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Search Results (2,353)

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17 pages, 9162 KiB  
Article
Estimating Cadmium Concentration in Agricultural Soils with ZY1-02D Hyperspectral Data: A Comparative Analysis of Spectral Transformations and Machine Learning Models
by Junwei Lv, Jing Geng, Xuanhong Xu, Yong Yu, Huajun Fang, Yifan Guo and Shulan Cheng
Agriculture 2024, 14(9), 1619; https://doi.org/10.3390/agriculture14091619 - 15 Sep 2024
Viewed by 227
Abstract
The accumulation of cadmium (Cd) in agricultural soils presents a significant threat to crop safety, emphasizing the critical necessity for effective monitoring and management of soil Cd levels. Despite technological advancements, accurately monitoring soil Cd concentrations using satellite hyperspectral technology remains challenging, particularly [...] Read more.
The accumulation of cadmium (Cd) in agricultural soils presents a significant threat to crop safety, emphasizing the critical necessity for effective monitoring and management of soil Cd levels. Despite technological advancements, accurately monitoring soil Cd concentrations using satellite hyperspectral technology remains challenging, particularly in efficiently extracting spectral information. In this study, a total of 304 soil samples were collected from agricultural soils surrounding a tungsten mine located in the Xiancha River basin, Jiangxi Province, Southern China. Leveraging hyperspectral data from the ZY1-02D satellite, this research developed a comprehensive framework that evaluates the predictive accuracy of nine spectral transformations across four modeling approaches to estimate soil Cd concentrations. The spectral transformation methods included four logarithmic and reciprocal transformations, two derivative transformations, and three baseline correction and normalization transformations. The four models utilized for predicting soil Cd were partial least squares regression (PLSR), support vector machine (SVM), bidirectional recurrent neural networks (BRNN), and random forest (RF). The results indicated that these spectral transformations markedly enhanced the absorption and reflection features of the spectral curves, accentuating key peaks and troughs. Compared to the original spectral curves, the correlation analysis between the transformed spectra and soil Cd content showed a notable improvement, particularly with derivative transformations. The combination of the first derivative (FD) transformation with the RF model yielded the highest accuracy (R2 = 0.61, RMSE = 0.37 mg/kg, MAE = 0.21 mg/kg). Furthermore, the RF model in multiple spectral transformations exhibited higher suitability for modeling soil Cd content compared to other models. Overall, this research highlights the substantial applicative potential of the ZY1-02D satellite hyperspectral data for detecting soil heavy metals and provides a framework that integrates optimal spectral transformations and modeling techniques to estimate soil Cd contents. Full article
(This article belongs to the Section Digital Agriculture)
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<p>Distribution of soil sampling sites in the study area: (<b>a</b>) Jiangxi Province, China; (<b>b</b>) Geographic location of the study area; (<b>c</b>) Distribution of sampling points and elevation within the study area. The top-right image shows the coverage of the study area by the original ZY1-02D imagery.</p>
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<p>(<b>a</b>) Original spectral curves and (<b>b</b>) Savitzky–Golay (SG) smoothed spectral curves of soil samples from hyperspectral images. Note: Each color represents a sampling point.</p>
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<p>The correlation coefficients between soil Cd and original soil spectral data, and after Savitzky–Golay (SG) smoothed spectral data.</p>
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<p>Nine spectral transformation curves of soil samples from hyperspectral images. (<b>a</b>) logarithmic transformation (LT), (<b>b</b>) reciprocal transformation (RT), (<b>c</b>) first derivative (FD), (<b>d</b>) logarithm of reciprocal transformation (LR), (<b>e</b>) reciprocal of logarithmic transformation (RL), (<b>f</b>) reciprocal of logarithmic and first derivative (RLFD), (<b>g</b>) standard normal variate (SNV), (<b>h</b>) continuum removal (CR), and (<b>i</b>) multiplicative scatter correction (MSC). Note: Each color represents a sampling point.</p>
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<p>The correlation coefficient curves between the spectra derived from nine spectral transformation methods and the soil Cd content. (<b>a</b>) logarithmic transformation (LT), (<b>b</b>) reciprocal transformation (RT), (<b>c</b>) first derivative (FD), (<b>d</b>) logarithm of reciprocal transformation (LR), (<b>e</b>) reciprocal of logarithmic transformation (RL), (<b>f</b>) reciprocal of logarithmic and first derivative (RLFD), (<b>g</b>) standard normal variate (SNV), (<b>h</b>) continuum removal (CR), and (<b>i</b>) multiplicative scatter correction (MSC).</p>
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<p>Spatial distribution of soil Cd content in the study area driven by the RF model constructed with first derivative-transformed spectral data. Note that this Cd distribution map has been masked with a cropland layer derived from the GlobeLand30 dataset (<a href="http://www.globallandcover.com/" target="_blank">http://www.globallandcover.com/</a>, accessed on 20 December 2022).</p>
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<p>Relative proportional and spatial extents of three soil pollution categories based on soil Cd contents.</p>
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18 pages, 4238 KiB  
Article
Combining Vegetation Indices to Identify the Maize Phenological Information Based on the Shape Model
by Huizhu Wu, Bing Liu, Bingxue Zhu, Zhijun Zhen, Kaishan Song and Jingquan Ren
Agriculture 2024, 14(9), 1608; https://doi.org/10.3390/agriculture14091608 - 14 Sep 2024
Viewed by 172
Abstract
Maize is the world’s largest food crop and plays a critical role in global food security. Accurate phenology information is essential for improving yield estimation and enabling timely field management. Yet, much of the research has concentrated on general crop growth periods rather [...] Read more.
Maize is the world’s largest food crop and plays a critical role in global food security. Accurate phenology information is essential for improving yield estimation and enabling timely field management. Yet, much of the research has concentrated on general crop growth periods rather than on pinpointing key phenological stages. This gap in understanding presents a challenge in determining how different vegetation indices (VIs) might accurately extract phenological information across these stages. To address this, we employed the shape model fitting (SMF) method to assess whether a multi-index approach could enhance the precision of identifying key phenological stages. By analyzing time-series data from various VIs, we identified five phenological stages (emergence, seven-leaf, jointing, flowering, and maturity stages) in maize cultivated in Jilin Province. The findings revealed that each VI had distinct advantages depending on the phenological stage, with the land surface water index (LSWI) being particularly effective for jointing and flowering stages due to its correlation with vegetation water content, achieving a root mean square error (RMSE) of three to four days. In contrast, the normalized difference vegetation index (NDVI) was more effective for identifying the emergence and seven-leaf stages, with an RMSE of four days. Overall, combining multiple VIs significantly improved the accuracy of phenological stage identification. This approach offers a novel perspective for utilizing diverse VIs in crop phenology, thereby enhancing the precision of agricultural monitoring and management practices. Full article
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<p>Map of the study area and sites.</p>
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<p>Division of vegetative and reproductive growth stages in maize phenology.</p>
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<p>Flowchart of phenological period identification.</p>
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<p>Relationship between field-observed and estimated phenological stages obtained from different indicators and the RMSE. (<b>a</b>,<b>c</b>,<b>e</b>) The data from 2003 to 2014 and (<b>b</b>,<b>d</b>,<b>f</b>) the data from 2015 to 2019. Both the x and y axes represent the DOY.</p>
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<p>Box plots of the errors in identifying phenological phases in different regions: (<b>a</b>) emergence, (<b>b</b>) seven-leaf stage, (<b>c</b>) jointing, (<b>d</b>) flowering, and (<b>e</b>) maturity. The errors are represented by residuals, with positive values indicating delayed predictions and negative values indicating earlier predictions.</p>
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<p>The target curve fitting reference curve in Baicheng City, Jilin Province, in 2019, where the orange curve is the reference curve, the blue curve is the target curve, and the green curve is the reference curve after deformation by the fitting function. In the subplots, (<b>a</b>,<b>d</b>,<b>g</b>,<b>j</b>,<b>m</b>) represent the fitting cases where NDVI is used as the reference curve for the shape model, (<b>b</b>,<b>e</b>,<b>h</b>,<b>k</b>,<b>n</b>) represent the cases with NDPI as the reference curve, and (<b>c</b>,<b>f</b>,<b>i</b>,<b>l</b>,<b>o</b>) represent the cases with LSWI as the reference curve, with each subplot labeled accordingly.</p>
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<p>Spatial distribution of the five phenological stages of maize obtained from the LSWI as a reference curve.</p>
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<p>Reference curves of different VIs in Jilin City.</p>
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<p>Reflectance values and reference curves at different phenological stages of different stations. (<b>a</b>) represents the case where the phenological stages of the stations correspond to NDVI values falling on the reference curve, (<b>b</b>) represents the case for NDPI values, and (<b>c</b>) represents the case for LSWI values.</p>
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16 pages, 5469 KiB  
Article
Agronomic Performance and Yield Stability of Elite White Guinea Yam (Dioscorea rotundata) Genotypes Grown in Multiple Environments in Nigeria
by Alice Adenike Olatunji, Andrew Saba Gana, Kehinde D. Tolorunse, Paterne A. Agre, Patrick Adebola and Asrat Asfaw
Agronomy 2024, 14(9), 2093; https://doi.org/10.3390/agronomy14092093 - 13 Sep 2024
Viewed by 464
Abstract
Yam (Dioscorea spp.) is a main staple tuber crop in Nigeria and the West African region. Its performance is determined by genotypes and also the environment of growth. This study assessed the agronomic performance and yield stability of elite white yam (Dioscorea [...] Read more.
