Grain Protein Content Phenotyping in Rice via Hyperspectral Imaging Technology and a Genome-Wide Association Study.

Efficient and accurate acquisition of the rice grain protein content (GPC) is important for selecting high-quality rice varieties, and remote sensing technology is an attractive potential method for this task. However, the majority of multispectral sensors are poor predictors of GPC due to their broad spectral bands. Hyperspectral technology provides a new analytical technology for bridging the gap between phenomics and genomics. However, the small size of typical datasets is a constraint for model construction for estimating GPC, limiting their accuracy and reducing their ability to generalize to a wide range of varieties. In this study, we used hyperspectral data of rice grains from 515 japonica varieties and deep convolution generative adversarial networks (DCGANs) to generate simulated data to improve the model accuracy. Features sensitive to GPC were extracted after applying a continuous wavelet transform (CWT), and the estimated GPC model was constructed by partial least squares regression (PLSR). Finally, a genome-wide association study (GWAS) was applied to the measured and generated datasets to detect GPC loci. The results demonstrated that the simulated GPC values generated after 8,000 epochs were closest to the measured values. The wavelet feature (WF1743, 2), obtained from the data with the addition of 200 simulated samples, exhibited the highest GPC estimation accuracy (R 2 = 0.58 and RRMSE = 6.70%). The GWAS analysis showed that the estimated values based on the simulated data detected the same loci as the measured values, including the OsmtSSB1L gene related to grain storage protein. This study provides a new technique for the efficient genetic study of phenotypic traits in rice based on hyperspectral technology.

Comparison of two novel methods for counting wheat ears in the field with terrestrial LiDAR.

BACKGROUND: The metrics for assessing the yield of crops in the field include the number of ears per unit area, the grain number per ear, and the thousand-grain weight. Typically, the ear number per unit area contributes the most to the yield. However, calculation of the ear number tends to rely on traditional manual counting, which is inefficient, labour intensive, inaccurate, and lacking in objectivity. In this study, two novel extraction algorithms for the estimation of the wheat ear number were developed based on the use of terrestrial laser scanning (TLS) in conjunction with the density-based spatial clustering (DBSC) algorithm based on the normal and the voxel-based regional growth (VBRG) algorithm. The DBSC involves two steps: (1) segmentation of the point clouds using differences in the normal vectors and (2) clustering of the segmented point clouds using a density clustering algorithm to calculate the ear number. The VBRG involves three steps: (1) voxelization of the point clouds, (2) construction of the topological relationships between the voxels as a connected region using the k-dimensional tree, and (3) detection of the wheat ears in the connected areas using a regional growth algorithm. RESULTS: The results demonstrated that DBSC and VBRG were promising in estimating the number of ears for different cultivars, planting densities, N fertilization rates, and growth stages of wheat (RMSE = 76 ~ 114 ears/m2, rRMSE = 18.62 ~ 27.96%, r = 0.76 ~ 0.84). Comparing the performance of the two algorithms, the overall accuracy of the DBSC (RMSE = 76 ears/m2, rRMSE = 18.62%, r = 0.84) was better than that of the VBRG (RMSE = 114 ears/m2, rRMSE = 27.96%, r = 0.76). It was found that with the DBSC, the calculation in points as units permitted more detailed information to be retained, and this method was more suitable for estimation of the wheat ear number in the field. CONCLUSIONS: The algorithms adopted in this study provide new approaches for non-destructive measurement and efficient acquisition of the ear number in the assessment of the wheat yield phenotype.

SPSI: A Novel Composite Index for Estimating Panicle Number in Winter Wheat before Heading from UAV Multispectral Imagery.

