Image-based phenotyping of seed architectural traits and prediction of seed weight using machine learning models in soybean.

Among seed attributes, weight is one of the main factors determining the soybean harvest index. Recently, the focus of soybean breeding has shifted to improving seed size and weight for crop optimization in terms of seed and oil yield. With recent technological advancements, there is an increasing application of imaging sensors that provide simple, real-time, non-destructive, and inexpensive image data for rapid image-based prediction of seed traits in plant breeding programs. The present work is related to digital image analysis of seed traits for the prediction of hundred-seed weight (HSW) in soybean. The image-based seed architectural traits (i-traits) measured were area size (AS), perimeter length (PL), length (L), width (W), length-to-width ratio (LWR), intersection of length and width (IS), seed circularity (CS), and distance between IS and CG (DS). The phenotypic investigation revealed significant genetic variability among 164 soybean genotypes for both i-traits and manually measured seed weight. Seven popular machine learning (ML) algorithms, namely Simple Linear Regression (SLR), Multiple Linear Regression (MLR), Random Forest (RF), Support Vector Regression (SVR), LASSO Regression (LR), Ridge Regression (RR), and Elastic Net Regression (EN), were used to create models that can predict the weight of soybean seeds based on the image-based novel features derived from the Red-Green-Blue (RGB)/visual image. Among the models, random forest and multiple linear regression models that use multiple explanatory variables related to seed size traits (AS, L, W, and DS) were identified as the best models for predicting seed weight with the highest prediction accuracy (coefficient of determination, R2=0.98 and 0.94, respectively) and the lowest prediction error, i.e., root mean square error (RMSE) and mean absolute error (MAE). Finally, principal components analysis (PCA) and a hierarchical clustering approach were used to identify IC538070 as a superior genotype with a larger seed size and weight. The identified donors/traits can potentially be used in soybean improvement programs.

Phenomics based prediction of plant biomass and leaf area in wheat using machine learning approaches.

Introduction: Phenomics has emerged as important tool to bridge the genotype-phenotype gap. To dissect complex traits such as highly dynamic plant growth, and quantification of its component traits over a different growth phase of plant will immensely help dissect genetic basis of biomass production. Based on RGB images, models have been developed to predict biomass recently. However, it is very challenging to find a model performing stable across experiments. In this study, we recorded RGB and NIR images of wheat germplasm and Recombinant Inbred Lines (RILs) of Raj3765xHD2329, and examined the use of multimodal images from RGB, NIR sensors and machine learning models to predict biomass and leaf area non-invasively. Results: The image-based traits (i-Traits) containing geometric features, RGB based indices, RGB colour classes and NIR features were categorized into architectural traits and physiological traits. Total 77 i-Traits were selected for prediction of biomass and leaf area consisting of 35 architectural and 42 physiological traits. We have shown that different biomass related traits such as fresh weight, dry weight and shoot area can be predicted accurately from RGB and NIR images using 16 machine learning models. We applied the models on two consecutive years of experiments and found that measurement accuracies were similar suggesting the generalized nature of models. Results showed that all biomass-related traits could be estimated with about 90% accuracy but the performance of model BLASSO was relatively stable and high in all the traits and experiments. The R2 of BLASSO for fresh weight prediction was 0.96 (both year experiments), for dry weight prediction was 0.90 (Experiment 1) and 0.93 (Experiment 2) and for shoot area prediction 0.96 (Experiment 1) and 0.93 (Experiment 2). Also, the RMSRE of BLASSO for fresh weight prediction was 0.53 (Experiment 1) and 0.24 (Experiment 2), for dry weight prediction was 0.85 (Experiment 1) and 0.25 (Experiment 2) and for shoot area prediction 0.59 (Experiment 1) and 0.53 (Experiment 2). Discussion: Based on the quantification power analysis of i-Traits, the determinants of biomass accumulation were found which contains both architectural and physiological traits. The best predictor i-Trait for fresh weight and dry weight prediction was Area_SV and for shoot area prediction was projected shoot area. These results will be helpful for identification and genetic basis dissection of major determinants of biomass accumulation and also non-invasive high throughput estimation of plant growth during different phenological stages can identify hitherto uncovered genes for biomass production and its deployment in crop improvement for breaking the yield plateau.

