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Application of visible/near-infrared spectroscopy and hyperspectral imaging with machine learning for high-throughput plant heavy metal stress phenotyping: a review 将可见/近红外光谱和高光谱成像技术与机器学习相结合,用于高通量植物重金属胁迫表型分析:综述
IF 6.5 1区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2023-11-21 DOI: 10.34133/plantphenomics.0124
Yuanning Zhai, Lei Zhou, Hengnian Qi, Pan Gao, Chu Zhang
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引用次数: 0
Functional-Structural Plant Model 'GreenLab': A State-of-the-Art Review 功能-结构植物模型“绿色实验室”:最新的回顾
1区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2023-11-13 DOI: 10.34133/plantphenomics.0118
Xiujuan Wang, Jing Hua, Mengzhen Kang, Haoyu Wang, Philippe de Reffye
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引用次数: 0
Estimating Compositions and Nutritional Values of Seed Mixes Based on Vision Transformers. 基于视觉变换的混合种子成分及营养价值估算。
IF 6.5 1区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2023-11-10 eCollection Date: 2023-01-01 DOI: 10.34133/plantphenomics.0112
Shamprikta Mehreen, Hervé Goëau, Pierre Bonnet, Sophie Chau, Julien Champ, Alexis Joly

The cultivation of seed mixtures for local pastures is a traditional mixed cropping technique of cereals and legumes for producing, at a low production cost, a balanced animal feed in energy and protein in livestock systems. By considerably improving the autonomy and safety of agricultural systems, as well as reducing their impact on the environment, it is a type of crop that responds favorably to both the evolution of the European regulations on the use of phytosanitary products and the expectations of consumers who wish to increase their consumption of organic products. However, farmers find it difficult to adopt it because cereals and legumes do not ripen synchronously and the harvested seeds are heterogeneous, making it more difficult to assess their nutritional value. Many efforts therefore remain to be made to acquire and aggregate technical and economical references to evaluate to what extent the cultivation of seed mixtures could positively contribute to securing and reducing the costs of herd feeding. The work presented in this paper proposes new Artificial Intelligence techniques that could be transferred to an online or smartphone application to automatically estimate the nutritional value of harvested seed mixes to help farmers better manage the yield and thus engage them to promote and contribute to a better knowledge of this type of cultivation. For this purpose, an original open image dataset has been built containing 4,749 images of seed mixes, covering 11 seed varieties, with which 2 types of recent deep learning models have been trained. The results highlight the potential of this method and show that the best-performing model is a recent state-of-the-art vision transformer pre-trained with self-supervision (Bidirectional Encoder representation from Image Transformer). It allows an estimation of the nutritional value of seed mixtures with a coefficient of determination R2 score of 0.91, which demonstrates the interest of this type of approach, for its possible use on a large scale.

