Root Pulling Force Across Drought in Maize Reveals Genotype by Environment Interactions and Candidate Genes

Abstract

High-throughput, field-based characterization of root systems for hundreds of genotypes in thousands of plots is necessary for breeding and identifying loci underlying variation in root traits and their plasticity. We designed a large-scale sampling of root pulling force, the vertical force required to extract the root system from the soil, in a maize diversity panel under differing irrigation levels for two growing seasons. We then characterized the root system architecture of the extracted root crowns. We found consistent patterns of phenotypic plasticity for root pulling force for a subset of genotypes under differential irrigation, suggesting that root plasticity is predictable. Using genome-wide association analysis, we identified 54 SNPs as statistically significant for six independent root pulling force measurements across two irrigation levels and four developmental timepoints. For every significant GWAS SNP for any trait in any treatment and timepoint we conducted post hoc tests for genotype-by-environment interaction, using a mixed model ANOVA. We found that 8 of the 54 SNPs showed significant GxE. Candidate genes underlying variation in root pulling force included those involved in nutrient transport. Although they are often treated separately, variation in the ability of plant roots to sense and respond to variation in environmental resources including water and nutrients may be linked by the genes and pathways underlying this variation. While functional validation of the identified genes is needed, our results expand the current knowledge of root phenotypic plasticity at the whole plant and gene levels, and further elucidate the complex genetic architecture of maize root systems.

The 2020 derecho revealed limited overlap between maize genes associated with root lodging and root system architecture

“…( Berry et al 2021 ). Further, we explored the phenotypic correlation of root lodging with a variety of published above-ground traits ( Leiboff et al 2015 ), RSA traits ( Zheng et al 2020 ), root pulling force (RPF) data ( Woods et al 2022 ), and previously unpublished brace root trait data we collected from prior years ( Supplemental Text S1 and Table S4 ). The correlations of these traits with root lodging were generally low (i.e.…”

“…( Shah et al 2019 ). For root strength, we compared the overlap between the 118 candidate genes identified in the current study with those from a GWAS for RPF, a proxy trait that reflects root strength under different irrigation treatments (Supplemental Table S4 of Woods et al 2022 ); only a single candidate gene Zm00001eb191650 was identified in both studies. This gene is a maize homolog of an Arabidopsis gene, AtPHO1 involved in both phosphate and cytokinin signaling pathways; a mutant of this gene exhibits reduced root length when compared with wild type ( Lan et al 2006 ).…”

Climate change challenges, plant science solutions

“… Quantitative variation in lignin content in maize root systems from a field study of 358 maize inbred lines. A description of the experiment can be found in Woods et al (2022) . …”