Genetic and genomic dissection of maize root development and architecture

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The complex architecture and plasticity of the maize root system is controlled by a plethora of genes. Mutant analyses have identified genes regulating shoot-borne root initiation (RTCS) and root hair elongation (RTH1 and RTH3). Quantitative trait locus (QTL) studies have highlighted the importance of seminal roots, lateral roots, and root hairs in phosphorus acquisition. Additionally, QTLs that influence root features were shown to affect yield under different water regimes and under flooding conditions. Finally, proteome and transcriptome analyses provided insights into maize root development and identified candidate genes associated with cell specification, and lateral root initiation in pericycle cells. The targeted application of forward-genetics and reverse-genetics approaches will accelerate the unraveling of the functional basis of root development and architecture.

Introduction

Maize constitutes a major source of starch for humans and livestock in many regions of the world and has become increasingly important for biofuel production. The unique structure of the maize root system efficiently secures water and nutrient uptake and provides anchorage in soil [1]. Hence, an in-depth understanding of the molecular basis of maize root formation is necessary to secure a staple food source for an increasing world population, particularly in view of the formidable challenges posed by climate change and higher costs for energy, fertilizers, and water. This review summarizes the current status of the genetic and genomic analysis of maize root development and architecture. The first part of the review highlights the cloning of genes that affect qualitative root traits via monogenic mutants and the dissection of quantitative features via quantitative trait locus (QTL) analysis. The second part surveys the adoption of high-throughput techniques to examine the expression patterns of genes and proteins involved in root development.

Section snippets

Root mutants of maize

The maize root system is composed of embryonic primary and seminal roots and postembryonic shoot-borne and lateral roots [2] that serve distinct functions during development (Figure 1). While embryonic roots are important for early vigor of the maize seedlings, toward flowering the maize root stock is dominated by shoot-borne nodal roots, which can have a significant influence on grain yield in water-limited conditions.

Several mutants specifically altered in the development of shoot-borne

QTLs associated with maize root architecture

Genomics-based approaches offer unprecedented opportunities to discover QTLs that govern natural variation in root traits and investigate to what extent this variation affects grain yield and other agronomic traits in maize grown under varying water and nutrient regimes [9, 10]. Once major QTLs are identified, the production of near-isogenic lines (NILs) at these QTLs [11] allows for their fine mapping and, eventually, cloning [12] an essential prerequisite for a more effective exploitation and

Cell-type-specific transcriptome analysis of maize root development

Several high-throughput ‘omics’ technologies have been recently employed to study maize root development. Among these, microarray technology stands out because of its resolution that allows for the simultaneous analysis of tens of thousands of transcripts while only a few hundred proteins or metabolites can be studied in a single experiment. Maize roots are composed of different tissues and cell-types, each providing unique global gene expression patterns related to their specific functions. To

Transcriptome analyses of maize root responses toward environmental stimuli

Maize root system architecture is significantly shaped by its interaction with the soil environment and its adaptability to changing environmental conditions. Recently, several studies analyzed transcriptome profiles of maize roots after exogenous stimulation.

In an effort to study local nitrate-induced lateral root formation in maize, strong interactions among hormonal pathways and local nitrate signaling pathways were demonstrated in microarray experiments [33]. Moreover, genes related to

Proteomic dissection of maize root formation

In recent years, proteomic studies have provided new insights into the regulation of maize root development [36]. These experiments either generated reference maps of the most abundant proteins of a particular stage of root development or compared differential protein accumulation levels between different genotypes or treatments of a particular root type. Most of these studies analyzed complete roots [37, 38, 39, 40, 41, 42, 43] while others focused on defined longitudinal zones [44, 45•],

Conclusions

The sequencing and annotation of the maize genome [46] will facilitate the positional cloning of root-related genes in maize, while the availability of reverse-genetics resources such as TILLING [47] will contribute novel root phenotypes. Moreover, recent advances in QTL approaches like NAM [28] will streamline the identification and cloning of QTLs associated with maize root architecture. In addition to phenotypic traits, gene expression and protein accumulation data related to maize root

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

Root research in FHs laboratory is supported by the German Science Foundation (DFG) grants HO1149/4, HO1149/6, HO1149/8, and SFB446 B16. Root research in RTs laboratory is supported by grants from Pioneer-DuPont and KWS. We thank Muhammad Saleem of the Hochholdinger lab for sharing unpublished data.

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