GSE131582
Time-Dependent Transcriptome Profiling Reveals the Importance of Multiple Transcription Factors in Brachypodium Root Development
The goal of this study was to examine the transcriptional events occuring during stress-free Brachypodium distachyon root development via illumina paired-end RNA-seq. 4 time-points were chosen that capture the transition from rapid vegetative growth into slower reproductive growth. Abstract - Root systems are dynamic, adaptable organs that play critical roles in plant development. Roots, however, remain understudied and therefore present opportunities for trait improvement in food and bioenergy crops. A comprehensive growth stage-based root phenotyping integrated with molecular signatures is required to advance our understanding of root growth and development. Here we studied Brachypodium distachyon rooting process by monitoring root biomass, length, branching, root-to-shoot ratio and Carbon-to-Nitrogen ratio during time. To provide insight into gene regulation that accompanies root development and biomass accumulation, we generated comprehensive transcript profiles of Brachypodium whole-root system at four initial developmental stages that capture the transition from vegetative to reproductive growth. Our stringent data analysis revealed that multiple biological processes and various families of transcription factors (TFs) were differentially expressed during root development. In particular, the AUX/IAA, ERFs, WRKY, NAC, and MADS TF family members were upregulated, while ARFs and GRFs were downregulated in a time-dependent manner. Our results suggested particular TF families and biological processes including trehalose metabolism as important factors possibly involved in root biomass accumulation. We introduced several Brachypodium root biomass-promoting genes which can be employed by the genome editing approaches for improving biomass productivity in grasses. Overall design: Brachypodium distachyon whole-root RNA-seq via illumina. 4 timepoints with 3 biological replicates each. Timepoints were collected 18, 25, 32, and 36 days post sowing.