Epigenetic Control of Drought Response in Sorghum (EPICON)
Dr. Peggy G. Lemaux, University of California, Berkeley (Principal Investigator)
Dr. Devin Coleman-Derr, University of California, Berkeley (Co-PI)
Dr. Jeffrey Dahlberg, University of California, Kearney Ag Research & Extension Center (Co-PI)
Dr. Robert Hutmacher, University of California, West Side Research & Extension Center (Co-PI)
Dr. Christer Jansson, Pacific Northwest National Laboratory (Co-PI)
Dr. Elizabeth Purdom, University of California, Berkeley (Co-PI)
Dr. John Taylor, University of California, Berkeley (Co-PI)
Dr. Chia-Lin Wei, Joint Genome Institute (Co-PI)

Genetic manipulation of crops to increase the presence or intensity of desirable traits has historically been critical to increasing agricultural productivity. These changes have primarily involved modification of the plant’s DNA sequence. However, there is increasing recognition that plant development and environmental responses are also mediated by epigenetics, a process that involves heritable changes in phenotype or gene expression without changes in DNA sequence. Specifically, epigenetic changes have been shown to play a major role in regulating plant responses to drought, an increasing problem for world agriculture due to climate change. In general, exposure of plants to abiotic stresses, including water limitation, triggers cascades of epigenetic changes, which include remodeling of chromatin, which is the network of DNA, RNA and various proteins making up chromosomes, and related modifications in regulatory mechanisms, including small non-coding RNAs. EPICON’s efforts will focus on unraveling the role over time that epigenetic signals play in acclimation to and recovery from drought through effects on individual transcription factors or transcriptional networks that direct entire metabolic pathways. To achieve this goal we will follow responses to water deprivation of two sorghum cultivars differing in their drought responses. Sorghum, a widely cultivated cereal with drought and flood tolerance, offers notable advantages as a bioenergy feedstock due to its relatively reduced environmental footprint versus its close relative, corn. Conducting drought studies with sorghum in California’s central valley offers the advantage that this region’s lack of summer rainfall makes well controlled, field-based drought studies possible. In EPICON’s three-year field trial, sorghum will be grown under controlled irrigation conditions. Phenotypic analyses will be conducted to chart growth, flowering time, grain and biomass yield, and other observable characteristics. Leaf and root samples will also be taken to perform molecular phenotyping to track spatiotemporal changes in epigenetic, transcriptomic, metabolomic and proteomic footprints. Analytical methods will include a whole portfolio of epigenomic analytical tools, i.e., RNA-Seq, smRNA-Seq, ChIP-Seq, BS-Seq, Orbitrap MS, MALDI-ToF MS and nano-DESI. As potential molecular mechanisms are identified from analyses of results, targeted engineering will be used to validate suggested findings. Shifts in sorghum-associated microbial community composition and activity throughout the drought period will also be studied to determine if changes in membership or functional capacity within the rhizosphere, root endosphere, and phyllosphere correlate with epigenetic, transcriptional or metabolomic variation in the plant. Investigating the sorghum microbiome will be done via Illumina itag sequencing of 16S rRNA and ITS, specific to prokaryotic and fungal microbes respectively, and via shotgun metagenomic and metatranscriptomic sequencing of rhizosphere communities. Knowledge and data generated in this project will be shared via Kbase, an open platform for comparative functional genomics that enables sharing results and methods with other scientists. Analysis of the entire data set will provide a better understanding of the epigenetic processes responsible for restructuring the metabolic and regulatory landscape of the sorghum genome, and their relationship to drought tolerance. This will lead to the achievement of our ultimate goal, which is to identify key transcriptional regulators and pathways controlling drought resistance and to characterize their mechanisms of action, both in the plant and in its associated microbial communities. Additionally, through our efforts we will uncover biomarkers associated with drought resistance, which can be used to monitor and follow phenotypic changes in large populations. The genetic targets and their regulatory pathways will be utilized in future efforts to improve growth and biomass production of sorghum and other crops in the field and in marginal lands under water-limiting conditions.