Abstract
Lateral roots are a major determinant of root architecture and are instrumental for the efficient uptake of water and nutrients. Lateral roots consist of multiple cell types each expressing a unique transcriptome at a given developmental stage. Therefore, transcriptome analyses of complete lateral roots provide only average gene expression levels integrated over all cell types. Such analyses have the risk to mask genes, pathways and networks specifically expressed in a particular cell type during lateral root formation. Cell type-specific transcriptomics paves the way for a holistic understanding of the programming and re-programming of cells such as pericycle cells, involved in lateral root initiation. Recent discoveries have advanced the molecular understanding of the intrinsic genetic control of lateral root initiation and elongation. Moreover, the impact of nitrate availability on the transcriptional regulation of lateral root formation in Arabidopsis and cereals has been studied. In this review, we will focus on the systemic dissection of lateral root formation and its interaction with environmental nitrate through cell type-specific transcriptome analyses. These novel discoveries provide a better mechanistic understanding of postembryonic lateral root development in plants.
Highlights
A key strategy of plants to adapt to changing moisture and nutrient availability in soil is the formation of a postembryonic root system
fluorescence activated cell sorting (FACS) sorting of xylem pole pericycle cells of Arabidopsis and subsequent transcriptome analyses, resulted in 1,920 genes differentially expressed at different stages of mitosis (De Smet et al, 2008)
These authors compared the phloem pole pericycle cell transcriptome of maize with transcriptomic profiles of xylem and phloem pole pericycle cells in Arabidopsis (Jansen et al, 2013). They showed that multiple genes including the gene LBD16/ASL18 were underrepresented in phloem pole pericycle cells of Arabidopsis, while the corresponding orthologs were induced upon lateral root induction in phloem pole pericycle cells of maize (Jansen et al, 2013). These findings indicated a shared identity between xylem pole pericycle cells of Arabidopsis and phloem pole pericycle cells of maize (Jansen et al, 2013)
Summary
A key strategy of plants to adapt to changing moisture and nutrient availability in soil is the formation of a postembryonic root system. Transcriptome analysis of lateral roots has been shown to be distinct from that of parent roots in both maize and rice, supporting the notion that fine lateral roots and thicker roots are functionally different (Gutjahr et al, 2015; Yu et al, 2018). Comparative transcriptome analyses of wild-type and mutant root systems in maize and rice have revealed molecular functions involved in auxin signaling and cell cycle regulation during lateral root formation (Zhang et al, 2014; Zhao et al, 2015). Organs or tissues are composite structures consisting of multiple cell types with different biological functions and disparate transcriptome profiles (Schnable et al, 2004)
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