为地方牧场种植混合种子是谷物和豆类的传统混合种植技术,以低生产成本生产牲畜系统中能量和蛋白质平衡的动物饲料。通过大大提高农业系统的自主性和安全性,以及减少对环境的影响,这种作物对欧洲植物检疫产品使用法规的演变和希望增加有机产品消费的消费者的期望都做出了积极的反应。然而,农民发现很难采用它,因为谷物和豆类不是同步成熟的,而且收获的种子是异质的,这使得评估它们的营养价值变得更加困难。因此,仍需作出许多努力来获取和收集技术和经济参考资料,以评价混合种子的种植在多大程度上能对确保和降低畜群饲养的费用作出积极贡献。本文提出的工作提出了新的人工智能技术,可以转移到在线或智能手机应用程序中,以自动估计收获的种子混合物的营养价值,以帮助农民更好地管理产量,从而使他们参与促进并有助于更好地了解这种类型的种植。为此,我们建立了一个原始的开放图像数据集,其中包含4749张种子混合图像,涵盖11个种子品种,并使用该数据集训练了2种最新的深度学习模型。结果突出了这种方法的潜力,并表明表现最好的模型是最近最先进的视觉变压器,预先训练了自我监督(来自Image transformer的双向编码器表示)。它可以估计混合种子的营养价值,决定系数R2得分为0.91,这表明了这种方法的兴趣,因为它可能被大规模使用。
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引用次数: 0
Quantification of the Cumulative Shading Capacity in a Maize-Soybean Intercropping System Using an Unmanned Aerial Vehicle. 玉米-大豆间作系统累积遮荫能力的无人机量化
IF 6.5 1区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2023-11-10 eCollection Date: 2023-01-01 DOI: 10.34133/plantphenomics.0095
Min Li, Pengcheng Hu, Di He, Bangyou Zheng, Yan Guo, Yushan Wu, Tao Duan

In intercropping systems, higher crops block direct radiation, resulting in inevitable shading on the lower crops. Cumulative shading capacity (CSC), defined as the amount of direct radiation shaded by higher crops during a growth period, affects the light interception and radiation use efficiency of crops. Previous studies investigated the light interception and distribution of intercropping. However, how to directly quantify the CSC and its inter-row heterogeneity is still unclear. Considering the canopy height differences (Hms, obtained using an unmanned aerial vehicle) and solar position, we developed a shading capacity model (SCM) to quantify the shading on soybean in maize-soybean intercropping systems. Our results indicated that the southernmost row of soybean had the highest shading proportion, with variations observed among treatments composed of strip configurations and plant densities (ranging from 52.44% to 57.44%). The maximum overall CSC in our treatments reached 123.77 MJ m-2. There was a quantitative relationship between CSC and the soybean canopy height increment (y = 3.61 × 10-2×ln(x)+6.80 × 10-1, P < 0.001). Assuming that the growth status of maize and soybean was consistent under different planting directions and latitudes, we evaluated the effects of factors (i.e., canopy height difference, latitude, and planting direction) on shading to provide insights for optimizing intercropping planting patterns. The simulation showed that increasing canopy height differences and latitude led to increased shading, and the planting direction with the least shading was about 90° to 120° at the experimental site. The newly proposed SCM offers a quantitative approach for better understanding shading in intercropping systems.

在间作系统中,较高的作物阻挡了直接辐射,从而不可避免地对较低的作物产生阴影。累积遮阳能力(CSC)是指高等作物在生育期遮阳的直接辐射量,影响作物的光截获和辐射利用效率。以往的研究对间作的截光和分布进行了研究。然而,如何直接量化CSC及其行间异质性尚不清楚。考虑到冠层高度差(Hms,利用无人机获得)和太阳位置,我们建立了遮阳能力模型(SCM)来量化玉米-大豆间作系统对大豆的遮阳。结果表明,大豆最南行遮阳比例最高,不同处理的遮阳比例在52.44% ~ 57.44%之间。我们处理的最大总CSC达到123.77 MJ -2。CSC与大豆冠层高度增量之间存在定量关系(y = 3.61 × 10-2×ln(x)+6.80 × 10-1, P < 0.001)。假设玉米和大豆在不同种植方向和纬度下的生长状况是一致的,我们评估了冠层高差、纬度和种植方向等因素对遮阳的影响,为优化间作种植模式提供参考。模拟结果表明,随着冠层高度差和纬度的增加,遮荫度增加,试验点遮荫度最小的种植方向约为90°~ 120°。新提出的SCM为更好地理解间作系统中的遮阳提供了定量方法。
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引用次数: 0
Combinatorial maps, a new framework to model agroforestry systems 组合图,一个新的框架来模拟农林业系统
1区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2023-11-07 DOI: 10.34133/plantphenomics.0120
Laetitia Lemiere, Marc Jaeger, Marie Gosme, Gérard Subsol
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引用次数: 0
A Pathway to Assess Genetic Variation of Wheat Germplasm by Multi-dimensional Traits with Digital Images 基于数字图像的小麦种质资源多维性状遗传变异评价途径
1区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2023-11-07 DOI: 10.34133/plantphenomics.0119
Tingting Wu, Peng Shen, Jianlong Dai, Yuntao Ma, Yi Feng