Yam (Dioscorea spp.) is a main staple tuber crop in Nigeria and the West African region. Its performance is determined by genotypes and also the environment of growth. This study assessed the agronomic performance and yield stability of elite white yam (Dioscorea rotundata) genotypes across diverse Nigerian environments. A total of 25 genotypes were evaluated at three locations in two consecutive growing seasons, 2022 and 2023, for fresh tuber yield, disease resistance, and tuber quality traits. The genotype’s performance and stability for the measured traits were assessed using various analytical tools such as additive main effects and multiplicative interaction (AMMI) and multi-trait stability index (MTSI). The AMMI analysis revealed significant differences among the genotypes and across the environments for all traits (p < 0.001, p < 0.01). The PCA revealed that the first two principal components (PC1 and PC2) explained a substantial portion of the total variation (49.84%). The MTSI identified four clones: G18, G19, G24, and G16 as promising candidates for improved yam production in Nigeria with high and stable performance for the multiple traits. Full article
(This article belongs to the Section Horticultural and Floricultural Crops)
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<p>Visual scale for yam mosaic virus disease scoring. (<b>1</b>) No visible symptoms of virus; (<b>2</b>) Mosaic on few spots; (<b>3</b>) Mild symptoms on leaf; (<b>4</b>) Severe mosaic on leaf; (<b>5</b>) Severe mosaic (bleaching) on leaf. Photo credit to first author.</p>
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<p>Boxplots of quantitative traits accessed on 25 yam genotypes. The black line and red diamond inside each boxplot represent the median and mean values, respectively. PLNV: plant vigor; AUDPCYAD: area under disease progression curve yam anthracnose disease; AUDPCYMV: area under disease progression curve yam mosaic virus, ATW: average tuber weight; TTY: total tuber yield; OXi30 and OXi180: intensity of tuber oxidation at 30 and 180 min and DMC: dry matter content.</p>
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<p>Pearson correlation coefficient among the agronomic traits for 25 white yam genotypes. PLNV: plant vigor; AUDPCYAD: area under disease progression curve yam anthracnose disease; AUDPCYMV: area under disease progression curve yam mosaic virus; ATW: average tuber weight; TTY: total tuber; OXi30 and OXi180: intensity of tuber oxidation at 30 and 180 min; and DMC: dry matter content.</p>
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<p>AMMI1 biplot view for best genotypes across six environments (<b>a</b>) fresh tuber yield (tha-1), (<b>b</b>) Dry matter content (%).</p>
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<p>Ammi2 biplot polygon view for best genotypes across six environments (<b>a</b>) total tuber yield, (<b>b</b>) dry matter content. The green lines represent the environmental vectors showing the direction of environmental influence on genotype performance. The dotted blue lines connecting between genotypes in vertical cortex, showing their relationship in terms of performances across the environments.</p>
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<p>Mean and stability biplot for fresh tuber yield (tha-1) (<b>a</b>), Fresh tuber yield, (<b>b</b>) and dry matter content.</p>
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<p>Twenty-five genotypes of white yam selected by multi-trait stability index. The selected stable genotypes are located on and beyond the red circle with red dots while the unselected are the black dots within the red circle. The FA1: TTY; FA2: AUDPCYMV, AUDPCYAD, DMC; FA3: Oxi30, Oxi180; FA4: PLNV, ATW. The dashed line from the strength and weakness view shows the theoretical value if all the factors had contributed equally.</p>
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19 pages, 18432 KiB  
Article
Low-Cost Lettuce Height Measurement Based on Depth Vision and Lightweight Instance Segmentation Model
by Yiqiu Zhao, Xiaodong Zhang, Jingjing Sun, Tingting Yu, Zongyao Cai, Zhi Zhang and Hanping Mao
Agriculture 2024, 14(9), 1596; https://doi.org/10.3390/agriculture14091596 - 13 Sep 2024
Viewed by 220
Abstract
Plant height is a crucial indicator of crop growth. Rapid measurement of crop height facilitates the implementation and management of planting strategies, ensuring optimal crop production quality and yield. This paper presents a low-cost method for the rapid measurement of multiple lettuce heights, [...] Read more.
Plant height is a crucial indicator of crop growth. Rapid measurement of crop height facilitates the implementation and management of planting strategies, ensuring optimal crop production quality and yield. This paper presents a low-cost method for the rapid measurement of multiple lettuce heights, developed using an improved YOLOv8n-seg model and the stacking characteristics of planes in depth images. First, we designed a lightweight instance segmentation model based on YOLOv8n-seg by enhancing the model architecture and reconstructing the channel dimension distribution. This model was trained on a small-sample dataset augmented through random transformations. Secondly, we proposed a method to detect and segment the horizontal plane. This method leverages the stacking characteristics of the plane, as identified in the depth image histogram from an overhead perspective, allowing for the identification of planes parallel to the camera’s imaging plane. Subsequently, we evaluated the distance between each plane and the centers of the lettuce contours to select the cultivation substrate plane as the reference for lettuce bottom height. Finally, the height of multiple lettuce plants was determined by calculating the height difference between the top and bottom of each plant. The experimental results demonstrated that the improved model achieved a 25.56% increase in processing speed, along with a 2.4% enhancement in mean average precision compared to the original YOLOv8n-seg model. The average accuracy of the plant height measurement algorithm reached 94.339% in hydroponics and 91.22% in pot cultivation scenarios, with absolute errors of 7.39 mm and 9.23 mm, similar to the sensor’s depth direction error. With images downsampled by a factor of 1/8, the highest processing speed recorded was 6.99 frames per second (fps), enabling the system to process an average of 174 lettuce targets per second. The experimental results confirmed that the proposed method exhibits promising accuracy, efficiency, and robustness. Full article
(This article belongs to the Special Issue Smart Agriculture Sensors and Monitoring Systems for Field Detection)
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<p>Lettuce growing environment.</p>
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<p>Plant height measurement tool.</p>
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<p>Examples of random transformations.</p>
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<p>YOLOv8n-seg structure.</p>
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<p>Structure of YOLOv8-seg with FasterNet as backbone.</p>
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<p>Hydroponics scenario: (<b>A</b>) distribution of depth image pixels along the depth axis, (<b>B</b>) histogram of depth image. Potting scenario: (<b>C</b>) distribution of depth image pixels along the depth axis, (<b>D</b>) histogram of depth image.</p>
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<p>(<b>A</b>,<b>C</b>) Results of plane detection based on pixel stacking. (<b>B</b>,<b>D</b>) Image region division based on crop center.</p>
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<p>Algorithm flow diagram.</p>
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<p>Model channel dimension comparisons (before multiplying the width coefficient of the model).</p>
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<p>mAP changes of 7 models during model training.</p>
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<p>Segmentation performance comparison of 7 models with target confidence scores.</p>
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<p>Heat maps of the last layer of different backbones.</p>
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<p>Lettuce height measurement outputs (mm).</p>
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<p>Plant height measurement results of hydroponics scenario.</p>
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<p>Plant height measurement results of potted lettuce.</p>
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<p>Segmentation comparison between vegetation index method and Model 5.</p>
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<p>Comparison of different plane detection algorithms.</p>
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19 pages, 6418 KiB  
Article
Evaluating Sugarcane Yield Estimation in Thailand Using Multi-Temporal Sentinel-2 and Landsat Data Together with Machine-Learning Algorithms
by Jaturong Som-ard, Savittri Ratanopad Suwanlee, Dusadee Pinasu, Surasak Keawsomsee, Kemin Kasa, Nattawut Seesanhao, Sarawut Ninsawat, Enrico Borgogno-Mondino and Filippo Sarvia
Land 2024, 13(9), 1481; https://doi.org/10.3390/land13091481 - 13 Sep 2024
Viewed by 433
Abstract
Updated and accurate crop yield maps play a key role in the agricultural environment. Their application enables the support for sustainable agricultural practices and the formulation of effective strategies to mitigate the impacts of climate change. Farmers can apply the maps to gain [...] Read more.
