The selection and promotion of high-yielding and nitrogen-efficient wheat varieties can reduce nitrogen fertilizer application while ensuring wheat yield and quality and contribute to the sustainable development of agriculture; thus, the mining and localization of nitrogen use efficiency (NUE) genes is particularly important, but the localization of NUE genes requires a large amount of phenotypic data support. In view of this, we propose the use of low-altitude aerial photography to acquire field images at a large scale, generate 3-dimensional (3D) point clouds and multispectral images of wheat plots, propose a wheat 3D plot segmentation dataset, quantify the plot canopy height via combination with PointNet++, and generate 4 nitrogen utilization-related vegetation indices via index calculations. Six height-related and 24 vegetation-index-related dynamic digital phenotypes were extracted from the digital phenotypes collected at different time points and fitted to generate dynamic curves. We applied height-derived dynamic numerical phenotypes to genome-wide association studies of 160 wheat cultivars (660,000 single-nucleotide polymorphisms) and found that we were able to locate reliable loci associated with height and NUE, some of which were consistent with published studies. Finally, dynamic phenotypes derived from plant indices can also be applied to genome-wide association studies and ultimately locate NUE- and growth-related loci. In conclusion, we believe that our work demonstrates valuable advances in 3D digital dynamic phenotyping for locating genes for NUE in wheat and provides breeders with accurate phenotypic data for the selection and breeding of nitrogen-efficient wheat varieties.

Grain filling is essential for wheat yield formation, but is very susceptible to environmental stresses, such as high temperatures, especially in the context of global climate change. Grain RGB images include rich color, shape, and texture information, which can explicitly reveal the dynamics of grain filling. However, it is still challenging to further quantitatively predict the days after anthesis (DAA) from grain RGB images to monitor grain development. Results: The WheatGrain dataset revealed dynamic changes in color, shape, and texture traits during grain development. To predict the DAA from RGB images of wheat grains, we tested the performance of traditional machine learning, deep learning, and few-shot learning on this dataset. The results showed that Random Forest (RF) had the best accuracy of the traditional machine learning algorithms, but it was far less accurate than all deep learning algorithms. The precision and recall of the deep learning classification model using Vision Transformer (ViT) were the highest, 99.03% and 99.00%, respectively. In addition, few-shot learning could realize fine-grained image recognition for wheat grains, and it had a higher accuracy and recall rate in the case of 5-shot, which were 96.86% and 96.67%, respectively. Materials and Methods: In this work, we proposed a complete wheat grain dataset, WheatGrain, which covers thousands of wheat grain images from 6 DAA to 39 DAA, which can characterize the complete dynamics of grain development. At the same time, we built different algorithms to predict the DAA, including traditional machine learning, deep learning, and few-shot learning, in this dataset, and evaluated the performance of all models. Conclusions: To obtain wheat grain filling dynamics promptly, this study proposed an RGB dataset for the whole growth period of grain development. In addition, detailed comparisons were conducted between traditional machine learning, deep learning, and few-shot learning, which provided the possibility of recognizing the DAA of the grain timely. These results revealed that the ViT could improve the performance of deep learning in predicting the DAA, while few-shot learning could reduce the need for a number of datasets. This work provides a new approach to monitoring wheat grain filling dynamics, and it is beneficial for disaster prevention and improvement of wheat production.

This study suggests a novel extraction pipeline based on terrestrial laser scanning across multiple growth stages to address the current deficiency of three-dimensional (3D) phenotypic traits for wheat populations derived from 3D point clouds. This study presents 3D Wheat Point-seg Net (3D WP-seg Net), a novel 3D point cloud segmentation network that incorporates an SA-CrossAttention module to address the difficulties presented by complex structures, background noise, non-uniform point distributions, and scale variations in plot-level wheat point cloud data. Plot height, canopy area, and volume are examples of common phenotypic parameters that are successfully extracted using this technique. Additionally, two new phenotypic parameters: plot extension distance and lodging angle are suggested by fusing the centroid and slice-skeletonization algorithms. A software platform called 3D Trait Analysis was created to facilitate multi-sensor 3D data processing and trait extraction. A genome-wide association study (GWAS) was then conducted using the extracted population-level traits to find potential genes linked to these new phenotypes. While the segmentation accuracies of 3D WP-seg Net achieved 93.1%, 88.3%, and 92.5% under various sensor systems, the results showed a strong correlation between the predicted and measured plot heights (R² = 0.954). Furthermore, four candidate genes linked to extension distance were found on chromosomes 1A, 2A, and 4A, and five putative genes controlling plot lodging angle were found on chromosomes 2D, 3A, and 7A. The multi-stage 3D phenotyping and analysis framework for wheat populations established by this study improves the accuracy of point cloud segmentation and trait quantification while offering a new and efficient method for the genetic analysis of important population-level traits.

Drought priming represents a potential strategy to bolster wheat yields in the face of recurring droughts, and there is a need to identify responsive cultivars and decipher the underlying mechanisms of priming. Here, the responses of 157 wheat cultivars to drought-priming were phenotyped using a high-throughput phenotyping (HTP) platform across two growing seasons, and a drought priming index (DPI) was devised to assess the priming sensitivity for each cultivar. A DPI comprehensive score (DPICS) was derived from 13 sensitive traits identified by principal component analysis, and significant variations in this score led to the classification of the cultivars into two distinct groups, one sensitive to drought priming and one not. The sensitive group contained 58 cultivars that had higher DPI values for traits including yield components, harvest index, post-anthesis assimilation, photochemical efficiency, canopy coverage, and normalized difference vegetation index, and lower DPI values for traits including remobilization of dry matter stored pre-anthesis, non-photochemical quenching, plant senescence reflectance index, and canopy temperature. A genome-wide association study (GWAS) based on the DPI identified 499 significant markers related to drought priming using a commercially Wheat660 SNP array. Notably, one marker situated on chromosome 5B consistently appeared in both the growing seasons that were studied. This marker resides within a 261.2 kb genomic block containing seven genes, including the candidate gene TraesCS5B03G1259700, which exhibited distinct transcriptional memory related to drought priming. Our results suggest that integrating HTP and GWAS has great potential for deciphering the genetic basis of acquired drought tolerance induced by priming and could facilitate the breeding of improved wheat varieties that can respond to recurring drought events.