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DOE OSTI2025

Leveraging transfer learning and leaf spectroscopy for leaf trait prediction with broad spatial, species, and temporal applicability

Accurate and reliable prediction of leaf traits is crucial for understanding plant adaptations to environmental variation, monitoring terrestrial ecosystems, and enhancing comprehension of functional diversity and ecosystem functioning. Currently, various approaches (e.g., statistical, physical models) have been developed to estimate leaf traits through hyperspectral remote sensing and leaf spectroscopy. However, the absence of high-performing, transferable, and stable models across various domains of space, plant functional types (PFTs) and seasons hinder our ability to quantify and comprehend spatiotemporal variations in leaf traits. This study proposes robust and highly transferable models for better predicting leaf traits with hyperspectral reflectance. Initially, three datasets were assembled, pairing common leaf traits — chlorophyll (Chla+b), carotenoids (Ccar), leaf mass per area (LAM), equivalent water thickness (EWT) — with leaf spectra measurements collected across diverse geographic locations in the U.S. and Europe, PFTs, and seasons. Measurements were acquired using spectroradiometers (e.g., ASD FieldSpec 3/4/Pro and SVC HR-1024i) with integrating spheres, leaf clips, and contact probes. Here, we then developed transfer learning-based hybrid models that incorporated the domain knowledge of radiative transfer models (RTMs) through pretraining processes and were well-constrained by fine-tuning with field measurements. Through comparison with other state-of-the-art statistical models, including partial-least squares regression (PLSR) and Gaussian Process Regression (GPR), as well as pure physical models, we found that the proposed transfer learning models achieved better predictive performance and higher transferability. Specifically, compared to other statistical models and pure RTMs, the transfer learning model exhibited higher coefficient of determination (R 2 ) values with range of 0.01 to 0.79, lower normalized root mean square error (NRMSE) with range of 0.06 % to 33.25 % in model performance. Additionally, the models exhibited improved transferability, with higher R 2 values range from 0.04 to 0.32, lower NRMSE range from 0.08 % to 30.81 %. The findings underscore that transfer learning models through integrating domain knowledge from RTMs and limited observations, can harness the advantages of both RTMs and statistical models and serve as a promising approach for effectively predicting leaf traits.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Climate change drives convergent evolution of root traits on Sky Island climate relicts

Roots are essential to the strategies plants use to survive in variable environments, yet we know little of how they vary within species. Experimental conditions demonstrate that intraspecific plant root traits respond strongly to variation in the environment; however, it is unclear when these responses can be characterized as evolution in response to selective pressures of climate change over many generations. Sky Islands are model, natural climate relict ecosystems to examine climate-change driven evolution. Utilizing a common garden with replicate genotypes of Populus angustifolia (Narrowleaf cottonwood) from six Sky Island (SI) populations and nine adjacent Mountain Chain (MC) populations across three genetic provenances, we hypothesized that SI root traits have diverged due to historical isolation in warmer, drier climates. When grown in common conditions, populations originating on SI’s showed convergent evolution across three distinct genetic provenances, which was characterized by 44.16% decreased total root length, 42.64% decreased average root volume, 43.31% decreased root surface area, and significantly less root trait variation, relative to adjacent mountain chains. Convergent evolution of root traits from trees originating on SI’s is correlated with changes in mean annual precipitation and potential evapotranspiration in the field over the past ~ 125 years. These results demonstrate a consistent pattern in root trait evolution at the landscape scale and the role of climate on the evolution of root traits in a genetic and geographic context relevant to climate change.