Rapid and accurate estimation of panicle number per unit ground area (PNPA) in winter wheat before heading is crucial to evaluate yield potential and regulate crop growth for increasing the final yield. The accuracies of existing methods were low for estimating PNPA with remotely sensed data acquired before heading since the spectral saturation and background effects were ignored. This study proposed a spectral-textural PNPA sensitive index (SPSI) from unmanned aerial vehicle (UAV) multispectral imagery for reducing the spectral saturation and improving PNPA estimation in winter wheat before heading. The effect of background materials on PNPA estimated by textural indices (TIs) was examined, and the composite index SPSI was constructed by integrating the optimal spectral index (SI) and TI. Subsequently, the performance of SPSI was evaluated in comparison with other indices (SI and TIs). The results demonstrated that green-pixel TIs yielded better performances than all-pixel TIs apart from TI[HOM], TI[ENT], and TI[SEM] among all indices from 8 types of textural features. SPSI, which was calculated by the formula DATT[850,730,675] + NDTICOR[850,730], exhibited the highest overall accuracies for any date in any dataset in comparison with DATT[850,730,675], TINDRE[MEA], and NDTICOR[850,730]. For the unified models assembling 2 experimental datasets, the RV2 values of SPSI increased by 0.11 to 0.23, and both RMSE and RRMSE decreased by 16.43% to 38.79% as compared to the suboptimal index on each date. These findings indicated that the SPSI is valuable in reducing the spectral saturation and has great potential to better estimate PNPA using high-resolution satellite imagery.

Fusarium head blight monitoring in wheat ears using machine learning and multimodal data from asymptomatic to symptomatic periods.

The growth of the fusarium head blight (FHB) pathogen at the grain formation stage is a deadly threat to wheat production through disruption of the photosynthetic processes of wheat spikes. Real-time nondestructive and frequent proxy detection approaches are necessary to control pathogen propagation and targeted fungicide application. Therefore, this study examined the ch\lorophyll-related phenotypes or features from spectral and chlorophyll fluorescence for FHB monitoring. A methodology is developed using features extracted from hyperspectral reflectance (HR), chlorophyll fluorescence imaging (CFI), and high-throughput phenotyping (HTP) for asymptomatic to symptomatic disease detection from two consecutive years of experiments. The disease-sensitive features were selected using the Boruta feature-selection algorithm, and subjected to machine learning-sequential floating forward selection (ML-SFFS) for optimum feature combination. The results demonstrated that the biochemical parameters, HR, CFI, and HTP showed consistent alterations during the spike-pathogen interaction. Among the selected disease sensitive features, reciprocal reflectance (RR=1/700) demonstrated the highest coefficient of determination (R 2) of 0.81, with root mean square error (RMSE) of 11.1. The multivariate k-nearest neighbor model outperformed the competing multivariate and univariate models with an overall accuracy of R 2 = 0.92 and RMSE = 10.21. A combination of two to three kinds of features was found optimum for asymptomatic disease detection using ML-SFFS with an average classification accuracy of 87.04% that gradually improved to 95% for a disease severity level of 20%. The study demonstrated the fusion of chlorophyll-related phenotypes with the ML-SFFS might be a good choice for crop disease detection.

Analysis and Evaluation of the Image Preprocessing Process of a Six-Band Multispectral Camera Mounted on an Unmanned Aerial Vehicle for Winter Wheat Monitoring.

Unmanned aerial vehicle (UAV)-based multispectral sensors have great potential in crop monitoring due to their high flexibility, high spatial resolution, and ease of operation. Image preprocessing, however, is a prerequisite to make full use of the acquired high-quality data in practical applications. Most crop monitoring studies have focused on specific procedures or applications, and there has been little attempt to examine the accuracy of the data preprocessing steps. This study focuses on the preprocessing process of a six-band multispectral camera (Mini-MCA6) mounted on UAVs. First, we have quantified and analyzed the components of sensor error, including noise, vignetting, and lens distortion. Next, different methods of spectral band registration and radiometric correction were evaluated. Then, an appropriate image preprocessing process was proposed. Finally, the applicability and potential for crop monitoring were assessed in terms of accuracy by measurement of the leaf area index (LAI) and the leaf biomass inversion under variable growth conditions during five critical growth stages of winter wheat. The results show that noise and vignetting could be effectively removed via use of correction coefficients in image processing. The widely used Brown model was suitable for lens distortion correction of a Mini-MCA6. Band registration based on ground control points (GCPs) (Root-Mean-Square Error, RMSE = 1.02 pixels) was superior to that using PixelWrench2 (PW2) software (RMSE = 1.82 pixels). For radiometric correction, the accuracy of the empirical linear correction (ELC) method was significantly higher than that of light intensity sensor correction (ILSC) method. The multispectral images that were processed using optimal correction methods were demonstrated to be reliable for estimating LAI and leaf biomass. This study provides a feasible and semi-automatic image preprocessing process for a UAV-based Mini-MCA6, which also serves as a reference for other array-type multispectral sensors. Moreover, the high-quality data generated in this study may stimulate increased interest in remote high-efficiency monitoring of crop growth status.

