Construction of Temperature Stress Networks in Brachypodium distachyon and Setaria viridis through High-Throughput Phenotyping

The geographical distribution of food and bioenergy crops is limited by several factors including temperature, soil salinity, and water availability. Grasses, such as rice, wheat, maize and sorghum, are the primary caloric intake for humans. Although research in the dicot model plant, Arabidopsis, has been successful in elucidating pathways for abiotic stress, key questions still remain. For example, it is still unknown how temperature is sensed in a plant. Mechanisms of temperature sensing are also critical for entrainment of the plant circadian clock. This study focuses on temperature perception and stress (cold and heat) under circadian regulation in the model grasses B. distachyon and S. viridis. In this study, physiological assays that measure membrane damage in response to temperature stress determine a physiologically relevant range of temperatures to examine B. distachyon and S. viridis.  Accessions of both B. distachyon and S. viridis are screened for interesting temperature phenotypes using a number of phenomics tools. Temperature stress and sub-optimal temperature expression profiling are systematically performed in B. distachyon and S. viridis using RNA-seq and are compared to publicly available expression datasets. Transcription factors are prioritized for misexpression (knock-out and over-expression) by filtering differentially expressed genes found in RNA-seq experiments by their circadian patterns. Misexpression lines are carefully phenotyped across stresses using high-throughput phenotyping tools. Finally, up and downstream targets of temperature genes are identified through yeast one-hybrid, ChIP-seq, and high-throughput sequencing.