Phenotype identification and genome-wide association study of ear-internode vascular bundles in maize (Zea mays).

The vascular bundle in the ear-internode of maize is a key conduit for transporting photosynthetic materials between "source" and "sink", making it critically important to examine its micro-phenotypes and genetic architecture to identify advantageous characteristics and cultivate high-yielding and high-quality varieties. Unfortunately, the limited observation methods and scope of study precludes any comprehensive and systematic investigations into the microscopic phenotypes and genetic mechanisms of vascular bundle in maize ear-internode. In this study, 47 phenotypic traits were extracted in 495 maize inbred lines using micro computed tomography (Micro-CT) scanning technology and a deep learning-based phenotype acquisition method for stem vascular bundle, which included stem slice-related, epidermis zone-related, periphery zone-related, inner zone-related and vascular bundles-related traits. Phenotypic analysis indicated that there was extensive phenotypic variation of vascular bundle traits in ear-internode, especially that in the inner zone. Of these, 30 phenotypic traits with heritability greater than 0.70 were conducted for GWAS, and a total of 4,225 significant SNPs and 416 candidate genes with detailed functional annotations were identified. Furthermore, 20 genes were highly expressed in stem-related tissues, especially in maize internodes. Functional analysis of candidate genes indicated that the pathways obtained for candidate genes of different trait groups were distinct, mainly involved in vitamin synthesis and metabolism, transport of substances, carbohydrate derivative catabolic process, protein transport and localization, and anatomical structure development. The results of this study will help to further understand the phenotypic traits of stem vascular bundles and provide a reference for revealing the genetic mechanism of maize ear-internode vascular bundles.

Using high-throughput phenotype platform MVS-Pheno to reconstruct the 3D morphological structure of wheat.

It is of great significance to study the plant morphological structure for improving crop yield and achieving efficient use of resources. Three dimensional (3D) information can more accurately describe the morphological and structural characteristics of crop plants. Automatic acquisition of 3D information is one of the key steps in plant morphological structure research. Taking wheat as the research object, we propose a point cloud data-driven 3D reconstruction method that achieves 3D structure reconstruction and plant morphology parameterization at the phytomer scale. Specifically, we use the MVS-Pheno platform to reconstruct the point cloud of wheat plants and segment organs through the deep learning algorithm. On this basis, we automatically reconstructed the 3D structure of leaves and tillers and extracted the morphological parameters of wheat. The results show that the semantic segmentation accuracy of organs is 95.2%, and the instance segmentation accuracy AP50 is 0.665. The R2 values for extracted leaf length, leaf width, leaf attachment height, stem leaf angle, tiller length, and spike length were 0.97, 0.80, 1.00, 0.95, 0.99, and 0.95, respectively. This method can significantly improve the accuracy and efficiency of 3D morphological analysis of wheat plants, providing strong technical support for research in fields such as agricultural production optimization and genetic breeding.

Three-Dimensional Modeling of Maize Canopies Based on Computational Intelligence.

The 3-dimensional (3D) modeling of crop canopies is fundamental for studying functional-structural plant models. Existing studies often fail to capture the structural characteristics of crop canopies, such as organ overlapping and resource competition. To address this issue, we propose a 3D maize modeling method based on computational intelligence. An initial 3D maize canopy is created using the t-distribution method to reflect characteristics of the plant architecture. The subsequent model considers the 3D phytomers of maize as intelligent agents. The aim is to maximize the ratio of sunlit leaf area, and by iteratively modifying the azimuth angle of the 3D phytomers, a 3D maize canopy model that maximizes light resource interception can be constructed. Additionally, the method incorporates a reflective approach to optimize the canopy and utilizes a mesh deformation technique for detecting and responding to leaf collisions within the canopy. Six canopy models of 2 varieties plus 3 planting densities was constructed for validation. The average R2 of the difference in azimuth angle between adjacent leaves is 0.71, with a canopy coverage error range of 7% to 17%. Another 3D maize canopy model constructed using 12 distinct density gradients demonstrates the proportion of leaves perpendicular to the row direction increases along with the density. The proportion of these leaves steadily increased after 9 × 104 plants ha-1. This study presents a 3D modeling method for the maize canopy. It is a beneficial exploration of swarm intelligence on crops and generates a new way for exploring efficient resources utilization of crop canopies.

