Nothing Special   »   [go: up one dir, main page]

You seem to have javascript disabled. Please note that many of the page functionalities won't work as expected without javascript enabled.
 
 
Sign in to use this feature.

Years

Between: -

Subjects

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Journals

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Article Types

Countries / Regions

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Search Results (2,590)

Search Parameters:
Keywords = crop mapping

Order results
Result details
Results per page
Select all
Export citation of selected articles as:
24 pages, 10412 KiB  
Article
Deep Learning for Weed Detection and Segmentation in Agricultural Crops Using Images Captured by an Unmanned Aerial Vehicle
by Josef Augusto Oberdan Souza Silva, Vilson Soares de Siqueira, Marcio Mesquita, Luís Sérgio Rodrigues Vale, Thiago do Nascimento Borges Marques, Jhon Lennon Bezerra da Silva, Marcos Vinícius da Silva, Lorena Nunes Lacerda, José Francisco de Oliveira-Júnior, João Luís Mendes Pedroso de Lima and Henrique Fonseca Elias de Oliveira
Remote Sens. 2024, 16(23), 4394; https://doi.org/10.3390/rs16234394 (registering DOI) - 24 Nov 2024
Abstract
Artificial Intelligence (AI) has changed how processes are developed, and decisions are made in the agricultural area replacing manual and repetitive processes with automated and more efficient ones. This study presents the application of deep learning techniques to detect and segment weeds in [...] Read more.
Artificial Intelligence (AI) has changed how processes are developed, and decisions are made in the agricultural area replacing manual and repetitive processes with automated and more efficient ones. This study presents the application of deep learning techniques to detect and segment weeds in agricultural crops by applying models with different architectures in the analysis of images captured by an Unmanned Aerial Vehicle (UAV). This study contributes to the computer vision field by comparing the performance of the You Only Look Once (YOLOv8n, YOLOv8s, YOLOv8m, and YOLOv8l), Mask R-CNN (with framework Detectron2), and U-Net models, making public the dataset with aerial images of soybeans and beans. The models were trained using a dataset consisting of 3021 images, randomly divided into test, validation, and training sets, which were annotated, resized, and increased using the Roboflow application interface. Evaluation metrics were used, which included training efficiency (mAP50 and mAP50-90), precision, accuracy, and recall in the model’s evaluation and comparison. The YOLOv8s variant achieved higher performance with an mAP50 of 97%, precision of 99.7%, and recall of 99% when compared to the other models. The data from this manuscript show that deep learning models can generate efficient results for automatic weed detection when trained with a well-labeled and large set. Furthermore, this study demonstrated the great potential of using advanced object segmentation algorithms in detecting weeds in soybean and bean crops. Full article
23 pages, 9861 KiB  
Article
A Synergistic Framework for Coupling Crop Growth, Radiative Transfer, and Machine Learning to Estimate Wheat Crop Traits in Pakistan
by Rana Ahmad Faraz Ishaq, Guanhua Zhou, Aamir Ali, Syed Roshaan Ali Shah, Cheng Jiang, Zhongqi Ma, Kang Sun and Hongzhi Jiang
Remote Sens. 2024, 16(23), 4386; https://doi.org/10.3390/rs16234386 (registering DOI) - 24 Nov 2024
Viewed by 297
Abstract
The integration of the Crop Growth Model (CGM), Radiative Transfer Model (RTM), and Machine Learning Algorithm (MLA) for estimating crop traits represents a cutting-edge area of research. This integration requires in-depth study to address RTM limitations, particularly of similar spectral responses from multiple [...] Read more.
The integration of the Crop Growth Model (CGM), Radiative Transfer Model (RTM), and Machine Learning Algorithm (MLA) for estimating crop traits represents a cutting-edge area of research. This integration requires in-depth study to address RTM limitations, particularly of similar spectral responses from multiple input combinations. This study proposes the integration of CGM and RTM for crop trait retrieval and evaluates the performance of CGM output-based RTM spectra generation for multiple crop traits estimation without biased sampling using machine learning models. Moreover, PROSAIL spectra as training against Harmonized Landsat Sentinel-2 (HLS) as testing was also compared with HLS data only as an alternative. It was found that satellite data (HLS, 80:20) not only consistently performed better, but PROSAIL (train) and HLS (test) also had satisfactory results for multiple crop traits from uniform training samples in spite of differences in simulated and real data. PROSAIL-HLS has an RMSE of 0.67 for leaf area index (LAI), 5.66 µg/cm2 for chlorophyll ab (Cab), 0.0003 g/cm2 for dry matter content (Cm), and 0.002 g/cm2 for leaf water content (Cw) against the HLS only, with an RMSE of 0.40 for LAI, 3.28 µg/cm2 for Cab, 0.0002 g/cm2 for Cm, and 0.001 g/cm2 for Cw. Optimized machine learning models, namely Extreme Gradient Boost (XGBoost) for LAI, Support Vector Machine (SVM) for Cab, and Random Forest (RF) for Cm and Cw, were deployed for temporal mapping of traits to be used for wheat productivity enhancement. Full article
(This article belongs to the Section Remote Sensing in Agriculture and Vegetation)
Show Figures

Figure 1

Figure 1
<p>Methodology flowchart.</p>
Full article ">Figure 2
<p>Location map.</p>
Full article ">Figure 3
<p>APSIM calibration for LAI.</p>
Full article ">Figure 4
<p>Scatterplots showing each model performance on Dataset-1 (PROSAIL-HLS) against each crop trait.</p>
Full article ">Figure 5
<p>Scatterplots showing each model performance on Dataset-2 (HLS only) against each crop trait.</p>
Full article ">Figure 6
<p>Temporal mapping of wheat crop traits.</p>
Full article ">Figure 7
<p>Reflectance differences and changes in traits over time (Abdul Sattar Village Massa Kota). (<b>a</b>) PROSAIL reflectance over time. (<b>b</b>) HLS reflectance over time. (<b>c</b>) LAI and Cab over time.</p>
Full article ">
19 pages, 6256 KiB  
Article
Major and Trace Airborne Elements and Ecological Risk Assessment: Georgia Moss Survey 2019–2023
by Omari Chaligava, Inga Zinicovscaia, Alexandra Peshkova, Nikita Yushin, Marina Frontasyeva, Konstantin Vergel, Makhabbat Nurkassimova and Liliana Cepoi
Plants 2024, 13(23), 3298; https://doi.org/10.3390/plants13233298 (registering DOI) - 23 Nov 2024
Viewed by 205
Abstract
The study, carried out as part of the International Cooperative Program on Effects of Air Pollution on Natural Vegetation and Crops, involved collecting 95 moss samples across the territory of Georgia during the period from 2019 to 2023. Primarily samples of Hypnum cupressiforme [...] Read more.
The study, carried out as part of the International Cooperative Program on Effects of Air Pollution on Natural Vegetation and Crops, involved collecting 95 moss samples across the territory of Georgia during the period from 2019 to 2023. Primarily samples of Hypnum cupressiforme were selected, with supplementary samples of Abietinella abietina, Pleurozium schreberi, and Hylocomium splendens in cases of the former’s absence. The content of 14 elements (Al, Ba, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, S, Sr, V, and Zn) was detected using Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES), while the Hg content was determined using a Direct Mercury Analyzer. To identify any relationships between chemical elements and to depict their sources, multivariate statistics was applied. Principal component analysis identified three main components: PC1 (geogenic, 43.4%), PC2 (anthropogenic, 13.3%), and PC3 (local anomalies, 8.5%). The results were compared with the first moss survey conducted in Georgia in the period from 2014 to 2017, offering insights into temporal trends of air quality. Utilizing GIS, a spatial map illustrating pollution levels across Georgia, based on the Pollution Load Index, was generated. The Potential Environmental Risk Index emphasized significant risks associated with mercury and cadmium at several locations. The study highlights the utility of moss biomonitoring in assessing air pollution and identifying hotspots of contamination. The findings from this study could be beneficial for future biomonitoring research in areas with varying physical and geographical conditions. Full article
Show Figures

