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Xue M, Huang S, Xu W, Xie T. Advanced deep learning models for phenotypic trait extraction and cultivar classification in lychee using photon-counting micro-CT imaging. Front Plant Sci 2024; 15:1358360. [PMID: 38486848 PMCID: PMC10937343 DOI: 10.3389/fpls.2024.1358360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024]
Abstract
Introduction In contemporary agronomic research, the focus has increasingly shifted towards non-destructive imaging and precise phenotypic characterization. A photon-counting micro-CT system has been developed, which is capable of imaging lychee fruit at the micrometer level and capturing a full energy spectrum, thanks to its advanced photon-counting detectors. Methods For automatic measurement of phenotypic traits, seven CNN-based deep learning models including AttentionUNet, DeeplabV3+, SegNet, TransUNet, UNet, UNet++, and UNet3+ were developed. Machine learning techniques tailored for small-sample training were employed to identify key characteristics of various lychee species. Results These models demonstrate outstanding performance with Dice, Recall, and Precision indices predominantly ranging between 0.90 and 0.99. The Mean Intersection over Union (MIoU) consistently falls between 0.88 and 0.98. This approach served both as a feature selection process and a means of classification, significantly enhancing the study's ability to discern and categorize distinct lychee varieties. Discussion This research not only contributes to the advancement of non-destructive plant analysis but also opens new avenues for exploring the intricate phenotypic variations within plant species.
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Affiliation(s)
- Mengjia Xue
- Institute of Radiation Medicine, Fudan University, Shanghai, China
| | - Siyi Huang
- Institute of Radiation Medicine, Fudan University, Shanghai, China
| | - Wenting Xu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tianwu Xie
- Institute of Radiation Medicine, Fudan University, Shanghai, China
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Ferrarezi JA, Defant H, de Souza LF, Azevedo JL, Hungria M, Quecine MC. Meta-omics integration approach reveals the effect of soil native microbiome diversity in the performance of inoculant Azospirillum brasilense. Front Plant Sci 2023; 14:1172839. [PMID: 37457347 PMCID: PMC10340089 DOI: 10.3389/fpls.2023.1172839] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/19/2023] [Indexed: 07/18/2023]
Abstract
Plant growth promoting bacteria (PGPB) have been used as integrative inputs to minimize the use of chemical fertilizers. However, a holistic comprehension about PGPB-plant-microbiome interactions is still incipient. Furthermore, the interaction among PGPB and the holobiont (host-microbiome association) represent a new frontier to plant breeding programs. We aimed to characterize maize bulk soil and rhizosphere microbiomes in irradiated soil (IS) and a native soil (NS) microbial community gradient (dilution-to-extinction) with Azospirillum brasilense Ab-V5, a PGPB commercial inoculant. Our hypothesis was that plant growth promotion efficiency is a result of PGPB niche occupation and persistence according to the holobiont conditions. The effects of Ab-V5 and NS microbial communities were evaluated in microcosms by a combined approach of microbiomics (species-specific qPCR, 16S rRNA metataxonomics and metagenomics) and plant phenomics (conventional and high-throughput methods). Our results revealed a weak maize growth promoting effect of Ab-V5 inoculation in undiluted NS, contrasting the positive effects of NS dilutions 10-3, 10-6, 10-9 and IS with Ab-V5. Alpha diversity in NS + Ab-V5 soil samples was higher than in all other treatments in a time course of 25 days after sowing (DAS). At 15 DAS, alpha diversity indexes were different between NS and IS, but similar in all NS dilutions in rhizospheric samples. These differences were not persistent at 25 DAS, demonstrating a stabilization process in the rhizobiomes. In NS 10-3 +Ab-V5 and NS 10-6 Ab-V5, Ab-V5 persisted in the maize rhizosphere until 15 DAS in higher abundances compared to NS. In NS + Ab-V5, abundance of six taxa were positively correlated with response to (a)biotic stresses in plant-soil interface. Genes involved in bacterial metabolism of riboses and amino acids, and cresol degradation were abundant on NS 10-3 + Ab-V5, indicating that these pathways can contribute to plant growth promotion and might be a result of Ab-V5 performance as a microbial recruiter of beneficial functions to the plant. Our results demonstrated the effects of holobiont on Ab-V5 performance. The meta-omics integration supported by plant phenomics opens new perspectives to better understanding of inoculants-holobiont interaction and for developing better strategies for optimization in the use of microbial products.