Plant microphenotype: from innovative imaging to computational analysis.

The microphenotype plays a key role in bridging the gap between the genotype and the complex macro phenotype. In this article, we review the advances in data acquisition and the intelligent analysis of plant microphenotyping and present applications of microphenotyping in plant science over the past two decades. We then point out several challenges in this field and suggest that cross-scale image acquisition strategies, powerful artificial intelligence algorithms, advanced genetic analysis, and computational phenotyping need to be established and performed to better understand interactions among genotype, environment, and management. Microphenotyping has entered the era of Microphenotyping 3.0 and will largely advance functional genomics and plant science.

Research on the evolutionary history of the morphological structure of cotton seeds: a new perspective based on high-resolution micro-CT technology.

Cotton (Gossypium hirsutum L.) seed morphological structure has a significant impact on the germination, growth and quality formation. However, the wide variation of cotton seed morphology makes it difficult to achieve quantitative analysis using traditional phenotype acquisition methods. In recent years, the application of micro-CT technology has made it possible to analyze the three-dimensional morphological structure of seeds, and has shown technical advantages in accurate identification of seed phenotypes. In this study, we reconstructed the seed morphological structure based on micro-CT technology, deep neural network Unet-3D model, and threshold segmentation methods, extracted 11 basics phenotypes traits, and constructed three new phenotype traits of seed coat specific surface area, seed coat thickness ratio and seed density ratio, using 102 cotton germplasm resources with clear year characteristics. Our results show that there is a significant positive correlation (P< 0.001) between the cotton seed size and that of the seed kernel and seed coat volume, with correlation coefficients ranging from 0.51 to 0.92, while the cavity volume has a lower correlation with other phenotype indicators (r<0.37, P< 0.001). Comparison of changes in Chinese self-bred varieties showed that seed volume, seed surface area, seed coat volume, cavity volume and seed coat thickness increased by 11.39%, 10.10%, 18.67%, 115.76% and 7.95%, respectively, while seed kernel volume, seed kernel surface area and seed fullness decreased by 7.01%, 0.72% and 16.25%. Combining with the results of cluster analysis, during the hundred-year cultivation history of cotton in China, it showed that the specific surface area of seed structure decreased by 1.27%, the relative thickness of seed coat increased by 8.70%, and the compactness of seed structure increased by 50.17%. Furthermore, the new indicators developed based on micro-CT technology can fully consider the three-dimensional morphological structure and cross-sectional characteristics among the indicators and reflect technical advantages. In this study, we constructed a microscopic phenotype research system for cotton seeds, revealing the morphological changes of cotton seeds with the year in China and providing a theoretical basis for the quantitative analysis and evaluation of seed morphology.

Using High-Throughput Phenotyping Analysis to Decipher the Phenotypic Components and Genetic Architecture of Maize Seedling Salt Tolerance.

Soil salinization is a worldwide problem that limits agricultural production. It is important to understand the salt stress tolerance ability of maize seedlings and explore the underlying related genetic resources. In this study, we used a high-throughput phenotyping platform with a 3D laser sensor (Planteye F500) to identify the digital biomass, plant height and normalized vegetation index under normal and saline conditions at multiple time points. The result revealed that a three-leaf period (T3) was identified as the key period for the phenotypic variation in maize seedlings under salt stress. Moreover, we mapped the salt-stress-related SNPs and identified candidate genes in the natural population via a genome-wide association study. A total of 44 candidate genes were annotated, including 26 candidate genes under normal conditions and 18 candidate genes under salt-stressed conditions. This study demonstrates the feasibility of using a high-throughput phenotyping platform to accurately, continuously quantify morphological traits of maize seedlings in different growing environments. And the phenotype and genetic information of this study provided a theoretical basis for the breeding of salt-resistant maize varieties and the study of salt-resistant genes.

Investigating the genetic basis of maize ear characteristics: a comprehensive genome-wide study utilizing high-throughput phenotypic measurement method and system.

