A novel way to validate UAS-based high-throughput phenotyping protocols using in silico experiments for plant breeding purposes.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Giovanni GalliRoberto Fritsche-Neto

Abstract

It is possible to make inferences regarding the feasibility and applicability of plant high-throughput phenotyping via computer simulations. Protocol validation has been a key challenge to the establishment of high-throughput phenotyping (HTP) in breeding programs. We add to this matter by proposing an innovative way for designing and validating aerial imagery-based HTP approaches with in silico 3D experiments for plant breeding purposes. The algorithm is constructed following a pipeline composed of the simulation of phenotypic values, three-dimensional modeling of trials, and image rendering. Our tool is exemplified by testing a set of experimental setups that are of interest in the context of maize breeding using a comprehensive case study. We report on how the choice of (percentile of) points in dense clouds, the experimental repeatability (heritability), the treatment variance (genetic variability), and the flight altitude affect the accuracy of high-throughput plant height estimation based on conventional structure-from-motion (SfM) and multi-view stereo (MVS) pipelines. The evaluation of both the algorithm and the case study was driven by comparisons of the computer-simulated (ground truth) and the HTP-estimated values us...Continue Reading

References

Jan 19, 2006·Nature Reviews. Genetics·Jennifer L ReedBernhard O Palsson
Oct 22, 2013·Trends in Plant Science·José Luis Araus, Jill E Cairns
May 24, 2016·Bio Systems·Christian Edlich-MuthJoachim Selbig
Aug 19, 2016·Frontiers in Plant Science·Maria TattarisScott C Chapman
Mar 21, 2018·Trends in Plant Science·José Luis ArausJill E Cairns

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Software Mentioned

QGIS
- View Stereo ( MVS
R Core Team
R
Agisoft
Metashape
Blender
Blender engine
Agisoft Metashape
bpy

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