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

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.

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