The morphology of maize ears plays a critical role in the breeding of new varieties and increasing yield. However, the study of traditional ear-related traits alone can no longer meet the requirements of breeding. In this study, 20 ear-related traits, including size, shape, number, and color, were obtained in 407 maize inbred lines at two sites using a high-throughput phenotypic measurement method and system. Significant correlations were found among these traits, particularly the novel trait ear shape (ES), which was correlated with traditional traits: kernel number per row and kernel number per ear. Pairwise comparison tests revealed that the inbred lines of tropical-subtropical were significantly different from other subpopulations in row numbers per ear, kernel numbers per ear, and ear color. A genome-wide association study identified 275, 434, and 362 Single nucleotide polymorphisms (SNPs) for Beijing, Sanya, and best linear unbiased prediction scenarios, respectively, explaining 3.78% to 24.17% of the phenotypic variance. Furthermore, 58 candidate genes with detailed functional descriptions common to more than two scenarios were discovered, with 40 genes being associated with color traits on chromosome 1. After analysis of haplotypes, gene expression, and annotated information, several candidate genes with high reliability were identified, including Zm00001d051328 for ear perimeter and width, zma-MIR159f for ear shape, Zm00001d053080 for kernel width and row number per ear, and Zm00001d048373 for the blue color channel of maize kernels in the red-green-blue color model. This study emphasizes the importance of researching novel phenotypic traits in maize by utilizing high-throughput phenotypic measurements. The identified genetic loci enrich the existing genetic studies related to maize ears.

Three-dimensional branch segmentation and phenotype extraction of maize tassel based on deep learning.

BACKGROUND: The morphological structure phenotype of maize tassel plays an important role in plant growth, reproduction, and yield formation. It is an important step in the distinctness, uniformity, and stability (DUS) testing to obtain maize tassel phenotype traits. Plant organ segmentation can be achieved with high-precision and automated acquisition of maize tassel phenotype traits because of the advances in the point cloud deep learning method. However, this method requires a large number of data sets and is not robust to automatic segmentation of highly adherent organ components; thus, it should be combined with point cloud processing technology. RESULTS: An innovative method of incomplete annotation of point cloud data was proposed for easy development of the dataset of maize tassels,and an automatic maize tassel phenotype analysis system: MaizeTasselSeg was developed. The tip feature of point cloud is trained and learned based on PointNet + + network, and the tip point cloud of tassel branch was automatically segmented. Complete branch segmentation was realized based on the shortest path algorithm. The Intersection over Union (IoU), precision, and recall of the segmentation results were 96.29, 96.36, and 93.01, respectively. Six phenotypic traits related to morphological structure (branch count, branch length, branch angle, branch curvature, tassel volume, and dispersion) were automatically extracted from the segmentation point cloud. The squared correlation coefficients (R2) for branch length, branch angle, and branch count were 0.9897, 0.9317, and 0.9587, respectively. The root mean squared error (RMSE) for branch length, branch angle, and branch count were 0.529 cm, 4.516, and 0.875, respectively. CONCLUSION: The proposed method provides an efficient scheme for high-throughput organ segmentation of maize tassels and can be used for the automatic extraction of phenotypic traits of maize tassel. In addition, the incomplete annotation approach provides a new idea for morphology-based plant segmentation.

Multi-Source Data Fusion Improves Time-Series Phenotype Accuracy in Maize under a Field High-Throughput Phenotyping Platform.

The field phenotyping platforms that can obtain high-throughput and time-series phenotypes of plant populations at the 3-dimensional level are crucial for plant breeding and management. However, it is difficult to align the point cloud data and extract accurate phenotypic traits of plant populations. In this study, high-throughput, time-series raw data of field maize populations were collected using a field rail-based phenotyping platform with light detection and ranging (LiDAR) and an RGB (red, green, and blue) camera. The orthorectified images and LiDAR point clouds were aligned via the direct linear transformation algorithm. On this basis, time-series point clouds were further registered by the time-series image guidance. The cloth simulation filter algorithm was then used to remove the ground points. Individual plants and plant organs were segmented from maize population by fast displacement and region growth algorithms. The plant heights of 13 maize cultivars obtained using the multi-source fusion data were highly correlated with the manual measurements (R2 = 0.98), and the accuracy was higher than only using one source point cloud data (R2 = 0.93). It demonstrates that multi-source data fusion can effectively improve the accuracy of time series phenotype extraction, and rail-based field phenotyping platforms can be a practical tool for plant growth dynamic observation of phenotypes in individual plant and organ scales.

Disentangling the Heterosis in Biomass Production and Radiation Use Efficiency in Maize: A Phytomer-Based 3D Modelling Approach.