Figure 1

Figure 1
<p>Correlation matrix between the elements of the entire initial data set. X stands for not significant.</p>
Full article ">Figure 2
<p>(<b>a</b>) Biplot of PC1 and PC2 denote the first two principal components explaining 56.7% of the variance in the data. (<b>b</b>) Biplot of PC2 and PC3 represent the second and third principal components explaining 21.8% of the variance in the data. Each point, distinguished by a unique combination of color and symbol, represents a sample of one of the four species. Arrows emanate from the origin, representing the variables.</p>
Full article ">Figure 2 Cont.
<p>(<b>a</b>) Biplot of PC1 and PC2 denote the first two principal components explaining 56.7% of the variance in the data. (<b>b</b>) Biplot of PC2 and PC3 represent the second and third principal components explaining 21.8% of the variance in the data. Each point, distinguished by a unique combination of color and symbol, represents a sample of one of the four species. Arrows emanate from the origin, representing the variables.</p>
Full article ">Figure 3
<p>PMF analysis factor fingerprint showing the percentage contribution of three identified factors (Factor 1, Factor 2, Factor 3) across various elements measured in the moss samples.</p>
Full article ">Figure 4
<p>Comparison of Contamination Factors (CF) between current (95 Samples) and previous (120 Samples) moss surveys in Georgia.</p>
Full article ">Figure 5
<p>Spatial distribution of the Pollution Load Index (PLI) across all sampling locations. The PLI is represented by colored dots on the map, with different colors indicating varying levels of pollution. Each dot corresponds to a specific sampling site, numbered for reference purposes.</p>
Full article ">Figure 6
<p>Boxplots of the Potential Ecological Risk Index (PERI) for selected elements accumulated by the mosses.</p>
Full article ">Figure 7
<p>Map of sampling locations with color-coded markers to indicate moss species collected. Red dots indicate <span class="html-italic">Abietinella abietina</span>, green—<span class="html-italic">Hylocomium splendens</span>, yellow—<span class="html-italic">Hypnum cupressiforme</span>, and blue—<span class="html-italic">Pleurozium schreberi</span>.</p>
Full article ">
17 pages, 5102 KiB  
Article
Application of Image-Based Phenotyping for QTL Identification of Tiller Angle in Rice (Oryza sativa L.)
by Yoon-Hee Jang, Song Lim Kim, Jeongho Baek, Hongseok Lee, Chaewon Lee, Inchan Choi, Nyunhee Kim, Tae-Ho Kim, Ye-Ji Lee, Hyeonso Ji and Kyung-Hwan Kim
Plants 2024, 13(23), 3288; https://doi.org/10.3390/plants13233288 - 22 Nov 2024
Viewed by 274
Abstract
Rice tiller angle is a key agronomic trait that regulates plant architecture and plays a critical role in determining rice yield. Given that tiller angle is regulated by multiple genes, it is important to identify quantitative trait loci (QTL) associated with tiller angle. [...] Read more.
Rice tiller angle is a key agronomic trait that regulates plant architecture and plays a critical role in determining rice yield. Given that tiller angle is regulated by multiple genes, it is important to identify quantitative trait loci (QTL) associated with tiller angle. Recently, with the advancement of imaging technology for plant phenotyping, it has become possible to quickly and accurately measure agronomic traits of breeding populations. In this study, we extracted tiller angle and various image-based parameters from Red-Green-Blue (RGB) images of a recombinant inbred line (RIL) population derived from a cross between Milyang23 (Indica) and Giho (Japonica). Correlations among the obtained data were analyzed, and through dynamic QTL mapping, five major QTLs (qTA1, qTA1-1, qTA2, qTA2-1, and qTA9) related to tiller angle were detected on chromosomes 1, 2, and 9. Among them, 26 candidate genes related to auxin signaling and plant growth, including the TAC1 (Tiller Angle Control 1) gene, were identified in qTA9 (RM257-STS09048). These results demonstrate the potential of image-based phenotyping to overcome the limitations of traditional manual measurements in crop structure research. Furthermore, the identification of key QTLs and candidate genes related to tiller angle provides valuable genetic insights for the development of high-yielding varieties through crop morphology control. Full article
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
19 pages, 53371 KiB  
Article
Efficient UAV-Based Automatic Classification of Cassava Fields Using K-Means and Spectral Trend Analysis
by Apinya Boonrang, Pantip Piyatadsananon and Tanakorn Sritarapipat
AgriEngineering 2024, 6(4), 4406-4424; https://doi.org/10.3390/agriengineering6040250 - 22 Nov 2024
Viewed by 284
Abstract
High-resolution images captured by Unmanned Aerial Vehicles (UAVs) play a vital role in precision agriculture, particularly in evaluating crop health and detecting weeds. However, the detailed pixel information in these images makes classification a time-consuming and resource-intensive process. Despite these challenges, UAV imagery [...] Read more.
High-resolution images captured by Unmanned Aerial Vehicles (UAVs) play a vital role in precision agriculture, particularly in evaluating crop health and detecting weeds. However, the detailed pixel information in these images makes classification a time-consuming and resource-intensive process. Despite these challenges, UAV imagery is increasingly utilized for various agricultural classification tasks. This study introduces an automatic classification method designed to streamline the process, specifically targeting cassava plants, weeds, and soil classification. The approach combines K-means unsupervised classification with spectral trend-based labeling, significantly reducing the need for manual intervention. The method ensures reliable and accurate classification results by leveraging color indices derived from RGB data and applying mean-shift filtering parameters. Key findings reveal that the combination of the blue (B) channel, Visible Atmospherically Resistant Index (VARI), and color index (CI) with filtering parameters, including a spatial radius (sp) = 5 and a color radius (sr) = 10, effectively differentiates soil from vegetation. Notably, using the green (G) channel, excess red (ExR), and excess green (ExG) with filtering parameters (sp = 10, sr = 20) successfully distinguishes cassava from weeds. The classification maps generated by this method achieved high kappa coefficients of 0.96, with accuracy levels comparable to supervised methods like Random Forest classification. This technique offers significant reductions in processing time compared to traditional methods and does not require training data, making it adaptable to different cassava fields captured by various UAV-mounted optical sensors. Ultimately, the proposed classification process minimizes manual intervention by incorporating efficient pre-processing steps into the classification workflow, making it a valuable tool for precision agriculture. Full article
(This article belongs to the Special Issue Computer Vision for Agriculture and Smart Farming)
Show Figures

