Development and Validation of a Phenotyping Computational Workflow to Predict the Biomass Yield of a Large Perennial Ryegrass Breeding Field Trial
Increasing dry matter yield (DMY) is the most important objective in perennial ryegrass breeding programs. Current yield assessment methods like cutting are time-consuming and destructive, non-destructive measures such as scoring yield on single plants by visual inspection may be subjective. These a...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2020-05-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2020.00689/full |
| _version_ | 1819014177945026560 |
|---|---|
| author | Alem Gebremedhin Alem Gebremedhin Pieter Badenhorst Junping Wang Fan Shi Ed Breen Khageswor Giri German C. Spangenberg German C. Spangenberg Kevin Smith Kevin Smith |
| author_facet | Alem Gebremedhin Alem Gebremedhin Pieter Badenhorst Junping Wang Fan Shi Ed Breen Khageswor Giri German C. Spangenberg German C. Spangenberg Kevin Smith Kevin Smith |
| author_sort | Alem Gebremedhin |
| collection | DOAJ |
| description | Increasing dry matter yield (DMY) is the most important objective in perennial ryegrass breeding programs. Current yield assessment methods like cutting are time-consuming and destructive, non-destructive measures such as scoring yield on single plants by visual inspection may be subjective. These assessments involve multiple measurements and selection procedures across seasons and years to evaluate biomass yield repeatedly. This contributes to the slow process of new cultivar development and commercialisation. This study developed and validated a computational phenotyping workflow for image acquisition, processing and analysis of spaced planted ryegrass and investigated sensor-based DMY yield estimation of individual plants through normalized difference vegetative index (NDVI) and ultrasonic plant height data extraction. The DMY of 48,000 individual plants representing 50 advanced breeding lines and commercial cultivars was accurately estimated at multiple harvests across the growing season. NDVI, plant height and predicted DMY obtained from aerial and ground-based sensors illustrated the variation within and between cultivars across different seasons. Combining NDVI and plant height of individual plants was a robust method to enable high-throughput phenotyping of biomass yield in ryegrass breeding. Similarly, the plot-level model indicated good to high-coefficients of determination (R2) between the predicted and measured DMY across three seasons with R2 between 0.19 and 0.81 and root mean square errors (RMSE) values ranging from 0.09 to 0.21 kg/plot. The model was further validated using a combined regression of the three seasons harvests. This study further sets a foundation for the application of sensor technologies combined with genomic studies that lead to greater rates of genetic gain in perennial ryegrass biomass yield. |
| first_indexed | 2024-12-21T02:11:42Z |
| format | Article |
| id | doaj.art-21f536430fb14a7cb65670b5a69bee74 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-21T02:11:42Z |
| publishDate | 2020-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-21f536430fb14a7cb65670b5a69bee742022-12-21T19:19:20ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2020-05-011110.3389/fpls.2020.00689530315Development and Validation of a Phenotyping Computational Workflow to Predict the Biomass Yield of a Large Perennial Ryegrass Breeding Field TrialAlem Gebremedhin0Alem Gebremedhin1Pieter Badenhorst2Junping Wang3Fan Shi4Ed Breen5Khageswor Giri6German C. Spangenberg7German C. Spangenberg8Kevin Smith9Kevin Smith10Agriculture Victoria, Hamilton Centre, Hamilton, VIC, AustraliaFaculty of Veterinary and Agricultural Sciences, School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, AustraliaAgriculture Victoria, Hamilton Centre, Hamilton, VIC, AustraliaAgriculture Victoria, Hamilton Centre, Hamilton, VIC, AustraliaAgriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, AustraliaAgriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, AustraliaAgriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, AustraliaAgriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, AustraliaSchool of Applied Systems Biology, La Trobe University, Bundoora, VIC, AustraliaAgriculture Victoria, Hamilton Centre, Hamilton, VIC, AustraliaFaculty of Veterinary and Agricultural Sciences, School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, AustraliaIncreasing dry matter yield (DMY) is the most important objective in perennial ryegrass breeding programs. Current yield assessment methods like cutting are time-consuming and destructive, non-destructive measures such as scoring yield on single plants by visual inspection may be subjective. These assessments involve multiple measurements and selection procedures across seasons and