Updated and accurate crop yield maps play a key role in the agricultural environment. Their application enables the support for sustainable agricultural practices and the formulation of effective strategies to mitigate the impacts of climate change. Farmers can apply the maps to gain an overview of the yield variability, improving farm management practices and optimizing inputs to increase productivity and sustainability such as fertilizers. Earth observation (EO) data make it possible to map crop yield estimations over large areas, although this will remain challenging for specific crops such as sugarcane. Yield data collection is an expensive and time-consuming practice that often limits the number of samples collected. In this study, the sugarcane yield estimation based on a small number of training datasets within smallholder crop systems in the Tha Khan Tho District, Thailand for the year 2022 was assessed. Specifically, multi-temporal satellite datasets from multiple sensors, including Sentinel-2 and Landsat 8/9, were involved. Moreover, in order to generate the sugarcane yield estimation maps, only 75 sampling plots were selected and surveyed to provide training and validation data for several powerful machine-learning algorithms, including multiple linear regression (MLR), stepwise multiple regression (SMR), partial least squares regression (PLS), random forest regression (RFR), and support vector regression (SVR). Among these algorithms, the RFR model demonstrated outstanding performance, yielding an excellent result compared to existing techniques, achieving an R-squared (R2) value of 0.79 and a root mean square error (RMSE) of 3.93 t/ha (per 10 m × 10 m pixel). Furthermore, the mapped yields across the region closely aligned with the official statistical data from the Office of the Cane and Sugar Board (with a range value of 36,000 ton). Finally, the sugarcane yield estimation model was applied to over 2100 sugarcane fields in order to provide an overview of the current state of the yield and total production in the area. In this work, the different yield rates at the field level were highlighted, providing a powerful workflow for mapping sugarcane yields across large regions, supporting sugarcane crop management and facilitating decision-making processes. Full article
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<p>Flow chart of the implemented methodology for mapping sugarcane yield in 2022 at Tha Khan Tho District, Thailand using multi-temporal Sentinel-2 (S2) and Landsat 8/9 (L8/9) dataset together with the several machine-learning methods.</p>
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<p>Study area (<b>a</b>): background shows Sentinel-2 (S2) imagery (image composites: during November 2022) with false color (Red = band 8: Green = band 4: Blue = band 3). The 60 yellow sampling plots are used for training datasets and remaining 15 blue plots were used for validating the mapped results. (<b>b</b>) is a location of the Tha Khan Tho District, Kalasin Province, Thailand (study region), (<b>c</b>) shows sampling plot with size of 10 m × 10 m.</p>
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<p>The sugarcane field dataset (2364 fields) was visually interpreted using very high-resolution imagery as Planet imagery during November 2022.</p>
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<p>The ranking importance of the features using the random forest (RF) method for the year 2022 with sampling plots and the multi-temporal Sentinel-2 (S2) and Landsat 8/Landsat 9 (L8/9) data.</p>
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<p>Zoom box of the estimated yield maps with yield value from 59 to 108 based on productive models: multiple linear regression (MLR) (<b>a</b>); stepwise multiple regression (SMR) (<b>b</b>); partial least squares regression (PLS) (<b>c</b>); random forest regression (RFR) (<b>d</b>); and support vector regression (SVR) (<b>e</b>). The sugarcane fields the entire study area (<b>f</b>) are shown.</p>
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<p>The scatter plots of sugarcane yield estimation results using five productive models together with multi-temporal Sentinel-2 (S2) and Landsat 8/9 (L8/9) data: multiple linear regression (MLR) (<b>a</b>); stepwise multiple regression (SMR) (<b>b</b>); partial least squares regression (PLS) (<b>c</b>); random forest regression (RFR) (<b>d</b>); and support vector regression (SVR) (<b>e</b>).</p>
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<p>A comparison of observed yield (t/ha) and estimated yield (t/ha) of 15 sampling fields across the study area based on the best random forest regression (RFR)-predictive model together with Sentinel-2 (S2) and Landsat data.</p>
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<p>The spatial distribution of estimated yield in 2022 using the best random forest regression (RFR) together with Sentinel-2 (S2) and Landsat data.</p>
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<p>Histogram of the frequency distribution of estimated yield (t/ha) across the Tha Khan Tho District, Thailand, from 10 m × 10 m Sentinel-2 (S2). The red dotted line is the mean value of the estimated yield in this region.</p>
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18 pages, 5133 KiB  
Article
Comprehensive Assessment of Climate Change Impacts on River Water Availability for Irrigation, Wheat Crop Area Coverage, and Irrigation Canal Hydraulic Capacity of Large-Scale Irrigation Scheme in Nepal
by Santosh Kaini, Matthew Tom Harrison, Ted Gardner and Ashok K. Sharma
Water 2024, 16(18), 2595; https://doi.org/10.3390/w16182595 - 13 Sep 2024
Viewed by 597
Abstract
While atmospheric warming intensifies the global water cycle, regionalised effects of climate change on water loss, irrigation supply, and food security are highly variable. Here, we elucidate the impacts of the climate crisis on irrigation water availability and cropping area in Nepal’s largest [...] Read more.
While atmospheric warming intensifies the global water cycle, regionalised effects of climate change on water loss, irrigation supply, and food security are highly variable. Here, we elucidate the impacts of the climate crisis on irrigation water availability and cropping area in Nepal’s largest irrigation scheme, the Sunsari Morang Irrigation Scheme (SMIS), by accounting for the hydraulic capacity of existing canal systems, and potential changes realised under future climates. To capture variability implicit in climate change projections, we invoke multiple Representative Concentration Pathways (RCPs; 4.5 and 8.5) across three time horizons (2016–2045, 2036–2065, and 2071–2100). We reveal that although climate change increases water availability to agriculture from December through March, the designed discharge of 60 m3/s would not be available in February-March for both RCPs under all three time horizons. Weed growth, silt deposition, and poor maintenance have reduced the current canal capacity from the design capacity of 60 m3/s to 53 m3/s up to 10.7 km from the canal intake (representing a 12% reduction in the discharge capacity of the canal). Canal flow is further reduced to 35 m3/s at 13.8 km from canal intake, representing a 27% reduction in flow capacity relative to the original design standards. Based on climate projections, and assuming ceteris paribus irrigation infrastructure, total wheat cropping area could increase by 12–19%, 23–27%, and 12–35% by 2016–2045, 2036–2065, and 2071–2100, respectively, due to increased water availability borne by the changing climate. The case for further investment in irrigation infrastructure via water diversion, or installation of efficient pumps at irrigation canal intakes is compelling. Such investment would catalyse a step-change in the agricultural economy that is urgently needed to sustain the Nepalese economy, and thus evoke beneficial cascading implications for global food security. Full article
(This article belongs to the Special Issue Model-Based Irrigation Management)
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<p>(<b>a</b>) Koshi River basin, Sunsari Morang Irrigation Scheme, and administrative boundary of Nepal, (<b>b</b>) Koshi River network and Sunsari Morang Irrigation Intake, (<b>c</b>) Sunsari Morang Irrigation Intake and Irrigation Canal Network. Discharge measurement chainages from 5.2 km to 25.4 km are shown in numbers (1–6) in (<b>c</b>).</p>
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<p>Overview of the study, including irrigation channels, flow discharge, and climate information modelling.</p>
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<p>Current meter (manual recorder) used for discharge measurement in the main irrigation canal.</p>
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<p>Observed and simulated discharge, velocity, and water depth for the (<b>a</b>) calibration and (<b>b</b>) validation periods. Locations of the Chainage 5.2 km, 11.8 km, 13 km, 15 km, 22.5 km, and 25.3 km in the main canal are shown in <a href="#water-16-02595-f001" class="html-fig">Figure 1</a>c.</p>
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<p>Stage–discharge relationship for the Koshi River at the irrigation canal intake, based on data available from 1996 to 2012. Crest level of the intake structure is 107 m above mean sea level.</p>
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<p>Headwork intake structure (12 rectangular orifices) of the Sunsari Morang Irrigation Scheme in the Koshi River (<b>a</b>) during the monsoon season, and (<b>b</b>) during the dry season (arrow shows the direction of river flow).</p>
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<p>Average monthly water available over the crests of the canal intake, which is then available for irrigation during the dry season (data averaged over 1982–2010).</p>
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<p>Projected average monthly minimum flows into the canal intake along with their standard deviation of the mean for different climate change scenarios (RCPSs) and future time periods, with reference (base) period flow for comparison.</p>
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13 pages, 1564 KiB  
Article
Genotype by Environment Interaction (GEI) Effect for Potato Tuber Yield and Their Quality Traits in Organic Multi-Environment Domains in Poland
by Beata Ewa Tatarowska, Jarosław Plich, Dorota Milczarek, Dominika Boguszewska-Mańkowska and Krystyna Zarzyńska
Agriculture 2024, 14(9), 1591; https://doi.org/10.3390/agriculture14091591 - 12 Sep 2024
Viewed by 281
Abstract
Potatoes (Solanum tuberosum L.) are an important plant crop, whose yield may vary significantly depending on pedo-climatic conditions and genotype. Therefore, the analysis of the genotype × environment interaction (GEI) is mandatory for the setup of high-yielding and stable potato genotypes. This [...] Read more.