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Affiliation(s)
- Jessica Aparecida Ferrarezi
- Laboratory of Genetics of Microorganisms “Prof. Joao Lucio de Azevedo”, Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Heloísa Defant
- Laboratory of Genetics of Microorganisms “Prof. Joao Lucio de Azevedo”, Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Leandro Fonseca de Souza
- Laboratory of Genetics of Microorganisms “Prof. Joao Lucio de Azevedo”, Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - João Lúcio Azevedo
- Laboratory of Genetics of Microorganisms “Prof. Joao Lucio de Azevedo”, Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Maria Carolina Quecine
- Laboratory of Genetics of Microorganisms “Prof. Joao Lucio de Azevedo”, Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
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Park E, Kim YS, Faqeerzada MA, Kim MS, Baek I, Cho BK. Hyperspectral reflectance imaging for nondestructive evaluation of root rot in Korean ginseng ( Panax ginseng Meyer). Front Plant Sci 2023; 14:1109060. [PMID: 36818876 PMCID: PMC9930644 DOI: 10.3389/fpls.2023.1109060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Root rot of Panax ginseng caused by Cylindrocarpon destructans, a soil-borne fungus is typically diagnosed by frequently checking the ginseng plants or by evaluating soil pathogens in a farm, which is a time- and cost-intensive process. Because this disease causes huge economic losses to ginseng farmers, it is important to develop reliable and non-destructive techniques for early disease detection. In this study, we developed a non-destructive method for the early detection of root rot. For this, we used crop phenotyping and analyzed biochemical information collected using the HSI technique. Soil infected with root rot was divided into sterilized and infected groups and seeded with 1-year-old ginseng plants. HSI data were collected four times during weeks 7-10 after sowing. The spectral data were analyzed and the main wavelengths were extracted using partial least squares discriminant analysis. The average model accuracy was 84% in the visible/near-infrared region (29 main wavelengths) and 95% in the short-wave infrared (19 main wavelengths). These results indicated that root rot caused a decrease in nutrient absorption, leading to a decline in photosynthetic activity and the levels of carotenoids, starch, and sucrose. Wavelengths related to phenolic compounds can also be utilized for the early prediction of root rot. The technique presented in this study can be used for the early and timely detection of root rot in ginseng in a non-destructive manner.
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Affiliation(s)
- Eunsoo Park
- Department of Biosystems Machinery Engineering, College of Agricultural and Life Science, Chungnam National University, Daejeon, Republic of Korea
| | - Yun-Soo Kim
- R&D Headquarters, Korea Ginseng Corporation, Yuseong, Daejeon, Republic of Korea
| | - Mohammad Akbar Faqeerzada
- Department of Biosystems Machinery Engineering, College of Agricultural and Life Science, Chungnam National University, Daejeon, Republic of Korea
| | - Moon S. Kim
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Insuck Baek
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Byoung-Kwan Cho
- Department of Biosystems Machinery Engineering, College of Agricultural and Life Science, Chungnam National University, Daejeon, Republic of Korea
- Department of Smart Agricultural System, College of Agricultural and Life Science, Chungnam National University, Daejeon, Republic of Korea
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Lu Y, Wang R, Hu T, He Q, Chen ZS, Wang J, Liu L, Fang C, Luo J, Fu L, Yu L, Liu Q. Nondestructive 3D phenotyping method of passion fruit based on X-ray micro-computed tomography and deep learning. Front Plant Sci 2023; 13:1087904. [PMID: 36714758 PMCID: PMC9878569 DOI: 10.3389/fpls.2022.1087904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Passion fruit is a tropical liana of the Passiflora family that is commonly planted throughout the world due to its abundance of nutrients and industrial value. Researchers are committed to exploring the relationship between phenotype and genotype to promote the improvement of passion fruit varieties. However, the traditional manual phenotyping methods have shortcomings in accuracy, objectivity, and measurement efficiency when obtaining large quantities of personal data on passion fruit, especially internal organization data. This study selected samples of passion fruit from three widely grown cultivars, which differed significantly in fruit shape, size, and other morphological traits. A Micro-CT system was developed to perform fully automated nondestructive imaging of the samples to obtain 3D models of passion fruit. A designed label generation method and segmentation method based on U-Net model were used to distinguish different tissues in the samples. Finally, fourteen traits, including fruit volume, surface area, length and width, sarcocarp volume, pericarp thickness, and traits of fruit type, were automatically calculated. The experimental results show that the segmentation accuracy of the deep learning model reaches more than 0.95. Compared with the manual measurements, the mean absolute percentage error of the fruit width and length measurements by the Micro-CT system was 1.94% and 2.89%, respectively, and the squares of the correlation coefficients were 0.96 and 0.93. It shows that the measurement accuracy of external traits of passion fruit is comparable to manual operations, and the measurement of internal traits is more reliable because of the nondestructive characteristics of our method. According to the statistical data of the whole samples, the Pearson analysis method was used, and the results indicated specific correlations among fourteen phenotypic traits of passion fruit. At the same time, the results of the principal component analysis illustrated that the comprehensive quality of passion fruit could be scored using this method, which will help to screen for high-quality passion fruit samples with large sizes and high sarcocarp content. The results of this study will firstly provide a nondestructive method for more accurate and efficient automatic acquisition of comprehensive phenotypic traits of passion fruit and have the potential to be extended to more fruit crops. The preliminary study of the correlation between the characteristics of passion fruit can also provide a particular reference value for molecular breeding and comprehensive quality evaluation.