years to evaluate biomass yield repeatedly. This contributes to the slow process of new cultivar development and commercialisation. This study developed and validated a computational phenotyping workflow for image acquisition, processing and analysis of spaced planted ryegrass and investigated sensor-based DMY yield estimation of individual plants through normalized difference vegetative index (NDVI) and ultrasonic plant height data extraction. The DMY of 48,000 individual plants representing 50 advanced breeding lines and commercial cultivars was accurately estimated at multiple harvests across the growing season. NDVI, plant height and predicted DMY obtained from aerial and ground-based sensors illustrated the variation within and between cultivars across different seasons. Combining NDVI and plant height of individual plants was a robust method to enable high-throughput phenotyping of biomass yield in ryegrass breeding. Similarly, the plot-level model indicated good to high-coefficients of determination (R2) between the predicted and measured DMY across three seasons with R2 between 0.19 and 0.81 and root mean square errors (RMSE) values ranging from 0.09 to 0.21 kg/plot. The model was further validated using a combined regression of the three seasons harvests. This study further sets a foundation for the application of sensor technologies combined with genomic studies that lead to greater rates of genetic gain in perennial ryegrass biomass yield.https://www.frontiersin.org/article/10.3389/fpls.2020.00689/fullhigh-throughput phenotypingbiomassperennial ryegrassNDVIplant heightcomputational workflow |
| spellingShingle | Alem Gebremedhin Alem Gebremedhin Pieter Badenhorst Junping Wang Fan Shi Ed Breen Khageswor Giri German C. Spangenberg German C. Spangenberg Kevin Smith Kevin Smith Development and Validation of a Phenotyping Computational Workflow to Predict the Biomass Yield of a Large Perennial Ryegrass Breeding Field Trial Frontiers in Plant Science high-throughput phenotyping biomass perennial ryegrass NDVI plant height computational workflow |
| title | Development and Validation of a Phenotyping Computational Workflow to Predict the Biomass Yield of a Large Perennial Ryegrass Breeding Field Trial |
| title_full | Development and Validation of a Phenotyping Computational Workflow to Predict the Biomass Yield of a Large Perennial Ryegrass Breeding Field Trial |
| title_fullStr | Development and Validation of a Phenotyping Computational Workflow to Predict the Biomass Yield of a Large Perennial Ryegrass Breeding Field Trial |
| title_full_unstemmed | Development and Validation of a Phenotyping Computational Workflow to Predict the Biomass Yield of a Large Perennial Ryegrass Breeding Field Trial |
| title_short | Development and Validation of a Phenotyping Computational Workflow to Predict the Biomass Yield of a Large Perennial Ryegrass Breeding Field Trial |
| title_sort | development and validation of a phenotyping computational workflow to predict the biomass yield of a large perennial ryegrass breeding field trial |
| topic | high-throughput phenotyping biomass perennial ryegrass NDVI plant height computational workflow |
| url | https://www.frontiersin.org/article/10.3389/fpls.2020.00689/full |
| work_keys_str_mv | AT alemgebremedhin developmentandvalidationofaphenotypingcomputationalworkflowtopredictthebiomassyieldofalargeperennialryegrassbreedingfieldtrial AT alemgebremedhin developmentandvalidationofaphenotypingcomputationalworkflowtopredictthebiomassyieldofalargeperennialryegrassbreedingfieldtrial AT pieterbadenhorst developmentandvalidationofaphenotypingcomputationalworkflowtopredictthebiomassyieldofalargeperennialryegrassbreedingfieldtrial AT junpingwang developmentandvalidationofaphenotypingcomputationalworkflowtopredictthebiomassyieldofalargeperennialryegrassbreedingfieldtrial AT fanshi developmentandvalidationofaphenotypingcomputationalworkflowtopredictthebiomassyieldofalargeperennialryegrassbreedingfieldtrial AT edbreen developmentandvalidationofaphenotypingcomputationalworkflowtopredictthebiomassyieldofalargeperennialryegrassbreedingfieldtrial AT khagesworgiri developmentandvalidationofaphenotypingcomputationalworkflowtopredictthebiomassyieldofalargeperennialryegrassbreedingfieldtrial AT germancspangenberg developmentandvalidationofaphenotypingcomputationalworkflowtopredictthebiomassyieldofalargeperennialryegrassbreedingfieldtrial AT germancspangenberg developmentandvalidationofaphenotypingcomputationalworkflowtopredictthebiomassyieldofalargeperennialryegrassbreedingfieldtrial AT kevinsmith developmentandvalidationofaphenotypingcomputationalworkflowtopredictthebiomassyieldofalargeperennialryegrassbreedingfieldtrial AT kevinsmith developmentandvalidationofaphenotypingcomputationalworkflowtopredictthebiomassyieldofalargeperennialryegrassbreedingfieldtrial |