A model for phenotyping crop fractional vegetation cover using imagery from unmanned aerial vehicles

Restoration of vegetation in the Yellow River Basin of Inner Mongolia is limited by geographic factors

Studying the relationships between vegetation cover and geography in the Mongolian region of the Yellow River Basin will help to optimize local vegetation recovery strategies and achieve harmonious human relations. Based on MOD13Q1 data, the spatial and temporal variations in fractional vegetation cover (FVC) in the Mongolian Yellow River Basin during 2000-2020 were investigated via trend and correlative analysis. The results are as follows: (1) From 2000 to 2020, the vegetation cover in the Mongolian section of the Yellow River Basin recovered well, the mean increase in the FVC was 0.001/a, the distribution of vegetation showed high coverage in the southeast and low coverage in the northwest, and 31.19% of the total area showed an extremely significant and significant increase in vegetation cover. (2) The explanatory power of each geographic factor significantly differed. Precipitation, soil type, air temperature, land use type and slope were the main driving factors influencing the spatial distribution of the vegetation cover, and for each factor, the explanatory power of its interaction with other factors was greater than that of the single factor. (3) The correlation coefficients between FVC and temperature and precipitation are mainly positive. The mean value of the FVC and its variation trend are characterized by differences in terrain and soil characteristics, population density and land use. Land use conversion can reflect the characteristics of human activities, and positive effects, such as returning farmland to forest and grassland and afforestation of unused land, promote the significant improvement of regional vegetation, while negative effects, such as urban expansion, inhibit the growth of vegetation.

Accurate estimation of fractional vegetation cover for winter wheat by integrated unmanned aerial systems and satellite images

Accurate estimation of fractional vegetation cover (FVC) is essential for crop growth monitoring. Currently, satellite remote sensing monitoring remains one of the most effective methods for the estimation of crop FVC. However, due to the significant difference in scale between the coarse resolution of satellite images and the scale of measurable data on the ground, there are significant uncertainties and errors in estimating crop FVC. Here, we adopt a Strategy of Upscaling-Downscaling operations for unmanned aerial systems (UAS) and satellite data collected during 2 growing seasons of winter wheat, respectively, using backpropagation neural networks (BPNN) as support to fully bridge this scale gap using highly accurate the UAS-derived FVC (FVCUAS) to obtain wheat accurate FVC. Through validation with an independent dataset, the BPNN model predicted FVC with an RMSE of 0.059, which is 11.9% to 25.3% lower than commonly used Long Short-Term Memory (LSTM), Random Forest Regression (RFR), and traditional Normalized Difference Vegetation Index-based method (NDVI-based) models. Moreover, all those models achieved improved estimation accuracy with the Strategy of Upscaling-Downscaling, as compared to only upscaling UAS data. Our results demonstrate that: (1) establishing a nonlinear relationship between FVCUAS and satellite data enables accurate estimation of FVC over larger regions, with the strong support of machine learning capabilities. (2) Employing the Strategy of Upscaling-Downscaling is an effective strategy that can improve the accuracy of FVC estimation, in the collaborative use of UAS and satellite data, especially in the boundary area of the wheat field. This has significant implications for accurate FVC estimation for winter wheat, providing a reference for the estimation of other surface parameters and the collaborative application of multisource data.

Dynamic UAV Phenotyping for Rice Disease Resistance Analysis Based on Multisource Data

Bacterial blight poses a threat to rice production and food security, which can be controlled through large-scale breeding efforts toward resistant cultivars. Unmanned aerial vehicle (UAV) remote sensing provides an alternative means for the infield phenotype evaluation of crop disease resistance to relatively time-consuming and laborious traditional methods. However, the quality of data acquired by UAV can be affected by several factors such as weather, crop growth period, and geographical location, which can limit their utility for the detection of crop disease and resistant phenotypes. Therefore, a more effective use of UAV data for crop disease phenotype analysis is required. In this paper, we used time series UAV remote sensing data together with accumulated temperature data to train the rice bacterial blight severity evaluation model. The best results obtained with the predictive model showed an R _p ² of 0.86 with an RMSE_p of 0.65. Moreover, model updating strategy was used to explore the scalability of the established model in different geographical locations. Twenty percent of transferred data for model training was useful for the evaluation of disease severity over different sites. In addition, the method for phenotypic analysis of rice disease we built here was combined with quantitative trait loci (QTL) analysis to identify resistance QTL in genetic populations at different growth stages. Three new QTLs were identified, and QTLs identified at different growth stages were inconsistent. QTL analysis combined with UAV high-throughput phenotyping provides new ideas for accelerating disease resistance breeding.

