From Images to Loci: Applying 3D Deep Learning to Enable Multivariate and Multitemporal Digital Phenotyping and Mapping the Genetics Underlying Nitrogen Use Efficiency in Wheat
The selection and promotion of high-yielding and nitrogen-efficient wheat varieties can reduce nitrogen fertilizer application while ensuring wheat yield and quality and contribute to the sustainable development of agriculture; thus, the mining and localization of nitrogen use efficiency (NUE) genes...
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| Format: | Article |
| Language: | English |
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American Association for the Advancement of Science (AAAS)
2024-01-01
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| Series: | Plant Phenomics |
| Online Access: | https://spj.science.org/doi/10.34133/plantphenomics.0270 |
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| author | Jiawei Chen Qing Li Dong Jiang |
| author_facet | Jiawei Chen Qing Li Dong Jiang |
| author_sort | Jiawei Chen |
| collection | DOAJ |
| description | The selection and promotion of high-yielding and nitrogen-efficient wheat varieties can reduce nitrogen fertilizer application while ensuring wheat yield and quality and contribute to the sustainable development of agriculture; thus, the mining and localization of nitrogen use efficiency (NUE) genes is particularly important, but the localization of NUE genes requires a large amount of phenotypic data support. In view of this, we propose the use of low-altitude aerial photography to acquire field images at a large scale, generate 3-dimensional (3D) point clouds and multispectral images of wheat plots, propose a wheat 3D plot segmentation dataset, quantify the plot canopy height via combination with PointNet++, and generate 4 nitrogen utilization-related vegetation indices via index calculations. Six height-related and 24 vegetation-index-related dynamic digital phenotypes were extracted from the digital phenotypes collected at different time points and fitted to generate dynamic curves. We applied height-derived dynamic numerical phenotypes to genome-wide association studies of 160 wheat cultivars (660,000 single-nucleotide polymorphisms) and found that we were able to locate reliable loci associated with height and NUE, some of which were consistent with published studies. Finally, dynamic phenotypes derived from plant indices can also be applied to genome-wide association studies and ultimately locate NUE- and growth-related loci. In conclusion, we believe that our work demonstrates valuable advances in 3D digital dynamic phenotyping for locating genes for NUE in wheat and provides breeders with accurate phenotypic data for the selection and breeding of nitrogen-efficient wheat varieties. |
| format | Article |
| id | doaj-art-791dc243fb754144bc3138ded694f8bd |
| institution | OA Journals |
| issn | 2643-6515 |
| language | English |
| publishDate | 2024-01-01 |
| publisher | American Association for the Advancement of Science (AAAS) |
| record_format | Article |
| series | Plant Phenomics |
| spelling | doaj-art-791dc243fb754144bc3138ded694f8bd2025-08-20T01:58:19ZengAmerican Association for the Advancement of Science (AAAS)Plant Phenomics2643-65152024-01-01610.34133/plantphenomics.0270From Images to Loci: Applying 3D Deep Learning to Enable Multivariate and Multitemporal Digital Phenotyping and Mapping the Genetics Underlying Nitrogen Use Efficiency in WheatJiawei Chen0Qing Li1Dong Jiang2Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, Collaborative Innovation Centre for Modern Crop Production, Co-sponsored by Province and Ministry, College of Agriculture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China.Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, Collaborative Innovation Centre for Modern Crop Production, Co-sponsored by Province and Ministry, College of Agriculture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China.Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, Collaborative Innovation Centre for Modern Crop Production, Co-sponsored by Province and Ministry, College of Agriculture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China.The selection and promotion of high-yielding and nitrogen-efficient wheat varieties can reduce nitrogen fertilizer application while ensuring wheat yield and quality and contribute to the sustainable development of agriculture; thus, the mining and localization of nitrogen use efficiency (NUE) genes is particularly important, but the localization of NUE genes requires a large amount of phenotypic data support. In view of this, we propose the use of low-altitude aerial photography to acquire field images at a large scale, generate 3-dimensional (3D) point clouds and multispectral images of wheat plots, propose a wheat 3D plot segmentation dataset, quantify the plot canopy height via combination with PointNet++, and generate 4 nitrogen utilization-related vegetation indices via index calculations. Six height-related and 24 vegetation-index-related dynamic digital phenotypes were extracted from the digital phenotypes collected at different time points and fitted to generate dynamic curves. We applied height-derived dynamic numerical phenotypes to genome-wide association studies of 160 wheat cultivars (660,000 single-nucleotide polymorphisms) and found that we were able to locate reliable loci associated with height and NUE, some of which were consistent with published studies. Finally, dynamic phenotypes derived from plant indices can also be applied to genome-wide association studies and ultimately locate NUE- and growth-related loci. In conclusion, we believe that our work demonstrates valuable advances in 3D digital dynamic phenotyping for locating genes for NUE in wheat and provides breeders with accurate phenotypic data for the selection and breeding of nitrogen-efficient wheat varieties.https://spj.science.org/doi/10.34133/plantphenomics.0270 |
| spellingShingle | Jiawei Chen Qing Li Dong Jiang From Images to Loci: Applying 3D Deep Learning to Enable Multivariate and Multitemporal Digital Phenotyping and Mapping the Genetics Underlying Nitrogen Use Efficiency in Wheat Plant Phenomics |
| title | From Images to Loci: Applying 3D Deep Learning to Enable Multivariate and Multitemporal Digital Phenotyping and Mapping the Genetics Underlying Nitrogen Use Efficiency in Wheat |
| title_full | From Images to Loci: Applying 3D Deep Learning to Enable Multivariate and Multitemporal Digital Phenotyping and Mapping the Genetics Underlying Nitrogen Use Efficiency in Wheat |
| title_fullStr | From Images to Loci: Applying 3D Deep Learning to Enable Multivariate and Multitemporal Digital Phenotyping and Mapping the Genetics Underlying Nitrogen Use Efficiency in Wheat |
| title_full_unstemmed | From Images to Loci: Applying 3D Deep Learning to Enable Multivariate and Multitemporal Digital Phenotyping and Mapping the Genetics Underlying Nitrogen Use Efficiency in Wheat |
| title_short | From Images to Loci: Applying 3D Deep Learning to Enable Multivariate and Multitemporal Digital Phenotyping and Mapping the Genetics Underlying Nitrogen Use Efficiency in Wheat |
| title_sort | from images to loci applying 3d deep learning to enable multivariate and multitemporal digital phenotyping and mapping the genetics underlying nitrogen use efficiency in wheat |
| url | https://spj.science.org/doi/10.34133/plantphenomics.0270 |
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