Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “traits”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

COMPILE: a GWAS computational pipeline for gene discovery in complex genomes

Abstract Background Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. Results COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer ( Ostrinia nubilalis ). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. Conclusions The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Classification of River Catchments in the Contiguous United States: Code, Dataset, Similarity Patterns, and Resulting Classes

This dataset serves as supplementary information for the paper by Ciulla F. and Varadharajan C. A Network Approach for Multiscale Catchment Classification using Traits (see reference 1). It contains environmental and physical catchment traits, such as temperatures, precipitation, land use and human interference, from 9067 sites across the contiguous United States (CONUS). The purpose of this dataset is to provide information for a better trait-based categorization of river catchments in the CONUS using networks as an analytical tool. The traits variables match the ones present in the GAGES-II dataset and the preprocessing steps are described in the Methods section (processed_dataset.csv). Additionally we include the topologies (nodes, edges and clusters, also referred as classes) of the catchment network and traits network generated by said dataset (csv and json files). A series of tables support the information carried by the network providing more detailed descriptions of cluster components (SI1.pdf). A summary of all the plots of clusters of catchments with at least 50 nodes is provided (SI2.pdf). The characteristic traits for each cluster of catchments is presented as z-score (traits_categories_zscores_per_catchment_class.csv). The link to the hydrological behavior of clusters of catchments is displayed by boxplots, each describing a particular river discharge index (SI3.pdf). Both csv and json files can be read by common text editors but the data contained into them can be better handled using programming languages like python and database oriented libraries like pandas. Pdf files can be read by any pdf reader software.[02-23-2024] Update: The code and datasets necessary to reproduce the results of the study are available as a zipped repository (code_datasets_catchments_similarity.zip).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

OPEN-Augmented Reality GUI for Bioenergy Crop Phenotyping and Precision Agriculture (Donald Danforth Plant Science Center Final Scientific Technical Report)

The project led by the Donald Danforth Plant Science Center, in collaboration with Arizona State University, George Washington University, and Saint Louis University, has made significant strides in advancing the phenotypic analysis of bioenergy crops through the development of an innovative AI processing pipeline. This initiative was primarily funded by ARPA-E, with additional cost-sharing provided by the participating institutions. The project successfully utilized a variety of sensors—3D scanners, thermal, RGB, and hyperspectral—to refine algorithms for data-driven trait signature identification and improve the classification and visualization of plant traits. The developed AI processing pipeline is capable of handling the complex, multidimensional data characteristic of dynamic agricultural environments. 1) Contributions to understanding: The research has advanced the field of plant phenomics by showcasing the synergistic use of various sensor data to enhance the precision of trait analysis in bioenergy crops. Through the integration of 3D scanners, thermal, RGB, and hyperspectral sensors, the project has developed robust data-driven trait signature algorithms and visualization techniques. These innovations have facilitated detailed monitoring and management of plant traits, providing vital insights into plant growth dynamics and stress responses. Further, the project has broadened our understanding of how machine learning can be effectively applied in multi-sensor environments to refine trait analysis. By leveraging diverse datasets, the research has not only improved the accuracy of phenotypic assessments but also established a versatile methodological framework that can be extended beyond agriculture to other fields requiring detailed phenotypic analysis. 2) Technical effectiveness and economic feasibility: The AI processing pipeline developed in this project demonstrated significant technical effectiveness, achieving high throughput analysis of extensive phenotypic data and meeting targeted accuracies. This system exemplified the capability of advanced machine learning technologies to efficiently manage and analyze large, complex datasets. Economically, the implementation of the project-developed pipelines may offer substantial cost savings across multiple sectors. It enhances data analysis processes and significantly reduces the need for manual data interpretation, thereby decreasing both the time and resources required. 3) Public benefit: The project has significantly broadened the scope of agricultural methodologies to enhance phenotypic analysis, with potential applications in various sectors beyond agriculture. Additionally, the initiative fostered an enriching educational and collaborative environment, significantly enhancing the technical skills of participants. It also made substantial contributions to the scientific community by providing open-access data sets and tools, encouraging ongoing research and development across various disciplines. Overall, the project not only met its scientific goals but also showcased the extensive utility of integrating advanced machine learning and sensor data analysis technologies. These advancements have proven instrumental in driving forward both theoretical research and practical applications, setting a strong foundation for future explorations and innovations in data-driven science.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Leaf-level physiological strategies related to productivity and plasticity of Populus in the Southeastern United States