Maize (Zea mays L.) benefits from heterosis in-yield formation and photosynthetic efficiency through optimizing canopy structure and improving leaf photosynthesis. However, the role of canopy structure and photosynthetic capacity in determining heterosis in biomass production and radiation use efficiency has not been separately clarified. We developed a quantitative framework based on a phytomer-based three-dimensional canopy photosynthesis model and simulated light capture and canopy photosynthetic production in scenarios with and without heterosis in either canopy structure or leaf photosynthetic capacity. The accumulated above-ground biomass of Jingnongke728 was 39% and 31% higher than its male parent, Jing2416, and female parent, JingMC01, while accumulated photosynthetically active radiation was 23% and 14% higher, correspondingly, leading to an increase of 13% and 17% in radiation use efficiency. The increasing post-silking radiation use efficiency was mainly attributed to leaf photosynthetic improvement, while the dominant contributing factor differs for male and female parents for heterosis in post-silking yield formation. This quantitative framework illustrates the potential to identify the key traits related to yield and radiation use efficiency and helps breeders to make selections for higher yield and photosynthetic efficiency.

Geometric Wheat Modeling and Quantitative Plant Architecture Analysis Using Three-Dimensional Phytomers.

The characterization, analysis, and evaluation of morphology and structure are crucial in wheat research. Quantitative and fine characterization of wheat morphology and structure from a three-dimensional (3D) perspective has great theoretical significance and application value in plant architecture identification, high light efficiency breeding, and cultivation. This study proposes a geometric modeling method of wheat plants based on the 3D phytomer concept. Specifically, 3D plant architecture parameters at the organ, phytomer, single stem, and individual plant scales were extracted based on the geometric models. Furthermore, plant architecture vector (PA) was proposed to comprehensively evaluate wheat plant architecture, including convergence index (C), leaf structure index (L), phytomer structure index (PHY), and stem structure index (S). The proposed method could quickly and efficiently achieve 3D wheat plant modeling by assembling 3D phytomers. In addition, the extracted PA quantifies the plant architecture differences in multi-scales among different cultivars, thus, realizing a shift from the traditional qualitative to quantitative analysis of plant architecture. Overall, this study promotes the application of the 3D phytomer concept to multi-tiller crops, thereby providing a theoretical and technical basis for 3D plant modeling and plant architecture quantification in wheat.

Design and Development of a Low-Cost UGV 3D Phenotyping Platform with Integrated LiDAR and Electric Slide Rail.

Unmanned ground vehicles (UGV) have attracted much attention in crop phenotype monitoring due to their lightweight and flexibility. This paper describes a new UGV equipped with an electric slide rail and point cloud high-throughput acquisition and phenotype extraction system. The designed UGV is equipped with an autopilot system, a small electric slide rail, and Light Detection and Ranging (LiDAR) to achieve high-throughput, high-precision automatic crop point cloud acquisition and map building. The phenotype analysis system realized single plant segmentation and pipeline extraction of plant height and maximum crown width of the crop point cloud using the Random sampling consistency (RANSAC), Euclidean clustering, and k-means clustering algorithm. This phenotyping system was used to collect point cloud data and extract plant height and maximum crown width for 54 greenhouse-potted lettuce plants. The results showed that the correlation coefficient (R2) between the collected data and manual measurements were 0.97996 and 0.90975, respectively, while the root mean square error (RMSE) was 1.51 cm and 4.99 cm, respectively. At less than a tenth of the cost of the PlantEye F500, UGV achieves phenotypic data acquisition with less error and detects morphological trait differences between lettuce types. Thus, it could be suitable for actual 3D phenotypic measurements of greenhouse crops.

LettuceGDB: The community database for lettuce genetics and omics.

