Identification of genetic effectors that control stem strength in arable crops using a comparative network approach.

Transcriptional regulatory networks (TRNs) define regulatory interactions between transcription factors (TFs) and target genes. To achieve plasticity in plant development, these networks process developmental and environmental signals which dynamically influence growth. Little is known about how TRNs have been influenced during speciation and selection. We hypothesise that similarities in gene content, connections, and signal flux within networks of different species will be present, as will important species-specific differences. Understanding such similarities and differences will be key to identifying targets for crop improvement. Here, we aim to test this hypothesis using plant vascular development as a model system.

Divisions in vascular meristems lead to formation of cells that take on either a phloem or xylem identity. Xylem cells are responsible for the majority of mechanical strength in plant stems. Lodging due to stem breakage is results in a significant reduction in yield. In the model plant Arabidopsis vascular development is generally well understood. By contrast, in monocots such as barley where vascular tissue is organised differently, much less is known. These differences will be reflected in species specific TRNs that underlie vascular development. The focus of this studentship will to compare and contrast Arabidopsis and barley TRNs.

To understand how gene expression is integrated at a transcriptional level in Arabidopsis vascular development, we have generated a TRN consisting of 690 TF-promoter interactions. The student will combine this network with transcriptomic data from unpublished RNA-seq experiments in the Etchells lab in a model that will allow is to understand how the network responds to perturbation. These experiments will enable us to predict the regulatory relationship between TF and target gene (activation or repression).

The student will then determine how the network differs in barley. RNA-seq over a vascular development time-course in mutants homologous to those for which we have transcriptiome data in Arabidopsis, and wild type controls will be performed. These barley mutants have already been obtained using genome editing. The student will model this new transcriptome data to predict which of those transcription factor-promoter interactions, present in our Arabidopsis TRN are likely to be conserved in barley. A subset of interactions will then be the subject of in planta confirmation studies. Time permitting, we will integrate all new knowledge into a biophysical dynamic model of growth patterning. Our comparative network approach may provide a blueprint for successfully transferring discoveries from model organisms into commercially important species such as barley.