Global Gene Expression Analysis of Brachypodium distachyon in Response to Cold, Drought, Salt, and Heat Stresses

Being sessile organisms, plants have evolved an exceptional ability to perceive, respond, and adapt to their environment. Understanding how plants respond to various abiotic stresses can lead to higher yields and more efficient crop productivity. Brachypodium distachyon is a temperate grass with close evolutionary relationships to economically important species including forage and turf grasses, temperate cereals, and potential biofuel feedstocks. Recently, Brachypodium has emerged as a model grass for functional genomics studies. In comparison to other grass species, characteristics of Brachypodium make it an excellent model system for global transcriptome profiling studies (short life cycle, small physical stature, simple growth requirements, and a sequenced and well annotated genome). Knowledge gained from transcriptomic studies in Brachypodium can provide information useful for the improvements of agriculturally important crops. We interrogated the Brachypodium transcriptome in response to cold, salt, drought, and heat stress after 1, 2, 5, 10, and 24 hours. We identified differentially expressed transcription factors as well as many potential cis-regulatory elements. We identified a large degree of crosstalk among the abiotic stress responses and observed an early- and late-response to abiotic stress, with distinct sets of genes differentially expressed within 5 hours and after longer exposure (10 – 24 hours). Analysis was extended to the BrachyCyc (http://www.gramene.org/pathway/brachycyc.html) database to identify differentially expressed genes of predicted metabolic pathway network. Overall, this work offers the first analysis of co-expressed, regulatory and metabolic genes in response to abiotic stress in Brachypodium and opens up new opportunities for closely related and agriculturally important grasses to study similar biological processes and gene networks.