As a globally popular leafy vegetable and a representative plant of the Asteraceae family, lettuce has great economic and academic significance. In the last decade, high-throughput sequencing, phenotyping, and other multi-omics data in lettuce have accumulated on a large scale, thus increasing the demand for an integrative lettuce database. Here, we report the establishment of a comprehensive lettuce database, LettuceGDB (https://www.lettucegdb.com/). As an omics data hub, the current LettuceGDB includes two reference genomes with detailed annotations; re-sequencing data from over 1000 lettuce varieties; a collection of more than 1300 worldwide germplasms and millions of accompanying phenotypic records obtained with manual and cutting-edge phenomics technologies; re-analyses of 256 RNA sequencing datasets; a complete miRNAome; extensive metabolite information for representative varieties and wild relatives; epigenetic data on the genome-wide chromatin accessibility landscape; and various lettuce research papers published in the last decade. Five hierarchically accessible functions (Genome, Genotype, Germplasm, Phenotype, and O-Omics) have been developed with a user-friendly interface to enable convenient data access. Eight built-in tools (Assembly Converter, Search Gene, BLAST, JBrowse, Primer Design, Gene Annotation, Tissue Expression, Literature, and Data) are available for data downloading and browsing, functional gene exploration, and experimental practice. A community forum is also available for information sharing, and a summary of current research progress on different aspects of lettuce is included. We believe that LettuceGDB can be a comprehensive functional database amenable to data mining and database-driven exploration, useful for both scientific research and lettuce breeding.

Prediction of vertical distribution of SPAD values within maize canopy based on unmanned aerial vehicles multispectral imagery.

Real-time monitoring of canopy chlorophyll content is significant in understanding crop growth status and guiding precision agricultural management. Remote sensing methods have demonstrated great potential in this regard. However, the spatiotemporal heterogeneity of chlorophyll content within crop canopies poses challenges to the accuracy and stability of remote sensing estimation models. Hence, this study aimed to develop a novel method for estimating canopy chlorophyll content (represented by SPAD values) in maize (Zea mays L.) canopies. Firstly, we investigated the spatiotemporal distribution patterns of maize canopy SPAD values under varying nitrogen application rates and different growth stages. The results revealed a non-uniform, "bell-shaped" curve distribution of maize canopy SPAD values in the vertical direction. Nitrogen application significantly influenced the distribution structure of SPAD values within the canopy. Secondly, we achieved satisfactory results by fitting the Lorentz peak distribution function to the SPAD values of different leaf positions in maize. The fitting performance, evaluated using R2 and RMSE, ranged from 0.69 to 0.98 and 0.45 to 3.59, respectively, for the year 2021, and from 0.69 to 0.77 and 2.38 to 6.51, respectively, for the year 2022.Finally, based on the correlation between canopy SPAD values and vegetation indices (VIs) at different growth stages, we identified the sensitive leaf positions for the selected CCCI (Canopy Chlorophyll Index) in each growth stage. The 6th (r = 0.662), 4th (r = 0.816), 12th (r = 0.722), and 12th (r = 0.874) leaf positions exhibited the highest correlations. Compared to the estimation model using canopy wide SPAD values, the model based on sensitive leaf positions showed improved accuracy, with increases of 34%, 3%, 20%, and 3% for each growth stage, respectively. In conclusion, the findings of this study contribute to the enhancement of chlorophyll content estimation models in crop canopies and provide valuable insights for the integration of crop growth models with remote sensing methods.

Characterization and genetic dissection of maize ear leaf midrib acquired by 3D digital technology.

The spatial morphological structure of plant leaves is an important index to evaluate crop ideotype. In this study, we characterized the three-dimensional (3D) data of the ear leaf midrib of maize at the grain-filling stage using the 3D digitization technology and obtained the phenotypic values of 15 traits covering four different dimensions of the ear leaf midrib, of which 13 phenotypic traits were firstly proposed for featuring plant leaf spatial structure. Cluster analysis results showed that the 13 traits could be divided into four groups, Group I, -II, -III and -IV. Group I contains HorizontalLength, OutwardGrowthMeasure, LeafAngle and DeviationTip; Group II contains DeviationAngle, MaxCurvature and CurvaturePos; Group III contains LeafLength and ProjectionArea; Group IV contains TipTop, VerticalHeight, UpwardGrowthMeasure, and CurvatureRatio. To investigate the genetic basis of the ear leaf midrib curve, 13 traits with high repeatability were subjected to genome-wide association study (GWAS) analysis. A total of 828 significantly related SNPs were identified and 1365 candidate genes were annotated. Among these, 29 candidate genes with the highest significant and multi-method validation were regarded as the key findings. In addition, pathway enrichment analysis was performed on the candidate genes of traits to explore the potential genetic mechanism of leaf midrib curve phenotype formation. These results not only contribute to further understanding of maize leaf spatial structure traits but also provide new genetic loci for maize leaf spatial structure to improve the plant type of maize varieties.

