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Abstract
Phenotypic analysis of cassava root crowns (CRCs) so far has been limited to visual inspection and very few measurements due to its laborious process in the field. Here, we developed a platform for acquiring 3D CRC models using close-range photogrammetry for phenotypic analysis. The state of the art is a low cost and easy to set up 3D acquisition requiring only a background sheet, a reference object and a camera, compatible with field experiments in remote areas. We tested different software with CRC samples, and Agisoft and Blender were the most suitable software for generating high-quality 3D models and data analysis, respectively. We optimized the workflow by testing different numbers of images for 3D reconstruction and found that a minimum of 25 images per CRC can provide high quality 3D models. Up to ten traits, including 3D crown volumes, 3D crown surface, root density, surface-to-volume ratio, root numbers, root angle, crown diameter, cylinder soil volume, CRC compactness and root length can be extracted providing novel parameters for studying cassava storage roots. We applied this platform to partial-inbred cassava populations and demonstrated that our platform provides reliable 3D CRC modelling for phenotypic analysis, analysis of genetic variances and supporting breeding selection.
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1 Kasetsart University, Department of Genetics, Faculty of Science, Bangkok, Thailand (GRID:grid.9723.f) (ISNI:0000 0001 0944 049X)
2 Kasetsart University, Department of Agronomy, Faculty of Agriculture, Bangkok, Thailand (GRID:grid.9723.f) (ISNI:0000 0001 0944 049X); Kasetsart University, Center for Advanced Studies of Agriculture and Food (CASAF), Bangkok, Thailand (GRID:grid.9723.f) (ISNI:0000 0001 0944 049X)
3 Kasetsart University, Department of Genetics, Faculty of Science, Bangkok, Thailand (GRID:grid.9723.f) (ISNI:0000 0001 0944 049X); Kasetsart University, Center of Advanced Studies for Tropical Natural Resources, Bangkok, Thailand (GRID:grid.9723.f) (ISNI:0000 0001 0944 049X); Kasetsart University (OmiKU), Omics Center for Agriculture, Bioresources, Food and Health, Bangkok, Thailand (GRID:grid.9723.f) (ISNI:0000 0001 0944 049X)
4 Kasetsart University, Department of Agronomy, Faculty of Agriculture, Bangkok, Thailand (GRID:grid.9723.f) (ISNI:0000 0001 0944 049X)
5 Kasetsart University, Department of Genetics, Faculty of Science, Bangkok, Thailand (GRID:grid.9723.f) (ISNI:0000 0001 0944 049X); Kasetsart University, Department of Agronomy, Faculty of Agriculture, Bangkok, Thailand (GRID:grid.9723.f) (ISNI:0000 0001 0944 049X); Kasetsart University, Center for Advanced Studies of Agriculture and Food (CASAF), Bangkok, Thailand (GRID:grid.9723.f) (ISNI:0000 0001 0944 049X); Kasetsart University, Center of Advanced Studies for Tropical Natural Resources, Bangkok, Thailand (GRID:grid.9723.f) (ISNI:0000 0001 0944 049X); The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia (GRID:grid.418348.2) (ISNI:0000 0001 0943 556X)
6 Kasetsart University, Department of Genetics, Faculty of Science, Bangkok, Thailand (GRID:grid.9723.f) (ISNI:0000 0001 0944 049X); Kasetsart University, Center for Advanced Studies of Agriculture and Food (CASAF), Bangkok, Thailand (GRID:grid.9723.f) (ISNI:0000 0001 0944 049X); Kasetsart University, Center of Advanced Studies for Tropical Natural Resources, Bangkok, Thailand (GRID:grid.9723.f) (ISNI:0000 0001 0944 049X); Kasetsart University (OmiKU), Omics Center for Agriculture, Bioresources, Food and Health, Bangkok, Thailand (GRID:grid.9723.f) (ISNI:0000 0001 0944 049X)