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Affiliation(s)
- Yuwei Lu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, China
- MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Rui Wang
- College of Tropical Crops, Hainan University, Haikou, China
| | - Tianyu Hu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, China
- MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qiang He
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - Zhou Shuai Chen
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - Jinhu Wang
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - Lingbo Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, China
- MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chuanying Fang
- College of Tropical Crops, Hainan University, Haikou, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Ling Fu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, China
- MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - Lejun Yu
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - Qian Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, China
- MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- School of Biomedical Engineering, Hainan University, Haikou, China
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Yu L, Liu L, Yang W, Wu D, Wang J, He Q, Chen Z, Liu Q. A non-destructive coconut fruit and seed traits extraction method based on Micro-CT and deeplabV3+ model. Front Plant Sci 2022; 13:1069849. [PMID: 36561444 PMCID: PMC9763456 DOI: 10.3389/fpls.2022.1069849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
With the completion of the coconut gene map and the gradual improvement of related molecular biology tools, molecular marker-assisted breeding of coconut has become the next focus of coconut breeding, and accurate coconut phenotypic traits measurement will provide technical support for screening and identifying the correspondence between genotype and phenotype. A Micro-CT system was developed to measure coconut fruits and seeds automatically and nondestructively to acquire the 3D model and phenotyping traits. A deeplabv3+ model with an Xception backbone was used to segment the sectional image of coconut fruits and seeds automatically. Compared with the structural-light system measurement, the mean absolute percentage error of the fruit volume and surface area measurements by the Micro-CT system was 1.87% and 2.24%, respectively, and the squares of the correlation coefficients were 0.977 and 0.964, respectively. In addition, compared with the manual measurements, the mean absolute percentage error of the automatic copra weight and total biomass measurements was 8.85% and 25.19%, respectively, and the adjusted squares of the correlation coefficients were 0.922 and 0.721, respectively. The Micro-CT system can nondestructively obtain up to 21 agronomic traits and 57 digital traits precisely.
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Affiliation(s)
- Lejun Yu
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - Lingbo Liu
- Wuhan National Laboratory for Optoelectronics, Britton Chance Center for Biomedical Photonics, Key Laboratory of Ministry of Education for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Dan Wu
- Wuhan National Laboratory for Optoelectronics, Britton Chance Center for Biomedical Photonics, Key Laboratory of Ministry of Education for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Jinhu Wang
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - Qiang He
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - ZhouShuai Chen
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - Qian Liu
- School of Biomedical Engineering, Hainan University, Haikou, China
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Tao H, Xu S, Tian Y, Li Z, Ge Y, Zhang J, Wang Y, Zhou G, Deng X, Zhang Z, Ding Y, Jiang D, Guo Q, Jin S. Proximal and remote sensing in plant phenomics: 20 years of progress, challenges, and perspectives. Plant Commun 2022; 3:100344. [PMID: 35655429 PMCID: PMC9700174 DOI: 10.1016/j.xplc.2022.100344] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/08/2022] [Accepted: 05/27/2022] [Indexed: 06/01/2023]
Abstract
Plant phenomics (PP) has been recognized as a bottleneck in studying the interactions of genomics and environment on plants, limiting the progress of smart breeding and precise cultivation. High-throughput plant phenotyping is challenging owing to the spatio-temporal dynamics of traits. Proximal and remote sensing (PRS) techniques are increasingly used for plant phenotyping because of their advantages in multi-dimensional data acquisition and analysis. Substantial progress of PRS applications in PP has been observed over the last two decades and is analyzed here from an interdisciplinary perspective based on 2972 publications. This progress covers most aspects of PRS application in PP, including patterns of global spatial distribution and temporal dynamics, specific PRS technologies, phenotypic research fields, working environments, species, and traits. Subsequently, we demonstrate how to link PRS to multi-omics studies, including how to achieve multi-dimensional PRS data acquisition and processing, how to systematically integrate all kinds of phenotypic information and derive phenotypic knowledge with biological significance, and how to link PP to multi-omics association analysis. Finally, we identify three future perspectives for PRS-based PP: (1) strengthening the spatial and temporal consistency of PRS data, (2) exploring novel phenotypic traits, and (3) facilitating multi-omics communication.