Figure 1

Figure 1
<p>Study area of cassava fields captured by the DJI Phantom 4 Pro sensor.</p>
Full article ">Figure 2
<p>Study area of cassava fields captured by the DJI Phantom 4 sensor.</p>
Full article ">Figure 3
<p>Proposed classification process.</p>
Full article ">Figure 4
<p>Boxplot of the spectral value of classes.</p>
Full article ">Figure 5
<p>Kappa coefficient of K-means, RF, and the proposed classification process.</p>
Full article ">Figure 6
<p>Classification results using the proposed classification process: (<b>a</b>) Plot 1, showing results from an area with patchy weeds and thin weed patches; (<b>b</b>) Plot 5, showing results from an area with fewer weed patches and dense weed coverage; (<b>c</b>) Plot 8, showing results from an area with varying light illumination.</p>
Full article ">
20 pages, 9880 KiB  
Article
Estimating Rice Leaf Nitrogen Content and Field Distribution Using Machine Learning with Diverse Hyperspectral Features
by Ting Tian, Jianliang Wang, Yueyue Tao, Fangfang Ji, Qiquan He, Chengming Sun and Qing Zhang
Agronomy 2024, 14(12), 2760; https://doi.org/10.3390/agronomy14122760 - 21 Nov 2024
Viewed by 208
Abstract
Leaf nitrogen content (LNC) is a vital agronomic parameter in rice, commonly used to evaluate photosynthetic capacity and diagnose crop nutrient levels. Nitrogen deficiency can significantly reduce yield, underscoring the importance of accurate LNC estimation for practical applications. This study utilizes hyperspectral UAV [...] Read more.
Leaf nitrogen content (LNC) is a vital agronomic parameter in rice, commonly used to evaluate photosynthetic capacity and diagnose crop nutrient levels. Nitrogen deficiency can significantly reduce yield, underscoring the importance of accurate LNC estimation for practical applications. This study utilizes hyperspectral UAV imagery to acquire rice canopy data, applying various machine learning regression algorithms (MLR) to develop an LNC estimation model and create a nitrogen concentration distribution map, offering valuable guidance for subsequent field nitrogen management. The analysis incorporates four types of spectral data extracted throughout the rice growth cycle: original reflectance bands (OR bands), vegetation indices (VIs), first-derivative spectral bands (FD bands), and hyperspectral variable parameters (HSPs) as model inputs, while measured nitrogen concentration serves as the output. Results demonstrate that the random forest regression (RFR) and gradient boosting decision tree (GBDT) algorithms performed effectively, with the GBDT achieving the highest average R2 of 0.76 across different nitrogen treatments. Among the nitrogen estimation models for various rice varieties, RFR exhibited superior accuracy, achieving an R2 of 0.95 for the SuXiangJing100 variety, while the GBDT reached 0.93. Meanwhile, the support vector machine regression (SVMR) showed slightly lower accuracy, and partial least-squares regression (PLSR) was the least effective. This study developed an LNC estimation method applicable to the whole growth stage of common rice varieties. The method is suitable for estimating rice LNC across different growth stages, varieties, and nitrogen treatments, and it also provides a reference for nitrogen estimation and fertilization planning at flight altitudes other than the 120 m used in this study. Full article
(This article belongs to the Special Issue Unmanned Farms in Smart Agriculture)
Show Figures

Graphical abstract

Graphical abstract
Full article ">Figure 1
<p>Study site and field experiment layout. Note: (<b>a</b>) is the location and latitude, longitude information of the province where the experiment was conducted; (<b>b</b>) is the location and latitude, longitude information of the city where the experiment was conducted; and (<b>c</b>) is the specific distribution of the experimental field and the design of the nitrogen fertiliser treatments, in (<b>c</b>), serial numbers 1-30 were divided into 15 fertiliser plots, with one nitrogen fertiliser treatment set up in each plot, and each nitrogen fertiliser treatment contained two varieties.</p>
Full article ">Figure 2
<p>Flow chart of the experimental treatments.</p>
Full article ">Figure 3
<p>Spectral reflectance and field-measured LNC results for the sample set throughout the whole growth stage. Note: (<b>a</b>–<b>d</b>) present the changes in the spectral curves of the rice canopy during the four different growth stages. The portion of the curve with large variations was selected using solid red rectangles, and the red dashed rectangles were used to select the red-bordered regions with increasing spectral reflectance. The red arrow in (<b>b</b>) indicates the slope of the spectral reflectance rise. Panel (<b>e</b>) presents field-measured LNC values across four growth stages, with 30 samples shown for each stage. The abbreviations represent the four growth stages: TE (tillering), JT (jointing), HD (heading), and MK (milky).</p>
Full article ">Figure 4
<p>Hyperspectral reflectance bands and feature screening results.</p>
Full article ">Figure 5
<p>Estimation performance of different regression algorithms for constructing nitrogen models.</p>
Full article ">Figure 6
<p>Estimation accuracy of rice whole growth stage models under different nitrogen fertilizer treatments.</p>
Full article ">Figure 7
<p>Distribution of LNC in the rice field. Note: The plots with high accuracy of model estimation are circled by red ellipses in (<b>a</b>). Rice samples were measured using a Konica Minolta SPAD-502plus handheld chlorophyll meter (Zhejiang Toppan Yunnong Science and Technology Co, Ltd, Hangzhou, China). Each leaf was measured three times at equal intervals, and the average was calculated. The SPAD value for each plot was then obtained by averaging the values from five leaves.</p>
Full article ">Figure 8
<p>Estimation effect of rice nitrogen model on different varieties.</p>
Full article ">Figure 9
<p>Effects of different flight altitudes on RFR nitrogen modeling. Note: Hyperspectral reflectance curves at different flight altitudes (60, 120, and 300m) show the results of 176 reflectance variations with flight efficiency scores and R<sup>2</sup> upper right corner.</p>
Full article ">
30 pages, 929 KiB  
Review
Drones in Precision Agriculture: A Comprehensive Review of Applications, Technologies, and Challenges
by Ridha Guebsi, Sonia Mami and Karem Chokmani
Drones 2024, 8(11), 686; https://doi.org/10.3390/drones8110686 - 19 Nov 2024
Viewed by 1087
Abstract
In the face of growing challenges in modern agriculture, such as climate change, sustainable resource management, and food security, drones are emerging as essential tools for transforming precision agriculture. This systematic review, based on an in-depth analysis of recent scientific literature (2020–2024), provides [...] Read more.
In the face of growing challenges in modern agriculture, such as climate change, sustainable resource management, and food security, drones are emerging as essential tools for transforming precision agriculture. This systematic review, based on an in-depth analysis of recent scientific literature (2020–2024), provides a comprehensive synthesis of current drone applications in the agricultural sector, primarily focusing on studies from this period while including a few notable exceptions of particular interest. Our study examines in detail the technological advancements in drone systems, including innovative aerial platforms, cutting-edge multispectral and hyperspectral sensors, and advanced navigation and communication systems. We analyze diagnostic applications, such as crop monitoring and multispectral mapping, as well as interventional applications like precision spraying and drone-assisted seeding. The integration of artificial intelligence and IoTs in analyzing drone-collected data is highlighted, demonstrating significant improvements in early disease detection, yield estimation, and irrigation management. Specific case studies illustrate the effectiveness of drones in various crops, from viticulture to cereal cultivation. Despite these advancements, we identify several obstacles to widespread drone adoption, including regulatory, technological, and socio-economic challenges. This study particularly emphasizes the need to harmonize regulations on beyond visual line of sight (BVLOS) flights and improve economic accessibility for small-scale farmers. This review also identifies key opportunities for future research, including the use of drone swarms, improved energy autonomy, and the development of more sophisticated decision-support systems integrating drone data. In conclusion, we underscore the transformative potential of drones as a key technology for more sustainable, productive, and resilient agriculture in the face of global challenges in the 21st century, while highlighting the need for an integrated approach combining technological innovation, adapted policies, and farmer training. Full article
(This article belongs to the Special Issue Advances of UAV in Precision Agriculture)
Show Figures