Use of 3D modeling to refine predictions of canopy light utilization: A comparative study on canopy photosynthesis models with different dimensions.

Canopy photosynthesis integrates leaf functional and structural traits in space and time and correlates positively with yield formation. Many models with different levels of architectural details ranging from zero-dimensional (0D) to three-dimensional (3D) have been developed to simulate canopy light interception and photosynthesis. Based on these models, a crop growth model can be used to assess crop yield in response to genetic improvement, optimized practices, and environmental change. However, to what extent do architectural details influence light interception, photosynthetic production, and grain yield remains unknown. Here, we show that a crop growth model with high-resolution upscaling approach in space reduces the departure of predicted yield from actual yield and refines the simulation of canopy photosynthetic production. We found crop yield predictions decreased by 12.0-48.5% with increasing the resolution of light simulation, suggesting that a crop growth model without architectural details may result in a considerable departure from the actual photosynthetic production. A dramatic difference in light interception and photosynthetic production of canopy between cultivars was captured by the proposed 3D model rather than the 0D, 1D, and 2D models. Furthermore, we found that the overestimation of crop yield by the 0D model is caused by the overestimation of canopy photosynthetically active radiation (PAR) interception and the RUE and that by the 1D and 2D model is caused by the overestimated canopy photosynthesis rate that is possibly related to higher predicted PAR and fraction of sunlit leaves. Overall, this study confirms the necessity of taking detailed architecture traits into consideration when evaluating the strategies of genetic improvement and canopy configuration in improving crop yield by crop modeling.

A miniaturized phenotyping platform for individual plants using multi-view stereo 3D reconstruction.

Plant phenotyping is essential in plant breeding and management. High-throughput data acquisition and automatic phenotypes extraction are common concerns in plant phenotyping. Despite the development of phenotyping platforms and the realization of high-throughput three-dimensional (3D) data acquisition in tall plants, such as maize, handling small-size plants with complex structural features remains a challenge. This study developed a miniaturized shoot phenotyping platform MVS-Pheno V2 focusing on low plant shoots. The platform is an improvement of MVS-Pheno V1 and was developed based on multi-view stereo 3D reconstruction. It has the following four components: Hardware, wireless communication and control, data acquisition system, and data processing system. The hardware sets the rotation on top of the platform, separating plants to be static while rotating. A novel local network was established to realize wireless communication and control; thus, preventing cable twining. The data processing system was developed to calibrate point clouds and extract phenotypes, including plant height, leaf area, projected area, shoot volume, and compactness. This study used three cultivars of wheat shoots at four growth stages to test the performance of the platform. The mean absolute percentage error of point cloud calibration was 0.585%. The squared correlation coefficient R 2 was 0.9991, 0.9949, and 0.9693 for plant height, leaf length, and leaf width, respectively. The root mean squared error (RMSE) was 0.6996, 0.4531, and 0.1174 cm for plant height, leaf length, and leaf width. The MVS-Pheno V2 platform provides an alternative solution for high-throughput phenotyping of low individual plants and is especially suitable for shoot architecture-related plant breeding and management studies.

Dissecting the Genetic Structure of Maize Leaf Sheaths at Seedling Stage by Image-Based High-Throughput Phenotypic Acquisition and Characterization.

The rapid development of high-throughput phenotypic detection techniques makes it possible to obtain a large number of crop phenotypic information quickly, efficiently, and accurately. Among them, image-based phenotypic acquisition method has been widely used in crop phenotypic identification and characteristic research due to its characteristics of automation, non-invasive, non-destructive and high throughput. In this study, we proposed a method to define and analyze the traits related to leaf sheaths including morphology-related, color-related and biomass-related traits at V6 stage. Next, we analyzed the phenotypic variation of leaf sheaths of 418 maize inbred lines based on 87 leaf sheath-related phenotypic traits. In order to further analyze the mechanism of leaf sheath phenotype formation, 25 key traits (2 biomass-related, 19 morphology-related and 4 color-related traits) with heritability greater than 0.3 were analyzed by genome-wide association studies (GWAS). And 1816 candidate genes of 17 whole plant leaf sheath traits and 1,297 candidate genes of 8 sixth leaf sheath traits were obtained, respectively. Among them, 46 genes with clear functional descriptions were annotated by single nucleotide polymorphism (SNPs) that both Top1 and multi-method validated. Functional enrichment analysis results showed that candidate genes of leaf sheath traits were enriched into multiple pathways related to cellular component assembly and organization, cell proliferation and epidermal cell differentiation, and response to hunger, nutrition and extracellular stimulation. The results presented here are helpful to further understand phenotypic traits of maize leaf sheath and provide a reference for revealing the genetic mechanism of maize leaf sheath phenotype formation.