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Affiliation(s)
- Haiyu Tao
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, National Engineering and Technology Center for Information Agriculture, Collaborative Innovation Centre for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Address: No. 1 Weigang, Xuanwu District, Nanjing 210095, China
| | - Shan Xu
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, National Engineering and Technology Center for Information Agriculture, Collaborative Innovation Centre for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Address: No. 1 Weigang, Xuanwu District, Nanjing 210095, China
| | - Yongchao Tian
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, National Engineering and Technology Center for Information Agriculture, Collaborative Innovation Centre for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Address: No. 1 Weigang, Xuanwu District, Nanjing 210095, China
| | - Zhaofeng Li
- The Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, Agriculture College, Shihezi University, Shihezi 832003, China
| | - Yan Ge
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, National Engineering and Technology Center for Information Agriculture, Collaborative Innovation Centre for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Address: No. 1 Weigang, Xuanwu District, Nanjing 210095, China
| | - Jiaoping Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Wang
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, National Engineering and Technology Center for Information Agriculture, Collaborative Innovation Centre for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Address: No. 1 Weigang, Xuanwu District, Nanjing 210095, China
| | - Guodong Zhou
- Sanya Research Institute of Nanjing Agriculture University, Sanya 572024, China
| | - Xiong Deng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ze Zhang
- The Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, Agriculture College, Shihezi University, Shihezi 832003, China
| | - Yanfeng Ding
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, National Engineering and Technology Center for Information Agriculture, Collaborative Innovation Centre for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Address: No. 1 Weigang, Xuanwu District, Nanjing 210095, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Sanya Research Institute of Nanjing Agriculture University, Sanya 572024, China
| | - Dong Jiang
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, National Engineering and Technology Center for Information Agriculture, Collaborative Innovation Centre for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Address: No. 1 Weigang, Xuanwu District, Nanjing 210095, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Sanya Research Institute of Nanjing Agriculture University, Sanya 572024, China
| | - Qinghua Guo
- Institute of Ecology, College of Urban and Environmental Science, Peking University, Beijing 100871, China
| | - Shichao Jin
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, National Engineering and Technology Center for Information Agriculture, Collaborative Innovation Centre for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Address: No. 1 Weigang, Xuanwu District, Nanjing 210095, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Sanya Research Institute of Nanjing Agriculture University, Sanya 572024, China; Jiangsu Provincial Key Laboratory of Geographic Information Science and Technology, International Institute for Earth System Sciences, Nanjing University, Nanjing, Jiangsu 210023, China.
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Arend D, Psaroudakis D, Memon JA, Rey-Mazón E, Schüler D, Szymanski JJ, Scholz U, Junker A, Lange M. From data to knowledge - big data needs stewardship, a plant phenomics perspective. Plant J 2022; 111:335-347. [PMID: 35535481 DOI: 10.1111/tpj.15804] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 06/14/2023]
Abstract
The research data life cycle from project planning to data publishing is an integral part of current research. Until the last decade, researchers were responsible for all associated phases in addition to the actual research and were assisted only at certain points by IT or bioinformaticians. Starting with advances in sequencing, the automation of analytical methods in all life science fields, including in plant phenotyping, has led to ever-increasing amounts of ever more complex data. The tasks associated with these challenges now often exceed the expertise of and infrastructure available to scientists, leading to an increased risk of data loss over time. The IPK Gatersleben has one of the world's largest germplasm collections and two decades of experience in crop plant research data management. In this article we show how challenges in modern, data-driven research can be addressed by data stewards. Based on concrete use cases, data management processes and best practices from plant phenotyping, we describe which expertise and skills are required and how data stewards as an integral actor can enhance the quality of a necessary digital transformation in progressive research.
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Affiliation(s)
- Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Dennis Psaroudakis
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Junaid Altaf Memon
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Elena Rey-Mazón
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Danuta Schüler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Jedrzej Jakub Szymanski
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
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Park E, Kim YS, Omari MK, Suh HK, Faqeerzada MA, Kim MS, Baek I, Cho BK. High-Throughput Phenotyping Approach for the Evaluation of Heat Stress in Korean Ginseng ( Panax ginseng Meyer) Using a Hyperspectral Reflectance Image. Sensors (Basel) 2021; 21:s21165634. [PMID: 34451076 PMCID: PMC8402434 DOI: 10.3390/s21165634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/15/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022]
Abstract
Panax ginseng has been used as a traditional medicine to strengthen human health for centuries. Over the last decade, significant agronomical progress has been made in the development of elite ginseng cultivars, increasing their production and quality. However, as one of the significant environmental factors, heat stress remains a challenge and poses a significant threat to ginseng plants’ growth and sustainable production. This study was conducted to investigate the phenotype of ginseng leaves under heat stress using hyperspectral imaging (HSI). A visible/near-infrared (Vis/NIR) and short-wave infrared (SWIR) HSI system were used to acquire hyperspectral images for normal and heat stress-exposed plants, showing their susceptibility (Chunpoong) and resistibility (Sunmyoung and Sunil). The acquired hyperspectral images were analyzed using the partial least squares-discriminant analysis (PLS-DA) technique, combining the variable importance in projection and successive projection algorithm methods. The correlation of each group was verified using linear discriminant analysis. The developed models showed 12 bands over 79.2% accuracy in Vis/NIR and 18 bands with over 98.9% accuracy at SWIR in validation data. The constructed beta-coefficient allowed the observation of the key wavebands and peaks linked to the chlorophyll, nitrogen, fatty acid, sugar and protein content regions, which differentiated normal and stressed plants. This result shows that the HSI with the PLS-DA technique significantly differentiated between the heat-stressed susceptibility and resistibility of ginseng plants with high accuracy.
