Work

A high-throughput UAV millimetric imaging pipeline for plant density phenotyping reveals high heritability in wheat-pea sole crops and intercrops

Year: 2026

Type: preprint

Abstract: 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. PLAIN LANGUAGE SUMMARY Growing two crops together in the same field such as wheat and pea is a promising way to make farming more sustainable. But breeding varieties suited to this practice remains difficult, because many interacting factors shape how the two crops perform together. One key factor is the number of plants that actually emerge in each plot: it reveals how many plants may ultimately contribute to yield, and it strongly affects how plants compete for resources. Counting plants by hand across thousands of small plots is impossible, so we used a drone to take very detailed photos of a large experiment involving 200 wheat varieties, grown alone or mixed with pea. From these images, we developed a method to estimate the number of plants in each plot wheat, pea, or both. Measuring this trait early and across hundreds of varieties can help breeders develop crops adapted to more diverse, environmentally friendly farming systems.

Source: bioRxiv (Cold Spring Harbor Laboratory)

DOI: 10.64898/2026.10.09.757598

Authors: V. Freitas, J. Enjalbert, T. Flutre, J.-M. Gilliot