Convergent evolution↗

DOE OSTI2024

Limits on the evolutionary rates of biological traits

Abstract This paper focuses on the maximum speed at which biological evolution can occur. I derive inequalities that limit the rate of evolutionary processes driven by natural selection, mutations, or genetic drift. These rate limits link the variability in a population to evolutionary rates. In particular, high variances in the fitness of a population and of a quantitative trait allow for fast changes in the trait’s average. In contrast, low variability makes a trait less susceptible to random changes due to genetic drift. The results in this article generalize Fisher’s fundamental theorem of natural selection to dynamics that allow for mutations and genetic drift, via trade-off relations that constrain the evolutionary rates of arbitrary traits. The rate limits can be used to probe questions in various evolutionary biology and ecology settings. They apply, for instance, to trait dynamics within or across species or to the evolution of bacteria strains. They apply to any quantitative trait, e.g., from species’ weights to the lengths of DNA strands.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Limits on the Evolutionary Rates of Biological Traits

This paper focuses on the maximum speed at which biological evolution can occur. I derive inequalities that limit the rate of evolutionary processes driven by natural selection, mutations, or genetic drift. These rate limits link the variability in a population to evolutionary rates. In particular, high variances in the fitness of a population and of a quantitative trait allow for fast changes in the trait’s average. In contrast, low variability makes a trait less susceptible to random changes due to genetic drift. The results in this article generalize Fisher’s fundamental theorem of natural selection to dynamics that allow for mutations and genetic drift, via trade-of relations that constrain the evolutionary rates of arbitrary traits. The rate limits can be used to probe questions in various evolutionary biology and ecology settings. They apply, for instance, to trait dynamics within or across species or to the evolution of bacteria strains. They apply to any quantitative trait, e.g., from species’ weights to the lengths of DNA strands.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

A systems genetic analysis identifies putative mechanisms and candidate genes regulating vessel traits in poplar wood

Wood is the water conducting tissue of tree stems. Like most angiosperm trees, poplar wood contains water-conducting vessel elements whose functional properties affect water transport and growth rates, as well as susceptibility to embolism and hydraulic failure during water stress and drought. Here we used a unique hybrid poplar pedigree carrying genomically characterized chromosomal insertions and deletions to undertake a systems genomics analysis of vessel traits. We assayed gene expression in wood forming tissues from clonal replicates of genotypes covering dosage quantitative trait loci with insertions and deletions, genotypes with extreme vessel trait phenotypes, and control genotypes. A gene co-expression analysis was used to assign genes to modules, which were then used in integrative analyses to identify modules associated with traits, to identify putative molecular and cellular processes associated with each module, and finally to identify candidate genes using multiple criteria including dosage responsiveness. These analyses identified known processes associated with vessel traits including stress response, abscisic acid and cell wall biosynthesis, and in addition identified previously unexplored processes including cell cycle and protein ubiquitination. We discuss our findings relative to component processes contributing to vessel trait variation including signaling, cell cycle, cell expansion, and cell differentiation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

The relationship between gene traits and transcription in soil microbial communities varies by environmental stimulus

Codon and nucleotide frequencies are known to relate to the rate of gene transcription, yet how these traits shape transcriptional profiles of soil microbial communities remains unclear. Here we test the prediction that functional genes with high codon optimization and energetically lower cost nucleotides (i.e., nucleotides requiring less adenosine triphosphate (ATP) for synthesis) have higher transcriptional expression in a soil microbial community. In laboratory incubations, we subjected an agricultural soil to two separate short-term environmental changes: labile carbon (glucose) addition or a sudden 30-min increase in temperature from 20 °C to 60 °C. Using the total genomic codon frequencies to predict preferred codon usage for each taxon, we then estimated codon optimization for each transcript. On the community level, we found a higher average level of codon optimization after the addition of glucose. Synonymous nucleotide composition in the transcript pool also shifted towards energetically cheaper nucleotides, favoring uracil (U) over adenine (A) and cytosine (C) over guanine (G). Similarly, we found that encoded amino acid usage shifted towards energetically cheaper amino acids in response to labile carbon. In contrast, in communities responding to heat shock, there were no significant differences in the averaged gene traits of expressed transcripts. We used metagenome-assembled-genomes to further examine the ability of gene traits to predict transcriptional responses within and between taxa. We found that traits of individual genes could not reliably predict the level of transcription of a gene within or between taxa—highlighting the limits of this approach. However, we did find that when traits were averaged across several related genes, codon optimization was able to predict levels of transcription in metabolic pathways associated with growth and nutrient uptake in response to glucose. Similar relationships were not observed in response to heat, or for functions associated with stress—such as genes associated with sporulation or heat shock. These results demonstrate that gene traits, such as codon usage, nucleotide selection, and amino acid selection, relate to the transcriptional expression of genes in soil microbial communities and suggests that these relationships may be dependent on both gene function and the specific type of environmental stimuli.