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Affiliation(s)
- Eunsoo Park
- Department of Biosystems Machinery Engineering, College of Agricultural and Life Science, Chungnam National University, Daejeon 34134, Korea; (E.P.); (M.K.O.); (M.A.F.)
| | - Yun-Soo Kim
- R&D Headquarters, Korea Ginseng Corporation, Daejeon 34128, Korea;
| | - Mohammad Kamran Omari
- Department of Biosystems Machinery Engineering, College of Agricultural and Life Science, Chungnam National University, Daejeon 34134, Korea; (E.P.); (M.K.O.); (M.A.F.)
| | - Hyun-Kwon Suh
- Department of Life Resources Industry, Dong-A University, Busan 49315, Korea;
| | - Mohammad Akbar Faqeerzada
- Department of Biosystems Machinery Engineering, College of Agricultural and Life Science, Chungnam National University, Daejeon 34134, Korea; (E.P.); (M.K.O.); (M.A.F.)
| | - Moon S. Kim
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville MD 20705, USA; (M.S.K.); (I.B.)
| | - Insuck Baek
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville MD 20705, USA; (M.S.K.); (I.B.)
| | - Byoung-Kwan Cho
- Department of Biosystems Machinery Engineering, College of Agricultural and Life Science, Chungnam National University, Daejeon 34134, Korea; (E.P.); (M.K.O.); (M.A.F.)
- Department of Smart Agriculture System, Chungnam National University, Daejeon 34134, Korea
- Correspondence:
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Nabwire S, Suh HK, Kim MS, Baek I, Cho BK. Review: Application of Artificial Intelligence in Phenomics. Sensors (Basel) 2021; 21:4363. [PMID: 34202291 DOI: 10.3390/s21134363] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 02/04/2023]
Abstract
Plant phenomics has been rapidly advancing over the past few years. This advancement is attributed to the increased innovation and availability of new technologies which can enable the high-throughput phenotyping of complex plant traits. The application of artificial intelligence in various domains of science has also grown exponentially in recent years. Notably, the computer vision, machine learning, and deep learning aspects of artificial intelligence have been successfully integrated into non-invasive imaging techniques. This integration is gradually improving the efficiency of data collection and analysis through the application of machine and deep learning for robust image analysis. In addition, artificial intelligence has fostered the development of software and tools applied in field phenotyping for data collection and management. These include open-source devices and tools which are enabling community driven research and data-sharing, thereby availing the large amounts of data required for the accurate study of phenotypes. This paper reviews more than one hundred current state-of-the-art papers concerning AI-applied plant phenotyping published between 2010 and 2020. It provides an overview of current phenotyping technologies and the ongoing integration of artificial intelligence into plant phenotyping. Lastly, the limitations of the current approaches/methods and future directions are discussed.
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10
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Rane J, Raina SK, Govindasamy V, Bindumadhava H, Hanjagi P, Giri R, Jangid KK, Kumar M, Nair RM. Use of Phenomics for Differentiation of Mungbean ( Vigna radiata L. Wilczek) Genotypes Varying in Growth Rates Per Unit of Water. Front Plant Sci 2021; 12:692564. [PMID: 34234800 PMCID: PMC8256871 DOI: 10.3389/fpls.2021.692564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/19/2021] [Indexed: 06/13/2023]
Abstract
In the human diet, particularly for most of the vegetarian population, mungbean (Vigna radiata L. Wilczek) is an inexpensive and environmentally friendly source of protein. Being a short-duration crop, mungbean fits well into different cropping systems dominated by staple food crops such as rice and wheat. Hence, knowing the growth and production pattern of this important legume under various soil moisture conditions gains paramount significance. Toward that end, 24 elite mungbean genotypes were grown with and without water stress for 25 days in a controlled environment. Top view and side view (two) images of all genotypes captured by a high-resolution camera installed in the high-throughput phenomics were analyzed to extract the pertinent parameters associated with plant features. We tested eight different multivariate models employing machine learning algorithms to predict fresh biomass from different features extracted from the images of diverse genotypes in the presence and absence of soil moisture stress. Based on the mean absolute error (MAE), root mean square error (RMSE), and R squared (R 2) values, which are used to assess the precision of a model, the partial least square (PLS) method among the eight models was selected for the prediction of biomass. The predicted biomass was used to compute the plant growth rates and water-use indices, which were found to be highly promising surrogate traits as they could differentiate the response of genotypes to soil moisture stress more effectively. To the best of our knowledge, this is perhaps the first report stating the use of a phenomics method as a promising tool for assessing growth rates and also the productive use of water in mungbean crop.
