Genetic Variability of Arabidopsis thaliana Mature Root System Architecture and Genome-Wide Association Study

Abstract

Root system architecture (RSA) has a direct influence on the efficiency of nutrient uptake and plant growth, but the genetics of RSA are often studied only at the seedling stage. To get an insight into the genetic blueprint of a more mature RSA, we exploited natural variation and performed a detailed in vitro study of 241 Arabidopsis thaliana accessions using large petri dishes. A comprehensive analysis of 17 RSA traits showed high variability among the different accessions, unveiling correlations between traits and conditions of the natural habitat of the plants. A sub-selection of these accessions was grown in water-limiting conditions in a rhizotron set-up, which revealed that especially the spatial distribution showed a high consistency between in vitro and ex vitro conditions, while in particular, a large root area in the lower zone favored drought tolerance. The collected RSA phenotype data were used to perform genome-wide association studies (GWAS), which stands out from the previous studies by its exhaustive measurements of RSA traits on more mature Arabidopsis accessions used for GWAS. As a result, we found not only several genes involved in the lateral root (LR) development or auxin signaling pathways to be associated with RSA traits but also new candidate genes that are potentially involved in the adaptation to the natural habitats.

LEADER (Leaf Element Accumulation from DEep Roots): A nondestructive phenotyping platform to estimate rooting depth in the field

“…Rooting depth is also exceedingly difficult to measure in soil. Rooting depth can be easily measured in (typically small) plants grown in artificial media, with the most extreme example being humid air (“aeroponics” [Awika et al., 2021; Eldridge et al., 2020]), but also commonly including agar plates (Guseman et al., 2016; Ogura et al., 2019), solution culture (Mathieu et al., 2015), paper growth pouches (Atkinson et al., 2015), or systems in which roots grow in solid media against a transparent surface (Deja‐Muylle et al., 2021; LaRue et al., 2022; Nagel et al., 2012; Rellán‐Álvarez et al., 2015; Yuan et al., 2016). Such systems are useful in specific contexts but may not be correlated with root phenotypes observed in natural soil, which has many characteristics capable of influencing root growth including, but not limited to, mechanical impedance, soil biota, and hypoxia (Poorter et al., 2016; Rich et al., 2020).…”

Plant Growth Regulators in Tree Rooting

“…Indeed, combination of imaging techniques with genetic studies might enhance our understanding of root development and help to identify new candidate genes involved in this process. In Arabidopsis, an integrated rhizotron imaging and GWAS analysis has allowed for the identification of genes that might be directly related to root system architecture [ 24 ]. However, examples in tree species are scarce at present.…”