Biological and medical sciences↗

DOE OSTI2024

Prediction of plant complex traits via integration of multi-omics data

The formation of complex traits is the consequence of genotype and activities at multiple molecular levels. However, connecting genotypes and these activities to complex traits remains challenging. Here, we investigate whether integrating genomic, transcriptomic, and methylomic data can improve prediction for six Arabidopsis traits. We find that transcriptome- and methylome-based models have performances comparable to those of genome-based models. However, models built for flowering time using different omics data identify different benchmark genes. Nine additional genes identified as important for flowering time from our models are experimentally validated as regulating flowering. Gene contributions to flowering time prediction are accession-dependent and distinct genes contribute to trait prediction in different genotypes. Models integrating multi-omics data perform best and reveal known and additional gene interactions, extending knowledge about existing regulatory networks underlying flowering time determination. These results demonstrate the feasibility of revealing molecular mechanisms underlying complex traits through multi-omics data integration.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Bacterial population-level trade-offs between drought tolerance and resource acquisition traits impact decomposition

Microbes drive fundamental ecosystem processes, such as decomposition. Environmental stressors are known to affect microbes, their fitness, and the ecosystem functions that they perform; yet, understanding the causal mechanisms behind this influence has been difficult. We used leaf litter on soil surface as a model in situ system to assess changes in bacterial genomic traits and decomposition rates for 18 months with drought as a stressor. We hypothesized that genome-scale trade-offs due to investment in stress tolerance traits under drought reduce the capacity for bacterial populations to carry out decomposition, and that these population-level trade-offs scale up to impact emergent community traits, thereby reducing decomposition rates. We observed drought tolerance mechanisms that were heightened in bacterial populations under drought, identified as higher gene copy numbers in metagenome-assembled genomes. A subset of populations under drought had reduced carbohydrate-active enzyme genes that suggested—as a trade-off—a decline in decomposition capabilities. These trade-offs were driven by community succession and taxonomic shifts as distinct patterns appeared in populations. We show that trait–trade-offs in bacterial populations under drought could scale up to reduce overall decomposition capabilities and litter decay rates. Using a trait-based approach to assess the population ecology of soil bacteria, we demonstrate genome-level trade-offs in response to drought with consequences for decomposition rates.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

A trait syndrome ties cell morphology to glycolysis across the yeast subphylum

Co-variation of traits provides fundamental insights into constraints governing their evolution. An inverse correlation between glucose uptake rates (GURs) and cell surface area-to-volume (SA:V) ratios across 11 yeast species was recently reported. Here, we expand the analysis to 282 species to assess the generalizability of this correlation across Saccharomycotina yeasts and the contribution of shared evolutionary history to the co-variation of these traits. Using phylogenetic regression models, we found extracellular acidification rates (ECARs, used as a proxy for GURs) were weakly, but significantly, correlated with SA:V across Saccharomycotina. ECARs were also correlated with genome sizes and growth rates. Our findings support the reported correlation between GURs and SA:V ratios, but suggest other associated traits, including genome sizes. Specifically, yeasts that consume glucose faster tend to have lower SA:V, faster growth rates, and larger genomes, suggesting a trait syndrome governing several metabolic, genomic, and morphological traits across the yeast subphylum.

