Potential of Hyperspectral and Thermal Proximal Sensing for Estimating Growth Performance and Yield of Soybean Exposed to Different Drip Irrigation Regimes Under Arid Conditions

Thermal imaging: The digital eye facilitates high-throughput phenotyping traits of plant growth and stress responses

Plant phenotyping is important for plants to cope with environmental changes and ensure plant health. Imaging techniques are perceived as the most critical and reliable tools for studying plant phenotypes. Thermal imaging has opened up new opportunities for nondestructive imaging of plant phenotyping. However, a comprehensive summary of thermal imaging in plant phenotyping is still lacking. Here we discuss the progress and future prospects of thermal imaging for assessing plant growth and stress responses. First, we classify thermal imaging into ground-based and aerial platforms based on their adaptability to different experimental environments (including laboratory, greenhouse, and field). It is convenient to collect phenotypic information of different dimensions. Second, in order to enhance the efficiency of thermal image processing, automatic algorithms based on deep learning are employed instead of traditional manual methods, greatly reducing the time cost of experiments. Considering its ease of implementation, handling and instant response, thermal imaging has been widely used in research on environmental stress, crop yield, and seed vigor. We have found that thermal imaging can detect thermal energy dissipation caused by living organisms (e.g., pests, viruses, bacteria, fungi, and oomycetes), enabling early disease diagnosis. It also recognizes changes leaf surface temperatures resulting from reduced transpiration rates caused by nutrient deficiency, drought, salinity, or freezing. Furthermore, thermal imaging predicts crop yield under different water states and forecasts the viability of dormant seeds after water absorption by monitoring temperature changes in the seeds. This work will assist biologists and agronomists in studying plant phenotypes and serve a guide for breeders to develop high-yielding, stress-tolerant, and superior crops.

Field phenotyping for African crops: overview and perspectives

Improvements in crop productivity are required to meet the dietary demands of the rapidly-increasing African population. The development of key staple crop cultivars that are high-yielding and resilient to biotic and abiotic stresses is essential. To contribute to this objective, high-throughput plant phenotyping approaches are important enablers for the African plant science community to measure complex quantitative phenotypes and to establish the genetic basis of agriculturally relevant traits. These advances will facilitate the screening of germplasm for optimum performance and adaptation to low-input agriculture and resource-constrained environments. Increasing the capacity to investigate plant function and structure through non-invasive technologies is an effective strategy to aid plant breeding and additionally may contribute to precision agriculture. However, despite the significant global advances in basic knowledge and sensor technology for plant phenotyping, Africa still lags behind in the development and implementation of these systems due to several practical, financial, geographical and political barriers. Currently, field phenotyping is mostly carried out by manual methods that are prone to error, costly, labor-intensive and may come with adverse economic implications. Therefore, improvements in advanced field phenotyping capabilities and appropriate implementation are key factors for success in modern breeding and agricultural monitoring. In this review, we provide an overview of the current state of field phenotyping and the challenges limiting its implementation in some African countries. We suggest that the lack of appropriate field phenotyping infrastructures is impeding the development of improved crop cultivars and will have a detrimental impact on the agricultural sector and on food security. We highlight the prospects for integrating emerging and advanced low-cost phenotyping technologies into breeding protocols and characterizing crop responses to environmental challenges in field experimentation. Finally, we explore strategies for overcoming the barriers and maximizing the full potential of emerging field phenotyping technologies in African agriculture. This review paper will open new windows and provide new perspectives for breeders and the entire plant science community in Africa.

Developing Novel Rice Yield Index Using UAV Remote Sensing Imagery Fusion Technology

