A high-throughput UAV millimetric imaging pipeline for plant density phenotyping reveals high heritability in wheat-pea sole crops and intercrops.
- 1INRAE - GQE-Le-Moulon
Abstract
Within-field diversification, notably through cereal legume intercropping, is a major lever of the agroecological transition. Breeding cultivars adapted to intercropping requires major changes in breeding practices, owing to strong genotype-by-stand-type interactions and the high spatial heterogeneity of low-input field trials. Part of this heterogeneity stems from variation in plant density, a first yield component that strongly influences resource competition and is critical to monitor in intercrops. Given the many plots in such platforms, high-throughput phenotyping of plant density is essential. Over two seasons, we designed a large field trial involving 200 wheat cultivars observed as sole crop as well as intercropped with two pea tester cultivars, in a pseudo-randomized complete block design. Plant density was manually counted on 40 cultivars, alongwith UAV flights at both high and low altitudes. We propose a method to predict plant density from millimeter-resolution RGB images, using linear regression on log-transformed fractional vegetation cover and additional colorimetric and textural indices. We predict total density of wheat or pea in sole crops, or the combined pea+wheat total density in intercrops with relative RMSE of 19.2% and 27.4% depending on season. Thanks to the pipeline, total plant density was predicted across the entire trial, comprising more than 1,000 microplots (200 varieties); this density showed high heritability (0.75-0.85). We provide guidelines regarding the composition of the training set for such intercrop trials. High-throughput phenotyping approaches such as the one proposed here can be instrumental in mobilizing genetic diversity for agroecology.
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BibTeX
@misc{freitas2026highthroughput,
title = {{A high-throughput UAV millimetric imaging pipeline for plant density phenotyping reveals high heritability in wheat-pea sole crops and intercrops.}},
author = {V. F. A. FREITAS and j. ENJALBERT and T. FLUTRE and J.-M. GILLIOT},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.09.757598},
url = {https://www.biorxiv.org/content/10.64898/2026.10.09.757598v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - A high-throughput UAV millimetric imaging pipeline for plant density phenotyping reveals high heritability in wheat-pea sole crops and intercrops.
AU - V. F. A. FREITAS
AU - j. ENJALBERT
AU - T. FLUTRE
AU - J.-M. GILLIOT
PY - 2026
DA - 2026/10/09
PB - bioRxiv
DO - 10.64898/2026.10.09.757598
UR - https://www.biorxiv.org/content/10.64898/2026.10.09.757598v1
AB - Within-field diversification, notably through cereal legume intercropping, is a major lever of the agroecological transition. Breeding cultivars adapted to intercropping requires major changes in breeding practices, owing to strong genotype-by-stand-type interactions and the high spatial heterogeneity of low-input field trials. Part of this heterogeneity stems from variation in plant density, a first yield component that strongly influences resource competition and is critical to monitor in intercrops. Given the many plots in such platforms, high-throughput phenotyping of plant density is essential. Over two seasons, we designed a large field trial involving 200 wheat cultivars observed as sole crop as well as intercropped with two pea tester cultivars, in a pseudo-randomized complete block design. Plant density was manually counted on 40 cultivars, alongwith UAV flights at both high and low altitudes. We propose a method to predict plant density from millimeter-resolution RGB images, using linear regression on log-transformed fractional vegetation cover and additional colorimetric and textural indices. We predict total density of wheat or pea in sole crops, or the combined pea+wheat total density in intercrops with relative RMSE of 19.2% and 27.4% depending on season. Thanks to the pipeline, total plant density was predicted across the entire trial, comprising more than 1,000 microplots (200 varieties); this density showed high heritability (0.75-0.85). We provide guidelines regarding the composition of the training set for such intercrop trials. High-throughput phenotyping approaches such as the one proposed here can be instrumental in mobilizing genetic diversity for agroecology.
ER -