Temporally resolved growth patterns reveal novel information about the polygenic nature of complex quantitative traits

Abstract

Plant height can be an indicator of plant health across environments and used to identify superior genotypes. Typically plant height is measured at a single timepoint when plants reach terminal height. Evaluating plant height using unoccupied aerial vehicles allows for measurements throughout the growing season, facilitating a better understanding of plant-environment interactions and the genetic basis of this complex trait. To assess variation throughout development, plant height data was collected from planting until terminal height at anthesis (14 flights 2018, 27 in 2019, 12 in 2020, and 11 in 2021) for a panel of ~500 diverse maize inbred lines. The percent variance explained in plant height throughout the season was significantly explained by genotype (9-48%), year (4-52%), and genotype-by-year interactions (14-36%) to varying extents throughout development. Genome-wide association studies revealed 717 significant single nucleotide polymorphisms associated with plant height and growth rate at different parts of the growing season specific to certain phases of vegetative growth. When plant height growth curves were compared to growth curves estimated from canopy cover, greater Fréchet distance stability was observed in plant height growth curves than for canopy cover. This indicated canopy cover may be more useful for understanding environmental modulation of overall plant growth and plant height better for understanding genotypic modulation of overall plant growth. This study demonstrated that substantial information can be gained from high temporal resolution data to understand how plants differentially interact with the environment and can enhance our understanding of the genetic basis of complex polygenic traits.

Keywords: Fréchet distance; Zea mays L; canopy cover; genome‐wide association studies; genotype‐by‐environment interaction; plant height; unoccupied aerial vehicles.

Figure 1

Temporal plant height and growth rate analysis of variance. (a) LOESS curves of plant height are broken into three phases of the growing season based on the performance of genotypes in each year. (b) Variance explained and heritability at each plant height timepoint throughout the growing season. (c) Variance explained and heritability at each growth rate timepoint throughout the growing season.

Figure 2

Fuzzy c‐means clustering of LOESS growth curves. (a) Fuzzy c‐means clusters of 2018 LOESS growth curves with shading equating goodness of fit for each curve into the specified cluster. (b) Upset plot showing overlap of genotypes between growth curve clusters across years. Each curve is classified into a cluster based on the highest fit for each curve. Cluster types are represented by identifying colors (yellow: tall to tall; blue: short to short; red: short to tall).

Figure 3

Fréchet distances for each genotype present in all 4 years. (a) Pairwise Fréchet distance values comparing plant height growth curves of the same genotype across different years. (b) Example genotype (PHG47) representing genotypes with consistently low Fréchet distance values and low variation in terminal height. (c) Example genotype (YING‐55) representing genotypes with high Fréchet distance values and low variation in terminal height. (d) Example genotype (PHN66) representing genotypes with high Fréchet distance values and high variation in terminal height.

Figure 4

Significant single nucleotide polymorphisms (SNPs) identified with genome‐wide association study (GWAS) across development. (a) Results from plant height GWAS at each growing degree day interval throughout the growing season shaded by percent variance explained (PVE) of the significant SNPs at that timepoint. (b) Results from growth rate GWAS at each growing degree day interval throughout the growing season shaded by PVE of the significant SNPs at that interval. (c) Number of timepoints (height) or intervals (rate) in which a SNP was identified as significant within a year.

Figure 5

Significant single nucleotide polymorphism (SNP) effects from genome‐wide association study (GWAS) conducted on plant height or growth rate across the growing season. (a) Absolute value of effect of significant SNPs from at least one timepoint‐by‐year assessed across all plant height GWAS iterations in every timepoint throughout the growing season in all four growing seasons. (b) Absolute value of effect of significant SNPs from at least one timepoint‐by‐year assessed across all growth rate GWAS iterations in every timepoint throughout the growing season in all four growing seasons. (c) Absolute value of effect of an example significant SNP from plant height located on Chr2 at position 169 140 523 in the B73 v4 reference genome assembly throughout each of the growing seasons.

Figure 6

Relationships between plant height and canopy cover. (a) Pearson correlation between plant height and canopy cover across all plots at each growing degree day (GDD) interval for each year. (b) Fréchet distance between the plant height growth curve and canopy cover growth curve within the same plot. (c) Fréchet distance between experimental entry replicates for plant height versus Fréchet distance between experimental entry replicates for canopy cover.

Figure 7

Unoccupied aerial vehicle (UAV) data processing and plant height extraction. (a) Pipeline for image acquisition and feature extraction from UAV images. (b) Extracted plant height normalized across timepoints for a single example plot with segmented views of the plot at each timepoint. (c) Pearson correlation between normalized mean extracted plot plant height and mean manual plot plant height measurements across all dates within a year for height extraction validation.