Potatoes (Solanum tuberosum L.) are an important plant crop, whose yield may vary significantly depending on pedo-climatic conditions and genotype. Therefore, the analysis of the genotype × environment interaction (GEI) is mandatory for the setup of high-yielding and stable potato genotypes. This research evaluated the tuber yield (t ha−1) and yield characteristic of nine potato cultivars over 3 years and 4 organic farms in Poland by additive main effects and multiplicative interactions (AMMIs) and genotype plus genotype environment interaction (GGE) biplot analyses. The results of these analyses indicated significant differentiation of tuber yield among genotypes in individual environments. It was found that the environment (E, where E = L (localization) × Y (year)), genotype (G) and GEI, but not replication, significantly affected tuber yield. The AMMI analysis showed that the environment factor explained the most considerable part of tuber yield variations (52.3%), while the GEI and G factors explained a much lower part of the variations. The AMMI and GGE analyses identified five cvs.: Twister (46.4 t ha−1), Alouette (35.8 t ha−1), Kokra (34.8 t ha−1), Levante (33.1 t ha−1), and Gardena (30.4 t ha−1), as leading cultivars in the studied organic farms due to their high productivity coupled with yield stability. The statistical measure Kang (YSi) showed that these cvs. can be considered as adaptable to a wide range of organic environments. In the case of morphological traits of tubers (tuber shape and depth of tuber eyes), the most important factor influencing both these traits was genotype (G). Influence of other factors, like localization (L), year (Y), and all interactions (double and triple), were much less significant or insignificant. In case of taste and non-darkening of tuber flesh, the main effects which significantly affected the values of these traits were genotype (G) and localization (L). We observed that cooking type can vary depending on the year (Y) and the localization (L). Full article
(This article belongs to the Section Crop Genetics, Genomics and Breeding)
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<p>Map of Poland with location of organic farms.</p>
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<p>Biplot analysis of GGE for first two IPC scores (IPC1 vs. IPC2) for tuber yield (2020–2022).</p>
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<p>Biplot analysis of GGE for the IPC1 scores and tuber yield of 9 potato cultivars across 12 environments (2020–2022).</p>
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<p>Taste of potato cultivars (2020–2021).</p>
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20 pages, 4752 KiB  
Article
Genome-Wide Identification and Characterization of Alternative Oxidase (AOX) Genes in Foxtail Millet (Setaria italica): Insights into Their Abiotic Stress Response
by Hui Zhang, Yidan Luo, Yujing Wang, Juan Zhao, Yueyue Wang, Yajun Li, Yihao Pu, Xingchun Wang, Xuemei Ren and Bo Zhao
Plants 2024, 13(18), 2565; https://doi.org/10.3390/plants13182565 - 12 Sep 2024
Viewed by 314
Abstract
Alternative oxidase (AOX) serves as a critical terminal oxidase within the plant respiratory pathway, playing a significant role in cellular responses to various stresses. Foxtail millet (Setaria italica), a crop extensively cultivated across Asia, is renowned for its remarkable [...] Read more.
Alternative oxidase (AOX) serves as a critical terminal oxidase within the plant respiratory pathway, playing a significant role in cellular responses to various stresses. Foxtail millet (Setaria italica), a crop extensively cultivated across Asia, is renowned for its remarkable tolerance to abiotic stresses and minimal requirement for fertilizer. In this study, we conducted a comprehensive genome-wide identification of AOX genes in foxtail millet genome, discovering a total of five SiAOX genes. Phylogenetic analysis categorized these SiAOX members into two subgroups. Prediction of cis-elements within the promoter regions, coupled with co-expression network analysis, intimated that SiAOX proteins are likely involved in the plant’s adaptive response to abiotic stresses. Employing RNA sequencing (RNA-seq) and real-time quantitative PCR (RT-qPCR), we scrutinized the expression patterns of the SiAOX genes across a variety of tissues and under multiple abiotic stress conditions. Specifically, our analysis uncovered that SiAOX1, SiAOX2, SiAOX4, and SiAOX5 display distinct tissue-specific expression profiles. Furthermore, SiAOX2, SiAOX3, SiAOX4, and SiAOX5 exhibit responsive expression patterns under abiotic stress conditions, with significant differences in expression levels observed between the shoot and root tissues of foxtail millet seedlings. Haplotype analysis of SiAOX4 and SiAOX5 revealed that these genes are in linkage disequilibrium, with Hap_2 being the superior haplotype for both, potentially conferring enhanced cold stress tolerance in the cultivar group. These findings suggest that both SiAOX4 and SiAOX5 may be targeted for selection in future breeding programs aimed at improving foxtail millet’s resilience to cold stress. Full article
(This article belongs to the Section Plant Molecular Biology)
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<p>Conserved motifs, functional domain, and gene structure of five SiAOX members in foxtail millet. These sizes could be estimated using the scale at bottom. (<b>A</b>) Gene tree. (<b>B</b>) Motif patterns. Conserved motifs in the SiAOX peptides are presented by different colored boxes. (<b>C</b>) Conserved domain. AOX domain is represented by pink box, other regions of SiAOX peptides are represented by lines. (<b>D</b>) Gene structure. Coding sequences (CDS) and untranslated region (UTR) are represented by different colored boxes, and introns are represented by lines.</p>
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<p>The three-dimensional models of AOX proteins in foxtail millet. All three-dimensional models are constructed using AlaphFold2 v2.3.2 and visualized by Pymol v2.5.5.</p>
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<p>Phylogenetic and collinearity analysis of AOXs in foxtail millet and other species. (<b>A</b>) Phylogenetic tree. Phylogenetic tree is constructed by AOX proteins of 17 species, including foxtail millet, rice, <span class="html-italic">Brachypodium distachyon</span>, <span class="html-italic">Triticum aestivum</span>, <span class="html-italic">Hordeum vulgare</span>, maize, sorghum, <span class="html-italic">Solanum tuberosum</span>, <span class="html-italic">Gossypium hirsutum</span>, <span class="html-italic">Brassica napus</span>, <span class="html-italic">Arabidopsis</span>, <span class="html-italic">Medicago sativa</span>, <span class="html-italic">Cicer arietinum</span>, <span class="html-italic">Cajanus cajan</span>, <span class="html-italic">Vigna unguiculata</span>, <span class="html-italic">Glycine max</span>, and <span class="html-italic">Solanum lycopersicum</span> with the neighbor-joining (NJ) method using MEGA11. Different colored ellipses represent different evolutionary clades and four clades are labeled with AOX1 (a, b, c), AOX1d, AOX2 (a, b, and c), and AOX2d. AOX proteins in foxtail millet are labeled in red. (<b>B</b>) Collinearity of <span class="html-italic">AOX</span> genes between foxtail millet, rice, and maize.</p>
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<p>Analysis of <span class="html-italic">cis</span>-elements in the <span class="html-italic">SiAOX</span> genes promoter regions. (<b>A</b>) The distribution of various <span class="html-italic">cis</span>-elements in the promoter regions. The different colored blocks represent the different types of <span class="html-italic">cis</span>-elements and their locations in upstream 2000 bp of <span class="html-italic">SiAOX</span> genes. (<b>B</b>) The <span class="html-italic">cis</span>-elements in the promoter regions of each <span class="html-italic">SiAOX</span> gene. The different colors and numbers in the grid indicate the numbers of different promoter elements in the <span class="html-italic">SiAOX</span> genes. Vertical bars with different colors indicate different <span class="html-italic">cis</span>-element types. (<b>C</b>) Count of three types of <span class="html-italic">cis</span>-elements in <span class="html-italic">SiAOX</span> genes promoter regions.</p>