In this paper, a new pathway was proposed to assess the germplasm genetic variation by multidimensional traits of wheat seeds generated from digital images. A machine vision platform was first established to reconstruct wheat germplasm 3D model from omnidirectional image sequences of wheat seeds. Then, multidimensional traits were conducted from the wheat germplasm 3D model, including seed length, width, thickness, surface area, volume, maximum projection area, roundness, and 2 new defined traits called cardioid-derived area and the index of adjustment (J index). To assess genetic variation of wheat germplasm, phenotypic coefficients of variation (PCVs), analysis of variance (ANOVA), clustering, and the defined genetic variation factor (GVF) were calculated using the extracted morphological traits of 15 wheat accessions comprising 13 offspring and 2 parents. The measurement accuracy of 3D reconstruction model is demonstrated by the correlation coefficient (R) and root mean square errors (RMSEs). Results of PCVs among all the traits show importance of multidimensional traits, as seed volume (22.4%), cardioid-derived area (16.97%), and maximum projection area (14.67%). ANOVA shows a highly significance difference among all accessions. The results of GVF innovatively reflect the connection between genotypic variance and phenotypic traits from parents to offspring. Our results confirmed that extracting multidimensional traits from digital images is a promising high-throughput and cost-efficient pathway that can be included as a valuable approach in genetic variation assessment, and it can provide useful information for genetic improvement, preservation, and evaluation of wheat germplasm.
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引用次数: 0
Semi-supervised Counting of Grape Berries in the Field Based on Density Mutual Exclusion 基于密度互斥的葡萄果实田间半监督计数
1区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2023-11-03 DOI: 10.34133/plantphenomics.0115
Yanan Li, Yuling Tang, Yifei Liu, Dingrun Zheng
Automated counting of grape berries has become one of the most important tasks in grape yield prediction. However, dense distribution of berries and the severe occlusion between berries bring great challenges to counting algorithm based on deep learning. The collection of data required for model training is also a tedious and expensive work. To address these issues and cost-effectively count grape berries, a semi-supervised counting of grape berries in the field based on density mutual exclusion (CDMENet) is proposed. The algorithm uses VGG16 as the backbone to extract image features. Auxiliary tasks based on density mutual exclusion are introduced. The tasks exploit the spatial distribution pattern of grape berries in density levels to make full use of unlabeled data. In addition, a density difference loss is designed. The feature representation is enhanced by amplifying the difference of features between different density levels. The experimental results on the field grape berry dataset show that CDMENet achieves less counting errors. Compared with the state of the arts, coefficient of determination (R2) is improved by 6.10%, and mean absolute error and root mean square error are reduced by 49.36% and 54.08%, respectively. The code is available at https://github.com/youth-tang/CDMENet-main.
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引用次数: 0
Phenomic Imaging Phenomic成像
1区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2023-11-03 DOI: 10.1007/s43657-023-00128-8
Lizhen Lan, Kai Feng, Yudan Wu, Wenbo Zhang, Ling Wei, Huiting Che, Le Xue, Yidan Gao, Ji Tao, Shufang Qian, Wenzhao Cao, Jun Zhang, Chengyan Wang, Mei Tian
Abstract Human phenomics is defined as the comprehensive collection of observable phenotypes and characteristics influenced by a complex interplay among factors at multiple scales. These factors include genes, epigenetics at the microscopic level, organs, microbiome at the mesoscopic level, and diet and environmental exposures at the macroscopic level. “Phenomic imaging” utilizes various imaging techniques to visualize and measure anatomical structures, biological functions, metabolic processes, and biochemical activities across different scales, both in vivo and ex vivo. Unlike conventional medical imaging focused on disease diagnosis, phenomic imaging captures both normal and abnormal traits, facilitating detailed correlations between macro- and micro-phenotypes. This approach plays a crucial role in deciphering phenomes. This review provides an overview of different phenomic imaging modalities and their applications in human phenomics. Additionally, it explores the associations between phenomic imaging and other omics disciplines, including genomics, transcriptomics, proteomics, immunomics, and metabolomics. By integrating phenomic imaging with other omics data, such as genomics and metabolomics, a comprehensive understanding of biological systems can be achieved. This integration paves the way for the development of new therapeutic approaches and diagnostic tools.