biological sciences↗

DOE OSTI2025

Drought increases microbial allocation to stress tolerance but with few tradeoffs among community-level traits

Climate change will increase soil drying, altering microbial communities via increasing water stress and decreasing resource availability. The responses of these microbial communities to changing environments could be governed by physiological tradeoffs between high yield, resource acquisition, and stress tolerance (YAS framework). We leveraged a unique field experiment that manipulates both drought and carbon availability across two years and three land uses, and we measured both physiological (with bioassays) and genetic (with metagenomics) microbial traits at the community level to test the following hypotheses: 1. Drought increases microbial allocation to stress tolerance functions, at both physiological and genetic levels. 2. Because microbes are resource-limited under drought, increased carbon will enable greater expression of stress tolerance. 3. All three key life history traits described in the YAS framework will trade off. Drought did increase microbial physiological investment in stress tolerance (measured via trehalose production), but we saw few other changes in microbial communities under drought. Adding carbon to plots increased resource acquisition (measured via enzyme activity and resource acquisition gene abundance) and stress tolerance (trehalose assay), but did so in both drought and average rainfall environments. Here, we found little evidence of trait tradeoffs, as a negative correlation between rRNA copy number and resource acquisition gene abundance was the only significant negative correlation between traits that we found that was consistent across years (for physiological or genetic traits). In summary, we found C addition, and to a lesser extent, drought, altered microbial community function and functional genes. However, resources did not alter drought response in a way that was consistent with theory of life history tradeoffs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Divergent trait controls on soluble sugars and starch underlie global strategies of tree carbohydrate storage

Nonstructural carbohydrate (NSC) stores buffer tree metabolism, osmotic regulation, and defense, thereby mediating tolerance and survival under climate extremes. Yet, the functional and evolutionary determinants of interspecific variation in NSC remain elusive, limiting understanding and prediction of forest carbon allocation and mortality under global change. Here, we present a cross-species synthesis of NSC concentrations across multiple organs for 281 woody species from 102 mixed forest communities worldwide, where we quantified species-specific deviations from community means to disentangle intrinsic trait effects from environmental and methodological variation. We found phylogenetic signals in NSC deviations, with coniferous gymnosperms and evergreen species consistently maintaining lower stem soluble sugars and starch concentrations than co-occurring angiosperms and deciduous species, respectively. A global pattern emerged where greater stomatal sensitivity to leaf water potential was associated with declines in the relative concentrations of both sugars and starch. In contrast, xylem hydraulic safety traits showed weak and organ-dependent relationships with NSC concentrations. Sugars increased with photosynthetic capacity and declined with wood density, whereas starch showed the reverse pattern, which aligned with the distinct functional-metabolic roles of sugars and starch. By integrating trait-based ecology with a community-centered framework, our study provides global evidence that stomatal regulation, photosynthetic capacity, specific leaf area, and wood density jointly govern interspecific NSC variation, through contrasting effects on sugars and starch. These are among the most broadly measured traits globally, thus the emergent carbohydrate–trait relationships can have broad applications toward understanding and predicting forest growth and survival under climate change.

tropic system↗

DOE OSTI2025

Optimizing genomic prediction for complex traits via investigating multiple factors in switchgrass

Genomic prediction has accelerated breeding processes and provided mechanistic insights into the genetic bases of complex traits. To further optimize genomic prediction, we assess the impact of genome assemblies, genotyping approaches, variant types, allelic complexities, polyploidy levels, and population structures on the prediction of 20 complex traits in switchgrass (Panicum virgatum L.), a perennial biofuel feedstock. Surprisingly, short read-based genome assembly performs comparably to or even better than long read-based assembly. Due to higher gene coverage, exome capture and multi-allelic variants outperform genotyping-by-sequencing and bi-allelic variants, respectively. Tetraploid models show higher prediction accuracy than octoploid models for most traits, likely due to the greater genetic distances among tetraploids. Depending on the trait in question, different types of variants need to be integrated for optimal predictions. Furthermore, our study provides insights into the factors influencing genomic prediction outcomes, guiding best practices for future studies and for improving agronomic traits in switchgrass and other species through selective breeding.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Climate adaptation in Populus trichocarpa : key adaptive loci identified for stomata and leaf traits