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<p>The spatiotemporal expression patterns of <span class="html-italic">SiAOX</span> genes in multiple tissues during the whole growth period in foxtail millet. The expression matrices (TPM values) of five <span class="html-italic">SiAOX</span> genes in 27 important tissues of foxtail millet during the whole growth period are retrieved from the foxtail millet multi-omics database (MDSi). The data presented were calculated using the log<sub>2</sub>TPM method. The visualization is achieved by TBtools II (v2.102), with blue to red representing the amount of expression from low to high.</p>
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<p>RT-qPCR analysis of <span class="html-italic">SiAOX</span> genes under various abiotic stress treatments in shoot and root tissues. (<b>A</b>) Expression pattern of <span class="html-italic">SiAOX</span> genes in shoot tissue under cold stress. (<b>B</b>) Expression pattern of <span class="html-italic">SiAOX</span> genes in shoot tissue under drought stress. (<b>C</b>) Expression pattern of <span class="html-italic">SiAOX</span> genes in shoot tissue under salt stress. (<b>D</b>) Expression pattern of <span class="html-italic">SiAOX</span> genes in root tissue under cold stress. (<b>E</b>) Expression pattern of <span class="html-italic">SiAOX</span> genes in root tissue under drought stress. (<b>F</b>) Expression pattern of <span class="html-italic">SiAOX</span> genes in root tissue under salt stress. The unstressed level (0 h) was used as a control. * Indicates a significant different at <span class="html-italic">p</span> &lt; 0.05, ** indicates a significant at <span class="html-italic">p</span> &lt; 0.01, *** indicates a significant at <span class="html-italic">p</span> &lt; 0.001, and **** indicates a significant at <span class="html-italic">p</span> &lt; 0.0001.</p>
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<p>Co-expression network of five <span class="html-italic">SiAOX</span> genes in foxtail millet. (<b>A</b>) <span class="html-italic">SiAOX1</span>. (<b>B</b>) <span class="html-italic">SiAOX2</span>. (<b>C</b>) <span class="html-italic">SiAOX3</span>. (<b>D</b>) <span class="html-italic">SiAOX4</span>. (<b>E</b>) <span class="html-italic">SiAOX5</span>. The blue circle indicates the core gene that is both belongs to the network and <span class="html-italic">SiAOX</span> genes family, and green circle indicates the reported abiotic stress-related genes, the red circle indicates the annotated transcription factors, the yellow circle indicates other genes.</p>
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<p>Haplotype analysis of <span class="html-italic">SiAOX4</span> and <span class="html-italic">SiAOX5</span> genes in foxtail millet. (<b>A</b>,<b>D</b>) SNPs identified for haplotype analysis of <span class="html-italic">SiAOX4</span> and <span class="html-italic">SiAOX5</span>, respectively. Haplotype information of foxtail millet resources are provided in <a href="#app1-plants-13-02565" class="html-app">Tables S4 and S5</a> for SiAOX4 and SiAOX5, respectively. Survive rate of <span class="html-italic">SiAOX4</span> and <span class="html-italic">SiAOX5</span> after cold stress treatment are provided in <a href="#app1-plants-13-02565" class="html-app">Table S6 and Table S7</a>, respectively. (<b>B</b>,<b>E</b>) The survive rate of Hap_1 and Hap_2 after cold stress in <span class="html-italic">SiAOX4</span>, <span class="html-italic">SiAOX5</span>, respectively. (<b>C</b>,<b>F</b>) The relative height of Hap_1 and Hap_2 after cold stress in <span class="html-italic">SiAOX4</span>, <span class="html-italic">SiAOX5</span>, respectively. Relative height of <span class="html-italic">SiAOX4</span> and <span class="html-italic">SiAOX5</span> after cold stress treatment are provided in <a href="#app1-plants-13-02565" class="html-app">Table S8 and Table S9</a>, respectively.</p>
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<p>Combination haplotype and LD analysis of the region surrounding <span class="html-italic">SiAOX4</span> and <span class="html-italic">SiAOX5</span> genes. (<b>A</b>–<b>C</b>) Venn of materials between <span class="html-italic">SiAOX4</span> and <span class="html-italic">SiAOX5</span> gene of Hap_1, Hap_2, and Hap_3, respectively. (<b>D</b>) LD analysis of <span class="html-italic">SiAOX3</span>, <span class="html-italic">SiAOX4</span>, and <span class="html-italic">SiAOX5</span> genes.</p>
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<p>Model of the <span class="html-italic">SiAOX</span> genes responding to abiotic stress in foxtail millet.</p>
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16 pages, 1402 KiB  
Review
Research Progress on miRNAs and Artificial miRNAs in Insect and Disease Resistance and Breeding in Plants
by Zengfeng Ma, Jianyu Wang and Changyan Li
Genes 2024, 15(9), 1200; https://doi.org/10.3390/genes15091200 - 12 Sep 2024
Viewed by 409
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that are expressed in a tissue- and temporal-specific manner during development. They have been found to be highly conserved during the evolution of different species. miRNAs regulate the expression of several genes in various organisms, with some [...] Read more.
MicroRNAs (miRNAs) are small, non-coding RNAs that are expressed in a tissue- and temporal-specific manner during development. They have been found to be highly conserved during the evolution of different species. miRNAs regulate the expression of several genes in various organisms, with some regulating the expression of multiple genes with similar or completely unrelated functions. Frequent disease and insect pest infestations severely limit agricultural development. Thus, cultivating resistant crops via miRNA-directed gene regulation in plants, insects, and pathogens is an important aspect of modern breeding practices. To strengthen the application of miRNAs in sustainable agriculture, plant endogenous or exogenous miRNAs have been used for plant breeding. Consequently, the development of biological pesticides based on miRNAs has become an important avenue for future pest control methods. However, selecting the appropriate miRNA according to the desired target traits in the target organism is key to successfully using this technology for pest control. This review summarizes the progress in research on miRNAs in plants and other species involved in regulating plant disease and pest resistance pathways. We also discuss the molecular mechanisms of relevant target genes to provide new ideas for future research on pest and disease resistance and breeding in plants. Full article
(This article belongs to the Special Issue Plant Small RNAs: Biogenesis and Functions)
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<p>Molecular mechanisms related to the regulation of endogenous miRNA expression in plants. Primary microRNA (pri-miRNA) is transcribed by Pol II from miRNA-encoding genes. In the nucleus, the RNase III family enzyme DCL1, along with HYL1 and SE, processes pre-miRNA into miRNA/miRNA double strands. The miRNA/miRNA* double strand is methylated at its 3′ end by the miRNA methyltransferase HEN1. Once methylated, the miRNA/miRNA* double strand is transported from the nucleus to the cytoplasm through HASTY. In the cytoplasm, the miRNA/miRNA* double-stranded guide strands are incorporated into RISC. This process is involved in miRNA degradation, as well as miRNA-mediated gene silencing through target cleavage and translational repression [<a href="#B6-genes-15-01200" class="html-bibr">6</a>].</p>
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<p>Functions of exogenous and endogenous miRNAs and amiRNAs in disease and insect resistance in plants. MiRNAs, miRNA target mimetics, and amiRNAs related to plant disease and pest resistance can be synthesized externally or directly transferred into the crop genome to enhance crop disease and pest resistance.</p>
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21 pages, 3913 KiB  
Article
Cotton Disease Recognition Method in Natural Environment Based on Convolutional Neural Network
by Yi Shao, Wenzhong Yang, Jiajia Wang, Zhifeng Lu, Meng Zhang and Danny Chen
Agriculture 2024, 14(9), 1577; https://doi.org/10.3390/agriculture14091577 - 11 Sep 2024
Viewed by 234
Abstract
As an essential component of the global economic crop, cotton is highly susceptible to the impact of diseases on its yield and quality. In recent years, artificial intelligence technology has been widely used in cotton crop disease recognition, but in complex backgrounds, existing [...] Read more.
