by both FM-PH and 3D-PH) represented potential novel loci. KASP markers for these QTLs were developed and validated. Furthermore, within the intervals of QPhzj.caas-5A and QPhzj.caas-3B (both were detected by 3D-PH), two candidate genes associated with PH regulation were identified: TaGL3-5A and Rht5, respectively. Corresponding KASP markers for these genes were also developed and validated. This study highlighted the advantages of 3D model and multi-level 3D-PH in elucidating the genetic basis of crop height, and provided a precise and objective basis for advancing wheat breeding programs.