Efficient and quick yield prediction is of great significance for ensuring world food security and crop breeding research. The rapid development of unmanned aerial vehicle (UAV) technology makes it more timely and accurate to monitor crops by remote sensing. The objective of this study was to explore the method of developing a novel yield index (YI) with wide adaptability for yield prediction by fusing vegetation indices (VIs), color indices (CIs), and texture indices (TIs) from UAV-based imagery. Six field experiments with 24 varieties of rice and 21 fertilization methods were carried out in three experimental stations in 2019 and 2020. The multispectral and RGB images of the rice canopy collected by the UAV platform were used to rebuild six new VIs and TIs. The performance of VI-based YI (MAPE = 13.98%) developed by quadratic nonlinear regression at the maturity stage was better than other stages, and outperformed that of CI-based (MAPE = 22.21%) and TI-based (MAPE = 18.60%). Then six VIs, six CIs, and six TIs were fused to build YI by multiple linear regression and random forest models. Compared with heading stage (R2 = 0.78, MAPE = 9.72%) and all stage (R2 = 0.59, MAPE = 22.21%), the best performance of YI was developed by random forest with fusing VIs + CIs + TIs at maturity stage (R2 = 0.84, MAPE = 7.86%). Our findings suggest that the novel YI proposed in this study has great potential in crop yield monitoring.

Combining Hyperspectral Reflectance and Multivariate Regression Models to Estimate Plant Biomass of Advanced Spring Wheat Lines in Diverse Phenological Stages under Salinity Conditions

An area of growing interest in wheat-breeding programs for abiotic stresses is the accurate and expeditious phenotyping of large genotype collections using nondestructive hyperspectral sensing tools. The main goal of this study was to use data from canopy spectral signatures (CSS) in the full-spectrum range (400–2500 nm) to estimate and predict the plant biomass dry weight at booting (BDW-BT) and anthesis (BDW-AN) growth stages, and biological yield (BY) of 64 spring wheat germplasms exposed to 150 mM NaCl using 13 spectral reflectance indices (SRIs, consisting of seven vegetation-related SRIs and six water-related SRIs) and partial least squares regression (PLSR). SRI and PLSR performance in estimating plant traits was evaluated during two years at BT, AN, and early milk grain (EMG) growth stages. Results showed significant genotypic differences between the three traits and SRIs, with highly significant two-way and three-way interactions between genotypes, years, and growth stages for all SRIs. Genotypic differences in CSS and the relationships between the three traits and a single wavelength over the full-spectrum range depended on the growth stage. Water-related SRIs were more strongly correlated with the three traits compared with vegetation-related SRIs at the BT stage; the opposite was found at the EMG stage. Both types of SRIs exhibited comparable associations with the three traits at the AN stage. Principal component analysis indicated that it is possible to assess plant biomass variations at an early stage (BT) through published and modified SRIs. SRIs coupled with PLSR models at the BT stage exhibited good prediction capacity of BDW-BT (57%), BDW-AN (82%), and BY (55%). Overall, results demonstrated that the integration of SRIs and multivariate models may present a feasible tool for plant breeders to increase the efficiency of the evaluation process and to improve the genetics for salt tolerance in wheat-breeding programs.

Potential Use of Hyperspectral Reflectance as a High-Throughput Nondestructive Phenotyping Tool for Assessing Salt Tolerance in Advanced Spring Wheat Lines under Field Conditions

The incorporation of stress tolerance indices (STIs) with the early estimation of grain yield (GY) in an expeditious and nondestructive manner can enable breeders for ensuring the success of genotype development for a wide range of environmental conditions. In this study, the relative performance of GY for sixty-four spring wheat germplasm under the control and 15.0 dS m^-1 NaCl were compared through different STIs, and the ability of a hyperspectral reflectance tool for the early estimation of GY and STIs was assessed using twenty spectral reflectance indices (SRIs; 10 vegetation SRIs and 10 water SRIs). The results showed that salinity treatments, genotypes, and their interactions had significant effects on the GY and nearly all SRIs. Significant genotypic variations were also observed for all STIs. Based on the GY under the control (GYc) and salinity (GYs) conditions and all STIs, the tested genotypes were classified into three salinity tolerance groups (salt-tolerant, salt-sensitive, and moderately salt-tolerant groups). Most vegetation and water SRIs showed strong relationships with the GYc, stress tolerance index (STI), and geometric mean productivity (GMP); moderate relationships with GYs and sometimes with the tolerance index (TOL); and weak relationships with the yield stability index (YSI) and stress susceptibility index (SSI). Obvious differences in the spectral reflectance curves were found among the three salinity tolerance groups under the control and salinity conditions. Stepwise multiple linear regressions identified three SRIs from each vegetation and water SRI as the most influential indices that contributed the most variation in the GY. These SRIs were much more effective in estimating the GYc (R² = 0.64 - 0.79) than GYs (R² = 0.38 - 0.47). They also provided a much accurate estimation of the GYc and GYs for the moderately salt-tolerant genotype group; YSI, SSI, and TOL for the salt-sensitive genotypes group; and STI and GMP for all the three salinity tolerance groups. Overall, the results of this study highlight the potential of using a hyperspectral reflectance tool in breeding programs for phenotyping a sufficient number of genotypes under a wide range of environmental conditions in a cost-effective, noninvasive, and expeditious manner. This will aid in accelerating the development of genotypes for salinity conditions in breeding programs.

