Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel
Abstract Estimates of plant traits derived from hyperspectral reflectance data have the potential to efficiently substitute for traits, which are time or labor intensive to manually score. Typical workflows for estimating plant traits from hyperspectral reflectance data employ supervised classificat...
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| Format: | Article |
| Language: | English |
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Wiley
2024-12-01
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| Series: | Plant Phenome Journal |
| Online Access: | https://doi.org/10.1002/ppj2.20106 |
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| author | Michael C. Tross Marcin W. Grzybowski Talukder Z. Jubery Ryleigh J. Grove Aime V. Nishimwe J. Vladimir Torres‐Rodriguez Guangchao Sun Baskar Ganapathysubramanian Yufeng Ge James C. Schnable |
| author_facet | Michael C. Tross Marcin W. Grzybowski Talukder Z. Jubery Ryleigh J. Grove Aime V. Nishimwe J. Vladimir Torres‐Rodriguez Guangchao Sun Baskar Ganapathysubramanian Yufeng Ge James C. Schnable |
| author_sort | Michael C. Tross |
| collection | DOAJ |
| description | Abstract Estimates of plant traits derived from hyperspectral reflectance data have the potential to efficiently substitute for traits, which are time or labor intensive to manually score. Typical workflows for estimating plant traits from hyperspectral reflectance data employ supervised classification models that can require substantial ground truth datasets for training. We explore the potential of an unsupervised approach, autoencoders, to extract meaningful traits from plant hyperspectral reflectance data using measurements of the reflectance of 2151 individual wavelengths of light from the leaves of maize (Zea mays) plants harvested from 1658 field plots in a replicated field trial. A subset of autoencoder‐derived variables exhibited significant repeatability, indicating that a substantial proportion of the total variance in these variables was explained by difference between maize genotypes, while other autoencoder variables appear to capture variation resulting from changes in leaf reflectance between different batches of data collection. Several of the repeatable latent variables were significantly correlated with other traits scored from the same maize field experiment, including one autoencoder‐derived latent variable (LV8) that predicted plant chlorophyll content modestly better than a supervised model trained on the same data. In at least one case, genome‐wide association study hits for variation in autoencoder‐derived variables were proximal to genes with known or plausible links to leaf phenotypes expected to alter hyperspectral reflectance. In aggregate, these results suggest that an unsupervised, autoencoder‐based approach can identify meaningful and genetically controlled variation in high‐dimensional, high‐throughput phenotyping data and link identified variables back to known plant traits of interest. |
| format | Article |
| id | doaj-art-2f45c21e70ec4f1aa738ded223ea579c |
| institution | DOAJ |
| issn | 2578-2703 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Wiley |
| record_format | Article |
| series | Plant Phenome Journal |
| spelling | doaj-art-2f45c21e70ec4f1aa738ded223ea579c2025-08-20T02:39:11ZengWileyPlant Phenome Journal2578-27032024-12-0171n/an/a10.1002/ppj2.20106Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panelMichael C. Tross0Marcin W. Grzybowski1Talukder Z. Jubery2Ryleigh J. Grove3Aime V. Nishimwe4J. Vladimir Torres‐Rodriguez5Guangchao Sun6Baskar Ganapathysubramanian7Yufeng Ge8James C. Schnable9Quantitative Life Sciences Initiative University of Nebraska‐Lincoln Lincoln Nebraska USAQuantitative Life Sciences Initiative University of Nebraska‐Lincoln Lincoln Nebraska USADepartment of Mechanical Engineering Iowa State University Ames Iowa USAQuantitative Life Sciences Initiative University of Nebraska‐Lincoln Lincoln Nebraska USAQuantitative Life Sciences Initiative University of Nebraska‐Lincoln Lincoln Nebraska USAQuantitative Life Sciences Initiative University of Nebraska‐Lincoln Lincoln Nebraska USAQuantitative Life Sciences Initiative University of Nebraska‐Lincoln Lincoln Nebraska USADepartment of Mechanical Engineering Iowa State University Ames Iowa USACenter for Plant Science Innovation University of Nebraska‐Lincoln Lincoln Nebraska USAQuantitative Life Sciences Initiative University of Nebraska‐Lincoln Lincoln Nebraska USAAbstract Estimates of plant traits derived from hyperspectral reflectance data have the potential to efficiently substitute for traits, which are time or labor intensive to manually score. Typical workflows for estimating plant traits from hyperspectral reflectance data employ supervised classification models that can require substantial ground truth datasets for training. We explore the potential of an unsupervised approach, autoencoders, to extract meaningful traits from plant hyperspectral reflectance data using measurements of the reflectance of 2151 individual wavelengths of light from the leaves of maize (Zea mays) plants harvested from 1658 field plots in a replicated field trial. A subset of autoencoder‐derived variables exhibited significant repeatability, indicating that a substantial proportion of the total variance in these variables was explained by difference between maize genotypes, while other autoencoder variables appear to capture variation resulting from changes in leaf reflectance between different batches of data collection. Several of the repeatable latent variables were significantly correlated with other traits scored from the same maize field experiment, including one autoencoder‐derived latent variable (LV8) that predicted plant chlorophyll content modestly better than a supervised model trained on the same data. In at least one case, genome‐wide association study hits for variation in autoencoder‐derived variables were proximal to genes with known or plausible links to leaf phenotypes expected to alter hyperspectral reflectance. In aggregate, these results suggest that an unsupervised, autoencoder‐based approach can identify meaningful and genetically controlled variation in high‐dimensional, high‐throughput phenotyping data and link identified variables back to known plant traits of interest.https://doi.org/10.1002/ppj2.20106 |
| spellingShingle | Michael C. Tross Marcin W. Grzybowski Talukder Z. Jubery Ryleigh J. Grove Aime V. Nishimwe J. Vladimir Torres‐Rodriguez Guangchao Sun Baskar Ganapathysubramanian Yufeng Ge James C. Schnable Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel Plant Phenome Journal |
| title | Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel |
| title_full | Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel |
| title_fullStr | Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel |
| title_full_unstemmed | Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel |
| title_short | Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel |
| title_sort | data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel |
| url | https://doi.org/10.1002/ppj2.20106 |
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