Integrating a crop growth model and radiative transfer model to improve estimation of crop traits based on deep learning

A major challenge for the estimation of crop traits (biophysical variables) from canopy reflectance is the creation of a high-quality training dataset. To address this problem, this research investigated a conceptual framework by integrating a crop growth model with a radiative transfer model to introduce biological constraints in a synthetic training dataset. In addition to the comparison of two datasets without and with biological constraints, we also investigated the effects of observation geometry, retrieval method, and wavelength range on estimation accuracy of four crop traits (leaf area index, leaf chlorophyll content, leaf dry matter, and leaf water content) of wheat. The theoretical analysis demonstrated potential advantages of adding biological constraints in synthetic training datasets as well as the capability of deep learning. Additionally, the predictive models were validated on real unmanned aerial vehicle-based multispectral images collected from wheat plots contrasting in canopy structure. The predictive model trained over a synthetic dataset with biological constraints enabled the prediction of leaf water content from using wavelengths in the visible to near infrared range based on the correlations between crop traits. Our findings presented the potential of the proposed conceptual framework in simultaneously retrieving multiple crop traits from canopy reflectance for applications in precision agriculture and plant breeding.

A novel method for cliff vegetation estimation based on the unmanned aerial vehicle 3D modeling

The cliff ecosystem is one of the least human-disturbed ecosystems in nature, and its inaccessible and often extreme habitats are home to many ancient and unique plant species. Because of the harshness of cliff habitats, their high elevation, steepness of slopes, and inaccessibility to humans, surveying cliffs is incredibly challenging. Comprehensive and systematic information on cliff vegetation cover is not unavailable but obtaining such information on these cliffs is fundamentally important and of high priority for environmentalists. Traditional coverage survey methods-such as large-area normalized difference vegetation index (NDVI) statistics and small-area quadratic sampling surveys-are not suitable for cliffs that are close to vertical. This paper presents a semi-automatic systematic investigation and a three-dimensional reconstruction of karst cliffs for vegetation cover evaluation. High-resolution imagery with structure from motion (SFM) was captured by a smart unmanned aerial vehicle (UAV). Using approximately 13,000 records retrieved from high-resolution images of 16 cliffs in the karst region Guilin, China, 16 models of cliffs were reconstructed. The results show that this optimized UAV photogrammetry method greatly improves modeling efficiency and the vegetation cover from the bottom to the top of cliffs is high-low-high, and very few cliffs have high-low cover at the top. This study highlights the unique vegetation cover of karst cliffs, which warrants further research on the use of SFM to retrieve cliff vegetation cover at large and global scales.

The field phenotyping platform's next darling: Dicotyledons

The genetic information and functional properties of plants have been further identified with the completion of the whole-genome sequencing of numerous crop species and the rapid development of high-throughput phenotyping technologies, laying a suitable foundation for advanced precision agriculture and enhanced genetic gains. Collecting phenotypic data from dicotyledonous crops in the field has been identified as a key factor in the collection of large-scale phenotypic data of crops. On the one hand, dicotyledonous plants account for 4/5 of all angiosperm species and play a critical role in agriculture. However, their morphology is complex, and an abundance of dicot phenotypic information is available, which is critical for the analysis of high-throughput phenotypic data in the field. As a result, the focus of this paper is on the major advancements in ground-based, air-based, and space-based field phenotyping platforms over the last few decades and the research progress in the high-throughput phenotyping of dicotyledonous field crop plants in terms of morphological indicators, physiological and biochemical indicators, biotic/abiotic stress indicators, and yield indicators. Finally, the future development of dicots in the field is explored from the perspectives of identifying new unified phenotypic criteria, developing a high-performance infrastructure platform, creating a phenotypic big data knowledge map, and merging the data with those of multiomic techniques.