Estimating the Leaf Water Status and Grain Yield of Wheat under Different Irrigation Regimes Using Optimized Two- and Three-Band Hyperspectral Indices and Multivariate Regression Models

Spectral reflectance indices (SRIs) often show inconsistency in estimating plant traits across different growth conditions; thus, it is still necessary to develop further optimized SRIs to guarantee the performance of SRIs as a simple and rapid approach to accurately estimate plant traits. The primary goal of this study was to develop optimized two- and three-band vegetation- and water-SRIs and to apply different multivariate regression models based on these SRIs for accurately estimating the relative water content (RWC), gravimetric water content (GWCF), and grain yield (GY) of two wheat cultivars evaluated under three irrigation regimes (100%, 75%, and 50% of crop evapotranspiration (ETc)) for two seasons. Results showed that the three plant traits and all SRIs showed significant differences (p < 0.05) between the three irrigation treatments for each wheat cultivar. The three-band water-SRIs (NWIs-3b) showed the best performance in estimating the three plant traits for both cultivars (R2 > 0.80), and RWC and GWCF under 75% ETc (R2 ≥ 0.65). Four out of six three-band vegetation-SRIs (NDVIs-3b) performed better than any other SRIs for estimating GY under 100% ETc and 50% ETC, and RWC under 100% ETc (R2 ≥ 0.60). All types of SRIs demonstrated excellent performance in estimating the three plant traits (R2 ≥ 0.70) when the data of all growth conditions were combined and analyzed together. The NWIs-3b coupled with Random Forest models predicted the three plant traits with satisfactory accuracy for the calibration (R2 ≥ 0.96) and validation (R2 ≥ 0.93) datasets. The overall results of this study elucidate that extracting an optimized NWIs-3b from the full spectrum data and combined with an appropriate regression technique could be a practical approach for managing deficit irrigation regimes of crops through accurately, timely, and non-destructively monitoring the water status and final potential yield.

Integration of Radiometric Ground-Based Data and High-Resolution QuickBird Imagery with Multivariate Modeling to Estimate Maize Traits in the Nile Delta of Egypt

In site-specific management, rapid and accurate identification of crop stress at a large scale is critical. Radiometric ground-based data and satellite imaging with advanced spatial and spectral resolution allow for a deeper understanding of crop stress and the level of stress in a given area. This research aimed to assess the potential of radiometric ground-based data and high-resolution QuickBird satellite imagery to determine the leaf area index (LAI), biomass fresh weight (BFW) and chlorophyll meter (Chlm) of maize across well-irrigated, water stress and salinity stress areas in the Nile Delta of Egypt. Partial least squares regression (PLSR) and multiple linear regression (MLR) were evaluated to estimate the three measured traits based on vegetation spectral indices (vegetation-SRIs) derived from these methods and their combination. Maize field visits were conducted during the summer seasons from 28 to 30 July 2007 to collect ground reference data concurrent with the acquisition of radiometric ground-based measurements and QuickBird satellite imagery. The results showed that the majority of vegetation-SRIs extracted from radiometric ground-based data and high-resolution satellite images were more effective in estimating LAI, BFW, and Chlm. In general, the vegetation-SRIs of radiometric ground-based data showed higher R² with measured traits compared to the vegetation-SRIs extracted from high-resolution satellite imagery. The coefficient of determination (R²) of the significant relationships between vegetation-SRIs of both methods and three measured traits varied from 0.64 to 0.89. For example, with QuickBird high-resolution satellite images, the relationships of the green normalized difference vegetation index (GNDVI) with LAI and BFW showed the highest R² of 0.80 and 0.84, respectively. Overall, the ground-based vegetation-SRIs and the satellite-based indices were found to be in good agreement to assess the measured traits of maize. Both the calibration (Cal.) and validation (Val.) models of PLSR and MLR showed the highest performance in predicting the three measured traits based on the combination of vegetation-SRIs from radiometric ground-based data and high-resolution QuickBird satellite imagery. For example, validation (Val.) models of PLSR and MLR showed the highest performance in predicting the measured traits based on the combination of vegetation-SRIs from radiometric ground-based data and high-resolution QuickBird satellite imagery with R² (0.91) of both methods for LAI, R² (0.91–0.93) for BFW respectively, and R² (0.82) of both methods for Chlm. The models of PLSR and MLR showed approximately the same performance in predicting the three measured traits and no clear difference was found between them and their combinations. In conclusion, the results obtained from this study showed that radiometric ground-based measurements and high spectral resolution remote-sensing imagery have the potential to offer necessary crop monitoring information across well-irrigated, water stress and salinity stress in regions suffering lack of freshwater resources.