Figure 1

Figure 1
<p>PRISMA flow diagram for the selection of articles on the use of drones in agriculture.</p>
Full article ">Figure 2
<p>Block diagram of a drone system.</p>
Full article ">Figure 3
<p>Data workflow in precision agriculture: from drone acquisition to farmer decision support.</p>
Full article ">
27 pages, 4822 KiB  
Review
Cadmium (Cd) Tolerance and Phytoremediation Potential in Fiber Crops: Research Updates and Future Breeding Efforts
by Adnan Rasheed, Pengliang He, Zhao Long, Syed Faheem Anjum Gillani, Ziqian Wang, Kareem Morsy, Mohamed Hashem and Yucheng Jie
Agronomy 2024, 14(11), 2713; https://doi.org/10.3390/agronomy14112713 - 17 Nov 2024
Viewed by 472
Abstract
Heavy metal pollution is one of the most devastating abiotic factors, significantly damaging crops and human health. One of the serious problems it causes is a rise in cadmium (Cd) toxicity. Cd is a highly toxic metal with a negative biological role, and [...] Read more.
Heavy metal pollution is one of the most devastating abiotic factors, significantly damaging crops and human health. One of the serious problems it causes is a rise in cadmium (Cd) toxicity. Cd is a highly toxic metal with a negative biological role, and it enters plants via the soil–plant system. Cd stress induces a series of disorders in plants’ morphological, physiological, and biochemical processes and initiates the inhibition of seed germination, ultimately resulting in reduced growth. Fiber crops such as kenaf, jute, hemp, cotton, and flax have high industrial importance and often face the issue of Cd toxicity. Various techniques have been introduced to counter the rising threats of Cd toxicity, including reducing Cd content in the soil, mitigating the effects of Cd stress, and genetic improvements in plant tolerance against this stress. For decades, plant breeders have been trying to develop Cd-tolerant fiber crops through the identification and transformation of novel genes. Still, the complex mechanism of Cd tolerance has hindered the progress of genetic breeding. These crops are ideal candidates for the phytoremediation of heavy metals in contaminated soils. Hence, increased Cd uptake, accumulation, and translocation in below-ground parts (roots) and above-ground parts (shoots, leaves, and stems) can help clean agricultural lands for safe use for food crops. Earlier studies indicated that reducing Cd uptake, detoxification, reducing the effects of Cd stress, and developing plant tolerance to these stresses through the identification of novel genes are fruitful approaches. This review aims to highlight the role of some conventional and molecular techniques in reducing the threats of Cd stress in some key fiber crops. Molecular techniques mainly involve QTL mapping and GWAS. However, more focus has been given to the use of transcriptome and TFs analysis to explore the potential genomic regions involved in Cd tolerance in these crops. This review will serve as a source of valuable genetic information on key fiber crops, allowing for further in-depth analyses of Cd tolerance to identify the critical genes for molecular breeding, like genetic engineering and CRISPR/Cas9. Full article
(This article belongs to the Section Agroecology Innovation: Achieving System Resilience)
Show Figures

Figure 1

Figure 1
<p>Cd is discharged from various sources, enters the soil, and is eventually taken up by plants through the roots and transported to the shoots. This Figure was made with <a href="http://BioRender.com" target="_blank">BioRender.com</a>.</p>
Full article ">Figure 2
<p>Cd toxicity decreases seed germination, seedling growth, and antioxidant activities and reduces protein content. Different factors, like organic acids and stress-related signaling, affect Cd uptake in plants. This Figure was made with <a href="http://BioRender.com" target="_blank">BioRender.com</a>.</p>
Full article ">Figure 3
<p>Conventional and molecular breeding tools are crucial in genetically improving Cd tolerance in fiber crops. The identification of Cd-tolerant genes led to an increase in the phytoremediation potential of fiber crops. This Figure was made with <a href="http://BioRender.com" target="_blank">BioRender.com</a>.</p>
Full article ">
17 pages, 3571 KiB  
Article
Geospatially Informed Water Pricing for Sustainability: A Mixed Methods Approach to the Increasing Block Tariff Model for Groundwater Management in Arid Regions of Northwest Bangladesh
by Ragib Mahmood Shuvo, Radwan Rahman Chowdhury, Sanchoy Chakroborty, Anutosh Das, Abdulla Al Kafy, Hamad Ahmed Altuwaijri and Muhammad Tauhidur Rahman
Water 2024, 16(22), 3298; https://doi.org/10.3390/w16223298 - 17 Nov 2024
Viewed by 465
Abstract
Groundwater depletion in arid regions poses a significant threat to agricultural sustainability and rural livelihoods. This study employs geospatial analysis and economic modeling to address groundwater depletion in the arid Barind region of Northwest Bangladesh, where 84% of the rural population depends on [...] Read more.
Groundwater depletion in arid regions poses a significant threat to agricultural sustainability and rural livelihoods. This study employs geospatial analysis and economic modeling to address groundwater depletion in the arid Barind region of Northwest Bangladesh, where 84% of the rural population depends on agriculture. Using remote sensing and GIS, we developed an elevation map revealing areas up to 60 m above sea level, exacerbating evaporation and aquifer dryness. Field data collected through Participatory Rural Appraisal tools showed farmers exhibiting “ignorant myopic” behavior, prioritizing short-term profits over resource conservation. To address this, an Increasing Block Tariff (IBT) water pricing model was developed, dividing water usage into three blocks based on irrigation hours: 1–275 h, 276–550 h, and 551+ h. The proposed IBT model significantly increases water prices across the three blocks: 117 BDT/hour for the first block (from current 100–110 BDT/hour), 120 BDT/hour for the second block, and 138 BDT/hour for the third block. A demand function (y = −0.1178x + 241.8) was formulated to evaluate the model’s impact. The results show potential reductions in groundwater consumption: 59 h in the first block, 26 h in the second block, and 158 h in the third block. These reductions align with the principles of integrated water resource management (IWRM): social equity, economic efficiency, and environmental integration. The model incorporates economic externalities (e.g., well lifting costs) and environmental externalities (e.g., crop pattern shifts), with total costs reaching 92,709,049 BDT for environmental factors. This research provides a framework for sustainable groundwater management in arid regions, potentially reducing overextraction while maintaining agricultural productivity. The proposed IBT model offers a locally driven solution to balance resource conservation with the livelihood needs of farming communities in the Barind tract. By combining remote sensing, GIS, and economic modeling, this research provides a framework for sustainable groundwater management in arid regions, demonstrating the power of geospatial technologies in addressing complex water resource challenges. Full article
Show Figures