Determination of optimal daily light integral (DLI) for indoor cultivation of iceberg lettuce in an indigenous vertical hydroponic system.

The indoor cultivation of lettuce in a vertical hydroponic system (VHS) under artificial lighting is an energy-intensive process incurring a high energy cost. This study determines the optimal daily light integral (DLI) as a function of photoperiod on the physiological, morphological, and nutritional parameters, as well as the resource use efficiency of iceberg lettuce (cv. Glendana) grown in an indoor VHS. Seedlings were grown in a photoperiod of 12 h, 16 h, and 20 h with a photosynthetic photon flux density (PPFD) of 200 µmol m-2 s-1 using white LED lights. The results obtained were compared with VHS without artificial lights inside the greenhouse. The DLI values for 12 h, 16 h, and 20 h were 8.64, 11.5, and 14.4 mol m-2 day-1, respectively. The shoot fresh weight at harvest increased from 275.5 to 393 g as the DLI increased from 8.64 to 11.5 mol m-2 day-1. DLI of 14.4 mol m-2 day-1 had a negative impact on fresh weight, dry weight, and leaf area. The transition from VHS without artificial lights to VHS with artificial lights resulted in a 60% increase in fresh weight. Significantly higher water use efficiency of 71 g FW/L and energy use efficiency of 206.31 g FW/kWh were observed under a DLI of 11.5 mol m-2 day-1. The study recommends an optimal DLI of 11.5 mol m-2 day-1 for iceberg lettuce grown in an indoor vertical hydroponic system.

Synthesis and Performance Evaluation of Novel Bentonite-Supported Nanoscale Zero Valent Iron for Remediation of Arsenic Contaminated Water and Soil.

Groundwater arsenic (As) pollution is a naturally occurring phenomenon posing serious threats to human health. To mitigate this issue, we synthesized a novel bentonite-based engineered nano zero-valent iron (nZVI-Bento) material to remove As from contaminated soil and water. Sorption isotherm and kinetics models were employed to understand the mechanisms governing As removal. Experimental and model predicted values of adsorption capacity (qe or qt) were compared to evaluate the adequacy of the models, substantiated by error function analysis, and the best-fit model was selected based on corrected Akaike Information Criterion (AICc). The non-linear regression fitting of both adsorption isotherm and kinetic models revealed lower values of error and lower AICc values than the linear regression models. The pseudo-second-order (non-linear) fit was the best fit among kinetic models with the lowest AICc values, at 57.5 (nZVI-Bare) and 71.9 (nZVI-Bento), while the Freundlich equation was the best fit among the isotherm models, showing the lowest AICc values, at 105.5 (nZVI-Bare) and 105.1 (nZVI-Bento). The adsorption maxima (qmax) predicted by the non-linear Langmuir adsorption isotherm were 354.3 and 198.5 mg g-1 for nZVI-Bare and nZVI-Bento, respectively. The nZVI-Bento successfully reduced As in water (initial As concentration = 5 mg L-1; adsorbent dose = 0.5 g L-1) to below permissible limits for drinking water (10 µg L-1). The nZVI-Bento @ 1% (w/w) could stabilize As in soils by increasing the amorphous Fe bound fraction and significantly diminish the non-specific and specifically bound fraction of As in soil. Considering the enhanced stability of the novel nZVI-Bento (upto 60 days) as compared to the unmodified product, it is envisaged that the synthesized product could be effectively used for removing As from water to make it safe for human consumption.

Leaf Count Aided Novel Framework for Rice (Oryza sativa L.) Genotypes Discrimination in Phenomics: Leveraging Computer Vision and Deep Learning Applications.

