Spatio-temporal modeling of high-throughput multi-spectral aerial images improves agronomic trait genomic prediction in hybrid maize

Design randomizations and spatial corrections have increased understanding of genotypic, spatial, and residual effects in field experiments, but precisely measuring spatial heterogeneity in the field remains a challenge. To this end, our study evaluated approaches to improve spatial modeling using high-throughput phenotypes (HTP) via unoccupied aerial vehicle (UAV) imagery. The normalized difference vegetation index (NDVI) was measured by a multi-spectral MicaSense camera and ImageBreed. Contrasting to baseline agronomic trait spatial correction and a baseline multi-trait model, a two-stage approach that quantified NDVI local environmental effects (NLEE) was proposed. Firstly, NLEE were separated from additive genetic effects over the growing season using two-dimensional spline (2DSpl), separable autoregressive (AR1) models, or random regression models (RR). Secondly, the NLEE were leveraged within agronomic trait genomic best linear unbiased prediction (GBLUP) either modeling an empirical covariance for random effects, or by modeling fixed effects as an average of NLEE across time or split among three growth phases. Modeling approaches were tested using simulation data and Genomes-to-Fields (G2F) hybrid maize (Zea mays L.) field experiments in 2015, 2017, 2019, and 2020 for grain yield, grain moisture, and ear height. The two-stage approach improved heritability, model fit, and genotypic effect estimation compared to all baseline models. Electrical conductance and elevation from a 2019 soil survey significantly improved model fit, while 2DSpl NLEE were most correlated to the soil parameters and grain yield 2DSpl effects. Simulation of field effects demonstrated improved specificity for RR models. In summary, NLEE increased experimental accuracy and understanding of field spatio-temporal heterogeneity.