Combining Thermal and RGB Imaging Indices with Multivariate and Data-Driven Modeling to Estimate the Growth, Water Status, and Yield of Potato under Different Drip Irrigation Regimes

Advances in proximal hyperspectral sensing tools, chemometric techniques, and data-driven modeling have enhanced precision irrigation management by facilitating the monitoring of several plant traits. This study investigated the performance of remote sensing indices derived from thermal and red-green-blue (RGB) images combined with stepwise multiple linear regression (SMLR) and an integrated adaptive neuro-fuzzy inference system with a genetic algorithm (ANFIS-GA) for monitoring the biomass fresh weight (BFW), biomass dry weight (BDW), biomass water content (BWC), and total tuber yield (TTY) of two potato varieties under 100%, 75%, and 50% of the estimated crop evapotranspiration (ETc). Results showed that the plant traits and indices varied significantly between the three irrigation regimes. Furthermore, all of the indices exhibited strong relationships with BFW, CWC, and TTY (R2 = 0.80–0.92) and moderate to weak relationships with BDW (R2 = 0.25–0.65) when considered for each variety across the irrigation regimes, for each season across the varieties and irrigation regimes, and across all data combined, but none of the indices successfully assessed any of the plant traits when considered for each irrigation regime across the two varieties. The SMLR and ANFIS-GA models gave the best predictions for the four plant traits in the calibration and testing stages, with the exception of the SMLR testing model for BDW. Thus, the use of thermal and RGB imaging indices with ANFIS-GA models could be a practical tool for managing the growth and production of potato crops under deficit irrigation regimes.

Integration of Spectral Reflectance Indices and Adaptive Neuro-Fuzzy Inference System for Assessing the Growth Performance and Yield of Potato under Different Drip Irrigation Regimes

Simultaneous and timely assessment of growth and water status-related plant traits is critical for precision irrigation management in arid regions. Here, we used proximal hyperspectral sensing tools to estimate biomass fresh weight (BFW), biomass dry weight (BDW), canopy water content (CWC), and total tuber yield (TTY) of two potato varieties irrigated with 100%, 75%, and 50% of the estimated crop evapotranspiration (ETc). Plant traits were assessed remotely using published and newly constructed vegetation and water spectral reflectance indices (SRIs). We integrated genetic algorithm (GA) and adaptive neuro-fuzzy inference system (ANFIS) models to predict the measured traits based on all SRIs. The different plant traits and SRIs varied significantly (p < 0.05) between the three irrigation regimes for the two varieties. The values of plant traits and majority SRIs showed a continuous decrease from the 100% ETc to the 50% ETc. Water-SRIs performed better than vegetation-SRIs for estimating the four plant traits. Almost all indices of the two SRI types had a weak relationship with the four plant traits (R2 = 0.00–0.37) under each irrigation regime. However, the majority of vegetation-SRIs and all water-SRIs showed strong relationships with BFW, CWC, and TTY (R2 ≥ 0.65) and moderate relationships with BDW (R2 ≥ 0.40) when the data of all irrigation regimes and varieties were analyzed together for each growing season or the data of all irrigation regimes, varieties, and seasons were combined together. The ANFIS-GA model predicted plant traits with satisfactory accuracy in both calibration (R2 = 1.0) and testing (R2 = 0.72–0.97) modes. The results indicate that SRI-based ANFIS models can improve plant trait estimation. This analysis also confirmed the benefits of applying GA to ANFIS to estimate plant responses to different growth conditions.