Estimation of area- and mass-based leaf nitrogen contents of wheat and rice crops from water-removed spectra using continuous wavelet analysis.

BACKGROUND: The visible and near infrared region has been widely used to estimate the leaf nitrogen (N) content based on the correlation of N with chlorophyll and deep absorption valleys of chlorophyll in this region. However, most absorption features related to N are located in the shortwave infrared (SWIR) region and the physical mechanism of leaf N estimation from fresh leaf reflectance spectra remains unclear. The use of SWIR region may help us reveal the underlying mechanism of casual relationships and better understand the spectral responses to N variation from fresh leaf reflectance spectra. This study combined continuous wavelet analysis (CWA) and water removal technique to improve the estimation of N content and leaf mass per area (LMA) by reducing the effect of water absorption and enhancing absorption signals in the SWIR region. The performance of the wavelet-based method was evaluated for estimating leaf N content and LMA of rice and wheat crops from fresh leaf reflectance spectra collected over a 2-year field experiment and compared with normalization difference (ND)-based spectral indices. RESULTS: The LMA and area-based N content (Narea) exhibited better correlations with the determined wavelet features derived from the water-removed (WR) spectra (LMA: R2 = 0.71, Narea: R2 = 0.77) than those from the measured reflectance (MR) spectra (LMA: R2 = 0.62, Narea: R2 = 0.64). The wavelet features performed remarkably better than the optimized ND indices for the estimations of LMA and Narea with MR spectra or WR spectra. Based on the best estimations of LMA and Narea with wavelet features from WR spectra, the mass-based N content (Nmass) could be retrieved with a high accuracy (R2 = 0.82, RMSE = 0.32%) in the indirect way. This accuracy was higher than that for Nmass obtained in the direct use of a single wavelet feature (R2 = 0.68, RMSE = 0.42%). CONCLUSIONS: The enhancement of absorption features in the SWIR region through the CWA applied to water-removed (WR) spectra was able to improve the spectroscopic estimation of leaf N content and LMA as compared to that obtained with the reflectance spectra of fresh leaves. The success in estimating LMA and N with this method would advance the spectroscopic estimations of grain quality parameters for staple crops and individual dry matter constituents for various vegetation types.

Assessing the Impact of Spatial Resolution on the Estimation of Leaf Nitrogen Concentration Over the Full Season of Paddy Rice Using Near-Surface Imaging Spectroscopy Data.

Timely monitoring nitrogen status of rice crops with remote sensing can help us optimize nitrogen fertilizer management and reduce environmental pollution. Recently, the use of near-surface imaging spectroscopy is emerging as a promising technology that can collect hyperspectral images with spatial resolutions ranging from millimeters to decimeters. The spatial resolution is crucial for the efficiency in the image sampling across rice plants and the separation of leaf signals from the background. However, the optimal spatial resolution of such images for monitoring the leaf nitrogen concentration (LNC) in rice crops remains unclear. To assess the impact of spatial resolution on the estimation of rice LNC, we collected ground-based hyperspectral images throughout the entire growing season over 2 consecutive years and generated ten sets of images with spatial resolutions ranging from 1.3 to 450 mm. These images were used to determine the sensitivity of LNC prediction to spatial resolution with three groups of vegetation indices (VIs) and two multivariate methods Gaussian Process regression (GPR) and Partial least squares regression (PLSR). The reflectance spectra of sunlit-, shaded-, and all-leaf leaf pixels separated from background pixels at each spatial resolution were used to predict LNC with VIs, GPR and PLSR, respectively. The results demonstrated all-leaf pixels generally exhibited more stable performance than sunlit- and shaded-leaf pixels regardless of estimation approaches. The predictions of LNC required stage-specific LNC~VI models for each vegetative stage but could be performed with a single model for all the reproductive stages. Specifically, most VIs achieved stable performances from all the resolutions finer than 14 mm for the early tillering stage but from all the resolutions finer than 56 mm for the other stages. In contrast, the global models for the prediction of LNC across the entire growing season were successfully established with the approaches of GPR or PLSR. In particular, GPR generally exhibited the best prediction of LNC with the optimal spatial resolution being found at 28 mm. These findings represent significant advances in the application of ground-based imaging spectroscopy as a promising approach to crop monitoring and understanding the effects of spatial resolution on the estimation of rice LNC.