We investigated adaptive genetic variation in Populus trichocarpa, a potential biofuel feedstock crop, to better understand how physiological traits may influence tolerance to water limitation. Our study focused on leaf and stomatal traits, given their roles in plant–water relations and adaptation. Using a diversity panel of over 1300 genotypes, we measured 14 leaf and stomatal traits under control (well-watered) and drought (water-limited) conditions. We conducted genome-wide association studies (GWAS), climate association analyses, and transcriptome (RNA-seq) profiling to identify genetic loci associated with phenotypic variation and adaptation. Stomatal traits, including size and density, were correlated with the climate of origin, with genotypes from more arid regions tending to have smaller but denser stomata. GWAS identified multiple loci associated with trait variation, including a major-effect region on chromosome 10 linked to stomatal size and abaxial contact angle. This locus overlapped with a tandem array of 3-ketoacyl-CoA synthase (KCS) genes and showed strong allele–climate and gene expression associations. Our findings reveal genetic and phenotypic variation consistent with local adaptation and suggest that future climates may favor alleles associated with smaller stomata, particularly under increasing aridity. This work provides insights into climate adaptation and breeding strategies for resilience in perennial crops.

Populus trichocarpa↗

DOE OSTI2024

Discovery of genes that positively affect biomass and stress associated traits in poplar

Woody biomass serves as a renewable resource for various industries, including pulp and paper production, construction, biofuels, and electricity generation. However, the molecular mechanisms behind biomass traits are poorly understood, which significantly curtails the speed and efficiency of their improvement. We used activation tagging to discover genes that can positively affect tree biomass-associated traits. We generated and screened under greenhouse conditions a population of 2,700 independent activation tagging lines. A total of 761 lines, which had significantly and positively affected at least one biomass-associated trait, were discovered. The tag was positioned in the genome for forty lines which were affected in multiple traits and activation of proximal genes validated for a subset. For two lines we fully recapitulated the phenotype of the original lines through overexpression. Moreover, the overexpression led to more pronounced and additional improvements, not observed in the original lines. Importantly, the overexpression of a Fasciclin-like gene (PtaFLA10) and a Patatin-like gene (PtaPAT) was found to substantially improve biomass, with a 40% increase in dry-stem weight, and enhance drought tolerance, respectively. Additionally, PtaPAT overexpression increased cellulose content, which is crucial for biofuel production. Our work shows that the activation tagging approach applied even on a non-genome saturation scale in a poplar tree can be successfully used for the discovery of genes positively modify biomass productivity. Such dominant forward genetics approaches can aid in biotechnological manipulation of woody biomass traits and help unravel the functions and mechanisms of individual genes, gene families, and regulatory modules.

Plant Sciences↗

DOE OSTI2026

Processed sap flow and fine-root trait data associated with summer drought responses in temperate trees in Lisle, Illinois, USA (2019–2021)

These data support the manuscript “Acquisitive root exploration strategies help maintain higher peak sap flux rates during summer drought, but more root biomass does not”. The dataset includes processed sap flow measurements and fine-root trait data collected between 2019 and 2021 from temperate monodominant tree plots established in the 1920s to 1930s ranging in size from 0.05 to 0.8 ha at The Morton Arboretum in Lisle, IL. Sap flow was measured with ICT sap flow sensors using the heat ratio method. Fine-root traits were measured from soil cores which includes specific root length (SRL), specific root area (SRA), diameter, biomass, and length for diameter classes ≤1 mm and ≤2 mm. The package contains comma separated value (CSV) data files and associated metadata that can be viewed and analyzed using common software such as spreadsheet programs, R, and Python. These data are used to investigate how variation in fine-root traits relate to tree water use and drought response during summer drought linking belowground root traits and aboveground physiological responses.