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Affiliation(s)
- Jagadish Rane
- School of Water Stress Management, Indian Council of Agricultural Research-National Institute of Abiotic Stress Management, Baramati, India
| | - Susheel Kumar Raina
- School of Water Stress Management, Indian Council of Agricultural Research-National Institute of Abiotic Stress Management, Baramati, India
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, Regional Station, Srinagar, India
| | - Venkadasamy Govindasamy
- School of Water Stress Management, Indian Council of Agricultural Research-National Institute of Abiotic Stress Management, Baramati, India
- Division of Microbiology, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
| | - Hanumantharao Bindumadhava
- World Vegetable Center, South Asia, International Crops Research Institute for the Semi-Arid Tropics Campus, Hyderabad, India
- Marri Channa Reddy Foundation (MCRF), Hyderabad, India
| | - Prashantkumar Hanjagi
- School of Water Stress Management, Indian Council of Agricultural Research-National Institute of Abiotic Stress Management, Baramati, India
- Division of Crop Physiology and Biochemistry, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, India
| | - Rajkumar Giri
- School of Water Stress Management, Indian Council of Agricultural Research-National Institute of Abiotic Stress Management, Baramati, India
| | - Krishna Kumar Jangid
- School of Water Stress Management, Indian Council of Agricultural Research-National Institute of Abiotic Stress Management, Baramati, India
| | - Mahesh Kumar
- School of Water Stress Management, Indian Council of Agricultural Research-National Institute of Abiotic Stress Management, Baramati, India
| | - Ramakrishnan M. Nair
- World Vegetable Center, South Asia, International Crops Research Institute for the Semi-Arid Tropics Campus, Hyderabad, India
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Rigoulot SB, Schimel TM, Lee JH, Sears RG, Brabazon H, Layton JS, Li L, Meier KA, Poindexter MR, Schmid MJ, Seaberry EM, Brabazon JW, Madajian JA, Finander MJ, DiBenedetto J, Occhialini A, Lenaghan SC, Stewart CN. Imaging of multiple fluorescent proteins in canopies enables synthetic biology in plants. Plant Biotechnol J 2021; 19:830-843. [PMID: 33179383 PMCID: PMC8051605 DOI: 10.1111/pbi.13510] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 10/31/2020] [Indexed: 05/24/2023]
Abstract
Reverse genetics approaches have revolutionized plant biology and agriculture. Phenomics has the prospect of bridging plant phenotypes with genes, including transgenes, to transform agricultural fields. Genetically encoded fluorescent proteins (FPs) have revolutionized plant biology paradigms in gene expression, protein trafficking and plant physiology. While the first instance of plant canopy imaging of green fluorescent protein (GFP) was performed over 25 years ago, modern phenomics has largely ignored fluorescence as a transgene expression device despite the burgeoning FP colour palette available to plant biologists. Here, we show a new platform for stand-off imaging of plant canopies expressing a wide variety of FP genes. The platform-the fluorescence-inducing laser projector (FILP)-uses an ultra-low-noise camera to image a scene illuminated by compact diode lasers of various colours, coupled with emission filters to resolve individual FPs, to phenotype transgenic plants expressing FP genes. Each of the 20 FPs screened in plants were imaged at >3 m using FILP in a laboratory-based laser range. We also show that pairs of co-expressed fluorescence proteins can be imaged in canopies. The FILP system enabled a rapid synthetic promoter screen: starting from 2000 synthetic promoters transfected into protoplasts to FILP-imaged agroinfiltrated Nicotiana benthamiana plants in a matter of weeks, which was useful to characterize a water stress-inducible synthetic promoter. FILP canopy imaging was also accomplished for stably transformed GFP potato and in a split-GFP assay, which illustrates the flexibility of the instrument for analysing fluorescence signals in plant canopies.
