Identification of transcription factors regulating senescence in wheat through gene regulatory network modelling

Abstract

10Senescence is a tightly regulated developmental programme which is coordinated by transcription 11 factors. Identifying these transcription factors in crops will provide opportunities to tailor the 12 senescence process to different environmental conditions and regulate the balance between yield and 13 grain nutrient content. Here we use ten time points of gene expression data alongside gene network 14 modelling to identify transcription factors regulating senescence in polyploid wheat. We observe two 15 main phases of transcription changes during senescence: early downregulation of housekeeping and 16 metabolic processes followed by upregulation of transport and hormone related genes. We have 17identified transcription factor families associated with these early and later waves of differential 18 expression. Using gene regulatory network modelling alongside complementary publicly available 19 datasets we identified candidate transcription factors for controlling senescence. We validated the 20 function of one of these candidate transcription factors in senescence using wheat chemically-induced 21 mutants. This study lays the ground work to understand the transcription factors which regulate 22 senescence in polyploid wheat and exemplifies the integration of time-series data with publicly 23 available expression atlases and networks to identify candidate regulatory genes. 24 25

The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat

“…This dataset was included in the generation of the GENIE3 network. The senescence-specific time course was first published in (Borrill et al 2019), from the spring wheat cultivar Bobwhite, and was not included in the GENIE3 network.…”

“…GO-term enrichment analysis was carried out as previously described in (Borrill et al 2019), using the GOSeq (v 1.34.1) package in R (Young et al 2010).…”

“…We have then compared these candidates with an independent senescence time-course (Borrill et al 2019), highlighting six candidate genes which were identified through both methods and are good candidates for further exploration. Moving forwards, information generated from networks such as the GENIE3 will need to be validated functionally and in planta.…”

Barley HISTIDINE KINASE 1 (HvHK1) coordinates transfer cell specification in the young endosperm

“…To specify direct targets of HvHK1 and the main regulatory links that govern regular ETC specification, GRNs of HvHK1 in WT and RNAi cells were generated by GENIE3. The GENIE3 algorithm uses random forest tree-based regression (Huynh-Thu et al, 2010) and was successfully applied to construct tissue-specific transcriptional networks in maize (Huang et al, 2018) and to predict TF targets in wheat (Borill et al, 2019). Separate GRNs were predicted using RNA-seq data from our experiments in combination with barley background data from the Sequence Read Archive (Data S3).…”

High-Resolution Mapping of the Novel Early Leaf Senescence Gene Els2 in Common Wheat

“…However, limited information is available about leaf senescence regulation in wheat. Several studies focused on the transcriptome of wheat leaf senescence [ 21 , 22 , 23 , 24 ]. These studies have provided global and potential gene dynamic expression changes and signalling pathways for leaf senescence regulation in wheat, but few genes involved in the regulation of wheat leaf senescence have been identified.…”