As an essential component of the global economic crop, cotton is highly susceptible to the impact of diseases on its yield and quality. In recent years, artificial intelligence technology has been widely used in cotton crop disease recognition, but in complex backgrounds, existing technologies have certain limitations in accuracy and efficiency. To overcome these challenges, this study proposes an innovative cotton disease recognition method called CANnet, and we independently collected and constructed an image dataset containing multiple cotton diseases. Firstly, we introduced the innovatively designed Reception Field Space Channel (RFSC) module to replace traditional convolution kernels. This module combines dynamic receptive field features with traditional convolutional features to effectively utilize spatial channel attention, helping CANnet capture local and global features of images more comprehensively, thereby enhancing the expressive power of features. At the same time, the module also solves the problem of parameter sharing. To further optimize feature extraction and reduce the impact of spatial channel attention redundancy in the RFSC module, we connected a self-designed Precise Coordinate Attention (PCA) module after the RFSC module to achieve redundancy reduction. In the design of the classifier, CANnet abandoned the commonly used MLP in traditional models and instead adopted improved Kolmogorov Arnold Networks-s (KANs) for classification operations. KANs technology helps CANnet to more finely utilize extracted features for classification tasks through learnable activation functions. This is the first application of the KAN concept in crop disease recognition and has achieved excellent results. To comprehensively evaluate the performance of CANnet, we conducted extensive experiments on our cotton disease dataset and a publicly available cotton disease dataset. Numerous experimental results have shown that CANnet outperforms other advanced methods in the accuracy of cotton disease identification. Specifically, on the self-built dataset, the accuracy reached 96.3%; On the public dataset, the accuracy reached 98.6%. These results fully demonstrate the excellent performance of CANnet in cotton disease identification tasks. Full article
(This article belongs to the Section Digital Agriculture)
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<p>Image display of self-built cotton disease dataset.</p>
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<p>Data preprocessing image display: (<b>a</b>) Self-built cotton disease dataset. (<b>b</b>) Public Cotton Disease Dataset.</p>
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<p>CANnet network architecture diagram. The feature extraction part mainly comprises the RFSC and PCA modules, and the KANs in the classifier part are the main innovations.</p>
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<p>RFSC module diagram.</p>
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<p>(<b>a</b>) The overall architecture of the PCA module. (<b>b</b>) The specific architecture of the SRU module. (<b>c</b>) The specific architecture of the CRU module.</p>
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<p>The confusion matrix diagram of CANnet on two datasets.</p>
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<p>(<b>a</b>) t-SNE plots of ResNet, MobileNetV2, and CANnet on self-built cotton disease datasets. (<b>b</b>) T-sne plots of ResNet, Mobile-Former, and CANnet on publicly available cotton disease datasets.</p>
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<p>(<b>a</b>) t-SNE plots of ResNet, MobileNetV2, and CANnet on self-built cotton disease datasets. (<b>b</b>) T-sne plots of ResNet, Mobile-Former, and CANnet on publicly available cotton disease datasets.</p>
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<p>Bar chart of specific species recognition accuracy using CANnet, ResNet18, and MobileNetV2 on a self-built cotton disease dataset.</p>
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<p>Bar chart of specific species recognition accuracy using CANnet, ResNet18, and Mobile-Former on a public cotton disease dataset.</p>
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<p>Attention visualization maps of ResNet, MobileNetV2, and CANnet on self-built cotton disease datasets. The darker the yellow, the better the attention effect.</p>
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<p>Attention visualization of ResNet, Mobile-Former, and CANnet on a public cotton disease dataset. The darker the yellow, the better the attention effect.</p>
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20 pages, 13462 KiB  
Article
Extraction of Garlic in the North China Plain Using Multi-Feature Combinations from Active and Passive Time Series Data
by Chuang Peng, Binglong Gao, Wei Wang, Wenji Zhu, Yongqi Chen and Chao Dong
Appl. Sci. 2024, 14(18), 8141; https://doi.org/10.3390/app14188141 - 10 Sep 2024
Viewed by 458
Abstract
Garlic constitutes a significant small-scale agricultural commodity in China. A key factor influencing garlic prices is the planted area, which can be accurately and efficiently determined using remote sensing technology. However, the spectral characteristics of garlic and winter wheat are easily confused, and [...] Read more.
Garlic constitutes a significant small-scale agricultural commodity in China. A key factor influencing garlic prices is the planted area, which can be accurately and efficiently determined using remote sensing technology. However, the spectral characteristics of garlic and winter wheat are easily confused, and the widespread intercropping of these crops in the study area exacerbates this issue, leading to significant challenges in remote sensing image analysis. Additionally, remote sensing data are often affected by weather conditions, spatial resolution, and revisit frequency, which can result in delayed and inaccurate area extraction. In this study, historical data were utilized to restore Sentinel-2 remote sensing images, aimed at mitigating cloud and rain interference. Feature combinations were devised, incorporating two vegetation indices into a comprehensive time series, along with Sentinel-1 synthetic aperture radar (SAR) time series and other temporal datasets. Multiple classification combinations were employed to extract garlic within the study area, and the accuracy of the classification results was systematically analyzed. First, we used passive satellite imagery to extract winter crops (garlic, winter wheat, and others) with high accuracy. Second, we identified garlic by applying various combinations of time series features derived from both active and passive remote sensing data. Third, we evaluated the classification outcomes of various feature combinations to generate an optimal garlic cultivation distribution map for each region. Fourth, we developed a garlic fragmentation index to assess the impact of landscape fragmentation on garlic extraction accuracy. The findings reveal that: (1) Better results in garlic extraction can be achieved using active–passive time series remote sensing. The performance of the classification model can be further enhanced by incorporating short-wave infrared bands or spliced time series data into the classification features. (2) Examination of garlic cultivation fragmentation using the garlic fragmentation index aids in elucidating variations in accuracy across the study area’s six counties. (3) Comparative analysis with validation samples demonstrated superior garlic extraction outcomes from the six primary garlic-producing counties of the North China Plain in 2021, achieving an overall precision exceeding 90%. This study offers a practical exploration of target crop identification using multi-source remote sensing data in mixed cropping areas. The methodology presented here demonstrates the potential for efficient, cost-effective, and accurate garlic classification, which is crucial for improving garlic production management and optimizing agricultural practices. Moreover, this approach holds promise for broader applications, such as nationwide garlic mapping. Full article
(This article belongs to the Special Issue Intelligent Computing and Remote Sensing—2nd Edition)
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<p>Diagram of garlic fertility period.</p>
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<p>Overview of the study area.</p>
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<p>Workflow of garlic extraction based on active–passive remote sensing time series data.</p>
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<p>The time series of Sentinel-2 NDVI for garlic and winter wheat. The curves in the figure represent the average NDVI values derived from the samples, while the upper and lower boundaries indicate the standard deviation.</p>
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<p>Time series of Sentinel-1 curves for garlic and winter wheat. (<b>a</b>) Time series data on the ratio of vertical–vertical (VV) and vertical–horizontal (VH) polarization in garlic and winter wheat. (<b>b</b>) Time series data of VV and VH polarization for garlic and winter wheat. The curves in the figure represent the average values derived from the samples.</p>
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<p>Winter crop distribution maps. This figure illustrates the winter vegetation classification results for each county within the study area. Green indicates areas of winter vegetation, while gray represents other land cover types.</p>
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<p>Winter crop distribution maps. This figure illustrates the winter vegetation classification results for each county within the study area. Green indicates areas of winter vegetation, while gray represents other land cover types.</p>
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<p>Garlic distribution maps. This figure illustrates the garlic classification results for each county within the study area. Blue indicates areas of garlic, while gray represents other land cover types.</p>
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11 pages, 1317 KiB  
Article
Biofortification of Cucumbers with Iron Using Bio-Chelates Derived from Spent Coffee Grounds: A Greenhouse Trial
by Ana Cervera-Mata, Leslie Lara-Ramos, José Ángel Rufián-Henares, Jesús Fernández-Bayo, Gabriel Delgado and Alejandro Fernández-Arteaga
Agronomy 2024, 14(9), 2063; https://doi.org/10.3390/agronomy14092063 - 9 Sep 2024
Viewed by 294
Abstract
The transformation of spent coffee grounds (SCGs) into hydrochars has been extensively studied in recent years to explore their potential in biofortifying foods and mitigating the plant toxicity associated with SCGs. This study aimed to evaluate the effects of adding activated (ASCG and [...] Read more.