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Affiliation(s)
- Stephen B. Rigoulot
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Tayler M. Schimel
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of MechanicalAerospace and Biomedical EngineeringUniversity of TennesseeKnoxvilleTNUSA
| | - Jun Hyung Lee
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Robert G. Sears
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Holly Brabazon
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Brabazon AppsKnoxvilleTNUSA
| | - Jessica S. Layton
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Li Li
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Kerry A. Meier
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Magen R. Poindexter
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Manuel J. Schmid
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Erin M. Seaberry
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | | | - Jonathan A. Madajian
- Mission Support and Test Services Special Technology LaboratorySanta BarbaraCAUSA
| | | | - John DiBenedetto
- Mission Support and Test Services Special Technology LaboratorySanta BarbaraCAUSA
| | - Alessandro Occhialini
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Food ScienceUniversity of TennesseeKnoxvilleTNUSA
| | - Scott C. Lenaghan
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Food ScienceUniversity of TennesseeKnoxvilleTNUSA
| | - C. Neal Stewart
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
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12
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Wu D, Guo Z, Ye J, Feng H, Liu J, Chen G, Zheng J, Yan D, Yang X, Xiong X, Liu Q, Niu Z, Gay AP, Doonan JH, Xiong L, Yang W. Combining high-throughput micro-CT-RGB phenotyping and genome-wide association study to dissect the genetic architecture of tiller growth in rice. J Exp Bot 2019; 70:545-561. [PMID: 30380099 PMCID: PMC6322582 DOI: 10.1093/jxb/ery373] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/24/2018] [Indexed: 05/20/2023]
Abstract
Manual phenotyping of rice tillers is time consuming and labor intensive, and lags behind the rapid development of rice functional genomics. Thus, automated, non-destructive methods of phenotyping rice tiller traits at a high spatial resolution and high throughput for large-scale assessment of rice accessions are urgently needed. In this study, we developed a high-throughput micro-CT-RGB imaging system to non-destructively extract 739 traits from 234 rice accessions at nine time points. We could explain 30% of the grain yield variance from two tiller traits assessed in the early growth stages. A total of 402 significantly associated loci were identified by genome-wide association study, and dynamic and static genetic components were found across the nine time points. A major locus associated with tiller angle was detected at time point 9, which contained a major gene, TAC1. Significant variants associated with tiller angle were enriched in the 3'-untranslated region of TAC1. Three haplotypes for the gene were found, and rice accessions containing haplotype H3 displayed much smaller tiller angles. Further, we found two loci containing associations with both vigor-related traits identified by high-throughput micro-CT-RGB imaging and yield. The superior alleles would be beneficial for breeding for high yield and dense planting.
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Affiliation(s)
- Di Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Zilong Guo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Junli Ye
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Hui Feng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Jianxiao Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Guoxing Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Jingshan Zheng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Dongmei Yan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, and Key Laboratory of Ministry of Education for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoquan Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, and Key Laboratory of Ministry of Education for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Xiong Xiong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, and Key Laboratory of Ministry of Education for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, and Key Laboratory of Ministry of Education for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiyou Niu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Alan P Gay
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - John H Doonan
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
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13
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Alaguero-Cordovilla A, Gran-Gómez FJ, Tormos-Moltó S, Pérez-Pérez JM. Morphological Characterization of Root System Architecture in Diverse Tomato Genotypes during Early Growth. Int J Mol Sci 2018; 19:E3888. [PMID: 30563085 PMCID: PMC6321557 DOI: 10.3390/ijms19123888] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/20/2022] Open
Abstract
Plant roots exploit morphological plasticity to adapt and respond to different soil environments. We characterized the root system architecture of nine wild tomato species and four cultivated tomato (Solanum lycopersicum L.) varieties during early growth in a controlled environment. Additionally, the root system architecture of six near-isogenic lines from the tomato 'Micro-Tom' mutant collection was also studied. These lines were affected in key genes of ethylene, abscisic acid, and anthocyanin pathways. We found extensive differences between the studied lines for a number of meaningful morphological traits, such as lateral root distribution, lateral root length or adventitious root development, which might represent adaptations to local soil conditions during speciation and subsequent domestication. Taken together, our results provide a general quantitative framework for comparing root system architecture in tomato seedlings and other related species.
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Affiliation(s)
| | | | - Sergio Tormos-Moltó
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain.
- OQOTECH Process Validation System, 03801 Alcoy, Spain.
