Comparative transcriptomics as a tool for the identification of root branching genes in maize

Abstract

Summary The root system is fundamental for plant development, is crucial for overall plant growth and is recently being recognized as the key for future crop productivity improvement. A major determinant of root system architecture is the initiation of lateral roots. While knowledge of the genetic and molecular mechanisms regulating lateral root initiation has mainly been achieved in the dicotyledonous plant Arabidopsis thaliana, only scarce data are available for major crop species, generally monocotyledonous plants. The existence of both similarities and differences at the morphological and anatomical level between plant species from both clades raises the question whether regulation of lateral root initiation may or may not be conserved through evolution. Here, we performed a targeted genome‐wide transcriptome analysis during lateral root initiation both in primary and in adventitious roots of Zea mays and found evidence for the existence of common transcriptional regulation. Further, based on a comparative analysis with Arabidopsis transcriptome data, a core of genes putatively conserved across angiosperms could be identified. Therefore, it is plausible that common regulatory mechanisms for lateral root initiation are at play in maize and Arabidopsis, a finding that might encourage the extrapolation of knowledge obtained in Arabidopsis to crop species at the level of root system architecture.

Cell Type-Specific Gene Expression Analyses by RNA Sequencing Reveal Local High Nitrate-Triggered Lateral Root Initiation in Shoot-Borne Roots of Maize by Modulating Auxin-Related Cell Cycle Regulation

“…The response of KRP3 deviated significantly from that of the other KRPs and was induced upon transfer to auxin, when it was highly expressed in actively dividing cells in Arabidopsis (De Veylder et al, 2001;Himanen et al, 2002). In contrast, in the stele of maize, the orthologous KRP3 gene showed a similar transcript pattern as the other KRP genes in response to auxin or nitrate (Jansen et al, 2013a; Fig. 2D).…”

“…In maize, these roots originate from concentric single-file layers of pericycle and endodermis cells (Fahn, 1990;Jansen et al, 2012). Lateral root initiation is the result of auxin-dependent cell cycle progression Jansen et al, 2013a). Most of the molecular changes during the cell cycle like, for instance, the induction of positive regulators, such as cyclins (CYCs) and cyclindependent kinases (CDKs), and the repression of Kiprelated proteins (KRPs), thus account for a reactivation of the cell cycle Himanen et al, 2002Himanen et al, , 2004.…”

“…Auxin responses in protoxylem or protophloem cells of the basal meristem coincide with the site of lateral root initiation (De Smet et al, 2007;Jansen et al, 2012). In these defined pericycle cells, the phloem pole pericycle founder cells are primed before auxin accumulation occurs (De Smet et al, 2007;Jansen et al, 2012Jansen et al, , 2013a. In contrast to dicots, the larger PIN family in monocots has a more divergent phylogenetic structure .…”

Conserved Gene Expression Programs in Developing Roots from Diverse Plants

“…Furthermore, global gene expression patterns have been defined for specific cells, tissues, and developmental stages of Arabidopsis roots, primarily using microarray-based methods (Galbraith and Birnbaum, 2006;Brady et al, 2007). Molecular studies of root development have also been conducted in other plants (Hochholdinger and Tuberosa, 2009;Jansen et al, 2013;Qiao and Libault, 2013;Karve and Iyer-Pascuzzi, 2015), although the extent to which the molecular mechanisms identified in Arabidopsis roots apply to other plants is not clear.…”

Branching Out in Roots: Uncovering Form, Function, and Regulation

“…Marker lines expressing red fluorescent protein under control of the DR5 promoter have indicated the presence of auxin response maxima in differentiating xylem cells and in cells surrounding the protophloem vessels (Jansen et al, 2012). Furthermore, targeted genome-wide transcriptome analysis of lateral root initiation has highlighted common transcriptional regulation between Arabidopsis and maize, suggesting the conservation of genes involved in lateral root initiation across angiosperms (Jansen et al, 2013).…”