Combining Canopy Coverage and Plant Height from UAV-Based RGB Images to Estimate Spraying Volume on Potato

Canopy coverage and plant height are the main crop canopy parameters, which can obviously reflect the growth status of crops on the field. The ability to identify canopy coverage and plant height quickly is critical for farmers or breeders to arrange their working schedule. In precision agriculture, choosing the opportunity and amount of farm inputs is the critical part, which will improve the yield and decrease the cost. The potato canopy coverage and plant height were quickly extracted, which could be used to estimate the spraying volume using the evaluation model obtained by indoor tests. The vegetation index approach was used to extract potato canopy coverage, and the color point cloud data method at different height rates was formed to estimate the plant height of potato at different growth stages. The original data were collected using a low-cost UAV, which was mounted on a high-resolution RGB camera. Then, the Structure from Motion (SFM) algorithm was used to extract the 3D point cloud from ordered images that could form a digital orthophoto model (DOM) and sparse point cloud. The results show that the vegetation index-based method could accurately estimate canopy coverage. Among EXG, EXR, RGBVI, GLI, and CIVE, EXG achieved the best adaptability in different test plots. Point cloud data could be used to estimate plant height, but when the potato coverage rate was low, potato canopy point cloud data underwent rarefaction; in the vigorous growth period, the estimated value was substantially connected with the measured value (R2 = 0.94). The relationship between the coverage area of spraying on potato canopy and canopy coverage was measured indoors to form the model. The results revealed that the model could estimate the dose accurately (R2 = 0.878). Therefore, combining agronomic factors with data extracted from the UAV RGB image had the ability to predict the field spraying volume.

Optical Property Mapping of Apples and the Relationship With Quality Properties

This paper reports on the measurement of optical property mapping of apples at the wavelengths of 460, 527, 630, and 710 nm using spatial-frequency domain imaging (SFDI) technique, for assessing the soluble solid content (SSC), firmness, and color parameters. A laboratory-based multispectral SFDI system was developed for acquiring SFDI of 140 "Golden Delicious" apples, from which absorption coefficient (μ _a ) and reduced scattering coefficient (μ _s ') mappings were quantitatively determined using the three-phase demodulation coupled with curve-fitting method. There was no noticeable spatial variation in the optical property mapping based on the resulting effect of different sizes of the region of interest (ROI) on the average optical properties. Support vector machine (SVM), multiple linear regression (MLR), and partial least square (PLS) models were developed based on μ _a , μ _s ' and their combinations (μ _a × μ _s ' and μ _eff ) for predicting apple qualities, among which SVM outperformed the best. Better prediction results for quality parameters based on the μ _a were observed than those based on the μ _s ', and the combinations further improved the prediction performance, compared to the individual μ _a or μ _s '. The best prediction models for SSC and firmness parameters [slope, flesh firmness (FF), and maximum force (Max.F)] were achieved based on the μ _a × μ _s ', whereas those for color parameters of b* and C* were based on the μ _eff , with the correlation coefficients of prediction as 0.66, 0.68, 0.73, 0.79, 0.86, and 0.86, respectively.

Advances in optical phenotyping of cereal crops

Optical sensors and sensing-based phenotyping techniques have become mainstream approaches in high-throughput phenotyping for improving trait selection and genetic gains in crops. We review recent progress and contemporary applications of optical sensing-based phenotyping (OSP) techniques in cereal crops and highlight optical sensing principles for spectral response and sensor specifications. Further, we group phenotypic traits determined by OSP into four categories - morphological, biochemical, physiological, and performance traits - and illustrate appropriate sensors for each extraction. In addition to the current status, we discuss the challenges of OSP and provide possible solutions. We propose that optical sensing-based traits need to be explored further, and that standardization of the language of phenotyping and worldwide collaboration between phenotyping researchers and other fields need to be established.