人类表型组学被定义为受多种因素复杂相互作用影响的可观察表型和特征的综合集合。这些因素包括微观水平上的基因、表观遗传学,中观水平上的器官、微生物组,宏观水平上的饮食和环境暴露。“现象成像”利用各种成像技术来可视化和测量不同尺度的解剖结构、生物功能、代谢过程和生化活动,包括体内和体外。与专注于疾病诊断的传统医学成像不同,表型成像捕获正常和异常特征,促进宏观和微观表型之间的详细相关性。这种方法在破译现象中起着至关重要的作用。本文综述了不同的表型成像方式及其在人类表型组学中的应用。此外,它还探讨了现象成像和其他组学学科之间的联系,包括基因组学、转录组学、蛋白质组学、免疫组学和代谢组学。通过将表型成像与其他组学数据(如基因组学和代谢组学)相结合,可以实现对生物系统的全面了解。这种整合为开发新的治疗方法和诊断工具铺平了道路。
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引用次数: 0
LiDAR is effective in characterizing vine growth and detecting associated genetic loci 激光雷达在表征葡萄生长和检测相关遗传位点方面是有效的
1区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2023-11-03 DOI: 10.34133/plantphenomics.0116
Eric Duchêne, Elsa Chedid, Komlan Avia, Vincent Dumas, Lionel Ley, Nicolas Reibel, Gisèle Butterlin, Maxime Soma, Raul Lopez-Lozano, Frédéric Baret, Didier Merdinoglu
The strong societal demand to reduce pesticide use and adaptation to climate change challenges the capacities of phenotyping new varieties in the vineyard. High-throughput phenotyping is a way to obtain meaningful and reliable information on hundreds of genotypes in a limited period. We evaluated traits related to growth in 209 genotypes from an interspecific grapevine biparental cross, between IJ119, a local genitor, and Divona, both in summer and in winter, using several methods: fresh pruning wood weight, exposed leaf area calculated from digital images, leaf chlorophyll concentration, and LiDAR-derived apparent volumes. Using high-density genetic information obtained by the genotyping by sequencing technology (GBS), we detected 6 regions of the grapevine genome [quantitative trait loci (QTL)] associated with the variations of the traits in the progeny. The detection of statistically significant QTLs, as well as correlations (R2) with traditional methods above 0.46, shows that LiDAR technology is effective in characterizing the growth features of the grapevine. Heritabilities calculated with LiDAR-derived total canopy and pruning wood volumes were high, above 0.66, and stable between growing seasons. These variables provided genetic models explaining up to 47% of the phenotypic variance, which were better than models obtained with the exposed leaf area estimated from images and the destructive pruning weight measurements. Our results highlight the relevance of LiDAR-derived traits for characterizing genetically induced differences in grapevine growth and open new perspectives for high-throughput phenotyping of grapevines in the vineyard.
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引用次数: 0
Point cloud completion of plant leaves under occlusion conditions based on deep learning 基于深度学习的遮挡条件下植物叶片点云补全
1区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2023-11-03 DOI: 10.34133/plantphenomics.0117
Haibo Chen, Shengbo Liu, Congyue Wang, Chaofeng Wang, Kangye Gong, Yuanhong Li, Yubin Lan
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引用次数: 0
期刊
Plant Phenomics
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