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

Nicolas Morales; Mahlet T Anche; Nicholas S Kaczmar; Nicholas Lepak; Pengzun Ni; Maria Cinta Romay; Nicholas Santantonio; Edward S Buckler; Michael A Gore; Lukas A Mueller; Kelly R Robbins

doi:10.1093/genetics/iyae037

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

Genetics. 2024 Mar 12:iyae037. doi: 10.1093/genetics/iyae037. Online ahead of print.

Authors

Nicolas Morales¹, Mahlet T Anche¹, Nicholas S Kaczmar¹, Nicholas Lepak², Pengzun Ni^{1

3}, Maria Cinta Romay⁴, Nicholas Santantonio^{1

5}, Edward S Buckler^{1

4

2}, Michael A Gore¹, Lukas A Mueller^{1

6}, Kelly R Robbins¹

Affiliations

¹ Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
² United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
³ College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China.
⁴ Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.
⁵ School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
⁶ Boyce Thompson Institute, Ithaca, NY, 14853, USA.

PMID: 38469622
DOI: 10.1093/genetics/iyae037

Abstract

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 processed using ImageBreed. Contrasting to baseline agronomic trait spatial correction and a baseline multi-trait model, a two-stage approach was proposed. Using longitudinal NDVI data, plot level permanent environment (PE) effects estimated spatial patterns in the field throughout the growing season. NDVI PE were separated from additive genetic effects using two-dimensional spline (2DSpl), separable autoregressive (AR1) models, or random regression models (RR). The PE 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 PE 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 baseline models. Electrical conductance and elevation from a 2019 soil survey significantly improved model fit, while 2DSpl PE were most strongly correlated with the soil parameters. Simulation of field effects demonstrated improved specificity for RR models. In summary, the use of longitudinal NDVI measurements increased experimental accuracy and understanding of field spatio-temporal heterogeneity.

Keywords: Unoccupied aerial vehicles; autoregressive; elevation; genomic prediction; high throughput phenotypes; permanent environment; random regression; soil curvature; soil electrical conductance; spatial correction; spatial heterogeneity; two-dimensional splines; vegetation indices.