Figure 1

Figure 1
<p>Study area map [<a href="#B17-water-16-03298" class="html-bibr">17</a>].</p>
Full article ">Figure 2
<p>(<b>a</b>) Left: elevation map and (<b>b</b>) right: groundwater fluctuation map of the study area.</p>
Full article ">Figure 3
<p>Distribution of farmland cultivated by the farmers.</p>
Full article ">Figure 4
<p>Calculated reduction in consumption hours of irrigation with the help of proposed water pricing model: (<b>a</b>) first block; (<b>b</b>) second block; (<b>c</b>) third block.</p>
Full article ">Figure 5
<p>Change in consumption of irrigation water (m<sup>3</sup>/hour) with the help of the proposed model.</p>
Full article ">
16 pages, 33569 KiB  
Article
Assessing Weed Canopy Cover in No-Till and Conventional Tillage Plots in Winter Wheat Production Using Drone Data
by Judith N. Oppong, Clement E. Akumu and Sam Dennis
Agronomy 2024, 14(11), 2706; https://doi.org/10.3390/agronomy14112706 - 16 Nov 2024
Viewed by 552
Abstract
Weed canopy cover assessment, particularly using drone-acquired data, plays a vital role in precision agriculture by providing accurate, timely, and spatially detailed information, enhancing weed management decision-making in response to environmental and management variables. Despite the significance of this approach, few studies have [...] Read more.
Weed canopy cover assessment, particularly using drone-acquired data, plays a vital role in precision agriculture by providing accurate, timely, and spatially detailed information, enhancing weed management decision-making in response to environmental and management variables. Despite the significance of this approach, few studies have investigated weed canopy cover through drone-based imagery. This study aimed to fill this gap by evaluating the effects of conventional tillage (CT) and no-till (NT) practices on weed canopy cover in a winter wheat field over two growing seasons. Results indicated that in the 2022–2023 season, weed populations were similar between tillage systems, with a high mean weed cover of 1.448 cm2 ± 0.241 in CT plots. In contrast, during the 2023–2024 season, NT plots exhibited a substantially higher mean weed cover (1.784 cm2 ± 0.167), with a significant overall variation (p < 0.05) in weed distribution between CT and NT plots. These differences suggest that, while CT practices initially mask weed emergence by burying seeds and disrupting root systems, NT practices encourage greater weed establishment over time by leaving seeds near the soil surface. These findings provide valuable insights for optimizing weed management practices, emphasizing the importance of comprehensive approaches to improve weed control and overall crop productivity. Full article
(This article belongs to the Special Issue Weed Ecology, Evolution and Management)
Show Figures

Figure 1

Figure 1
<p>Location of the study area with an insert of the study field.</p>
Full article ">Figure 2
<p>Schematic illustration of the methodology used for this study.</p>
Full article ">Figure 3
<p>No-till and conventional tillage plot layout for winter wheat production.</p>
Full article ">Figure 4
<p>West-to-east drone flight path for field image acquisition.</p>
Full article ">Figure 5
<p>Classified weed canopy cover map derived from the 2022–2023 tillering growth stage.</p>
Full article ">Figure 6
<p>Classified weed canopy cover map derived from the 2022–2023 jointing growth stage.</p>
Full article ">Figure 7
<p>Classified weed canopy cover map derived from the 2022–2023 booting growth stage.</p>
Full article ">Figure 8
<p>Classified weed canopy cover map derived from the 2022–2023 mature growth stage.</p>
Full article ">Figure 9
<p>Classified weed canopy cover map derived from the 2023–2024 tillering growth stage.</p>
Full article ">Figure 10
<p>Classified weed canopy cover map derived from the 2023–2024 jointing growth stage.</p>
Full article ">Figure 11
<p>Classified weed canopy cover map derived from the 2023–2024 booting growth stage.</p>
Full article ">Figure 12
<p>Classified weed canopy cover map derived from the 2023–2024 mature growth stage.</p>
Full article ">Figure 13
<p>Mean canopy cover of weeds for conventional tillage and no-till over the study period. Error bars = standard error of mean (SE).</p>
Full article ">
19 pages, 6561 KiB  
Article
Early Detection of Surface Mildew in Maize Kernels Using Machine Vision Coupled with Improved YOLOv5 Deep Learning Model
by Yu Xia, Ao Shen, Tianci Che, Wenbo Liu, Jie Kang and Wei Tang
Appl. Sci. 2024, 14(22), 10489; https://doi.org/10.3390/app142210489 - 14 Nov 2024
Viewed by 394
Abstract
Mildew in maize kernels is typically caused by various fungi, necessitating prompt detection and treatment to minimize losses during harvest and storage. In this study, a deep learning YOLOv5s algorithm based on machine vision technology was employed to develop a maize seed surface [...] Read more.
Mildew in maize kernels is typically caused by various fungi, necessitating prompt detection and treatment to minimize losses during harvest and storage. In this study, a deep learning YOLOv5s algorithm based on machine vision technology was employed to develop a maize seed surface mildew detection model and to enhance its portability for deployment on additional mobile devices. To guarantee the fruitful progression of this research, an initial experiment was conducted on maize seeds to obtain a sufficient number of images of mildewed maize kernels, which were classified into three grades (sound, mild, and severe). Subsequently, a maize seed image was extracted to create an image of a single maize seed, which was then divided to establish the data set. An enhanced YOLOv5s–ShuffleNet–CBAM model was ultimately developed. The results demonstrated that the model achieved with an mAP50 value of 0.955 and a model size of 2.4 MB. This resulted in a notable reduction in the model parameters and calculation amount while simultaneously enhancing model precision. Furthermore, K-fold cross-validation demonstrated the model stability, and Grad-CAM validated the model effectiveness. In the future, the proposed lightweight model in this study can be applied to other crops in the context of portable or online inspection systems, thus advancing effective and high-quality agricultural applications. Full article
Show Figures