Combining Unmanned Aerial Vehicle (UAV)-Based Multispectral Imagery and Ground-Based Hyperspectral Data for Plant Nitrogen Concentration Estimation in Rice.

Plant nitrogen concentration (PNC) is a critical indicator of N status for crops, and can be used for N nutrition diagnosis and management. This work aims to explore the potential of multispectral imagery from unmanned aerial vehicle (UAV) for PNC estimation and improve the estimation accuracy with hyperspectral data collected in the field with a hyperspectral radiometer. In this study we combined selected vegetation indices (VIs) and texture information to estimate PNC in rice. The VIs were calculated from ground and aerial platforms and the texture information was obtained from UAV-based multispectral imagery. Two consecutive years (2015 & 2016) of experiments were conducted, involving different N rates, planting densities and rice cultivars. Both UAV flights and ground spectral measurements were taken along with destructive samplings at critical growth stages of rice (Oryza sativa L.). After UAV imagery preprocessing, both VIs and texture measurements were calculated. Then the optimal normalized difference texture index (NDTI) from UAV imagery was determined for separated stage groups and the entire season. Results demonstrated that aerial VIs performed well only for pre-heading stages (R2 = 0.52-0.70), and photochemical reflectance index and blue N index from ground (PRIg and BNIg) performed consistently well across all growth stages (R2 = 0.48-0.65 and 0.39-0.68). Most texture measurements were weakly related to PNC, but the optimal NDTIs could explain 61 and 51% variability of PNC for separated stage groups and entire season, respectively. Moreover, stepwise multiple linear regression (SMLR) models combining aerial VIs and NDTIs did not significantly improve the accuracy of PNC estimation, while models composed of BNIg and optimal NDTIs exhibited significant improvement for PNC estimation across all growth stages. Therefore, the integration of ground-based narrow band spectral indices with UAV-based textural information might be a promising technique in crop growth monitoring.

Using an Active-Optical Sensor to Develop an Optimal NDVI Dynamic Model for High-Yield Rice Production (Yangtze, China).

The successful development of an optimal canopy vegetation index dynamic model for obtaining higher yield can offer a technical approach for real-time and nondestructive diagnosis of rice (Oryza sativa L) growth and nitrogen (N) nutrition status. In this study, multiple rice cultivars and N treatments of experimental plots were carried out to obtain: normalized difference vegetation index (NDVI), leaf area index (LAI), above-ground dry matter (DM), and grain yield (GY) data. The quantitative relationships between NDVI and these growth indices (e.g., LAI, DM and GY) were analyzed, showing positive correlations. Using the normalized modeling method, an appropriate NDVI simulation model of rice was established based on the normalized NDVI (RNDVI) and relative accumulative growing degree days (RAGDD). The NDVI dynamic model for high-yield production in rice can be expressed by a double logistic model: RNDVI = ( 1 + e - 15.2829 × ( R A G D D i - 0.1944 ) ) - 1 - ( 1 + e - 11.6517 × ( R A G D D i - 1.0267 ) ) - 1 (R2 = 0.8577**), which can be used to accurately predict canopy NDVI dynamic changes during the entire growth period. Considering variation among rice cultivars, we constructed two relative NDVI (RNDVI) dynamic models for Japonica and Indica rice types, with R2 reaching 0.8764** and 0.8874**, respectively. Furthermore, independent experimental data were used to validate the RNDVI dynamic models. The results showed that during the entire growth period, the accuracy (k), precision (R2), and standard deviation of RNDVI dynamic models for the Japonica and Indica cultivars were 0.9991, 1.0170; 0.9084**, 0.8030**; and 0.0232, 0.0170, respectively. These results indicated that RNDVI dynamic models could accurately reflect crop growth and predict dynamic changes in high-yield crop populations, providing a rapid approach for monitoring rice growth status.