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14
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Jimenez-Berni JA, Deery DM, Rozas-Larraondo P, Condon A(TG, Rebetzke GJ, James RA, Bovill WD, Furbank RT, Sirault XRR. High Throughput Determination of Plant Height, Ground Cover, and Above-Ground Biomass in Wheat with LiDAR. Front Plant Sci 2018; 9:237. [PMID: 29535749 PMCID: PMC5835033 DOI: 10.3389/fpls.2018.00237] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/09/2018] [Indexed: 05/18/2023]
Abstract
Crop improvement efforts are targeting increased above-ground biomass and radiation-use efficiency as drivers for greater yield. Early ground cover and canopy height contribute to biomass production, but manual measurements of these traits, and in particular above-ground biomass, are slow and labor-intensive, more so when made at multiple developmental stages. These constraints limit the ability to capture these data in a temporal fashion, hampering insights that could be gained from multi-dimensional data. Here we demonstrate the capacity of Light Detection and Ranging (LiDAR), mounted on a lightweight, mobile, ground-based platform, for rapid multi-temporal and non-destructive estimation of canopy height, ground cover and above-ground biomass. Field validation of LiDAR measurements is presented. For canopy height, strong relationships with LiDAR (r2 of 0.99 and root mean square error of 0.017 m) were obtained. Ground cover was estimated from LiDAR using two methodologies: red reflectance image and canopy height. In contrast to NDVI, LiDAR was not affected by saturation at high ground cover, and the comparison of both LiDAR methodologies showed strong association (r2 = 0.92 and slope = 1.02) at ground cover above 0.8. For above-ground biomass, a dedicated field experiment was performed with destructive biomass sampled eight times across different developmental stages. Two methodologies are presented for the estimation of biomass from LiDAR: 3D voxel index (3DVI) and 3D profile index (3DPI). The parameters involved in the calculation of 3DVI and 3DPI were optimized for each sample event from tillering to maturity, as well as generalized for any developmental stage. Individual sample point predictions were strong while predictions across all eight sample events, provided the strongest association with biomass (r2 = 0.93 and r2 = 0.92) for 3DPI and 3DVI, respectively. Given these results, we believe that application of this system will provide new opportunities to deliver improved genotypes and agronomic interventions via more efficient and reliable phenotyping of these important traits in large experiments.
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Affiliation(s)
- Jose A. Jimenez-Berni
- High Resolution Plant Phenomics Centre, Commonwealth Scientific and Industrial Research Organisation Agriculture and Food Agriculture and Food, Canberra, ACT, Australia
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, ACT, Australia
| | - David M. Deery
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
| | - Pablo Rozas-Larraondo
- High Resolution Plant Phenomics Centre, Commonwealth Scientific and Industrial Research Organisation Agriculture and Food Agriculture and Food, Canberra, ACT, Australia
| | - Anthony (Tony) G. Condon
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, ACT, Australia
| | - Greg J. Rebetzke
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
| | - Richard A. James
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
| | - William D. Bovill
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
| | - Robert T. Furbank
- High Resolution Plant Phenomics Centre, Commonwealth Scientific and Industrial Research Organisation Agriculture and Food Agriculture and Food, Canberra, ACT, Australia
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, ACT, Australia
| | - Xavier R. R. Sirault
- High Resolution Plant Phenomics Centre, Commonwealth Scientific and Industrial Research Organisation Agriculture and Food Agriculture and Food, Canberra, ACT, Australia
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, ACT, Australia
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15
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Großkinsky DK, Pieruschka R, Svensgaard J, Rascher U, Christensen S, Schurr U, Roitsch T. Phenotyping in the fields: dissecting the genetics of quantitative traits and digital farming. New Phytol 2015; 207:950-2. [PMID: 26235487 DOI: 10.1111/nph.13529] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Affiliation(s)
- Dominik K Großkinsky
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé 13, 2630, Taastrup, Denmark
| | - Roland Pieruschka
- European Plant Phenotyping Network and Forschungszentrum Jülich GmbH, Institut für Bio- und Geowissenschaften, IBG-2, Pflanzenwissenschaften, D-52425, Jülich, Germany
| | - Jesper Svensgaard
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé 13, 2630, Taastrup, Denmark
| | - Uwe Rascher
- European Plant Phenotyping Network and Forschungszentrum Jülich GmbH, Institut für Bio- und Geowissenschaften, IBG-2, Pflanzenwissenschaften, D-52425, Jülich, Germany
| | - Svend Christensen
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé 13, 2630, Taastrup, Denmark
| | - Ulrich Schurr
- European Plant Phenotyping Network and Forschungszentrum Jülich GmbH, Institut für Bio- und Geowissenschaften, IBG-2, Pflanzenwissenschaften, D-52425, Jülich, Germany
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé 13, 2630, Taastrup, Denmark
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16
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Dhondt S, Wuyts N, Inzé D. Cell to whole-plant phenotyping: the best is yet to come. Trends Plant Sci 2013; 18:428-39. [PMID: 23706697 DOI: 10.1016/j.tplants.2013.04.008] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/18/2013] [Accepted: 04/22/2013] [Indexed: 05/18/2023]
Abstract
Imaging and image processing have revolutionized plant phenotyping and are now a major tool for phenotypic trait measurement. Here we review plant phenotyping systems by examining three important characteristics: throughput, dimensionality, and resolution. First, whole-plant phenotyping systems are highlighted together with advances in automation that enable significant throughput increases. Organ and cellular level phenotyping and its tools, often operating at a lower throughput, are then discussed as a means to obtain high-dimensional phenotypic data at elevated spatial and temporal resolution. The significance of recent developments in sensor technologies that give access to plant morphology and physiology-related traits is shown. Overall, attention is focused on spatial and temporal resolution because these are crucial aspects of imaging procedures in plant phenotyping systems.
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Affiliation(s)
- Stijn Dhondt
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium
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