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

2024 Abstracts

Intraspecific Genetic Variation in Populus trichocarpa Influences Above and Belowground Plant Chemistry and Influences Plant-Soil Interactions


Udaya C. Kalluri1,3* ([email protected]), Anne E. Ware2, Sara Jawdy1,3, Kai Feng1,3, Matthew Craig3, John Field1,3, Brandon Sloan1,3, Wellington Muchero1,3, Gerald A. Tuskan1,3


1Center for Bioenergy Innovation, Oak Ridge National Laboratory; 2National Renewable Energy Laboratory; 3Oak Ridge National Laboratory



The Center for Bioenergy Innovation (CBI) vision is to accelerate domestication of bioenergy-relevant, non-model plants and microbes to enable high-impact innovations along the bioenergy and bioproduct supply chain, while focusing on sustainable aviation fuels (SAF). CBI has four overarching innovation targets: (1) develop sustainable, process-advantaged biomass feedstocks; (2) refine consolidated bioprocessing with cotreatment to create fermentation intermediates; (3) advance lignin valorization for bio-based products and aviation fuel feedstocks; and (4) improve catalytic upgrading for SAF blendstocks certification.


Gaining a predictive understanding of above- and belowground plant system performance is critical to developing, climate smart and sustainable bioenergy crops for SAF. Plant and soil (including microbial) interactions are known to influence nutrient and water uptake, microbial association, biomass productivity, climate adaptability, and soil carbon storage. Current understanding of variability and correlations among aboveground properties of bioenergy crops and their underlying genetics is far greater in comparison to that of the belowground properties (root, soil, and microbes), which is explained by data asymmetries between above- and belowground datasets. The challenges of laborious sampling, lack of standardized methods, and sparse measurements are further confounding to available belowground empirical data. To achieve a holistic understanding of bioenergy crop performance, researchers are undertaking laboratory- and field-based belowground performance evaluations of natural genotypes of the perennial woody bioenergy crop species, Populus trichocarpa. This project presents the results from two such studies, one at greenhouse-scale and another at field-scale.

The utility of genome-wide association study (GWAS) analysis in identifying single nucleotide polymorphisms (SNPs) associated with variation in traits of interest in Populus has been previously demonstrated with remarkable genomic resolution for aboveground traits such as biomass yield, phenology, and lignin content (Evans et al. 2014; Xie et al. 2018). There has been limited progress, however, in defining the genetic components of belowground root-related traits. Researchers undertook a GWAS of greenhouse root chemistry and coassessment of below- and aboveground traits. The results showed that above- and belowground chemistry is largely independently controlled and generated the first comprehensive collection of genes and SNPs associated with variation in root chemistry of a bioenergy crop species. Furthermore, the team identified a subset of SNPs and genotypes that are coevolved in trait combinations potentially favorable to aboveground valorization of biomass and belowground storage of carbon (C). The discovery of both colocated or independent SNPs and naturally superior genotypes from the analyses serve as high potential springboard levers in advanced synthetic biology and breeding strategies for desirable below- and aboveground traits.

Researchers undertook a pilot empirical evaluation study to inform a planned population-wide sampling effort and iterative modeling designed to understand plant-soil interactions in a mature, common garden stand of the same GWAS population in the Pacific Northwest. This study, using four different P. trichocarpa genotypes (population extremes in lignin content), demonstrates the value of leveraging mature GWAS common garden sites and the potential of focal tree soil sampling for detecting genotype-specific associations with soil biogeochemistry (e.g., C; nitrogen; N, phosphorus; P, and a range of soil micro- and macronutrient elements) and soil-bulk density, as well as the extent of correlations between above- and belowground traits. This analyses revealed positive relationships between root C and soil C; root C: N and soil calcium (Ca), and a negative relationship of soil C with soil pH, K, and P. In the future, expansion of such species-, age- and region-specific efforts will enhance predictability of plant-microbe-soil interactions in bioenergy crop systems. This will ultimately accelerate the identification of genetic and edaphic factors that can enhance bioproduct yield, C storage, and sustainability.


Evans L.M., et al. 2014. “Population Genomics of Populus Trichocarpa Identifies Signatures of Selection and Adaptive Trait Associations,” Nature Genetics 46(10), 1089–96.

Xie M., et al. 2018. “A 5-Enolpyruvylshikimate 3-Phosphate Synthase Functions as a Transcriptional Repressor in Populus,” Plant Cell 30(7), 1645–60.

Funding Information

Funding was provided by the Center for Bioenergy Innovation (CBI) led by Oak Ridge National Laboratory (ORNL). CBI is funded as a DOE Bioenergy Research Centers supported by the BER program in the DOE Office of Science under FWP ERKP886. ORNL is managed by UT-Battelle, LLC for the DOE  under contract no. DE-AC05-00OR22725.