Figure 1

Figure 1
<p>Annual maize production of China from 1978 to 2023.</p>
Full article ">Figure 2
<p>Image acquisition device (<b>a</b>) and its internal LED light strip (<b>b</b>).</p>
Full article ">Figure 3
<p>Raw image of maize seeds.</p>
Full article ">Figure 4
<p>Otsu method image binarization.</p>
Full article ">Figure 5
<p>Image after open and close operations.</p>
Full article ">Figure 6
<p>Maize external matrix.</p>
Full article ">Figure 7
<p>ShuffleNet V2 basic unit.</p>
Full article ">Figure 8
<p>Convolutional block attention module.</p>
Full article ">Figure 9
<p>YOLOv5s–ShuffleNet–CBAM model.</p>
Full article ">Figure 10
<p>Five-fold cross-validation.</p>
Full article ">Figure 11
<p>Improved YOLOv5s model: (<b>a</b>) <span class="html-italic">mAP50</span> growth curve, (<b>b</b>) <span class="html-italic">Precision</span> growth curve, and (<b>c</b>) <span class="html-italic">Recall</span> growth curve in 1000 epochs.</p>
Full article ">Figure 12
<p>Grad-CAM analysis: (<b>a</b>–<b>d</b>) “Sound”, (<b>e</b>–<b>h</b>) “Mild”, and (<b>i</b>–<b>l</b>) “Severe”.</p>
Full article ">Figure 13
<p>The detection of mold in maize: (0) “Sound”, (1) “Mild”, and (2) “Severe”.</p>
Full article ">
14 pages, 3019 KiB  
Article
A New Proposal for Soybean Plant Stand: Variation Based on the Law of the Minimum
by Fábio Henrique Rojo Baio, Ricardo Gava, Larissa Pereira Ribeiro Teodoro, Rita de Cássia Félix Alvarez, Marcos Eduardo Miranda Alves, Dthenifer Cordeiro Santana, Cid Naudi Silva Campos, Ana Carina da Silva Cândido and Paulo Eduardo Teodoro
Plants 2024, 13(22), 3193; https://doi.org/10.3390/plants13223193 - 14 Nov 2024
Viewed by 396
Abstract
The hypothesis of this study is that it is possible to determine the plant stand in the soybean (Glycine max L. Merril) crop based on the spatial variability of management units, which are limiting factors in maximizing crop yield. Our objectives were [...] Read more.
The hypothesis of this study is that it is possible to determine the plant stand in the soybean (Glycine max L. Merril) crop based on the spatial variability of management units, which are limiting factors in maximizing crop yield. Our objectives were as follows: (I) to evaluate the relationship between soil physical and chemical attributes to establish potential management units for variable-rate seeding; (II) to propose a method for varying plant stands based on the law of minimum soil nutrients; an (III) to relate the interaction between different plant stands on soybean grain yield, taking into account the interaction between the spatial variability of the mapped attributes. Field experiments were carried out on two plots over two agricultural years. The areas were seeded by randomly varying the soybean stand across strips in the first year. The most limiting soil nutrient was established and used, together with the soil CEC, to determine management units (MUs), which were also used to seed soybeans in VRT (Variable Rate Technology) in the same plots in the second year. MUs with the lowest restriction for maximizing yield were sown in the second year with the lowest plant stand. Data were processed using multivariate statistics. Our findings reveal that it is possible to establish MUs for seeding soybeans with different stands following the spatial variability of limiting soil nutrients according to the law of the minimum and thus increase the crop grain yield. Spatial variability of potassium (K) in the plot, identified as limiting, affected the spatial variability of grain yield. Decreasing plant stands in MUs with the lowest limitation level increases yield. However, increasing the stand in MUs with a higher limitation level can lead to increased intraspecific competition, affecting yield as well as increasing input costs. Full article
(This article belongs to the Special Issue Precision Agriculture Technology, Benefits & Application)
Show Figures

Figure 1

Figure 1
<p>Location of the experimental fields (<b>A</b>), Normalized Difference Vegetation Index (NDVI) from the Variable Rate Technology (VRT), and Control Fields during the first crop season (<b>B</b>), and during the second crop season (<b>C</b>).</p>
Full article ">Figure 2
<p>Rainfall (mm) and average temperature (°C) in ten-day periods in each month during soybean cultivation in the two experimental periods (crop seasons 2023 and 2024).</p>
Full article ">Figure 3
<p>Spatial variability of the map resulting from the algebra between the K map and the CEC map (<b>A</b>) and the soybean seed prescription map (<b>B</b>).</p>
Full article ">Figure 4
<p>Pearson’s correlation network (<b>a</b>) between the yield variables grain yield, 100-grain weight, and green plant weight; soil variables apparent soil electrical conductivity (ECa), cation exchange capacity (CEC), calcium (Ca), magnesium (Mg), potassium (K), and phosphorus (P) levels; and vegetation indices NDVI, NDRE, SCCI, and GNDVI, evaluated in the first experimental year. Canonical variable analysis (<b>b</b>) as a function of plant stands varying between 170,000 plants ha<sup>−1</sup> (170) and 310,000 plants ha<sup>−1</sup> (310), evaluated in the first experimental year. In (<b>a</b>) green lines indicate positive correlations, while red lines indicate negative correlations.</p>
Full article ">Figure 5
<p>Relationship between soybean grain yield in the first experimental year (strip sowing), NDVI levels, and plant green mass, according to the different plant stands. Equal letters in each response variable represent statistical similarity, according to Duncan’s test at 5% probability.</p>
Full article ">Figure 6
<p>Pearson’s correlation network (<b>a</b>) between the yield variables 100-grain weight, pods per plant, plant height and grain yield, and vegetation indices NDVI and NDRE, evaluated in the second experimental year. Canonical variable analysis (<b>b</b>) as a function of plant stands varying between 190,000 plants ha<sup>−1</sup> (Low pop.), 220,000 (Mean pop.), and 250,000 plants ha<sup>−1</sup> (High pop.), evaluated in the second experimental year. In (<b>a</b>) green lines indicate positive correlations, while red lines indicate negative correlations.</p>
Full article ">Figure 7
<p>Spatial variability and means of yield (<b>a1</b>,<b>a2</b>, respectively), pods per plant (<b>b1</b>,<b>b2</b>, respectively), and plant height (<b>c1</b>,<b>c2</b>, respectively) in the different management units seeded with soybean plant stand variation (low, mean, and high populations), and comparison of the means for these variables. Equal letters represent statistical similarity by Duncan’s test at 5% probability.</p>
Full article ">
15 pages, 38365 KiB  
Article
Functional Analysis of CsWOX4 Gene Mutation Leading to Maple Leaf Type in Cucumber (Cucumis sativus L.)
by Huizhe Wang, Bo Wang, Yiheng Wang, Qiang Deng, Guoqing Lu, Mingming Cao, Wancong Yu, Haiyan Zhao, Mingjie Lyu and Ruihuan Yang
Int. J. Mol. Sci. 2024, 25(22), 12189; https://doi.org/10.3390/ijms252212189 - 13 Nov 2024
Viewed by 319
Abstract
The leaf morphology is an important agronomic trait in crop production. Our study identified a maple leaf type (mlt) cucumber mutant and located the regulatory gene for leaf shape changes through BSA results. Hybrid F1 and F2 populations were generated by [...] Read more.
The leaf morphology is an important agronomic trait in crop production. Our study identified a maple leaf type (mlt) cucumber mutant and located the regulatory gene for leaf shape changes through BSA results. Hybrid F1 and F2 populations were generated by F1 self-crossing, and the candidate mlt genes were identified within the 2.8 Mb region of chromosome 2 using map cloning. Through the sequencing and expression analysis of genes within the bulk segregant analysis (BSA) region, we identified the target gene for leaf shape regulation as CsWOX4 (CsaV3_2G026510). The change from base C to T in the original sequence led to frameshift mutations and the premature termination of translation, resulting in shortened encoded proteins and conserved WUSCHEL (WUS) box sequence loss. The specific expression analysis of the CsWOX4/Cswox4 genes in the roots, stems, leaves and other tissue types of wild-type (WT) and mutant plants revealed that CsWOX4 was higher in the root, but Cswox4 (mutant gene) was significantly higher in the leaf. Subcellular localization analysis revealed that CsWOX4 was localized in the nucleus. RNA-seq analysis revealed that the differentially expressed genes were mainly enriched in the mitochondrial cell cycle phase transition, nucleosome and microtubule binding pathways. Simultaneously, the quantitative analysis of the expression trends of 25 typical genes regulating the leaf types revealed the significant upregulation of CsPIN3. In our study, we found that the conserved domain of CsWOX4 was missing in the mutant, and the transcriptome data revealed that the expression of some genes, such as CsPIN3, changed simultaneously, thereby jointly regulating changes in the cucumber leaf type. Full article
(This article belongs to the Special Issue Vegetable Genetics and Genomics, 3rd Edition)
Show Figures

