Factors Driving Diversity in Gene Regulatory Networks at Genome Scale[ASE]

Gene expression is a quantitative trait under the control of genetic and environmental factors and their interaction, so-called GxE. Understanding the mechanisms driving GxE is fundamental for ensuring stable crop performance across environments, and for predicting the response of natural populations to climate change. Gene expression is regulated through complex molecular networks, however environmental and genotypic effects on genome-wide regulatory networks are rarely considered. In this study, we model genome-scale gene expression variation between two natural accessions of the model grass Brachypodium distachyon and their response to soil drying. We identified genotypic, environmental, and GxE responses in physiological, metabolic, and gene expression traits. We then identified gene regulation conservation and variation among conditions and genotypes, simplified as co-expression clusters found unique in or conserved across library types. Putative gene regulatory interactions are inferred as network edges with a graphical model approach, resulting in hypotheses about gene-gene interactions which are then found to be specific to or with higher affinity in one genotype (G regulation), one environmental treatment (E regulation), or in one genotype under treatment (GxE regulation). Some gene-gene interactions are conserved across conditions so the differential expression is accordingly transmitted to target genes. These variably detected edges cluster together in co-expression modules, suggestive of different constraints or selection strength acting on specific pathways. We further applied our graphical model approach to identify putative, E-dependent regulatory mechanisms of leaf glucose content as an exemplar metabolite. Our study highlights an approach to identify variable features of gene regulatory networks and thereby identify key components for later genomic intervention to elucidate function or modulate environmental response. Our results also suggest possible targets of evolutionary change in gene regulatory networks associated with environmental plasticity. Overall design: To study regulation mechanism of how different genotypes of Brachypodium (Bd21 and Bd3-1) response to soil water deficit differently, we generated hybrid of the two genotypes and applied same treatments and harvest samples for RNA sequencing. We started gradual dry-down on 33rd day with a soil water content ended up 55% for drought and 85% for control after 6 days. The youngest fully expanded leaves from 5 replicates of hybrids under drought and control treatment, and 2 control Bd3-1 samples were harvested at a single time point 1-2:30pm of the day for RNA sequencing. These along with 12 samples (each genotype and condition, replicated three times) from the main experiment with exact same treatments are sequenced. We did gene expression profiling analysis and differential expression by fitting models using DESeq2 to infer gene regulation mechanism. Grant: IOS 2239070 Grant title: NSF CAREER Award Grantee: David Des Marais Funding agency: National Science Foundation