Use of Hyperspectral Reflectance Sensing for Assessing Growth and Chlorophyll Content of Spring Wheat Grown under Simulated Saline Field Conditions

The application of proximal hyperspectral sensing, using simple vegetation indices, offers an easy, fast, and non-destructive approach for assessing various plant variables related to salinity tolerance. Because most existing indices are site- and species-specific, published indices must be further validated when they are applied to other conditions and abiotic stress. This study compared the performance of various published and newly constructed indices, which differ in algorithm forms and wavelength combinations, for remotely assessing the shoot dry weight (SDW) as well as chlorophyll a (Chla), chlorophyll b (Chlb), and chlorophyll a+b (Chlt) content of two wheat genotypes exposed to three salinity levels. Stepwise multiple linear regression (SMLR) was used to extract the most influential indices within each spectral reflectance index (SRI) type. Linear regression based on influential indices was applied to predict plant variables in distinct conditions (genotypes, salinity levels, and seasons). The results show that salinity levels, genotypes, and their interaction had significant effects (p ≤ 0.05 and 0.01) on all plant variables and nearly all indices. Almost all indices within each SRI type performed favorably in estimating the plant variables under both salinity levels (6.0 and 12.0 dS m⁻¹) and for the salt-sensitive genotype Sakha 61. The most effective indices extracted from each SRI type by SMLR explained 60%–81% of the total variability in four plant variables. The various predictive models provided a more accurate estimation of Chla and Chlt content than of SDW and Chlb under both salinity levels. They also provided a more accurate estimation of SDW than of Chl content for salt-tolerant genotype Sakha 93, exhibited strong performance for predicting the four variables for Sakha 61, and failed to predict any variables under control and Chlb for Sakha 93. The overall results indicate that the simple form of indices can be used in practice to remotely assess the growth and chlorophyll content of distinct wheat genotypes under saline field conditions.

Entropy Weight Ensemble Framework for Yield Prediction of Winter Wheat Under Different Water Stress Treatments Using Unmanned Aerial Vehicle-Based Multispectral and Thermal Data

Crop breeding programs generally perform early field assessments of candidate selection based on primary traits such as grain yield (GY). The traditional methods of yield assessment are costly, inefficient, and considered a bottleneck in modern precision agriculture. Recent advances in an unmanned aerial vehicle (UAV) and development of sensors have opened a new avenue for data acquisition cost-effectively and rapidly. We evaluated UAV-based multispectral and thermal images for in-season GY prediction using 30 winter wheat genotypes under 3 water treatments. For this, multispectral vegetation indices (VIs) and normalized relative canopy temperature (NRCT) were calculated and selected by the gray relational analysis (GRA) at each growth stage, i.e., jointing, booting, heading, flowering, grain filling, and maturity to reduce the data dimension. The elastic net regression (ENR) was developed by using selected features as input variables for yield prediction, whereas the entropy weight fusion (EWF) method was used to combine the predicted GY values from multiple growth stages. In our results, the fusion of dual-sensor data showed high yield prediction accuracy [coefficient of determination (R ²) = 0.527-0.667] compared to using a single multispectral sensor (R ² = 0.130-0.461). Results showed that the grain filling stage was the optimal stage to predict GY with R ² = 0.667, root mean square error (RMSE) = 0.881 t ha^-1, relative root-mean-square error (RRMSE) = 15.2%, and mean absolute error (MAE) = 0.721 t ha^-1. The EWF model outperformed at all the individual growth stages with R ² varying from 0.677 to 0.729. The best prediction result (R ² = 0.729, RMSE = 0.831 t ha^-1, RRMSE = 14.3%, and MAE = 0.684 t ha^-1) was achieved through combining the predicted values of all growth stages. This study suggests that the fusion of UAV-based multispectral and thermal IR data within an ENR-EWF framework can provide a precise and robust prediction of wheat yield.