Figure 1

Figure 1
<p>Mature and seedling stage characteristics of wild-type “J128” and K39 mutants. (<b>A</b>) Phenotypes of wild type and mutant during the seedling stage. (<b>B</b>), Different phenotypes of wild-type and mutant leaves. Top right: Leaf phenotype of ”J128” wild-type seedlings in the field. Lower right: Leaf phenotype of “K39” seedlings in the field. (<b>C</b>) J128 field growing leaf morphology. (<b>D</b>) K39 field growing leaf morphology.</p>
Full article ">Figure 2
<p>MutMap analysis and gene structure analysis of <span class="html-italic">CsWOX4</span>. (<b>A</b>) The distribution of the G-index in 7 chromosomes. The horizontal axis represents the name and length of each chromosome, the vertical axis represents the G-index value, and the red line represents the threshold line corresponding to 95%. (<b>B</b>) Gene structure of <span class="html-italic">CsWOX4</span>. Black boxes represent exons and black lines represent introns. (<b>C</b>) Predicted protein domain of <span class="html-italic">CsWOX4</span>. (<b>D</b>) Coding sequence and amino acid sequence alignment of <span class="html-italic">CsWOX4</span>. Black represents the complete sequence information of <span class="html-italic">CsWOX4,</span> blue represents the amino acids expressed by the mutant cswox4, and * represents the stop codon of <span class="html-italic">cswox4</span>.</p>
Full article ">Figure 3
<p>Subcellular localization of <span class="html-italic">CsWOX4</span> protein. Green fluorescent protein GFP: excitation light 488 nm, emission light 510 nm. Red fluorescent protein mKATE excitation light 561 nm emission light 580 nm. Scale bar 10 μm.</p>
Full article ">Figure 4
<p>Expression profiles of <span class="html-italic">CsWOX4</span> gene in different tissue types of J128 and K39 mutants detected by qPCR. Values shown are mean ± SD calculated from three biological and three technical replicates. Statistical significance is denoted as *** for <span class="html-italic">p</span> &lt; 0.001 as determined by Student’s <span class="html-italic">t</span>-test.</p>
Full article ">Figure 5
<p>SDS–PAGE analysis of CsWOX4 and Cswox4 fusion proteins. M: On the left side is Protein pre-staining marker; IPTG-induced CsWOX4 fusion protein; IPTG-induced Cswox4 fusion protein.</p>
Full article ">Figure 6
<p>Transcriptome data analysis of J128 and K39. (<b>A</b>) Differential expression display of “J128” and K39 genomics. (<b>B</b>) Differential gene GO annotation analysis.</p>
Full article ">Figure 7
<p>Analysis of key gene expression levels in different regulatory pathways of leaf types. (<b>A</b>) qPCR expression level detection of key genes. (<b>B</b>) Heat map analysis of key gene expression patterns in transcriptome. Values shown are mean ± SD calculated from three biological and three technical replicates. Statistical significance is denoted as * for <span class="html-italic">p</span> &lt; 0.05 and ** for <span class="html-italic">p</span> &lt; 0.01, as determined by Student’s <span class="html-italic">t</span>-test.</p>
Full article ">
19 pages, 16510 KiB  
Article
Mapping Crop Types for Beekeepers Using Sentinel-2 Satellite Image Time Series: Five Essential Crops in the Pollination Services
by Navid Mahdizadeh Gharakhanlou, Liliana Perez and Nico Coallier
Remote Sens. 2024, 16(22), 4225; https://doi.org/10.3390/rs16224225 - 13 Nov 2024
Viewed by 430
Abstract
Driven by the widespread adoption of deep learning (DL) in crop mapping with satellite image time series (SITS), this study was motivated by the recent success of temporal attention-based approaches in crop mapping. To meet the needs of beekeepers, this study aimed to [...] Read more.
Driven by the widespread adoption of deep learning (DL) in crop mapping with satellite image time series (SITS), this study was motivated by the recent success of temporal attention-based approaches in crop mapping. To meet the needs of beekeepers, this study aimed to develop DL-based classification models for mapping five essential crops in pollination services in Quebec province, Canada, by using Sentinel-2 SITS. Due to the challenging task of crop mapping using SITS, this study employed three DL-based models, namely one-dimensional temporal convolutional neural networks (CNNs) (1DTempCNNs), one-dimensional spectral CNNs (1DSpecCNNs), and long short-term memory (LSTM). Accordingly, this study aimed to capture expert-free temporal and spectral features, specifically targeting temporal features using 1DTempCNN and LSTM models, and spectral features using the 1DSpecCNN model. Our findings indicated that the LSTM model (macro-averaged recall of 0.80, precision of 0.80, F1-score of 0.80, and ROC of 0.89) outperformed both 1DTempCNNs (macro-averaged recall of 0.73, precision of 0.74, F1-score of 0.73, and ROC of 0.85) and 1DSpecCNNs (macro-averaged recall of 0.78, precision of 0.77, F1-score of 0.77, and ROC of 0.88) models, underscoring its effectiveness in capturing temporal features and highlighting its suitability for crop mapping using Sentinel-2 SITS. Furthermore, applying one-dimensional convolution (Conv1D) across the spectral domain demonstrated greater potential in distinguishing land covers and crop types than applying it across the temporal domain. This study contributes to providing insights into the capabilities and limitations of various DL-based classification models for crop mapping using Sentinel-2 SITS. Full article
(This article belongs to the Section AI Remote Sensing)
Show Figures