Hyperspectral Technique Combined With Deep Learning Algorithm for Prediction of Phenotyping Traits in Lettuce.

The currently available methods for evaluating most biochemical traits of plant phenotyping are destructive and have extremely low throughput. However, hyperspectral techniques can non-destructively obtain the spectral reflectance characteristics of plants, which can provide abundant biophysical and biochemical information. Therefore, plant spectra combined with machine learning algorithms can be used to predict plant phenotyping traits. However, the raw spectral reflectance characteristics contain noise and redundant information, thus can easily affect the robustness of the models developed via multivariate analysis methods. In this study, two end-to-end deep learning models were developed based on 2D convolutional neural networks (2DCNN) and fully connected neural networks (FCNN; Deep2D and DeepFC, respectively) to rapidly and non-destructively predict the phenotyping traits of lettuces from spectral reflectance. Three linear and two nonlinear multivariate analysis methods were used to develop models to weigh the performance of the deep learning models. The models based on multivariate analysis methods require a series of manual feature extractions, such as pretreatment and wavelength selection, while the proposed models can automatically extract the features in relation to phenotyping traits. A visible near-infrared hyperspectral camera was used to image lettuce plants growing in the field, and the spectra extracted from the images were used to train the network. The proposed models achieved good performance with a determination coefficient of prediction ( R p 2 ) of 0.9030 and 0.8490 using Deep2D for soluble solids content and DeepFC for pH, respectively. The performance of the deep learning models was compared with five multivariate analysis method. The quantitative analysis showed that the deep learning models had higher R p 2 than all the multivariate analysis methods, indicating better performance. Also, wavelength selection and different pretreatment methods had different effects on different multivariate analysis methods, and the selection of appropriate multivariate analysis methods and pretreatment methods increased more time and computational cost. Unlike multivariate analysis methods, the proposed deep learning models did not require any pretreatment or dimensionality reduction and thus are more suitable for application in high-throughput plant phenotyping platforms. These results indicate that the deep learning models can better predict phenotyping traits of plants using spectral reflectance.

High-Throughput Phenotyping Accelerates the Dissection of the Phenotypic Variation and Genetic Architecture of Shank Vascular Bundles in Maize (Zea mays L.).

The vascular bundle of the shank is an important 'flow' organ for transforming maize biological yield to grain yield, and its microscopic phenotypic characteristics and genetic analysis are of great significance for promoting the breeding of new varieties with high yield and good quality. In this study, shank CT images were obtained using the standard process for stem micro-CT data acquisition at resolutions up to 13.5 µm. Moreover, five categories and 36 phenotypic traits of the shank including related to the cross-section, epidermis zone, periphery zone, inner zone and vascular bundle were analyzed through an automatic CT image process pipeline based on the functional zones. Next, we analyzed the phenotypic variations in vascular bundles at the base of the shank among a group of 202 inbred lines based on comprehensive phenotypic information for two environments. It was found that the number of vascular bundles in the inner zone (IZ_VB_N) and the area of the inner zone (IZ_A) varied the most among the different subgroups. Combined with genome-wide association studies (GWAS), 806 significant single nucleotide polymorphisms (SNPs) were identified, and 1245 unique candidate genes for 30 key traits were detected, including the total area of vascular bundles (VB_A), the total number of vascular bundles (VB_N), the density of the vascular bundles (VB_D), etc. These candidate genes encode proteins involved in lignin, cellulose synthesis, transcription factors, material transportation and plant development. The results presented here will improve the understanding of the phenotypic traits of maize shank and provide an important phenotypic basis for high-throughput identification of vascular bundle functional genes of maize shank and promoting the breeding of new varieties with high yield and good quality.