Drought is a detrimental factor to gaining higher yields in rice (Oryza sativa L.), especially amid the rising occurrence of drought across the globe. To combat this situation, it is essential to develop novel drought-resilient varieties. Therefore, screening of drought-adaptive genotypes is required with high precision and high throughput. In contemporary emerging science, high throughput plant phenotyping (HTPP) is a crucial technology that attempts to break the bottleneck of traditional phenotyping. In traditional phenotyping, screening significant genotypes is a tedious task and prone to human error while measuring various plant traits. In contrast, owing to the potential advantage of HTPP over traditional phenotyping, image-based traits, also known as i-traits, were used in our study to discriminate 110 genotypes grown for genome-wide association study experiments under controlled (well-watered), and drought-stress (limited water) conditions, under a phenomics experiment in a controlled environment with RGB images. Our proposed framework non-destructively estimated drought-adaptive plant traits from the images, such as the number of leaves, convex hull, plant-aspect ratio (plant spread), and similarly associated geometrical and morphological traits for analyzing and discriminating genotypes. The results showed that a single trait, the number of leaves, can also be used for discriminating genotypes. This critical drought-adaptive trait was associated with plant size, architecture, and biomass. In this work, the number of leaves and other characteristics were estimated non-destructively from top view images of the rice plant for each genotype. The estimation of the number of leaves for each rice plant was conducted with the deep learning model, YOLO (You Only Look Once). The leaves were counted by detecting corresponding visible leaf tips in the rice plant. The detection accuracy was 86-92% for dense to moderate spread large plants, and 98% for sparse spread small plants. With this framework, the susceptible genotypes (MTU1010, PUSA-1121 and similar genotypes) and drought-resistant genotypes (Heera, Anjali, Dular and similar genotypes) were grouped in the core set with a respective group of drought-susceptible and drought-tolerant genotypes based on the number of leaves, and the leaves' emergence during the peak drought-stress period. Moreover, it was found that the number of leaves was significantly associated with other pertinent morphological, physiological and geometrical traits. Other geometrical traits were measured from the RGB images with the help of computer vision.

SpikeSegNet-a deep learning approach utilizing encoder-decoder network with hourglass for spike segmentation and counting in wheat plant from visual imaging.

BACKGROUND: High throughput non-destructive phenotyping is emerging as a significant approach for phenotyping germplasm and breeding populations for the identification of superior donors, elite lines, and QTLs. Detection and counting of spikes, the grain bearing organs of wheat, is critical for phenomics of a large set of germplasm and breeding lines in controlled and field conditions. It is also required for precision agriculture where the application of nitrogen, water, and other inputs at this critical stage is necessary. Further, counting of spikes is an important measure to determine yield. Digital image analysis and machine learning techniques play an essential role in non-destructive plant phenotyping analysis. RESULTS: In this study, an approach based on computer vision, particularly object detection, to recognize and count the number of spikes of the wheat plant from the digital images is proposed. For spike identification, a novel deep-learning network, SpikeSegNet, has been developed by combining two proposed feature networks: Local Patch extraction Network (LPNet) and Global Mask refinement Network (GMRNet). In LPNet, the contextual and spatial features are learned at the local patch level. The output of LPNet is a segmented mask image, which is further refined at the global level using GMRNet. Visual (RGB) images of 200 wheat plants were captured using LemnaTec imaging system installed at Nanaji Deshmukh Plant Phenomics Centre, ICAR-IARI, New Delhi. The precision, accuracy, and robustness (F1 score) of the proposed approach for spike segmentation are found to be 99.93%, 99.91%, and 99.91%, respectively. For counting the number of spikes, "analyse particles"-function of imageJ was applied on the output image of the proposed SpikeSegNet model. For spike counting, the average precision, accuracy, and robustness are 99%, 95%, and 97%, respectively. SpikeSegNet approach is tested for robustness with illuminated image dataset, and no significant difference is observed in the segmentation performance. CONCLUSION: In this study, a new approach called as SpikeSegNet has been proposed based on combined digital image analysis and deep learning techniques. A dedicated deep learning approach has been developed to identify and count spikes in the wheat plants. The performance of the approach demonstrates that SpikeSegNet is an effective and robust approach for spike detection and counting. As detection and counting of wheat spikes are closely related to the crop yield, and the proposed approach is also non-destructive, it is a significant step forward in the area of non-destructive and high-throughput phenotyping of wheat.