The transformation of spent coffee grounds (SCGs) into hydrochars has been extensively studied in recent years to explore their potential in biofortifying foods and mitigating the plant toxicity associated with SCGs. This study aimed to evaluate the effects of adding activated (ASCG and AH160) and functionalized SCGs, as well as SCG-derived hydrochars (ASCG-Fe and AH160-Fe), on cucumber production and plant iron content. To achieve this, SCGs and SCG-derived hydrochars activated and functionalized with Fe were incorporated into cucumber crops grown in a greenhouse over multiple harvests. Among the treatments, SCG-Fe proved to be the most promising for cucumber production, yielding an average of 25 kg of cumulative production per treatment across three harvests. Regarding iron content, the average results across all harvests showed that SCGs and functionalized SCG-hydrochars matched the performance of the commercial chelate (0.108 vs. 0.11 mg Fe/100 g fresh weight). However, in subsequent harvests, iron appeared to leach out, with the activated bio-products (ASCG and AH160) leaving the highest iron reserves in the soil. Additionally, the hydrochar activated at 160 °C demonstrated the highest utilization efficiency. In conclusion, the incorporation of SCG residues and second-generation residues (hydrochars) shows promise as agents for biofortifying cucumbers. Full article
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<p>Cumulative production of cucumbers during the trial per treatment. AH160: activated hydrochar at 160 °C; AH160-Fe: activated and functionalized hydrochar at 160 °C; ASCG: activated spent coffee grounds; ASCG-Fe: activated and functionalized spent coffee grounds.</p>
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<p>Average Fe content in cucumbers per treatment. AH160: activated hydrochar at 160 °C; AH160-Fe: activated and functionalized hydrochar at 160 °C; ASCG: activated spent coffee grounds; ASCG-Fe: activated and functionalized spent coffee grounds. Different letters indicated statistically significant differences (<span class="html-italic">p</span> &lt; 0.05).</p>
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<p>Fe content in cucumbers per treatment, per harvest. AH160: activated hydrochar at 160 °C; AH160-Fe: activated and functionalized hydrochar at 160 °C; ASCG: activated spent coffee grounds; ASCG-Fe: activated and functionalized spent coffee grounds. Different letters indicated statistically significant differences between different harvests (<span class="html-italic">p</span> &lt; 0.05).</p>
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19 pages, 5717 KiB  
Article
Remote Prediction of Soybean Yield Using UAV-Based Hyperspectral Imaging and Machine Learning Models
by Adilson Berveglieri, Nilton Nobuhiro Imai, Fernanda Sayuri Yoshino Watanabe, Antonio Maria Garcia Tommaselli, Glória Maria Padovani Ederli, Fábio Fernandes de Araújo, Gelci Carlos Lupatini and Eija Honkavaara
AgriEngineering 2024, 6(3), 3242-3260; https://doi.org/10.3390/agriengineering6030185 - 9 Sep 2024
Viewed by 433
Abstract
Early soybean yield estimation has become a fundamental tool for market policy and food security. Considering a heterogeneous crop, this study investigates the spatial and spectral variability in soybean canopy reflectance to achieve grain yield estimation. Besides allowing crop mapping, remote sensing data [...] Read more.
Early soybean yield estimation has become a fundamental tool for market policy and food security. Considering a heterogeneous crop, this study investigates the spatial and spectral variability in soybean canopy reflectance to achieve grain yield estimation. Besides allowing crop mapping, remote sensing data also provide spectral evidence that can be used as a priori knowledge to guide sample collection for prediction models. In this context, this study proposes a sampling design method that distributes sample plots based on the spatial and spectral variability in vegetation spectral indices observed in the field. Random forest (RF) and multiple linear regression (MLR) approaches were applied to a set of spectral bands and six vegetation indices to assess their contributions to the soybean yield estimates. Experiments were conducted with a hyperspectral sensor of 25 contiguous spectral bands, ranging from 500 to 900 nm, carried by an unmanned aerial vehicle (UAV) to collect images during the R5 soybean growth stage. The tests showed that spectral indices specially designed from some bands could be adopted instead of using multiple bands with MLR. However, the best result was obtained with RF using spectral bands and the height attribute extracted from the photogrammetric height model. In this case, Pearson’s correlation coefficient was 0.91. The difference between the grain yield productivity estimated with the RF model and the weight collected at harvest was 1.5%, indicating high accuracy for yield prediction. Full article
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<p>Study area with soybean planting delimited by the red line—located in the western region of the state of São Paulo, Brazil. Image sources: Google Earth (on the <b>left</b>) and RGB image collected on 25 January 2020, with a UAV Phantom 3—DJI (on the <b>right</b>).</p>
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<p>Timeline presenting the progress of data collection in the study area.</p>
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<p>(<b>a</b>) FPI camera; (<b>b</b>) UAV in operation to acquire hyperspectral images.</p>
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<p>Image block adjustment of a hyperspectral band, showing two flying strips and six GCPs.</p>
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<p>(<b>a</b>) DTM. (<b>b</b>) Example of a cross-section in the CHM.</p>
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<p>Positions selected for 30 sample plots following the variability evidenced by the spectral indices: (<b>a</b>) NDVI; (<b>b</b>) SR; and (<b>c</b>) TCARI.</p>
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<p>(<b>a</b>) Descriptive statistics; (<b>b</b>) confidence interval; (<b>c</b>) normality test chart (red dots are the observed values).</p>
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<p>Grain yield production in kg/ha estimated from each sample plot, following the spatial distribution of <a href="#agriengineering-06-00185-f006" class="html-fig">Figure 6</a>.</p>
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<p>Comparison of results with the RF model when the height attribute is used with each vegetation index.</p>
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<p>Maps of grain productivity generated by the predictor models: (<b>a</b>) RF and (<b>b</b>) MLR.</p>
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21 pages, 10577 KiB  
Article
Evaluation of Sugarcane Crop Growth Monitoring Using Vegetation Indices Derived from RGB-Based UAV Images and Machine Learning Models
by P. P. Ruwanpathirana, Kazuhito Sakai, G. Y. Jayasinghe, Tamotsu Nakandakari, Kozue Yuge, W. M. C. J. Wijekoon, A. C. P. Priyankara, M. D. S. Samaraweera and P. L. A. Madushanka
Agronomy 2024, 14(9), 2059; https://doi.org/10.3390/agronomy14092059 - 9 Sep 2024
Viewed by 322
Abstract
Crop monitoring with unmanned aerial vehicles (UAVs) has the potential to reduce field monitoring costs while increasing monitoring frequency and improving efficiency. However, the utilization of RGB-based UAV imagery for crop-specific monitoring, especially for sugarcane, remains limited. This work proposes a UAV platform [...] Read more.