Figure 1

Figure 1
<p>The flowchart of the research methodology.</p>
Full article ">Figure 2
<p>Geographic location of the study area with a true-color median composite of Sentinel-2 satellite imagery generated for 1–10 April 2021.</p>
Full article ">Figure 3
<p>The macro-average of the F1-score for the 100 designed architectures on the validation dataset for (<b>a</b>) 1DTempCNN, (<b>b</b>) 1DSpecCNN, and (<b>c</b>) LSTM models.</p>
Full article ">Figure 3 Cont.
<p>The macro-average of the F1-score for the 100 designed architectures on the validation dataset for (<b>a</b>) 1DTempCNN, (<b>b</b>) 1DSpecCNN, and (<b>c</b>) LSTM models.</p>
Full article ">Figure 4
<p>The 1DTempCNN architecture with optimal performance.</p>
Full article ">Figure 5
<p>The 1DSpecCNN architecture with optimal performance.</p>
Full article ">Figure 6
<p>The LSTM architecture with optimal performance.</p>
Full article ">Figure 7
<p>(<b>a</b>) The ground reference map; and (<b>b</b>) the LSTM-provided map of land cover and crop type across the entire study area.</p>
Full article ">Figure A1
<p>Confusion matrix of the top-performing DL model (i.e., LSTM) in predicting land cover and crop type on the test dataset.</p>
Full article ">
17 pages, 5188 KiB  
Article
Detection of Candidate Genes and Development of KASP Markers for Pod Length and Pod Width by Combining Genome-Wide Association and Transcriptome Sequencing in Vegetable Soybean
by Dongqing Dai, Lu Huang, Xiaoyan Zhang, Jinyang Liu, Shiqi Zhang, Xingxing Yuan, Xin Chen and Chenchen Xue
Agronomy 2024, 14(11), 2654; https://doi.org/10.3390/agronomy14112654 - 11 Nov 2024
Viewed by 399
Abstract
Vegetable soybeans are one of the most important vegetable types in East Asia. The yield of vegetable soybeans is considerably influenced by the size of their pods. To facilitate the understanding of the genetic basis of the pod length and width in vegetable [...] Read more.
Vegetable soybeans are one of the most important vegetable types in East Asia. The yield of vegetable soybeans is considerably influenced by the size of their pods. To facilitate the understanding of the genetic basis of the pod length and width in vegetable soybeans, we conducted a genome-wide association study (GWAS) and transcriptome sequencing. Four quantitative trait loci, namely, qGPoL1, qGPoL2, qGPoW1, and qGPoW2, were mapped via GWAS analysis. Through the integration of gene function annotation, transcriptome sequencing, and expression pattern analysis, we identified Glyma.06G255000 and Glyma.13G007000 as the key determinants of the pod length and width in vegetable soybeans, respectively. Furthermore, two kompetitive allele-specific polymerase chain reaction (KASP) markers, namely, S06-42138365 (A/T) and S13_628331 (A/T), were developed and effectively validated in 27 vegetable soybean accessions. Overall, our research identified genes that regulate the pod length and width and determined KASP markers for molecular marker-assisted selection breeding. These findings have crucial implications for the improvement of soybean crops and can contribute to the development of efficient breeding strategies. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Soybeans)
Show Figures

Figure 1

Figure 1
<p>Correlation analysis of pod length and width. Correlation coefficient of pod length and width across six growth environments; the diagonals represent the distribution of different pod traits. * indicates a significant correlation (<span class="html-italic">p</span> &lt;  0.05), ** indicates a significant correlation (<span class="html-italic">p</span> &lt;  0.01), *** indicates a significant correlation (<span class="html-italic">p</span> &lt;  0.001). PoL, pod length; PoW, pod width; 2021XW, Xuanwu in 2021; 2022XW, Xuanwu in 2022; 2021LS, Lishui in 2021; 2022LS, Lishui in 2022; 2021LH, Liuhe in 2021; 2022LH, Liuhe in 2022.</p>
Full article ">Figure 2
<p>SNP distribution and population structural analysis. (<b>A</b>) Distribution density of 277022 high-quality SNPs on chromosomes. (<b>B</b>) Population structural analysis using SRUCTURE with k = 2 to 5.</p>
Full article ">Figure 3
<p>GWAS of the pod length and width. (<b>A</b>,<b>B</b>) Manhattan plot of MLM for pod length (<b>A</b>) and width (<b>B</b>). (<b>C</b>,<b>D</b>) QQ plot of pod length (<b>C</b>) and width (<b>D</b>).</p>
Full article ">Figure 4
<p>SNP haplotype analysis associated with pod length and width traits. (<b>A</b>,<b>B</b>) Significant haplotype of pod length; (<b>C</b>,<b>D</b>) significant haplotype of pod width. Asterisks indicate significant differences between different haplotypes (*** <span class="html-italic">p</span> &lt; 0.001).</p>
Full article ">Figure 5
<p>Genotyping of KASP markers. (<b>A</b>,<b>B</b>) Genotyping of S06_42138365 and S13_628331, respectively. NTC, negative control.</p>
Full article ">Figure 6
<p>Transcriptome analysis of pods of different sizes. (<b>A</b>,<b>B</b>) Pod length (<b>A</b>) and width (<b>B</b>) of various lines. (<b>C</b>) Heat map showing the expressions of up-/down-regulated genes in short and long pods. S, short pod; L, long pod. (<b>D</b>) Heat map showing the expressions of up-/down-regulated genes in narrow and wide pods. N, narrow pod, W, wide pod.</p>
Full article ">Figure 7
<p>GO and KEGG classification of different groups. GO classification of DEGs between short- and long-pod groups (<b>A</b>); narrow and wide pod groups (<b>B</b>); KEGG classification of short- and long-pod groups (<b>C</b>); narrow- and wide-pod groups (<b>D</b>). Each bubble represents a GO term or a pathway. Above the yellow line are significantly enriched GO terms or pathways, and the bubble size indicates the number of enriched genes.</p>
Full article ">Figure 8
<p>Expression analysis of candidate genes. Expression analysis of candidate genes for pod length (<b>A</b>) and width (<b>B</b>). S, short pod; L, long pod; N, narrow pod; W, wide pod.</p>
Full article ">Figure 9
<p>Analysis of expression patterns of candidate genes. The expression levels of <span class="html-italic">Glyma.06G255000</span> (<b>A</b>), <span class="html-italic">Glyma.13G007000</span> (<b>B</b>) and <span class="html-italic">Glyma.17G173000</span> (<b>C</b>) in various soybean tissues.</p>
Full article ">
Back to TopTop