Nature and Nurture: Genotype-Dependent Differential Responses of Root Architecture to Agar and Soil Environments.

Merijn Kerstens,Andrea Bimbo,Stephen Grigg,Vera Hesen,Tom Beeckman,Davy Opdenacker,Viola Willemsen,Kavya Yalamanchili,Renze Heidstra

doi:10.3390/genes12071028

Abstract

Root development is crucial for plant growth and therefore a key factor in plant performance and food production. Arabidopsis thaliana is the most commonly used system to study root system architecture (RSA). Growing plants on agar-based media has always been routine practice, but this approach poorly reflects the natural situation, which fact in recent years has led to a dramatic shift toward studying RSA in soil. Here, we directly compare RSA responses to agar-based medium (plates) and potting soil (rhizotrons) for a set of redundant loss-of-function plethora (plt) CRISPR mutants with variable degrees of secondary root defects. We demonstrate that plt3plt7 and plt3plt5plt7 plants, which produce only a handful of emerged secondary roots, can be distinguished from other genotypes based on both RSA shape and individual traits on plates and rhizotrons. However, in rhizotrons the secondary root density and the total contribution of the side root system to the RSA is increased in these two mutants, effectively rendering their phenotypes less distinct compared to WT. On the other hand, plt3, plt3plt5, and plt5plt7 mutants showed an opposite effect by having reduced secondary root density in rhizotrons. This leads us to believe that plate versus rhizotron responses are genotype dependent, and these differential responses were also observed in unrelated mutants short-root and scarecrow. Our study demonstrates that the type of growth system affects the RSA differently across genotypes, hence the optimal choice of growth conditions to analyze RSA phenotype is not predetermined.

Highlights

Plant roots are responsible for nutrient and water uptake and are critical components of overall plant productivity [1]
We revealed that the root system architecture (RSA) of plt CRISPR mutants responded in a genotype-specific manner to plates and rhizotrons by analyzing overall shape and individual traits
We investigated whether certain plt mutants possessed divergent RSA shapes for plates and rhizotrons separately (Figure 3D)

Summary

Introduction

Plant roots are responsible for nutrient and water uptake and are critical components of overall plant productivity [1]. Understanding the fundamental mechanisms regulating root system architecture (RSA) is important for future crop improvement [2]. Arabidopsis thaliana (Arabidopsis) is the most widely used plant model for studying fundamental processes in plant biology. The relative simplicity of the Arabidopsis root system makes it an ideal candidate to identify new players in RSA and to study the impact of endogenous traits and/or exogenous factors on root development. The Arabidopsis root system consists of two main classes of roots that together constitute the RSA, the primary root and the side roots. Side roots can be further classified into secondary roots that branch off the primary root directly and higher-order roots. Depending on the molecular pathway and tissue of origin, secondary roots can be either lateral roots (LRs) or lateral adventitious roots. If side roots are derived from non-root tissue, they are called adventitious roots [3]

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Conclusion