Crop monitoring with unmanned aerial vehicles (UAVs) has the potential to reduce field monitoring costs while increasing monitoring frequency and improving efficiency. However, the utilization of RGB-based UAV imagery for crop-specific monitoring, especially for sugarcane, remains limited. This work proposes a UAV platform with an RGB camera as a low-cost solution to monitor sugarcane fields, complementing the commonly used multi-spectral methods. This new approach optimizes the RGB vegetation indices for accurate prediction of sugarcane growth, providing many improvements in scalable crop-management methods. The images were captured by a DJI Mavic Pro drone. Four RGB vegetation indices (VIs) (GLI, VARI, GRVI, and MGRVI) and the crop surface model plant height (CSM_PH) were derived from the images. The fractional vegetation cover (FVC) values were compared by image classification. Sugarcane plant height predictions were generated using two machine learning (ML) algorithms—multiple linear regression (MLR) and random forest (RF)—which were compared across five predictor combinations (CSM_PH and four VIs). At the early stage, all VIs showed significantly lower values than later stages (p < 0.05), indicating an initial slow progression of crop growth. MGRVI achieved a classification accuracy of over 94% across all growth phases, outperforming traditional indices. Based on the feature rankings, VARI was the least sensitive parameter, showing the lowest correlation (r < 0.5) and mutual information (MI < 0.4). The results showed that the RF and MLR models provided better predictions for plant height. The best estimation results were observed withthe combination of CSM_PH and GLI utilizing RF model (R2 = 0.90, RMSE = 0.37 m, MAE = 0.27 m, and AIC = 21.93). This study revealed that VIs and the CSM_PH derived from RGB images captured by UAVs could be useful in monitoring sugarcane growth to boost crop productivity. Full article
(This article belongs to the Section Precision and Digital Agriculture)
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<p>Location of the study area: (<b>a</b>) Google location map of Sri Lanka, and (<b>b</b>) map of Galoya Plantations, Hingurana, Sri Lanka.</p>
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<p>(<b>a</b>) DJI Mavic Pro drone mounted with RGB bands along with its controlling mechanism (source: <a href="https://www.dji.com" target="_blank">https://www.dji.com</a>, accessed on 2 August 2021) and (<b>b</b>) artificial markings for GCPs measurement using GNSS receiver.</p>
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<p>Workflow for flight planning and image acquisition.</p>
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<p>The conceptual framework developed for the whole study (AOI, area of interest; DSM, digital surface model; DTM, digital terrain model; CSM, crop surface model; PH, plant height; VI, vegetation index; <span class="html-italic">r</span>, Pearson correlation of coefficient; MI, mutual information; MLR, multiple linear regression and RF, random forest).</p>
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<p>RGB mosaic images at different growth stages (F1 = tillering stage, F2 = early grand growth stage, F3 = later grand growth stage, F4 = ripening stage).</p>
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<p>The site appearance of a barren area in the field.</p>
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<p>Vegetation pattern distribution based on the vegetation indices at the later grand growth stage: (<b>a</b>) GLI, (<b>b</b>) VARI, (<b>c</b>) GRVI, (<b>d</b>) MGRVI. Red areas are row spaces, inter-plot regions, and barren areas; green areas are vegetation.</p>
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<p>Crop growth development is based on the vegetation cover. (F1, tillering stage; F2, early grand growth stage; F3, later grand growth stage; F4, ripening stage).</p>
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<p>Plant height model prediction results for multiple linear regression (MLR) and random forest (RF) algorithms:(<b>A</b>) coefficient of determination, (<b>B</b>) root mean square error (RMSE) and (<b>C</b>) mean absolute error (MAE). The models were predicted using four variable combinations: (a) single best (CSM_PH), (b) two best (CSM_PH + GLI), (c) three best (CSM_PH + GLI + GRVI), and (d) four best (CSM_PH + GLI + GRVI + MGRVI).</p>
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<p>Akaike’s information criterion (AIC) results for the plant height prediction results using the RF models; (1) single best (CSM_PH), (2) two best (CSM_PH + GLI), (3) three best (CSM_PH + GLI + GRVI), and (4) four best (CSM_PH + GLI + GRVI + MGRVI).</p>
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<p>Scatter plot of RF-predicted plant height vs. field-observed plant height for RF model, and CSM-derived plant height vs. field-measured plant height. The RF plots are based on the selection of the two best variables (CSM_PH + GLI) combination (Model 2). The dashed line is a 1:1 line.</p>
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24 pages, 8373 KiB  
Article
Hyperspectral Estimation of Chlorophyll Content in Wheat under CO2 Stress Based on Fractional Order Differentiation and Continuous Wavelet Transforms
by Liuya Zhang, Debao Yuan, Yuqing Fan, Renxu Yang, Maochen Zhao, Jinbao Jiang, Wenxuan Zhang, Ziyi Huang, Guidan Ye and Weining Li
Remote Sens. 2024, 16(17), 3341; https://doi.org/10.3390/rs16173341 - 9 Sep 2024
Viewed by 533
Abstract
The leaf chlorophyll content (LCC) of winter wheat, an important food crop widely grown worldwide, is a key indicator for assessing its growth and health status in response to CO2 stress. However, the remote sensing quantitative estimation of winter wheat LCC under [...] Read more.
The leaf chlorophyll content (LCC) of winter wheat, an important food crop widely grown worldwide, is a key indicator for assessing its growth and health status in response to CO2 stress. However, the remote sensing quantitative estimation of winter wheat LCC under CO2 stress conditions also faces challenges such as an unclear spectral sensitivity range, baseline drift, overlapping spectral peaks, and complex spectral response due to CO2 stress changes. To address these challenges, this study introduced the fractional order derivative (FOD) and continuous wavelet transform (CWT) techniques into the estimation of winter wheat LCC. Combined with the raw hyperspectral data, we deeply analyzed the spectral response characteristics of winter wheat LCC under CO2 stress. We proposed a stacking model including multiple linear regression (MLR), decision tree regression (DTR), random forest (RF), and adaptive boosting (AdaBoost) to filter the optimal combination from a large number of feature variables. We use a dual-band combination and vegetation index strategy to achieve the accurate estimation of LCC in winter wheat under CO2 stress. The results showed that (1) the FOD and CWT methods significantly improved the correlation between the raw spectral reflectance and LCC of winter wheat under CO2 stress. (2) The 1.2-order derivative dual-band index (RVI (R720, R522)) constructed by combining the sensitive spectral bands of the CO2 response of winter wheat leaves achieved a high-precision estimation of the LCC under CO2 stress conditions (R2 = 0.901). Meanwhile, the red-edged vegetation stress index (RVSI) constructed based on the CWT technique at specific scales also demonstrated good performance in LCC estimation (R2 = 0.880), verifying the effectiveness of the multi-scale analysis in revealing the mechanism of the CO2 impact on winter wheat. (3) By stacking the sensitive spectral features extracted by combining the FOD and CWT methods, we further improved the LCC estimation accuracy (R2 = 0.906). This study not only provides a scientific basis and technical support for the accurate estimation of LCC in winter wheat under CO2 stress but also provides new ideas and methods for coping with climate change, optimizing crop-growing conditions, and improving crop yield and quality in agricultural management. The proposed method is also of great reference value for estimating physiological parameters of other crops under similar environmental stresses. Full article
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Graphical abstract

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<p>Research zone.</p>
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<p>Spatial distribution of experimental sites. Note: the spatial distribution of experimental sites is adapted with permission from Ref. [<a href="#B21-remotesensing-16-03341" class="html-bibr">21</a>]. 2024, Liuya Zhang.</p>
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<p>Gas concentration measurement points.</p>
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<p>LCC of wheat under different (<b>a</b>) reproductive and (<b>b</b>) CO<sub>2</sub> stresses. Different uppercase letters indicate significant differences among the four treatments, and different lowercase letters indicate significant differences among the same treatment over the four reproductive periods (<span class="html-italic">p</span> &lt; 0.05).</p>
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<p>Canopy spectra of wheat under different CO<sub>2</sub> stresses at the (<b>a</b>) joining, (<b>b</b>) tasseling, (<b>c</b>) flowering, and (<b>d</b>) grouting stages.</p>
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<p>FOD-based reflectance spectral profiles of wheat leaves of different orders (<b>a</b>) raw spectra (<b>b</b>–<b>k</b>) 0.2–2 orders with different order derivatives in steps of 0.2.</p>
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<p>Correlation coefficients between LCC and different orders of spectra within FOD.</p>
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<p>CWT-based reflectance spectral profiles of wheat leaves at different scales. (<b>a</b>) Original spectral profile, (<b>b</b>–<b>k</b>) spectral profile on scales 1–10, and (<b>l</b>) localized magnification at the 10th scale.</p>
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<p>Correlation coefficients between LCC and different scale spectra within the CWT.</p>
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<p>Correlation coefficients of LCC and vegetation indices at different scales under CWT.</p>
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<p>MLR-based regression analyses for single-band, dual-band, and vegetation index features. Dual-band MLR model based on (<b>a</b>) FOD and (<b>d</b>) raw spectra, single-band MLR model based on (<b>b</b>) FOD and (<b>e</b>) raw spectra, and MLR model for vegetation indices based on (<b>c</b>) CWT and (<b>f</b>) raw spectra, with dotted lines in the graphs showing the 1:1 fit line between the predicted and measured LCC values.</p>
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<p>Stacking-based RVI estimation results for 1.2 order derivatives. (<b>a</b>–<b>d</b>) Comparison of R<sup>2</sup>, RMSE, and MAE between training and test sets for evaluating LCC under 4 models of DTR, RF, Adaboost, and stacking; the dashed line in the figure is the 1:1 fit line between the predicted and measured LCC. (<b>e</b>) Comparison of predicted and measured LCC for the stacking model.</p>
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<p>Stacking-based RVSI estimation results. (<b>a</b>–<b>d</b>) Comparison of R<sup>2</sup>, RMSE, and MAE between training and test sets for evaluating LCC under 4 models of DTR, RF, Adaboost, and stacking. The dashed line in the figure is the 1:1 fit line between the predicted and measured LCC values. (<b>e</b>) Comparison of predicted and measured LCC values for the stacking model.</p>
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<p>Stacking-based RVI and RVSI estimation results. (<b>a</b>–<b>d</b>) Comparison of R<sup>2</sup>, RMSE, and MAE between training and test sets for evaluating LCC under 4 models of DTR, RF, Adaboost, and stacking. The dashed line in the figure is the 1:1 fit line between the predicted and measured LCC values. (<b>e</b>) Comparison of predicted and measured LCC values for the stacking model.</p>
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<p>Further analysis of deviation values of LCC values. (<b>a</b>) Comparison of the deviation of LCC values for 1.2-order RVI and cwt8_RVSI, (<b>b</b>) Comparison of the deviation of LCC values for 1.2-order RVI and RVI combined with cwt8_RVSI, and (<b>c</b>) Comparison of the deviation of LCC values for cwt8_RVSI and 1.2-order RVI combined withcwt8_RVSI.</p>
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