drought↗

DOE OSTI2025

Volatile traits expand the microbial playbook

Microbial metabolic functions are increasingly conceptualized as fitness-regulating traits. However, volatile compounds (the volatilome), despite their key roles in metabolism and ecology, are often overlooked in trait-based frameworks. We propose that volatile traits not only reflect ecological strategies but also shape them by mediating responses to selection pressures. Their volatility affects diffusion, substrate access, and interactions across space, conferring selective advantages as resources or waste products. We outline approaches to incorporate volatile traits into predictive models to improve understanding of microbial selection and community dynamics. Furthermore, this integration enables a more holistic view of microbial life by accounting for the ecological and evolutionary consequences of volatile-mediated processes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Induced and natural variation affect traits independently in hybrid Populus

Abstract The genetic control of many plant traits can be highly complex. Both allelic variation (sequence change) and dosage variation (copy number change) contribute to a plant's phenotype. While numerous studies have investigated the effect of allelic or dosage variation, very few have documented both within the same system, leaving their relative contribution to phenotypic effects unclear. The Populus genome is highly polymorphic, and poplars are fairly tolerant of gene dosage variation. Here, using a previously established Populus hybrid F1 population, we assessed and compared the effect of natural allelic variation and induced dosage variation on biomass, phenology, and leaf morphology traits. We identified QTLs for many of these traits, but our results indicate limited overlap between the QTLs associated with natural allelic variation and induced dosage variation. Additionally, the integration of data from both allelic and dosage variation identifies a larger set of QTLs that together explain a larger percentage of the phenotypic variance. Finally, our results suggest that the effect of the large indels might mask that of allelic QTLs. Our study helps clarify the relationship between allelic and dosage variation and their effects on quantitative traits.

Guo, Weier (ORCID:0000000251789334)↗

DOE OSTI2024

Leaf functional traits highlight phenotypic variation of two tree species in the urban environment

Urbanization is transforming landscapes globally, altering environmental conditions that affect ecosystem functioning, particularly in urban areas where trees are crucial for regulating microclimates, improving air quality, and sustaining biodiversity. This study investigates the environmental differences and tree leaf structure and morphology in urban and suburban sites in the Chicago Metropolitan Region. The leaf functional traits of Norway Maple and Little − leaved Linden were studied in three locations in the summer of 2023: an urban park (University of Illinois Chicago, Chicago, IL), a suburban park (Morton Arboretum, Lisle, IL), and a suburban residential site (Lombard, IL). The urban site had higher daytime and nighttime air, and land surface temperatures compared to the suburban sites with significant fluctuations observed across the sites. Cumulative growing degree days, a measure of potential photosynthetically active days, were also higher in the urban park than in the suburban sites between March and August. Norway Maple trees growing in the urban site displayed higher specific leaf area (SLA) and lower leaf dry matter content (LDMC) than in the suburban sites, resulting in thinner leaves. Similarly, Little−leaved Linden trees in the suburban residential site displayed higher SLA and lower LDMC than those in the suburban park. The values of gas exchange traits − namely photosynthetic assimilation, transpiration rates, and stomatal conductance − of Norway Maple were higher at the urban site compared to suburban sites as temperatures increased during the summer. Norway Maple gas exchange values decreased as the growing season progressed, as expected by ontogeny. In contrast, Little−leaved Linden maintained similar leaf gas exchange values throughout the growing season. Both species in the urban site exhibited lower instantaneous water use efficiency and reduced LDMC, suggesting greater water loss in response to elevated temperatures compared to suburban park and residential sites. Comparisons with existing global trait databases emphasize the need for localized data to accurately capture site−specific responses. Although some traits aligned with database values, others deviated significantly, underscoring the importance of comprehensive, site−specific datasets for robust ecosystem modeling and management strategies.

Cho, Ahram↗