Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Integrating Functional Genomics with Molecular-Level Experimentation to Understand Adaptation to Nutrient Stress in Poplar and Sorghum


Tim Paape1(, Meng Xie1, Qun Liu1, Crysten E. Blaby-Haas1, Doreen Ware4,5, Daifeng Wang3, Sam Seaver2, Lifang Zhang4, Dimiru Tadesse1, Michael Regulski4, Miriam Pasquini1, Changxu Pang1, Sunita Kumari4, Desigan Kumaran1, Chiarg Gupta3, Nicolas Grosjean1, Nicolas Gladman4, Aditi Bhat1, and Jeremiah Anderson1


1Brookhaven National Laboratory; 2Argonne National Laboratory; 3University of Wisconsin–Madison; 4Cold Spring Harbor Laboratory; and 5U.S. Department of Agriculture, Agricultural Research Service, Ithaca, NY


The Quantitative Plant Science Initiative (QPSI) is a capability that aims to bridge the knowledge gap between genes and their functions. A central aspect of QPSI strategy is combining genome-wide experimentation and comparative genomics with molecular-level experimentation. In this way, researchers leverage the scalability of omics data and bioinformatic approaches to capture system-level information while generating sequence-specific understanding of gene and protein function. By incorporating molecular-level experimentation into the workflow, team members are addressing the question of how a protein functions and establishing mechanistic insight into how sequence variation impacts phenotype. This knowledge serves as a touchstone for accurate genome-based computational propagation across sequenced genomes and forms the foundation for robust predictive modeling of plant productivity in diverse environments.


Micro- and macronutrient stress is a growing importance in maximizing bioenergy/bioproduction crop yield in marginal soil. Bioavailability in the soil is dynamic and variable, and yield-impacting deficiencies are poorly understood. Because micronutrients are essential for the proper assimilation and metabolism of macronutrients such as nitrogen, metal deficiencies and other soil stresses can result in poor macronutrient availability. To support the development of bioenergy crops with improved nutrient stress resilience, the goal during the current 3-year period is to develop a genome-based, molecular-level and system-level understanding for the adaptation to micronutrient stress. Focusing on the bioenergy crops poplar and sorghum, researchers have completed a large-scale transcriptomics time-course experiment to understand how these plants respond to different nutrient stresses in their environment. Team members are also employing an interdisciplinary approach to provide a layer of experimentally grounded sequence-specific understanding of molecular-level functions for major players involved in plant homeostasis. Comparative genomics provides an in silico platform to generate protein function hypotheses. Hypotheses are tested with reverse genetics in model organisms and biochemical assays of protein family members. Structure-function studies supply mechanistic insight into how sequence space translates into molecular function. While working with micronutrient stresses in the current phase, there will be subsequent opportunities to incorporate other real-world conditions with the addition of field experiments addressing the impact of the soil geochemistry, microbiome and rhizosphere, and studying macro- and micro-nutrient interactions.


Funding Information

This research was supported by the DOE Office of Science, Biological and Environmental Research (BER) Program.