Introduction: Populus and its hybrids are attractive bioenergy crops and the southeastern United States has broad ability to supply bioenergy markets with woody biomass. Breeding and hybridization have led to superior eastern cottonwood (Populus deltoides W. Bartram ex Marshall) and hybrid poplars adapted to a wide variety of site types not suited for agricultural production. In order to maximize productivity and minimize inputs, genotypes need to efficiently use available site resources and tolerate environmental stresses. In addition, we need to determine plasticity of traits and their coordination across sites to select traits that will broadly characterize genotypes. Therefore, our study objectives were to determine (1) which leaf traits were correlated with growth, (2) if traits and genotypes exhibited significant plasticity across sites, and (3) how traits were coordinated within and across sites and Populus taxa. Methods: We measured trees at two sites in northeastern Mississippi, United States: one upland and one alluvial terrace site. Genotypes included eastern cottonwoods as well as F 1 crosses of eastern cottonwood and P. maximowiczii (Henry), P. nigra (L.) and P. trichocarpa (Torr. & Gray). Results: We found that sites differed in which leaf traits were correlated with productivity; with water use efficiency specifically being positively correlated with growth at an alluvial terrace site, but negatively correlated with growth at an upland site. Tree height growth, leaf isotope composition (δ 13 C and δ 15 N), as well as leaf mass per area (LMA) exhibited the least plasticity across sites, while physiological gas exchange parameters and leaf nitrogen concentration exhibited the highest plasticity. Broadly across taxa, leaf carbon isotope ratios were correlated with intrinsic water use efficiency, and stomatal conductance was positively correlated with photosynthetic nitrogen use efficiency across sites, while leaf nitrogen isotope ratios exhibited contrasting relationships with leaf nitrogen concentration. Discussion: Overall, these results allow us to refine selections of productive genotypes based on site conditions and site-specific relationships with physiological parameters to better match Populus taxa with sites and landowner objectives.

bioenergy feedstocks↗
DOE OSTI2022

Dissecting the Genetic Architecture of Carbon Partitioning in Sorghum Using Multiscale Phenotypes

Carbon partitioning in plants may be viewed as a dynamic process composed of the many interactions between sources and sinks. The accumulation and distribution of fixed carbon is not dictated simply by the sink strength and number but is dependent upon the source, pathways, and interactions of the system. As such, the study of carbon partitioning through perturbations to the system or through focus on individual traits may fail to produce actionable developments or a comprehensive understanding of the mechanisms underlying this complex process. Using the recently published sorghum carbon-partitioning panel, we collected both macroscale phenotypic characteristics such as plant height, above-ground biomass, and dry weight along with microscale compositional traits to deconvolute the carbon-partitioning pathways in this multipurpose crop. Multivariate analyses of traits resulted in the identification of numerous loci associated with several distinct carbon-partitioning traits, which putatively regulate sugar content, manganese homeostasis, and nitrate transportation. Using a multivariate adaptive shrinkage approach, we identified several loci associated with multiple traits suggesting that pleiotropic and/or interactive effects may positively influence multiple carbon-partitioning traits, or these overlaps may represent molecular switches mediating basal carbon allocating or partitioning networks. Conversely, we also identify a carbon tradeoff where reduced lignin content is associated with increased sugar content. The results presented here support previous studies demonstrating the convoluted nature of carbon partitioning in sorghum and emphasize the importance of taking a holistic approach to the study of carbon partitioning by utilizing multiscale phenotypes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Modeling the Effects of Global Change on Ecosystem Processes in a Tropical Rainforest

Ongoing land-use change and climate change in wet tropical forests can potentially drive shifts in tree species composition, representing a change in individual species within a functional group, tropical evergreen trees. The impacts on the global carbon cycle are potentially large, but unclear. We explored the differential effects of species within this functional group, in comparison with the effects of climate change, using the Century model as a research tool. Simulating effects of individual tree species on biome-level biogeochemical cycles constituted a novel application for Century. Background and Objectives: A unique, long-term, replicated field experiment containing five evergreen tree species in monodominant stands under similar environmental conditions in a Costa Rican wet forest provided data for model evaluation. Our objectives were to gain insights about this forest’s biogeochemical cycles and effects of tree species within this functional group, in comparison with climate change. Materials and Methods: We calibrated Century, using long-term meteorological, soil, and plant data from the field-based experiment. In modeling experiments, we evaluated effects on forest biogeochemistry of eight plant traits that were both observed and modeled. Climate-change simulation experiments represented two climate-change aspects observed in this region. Results: Model calibration revealed that unmodeled soil processes would be required to sustain observed P budgets. In species-traits experiments, three separate plant traits (leaf death rate, leaf C:N, and allocation to fine roots) resulted in modeled biomass C stock changes of >50%, compared with a maximum 21% change in the climate-change experiments. Conclusions: Modeled ecosystem properties and processes in Century were sensitive to changes in plant traits and nutrient limitations to productivity. Realistic model output was attainable for some species, but unusual plant traits thwarted predictions for one species. Including more plant traits and soil processes could increase realism, but less-complex models provide an accessible means for exploring plant-soil-atmosphere interactions.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2009

The Crop Evaluation Research for Environmental Strategies (CERES) Remote Sensing 2008 Project Activities

In recent years, the use of Plant Incorporated Protectant (PIP) corn by American producers has been increasing dramatically. PIP corn contains genetically inserted traits that produce toxins in the plant that provide narrowly targeted protection against specific insect pests. The plant producing t oxms can offer significant reductions in the application of broad -spectrum pesticides that have ecological and human health consequences. PIP corn as a percentage of total corn acreage planted in the US is expected to continue to increase as these protective traits are "stacked" with other desirable traits by seed companies, and producers are seeing considerable increases in corn yield as a result. The introduction of corn as a bio-fuel source for ethanol has increased production by over 6 million hectares in 2007. The United States Environmental Protection Agency (USEPA), which is responsible for the registration of PIP crops under the Federal Insecticide, Fungicide and Rodenticide Act, views the use of PIP corn as positive. Broad spectrum pesticide use has declined since the PIP traits have been introduced. As the agricultural landscape sees a higher percentage of corn acres using the PIP technology, the risk of the targeted insect pest populations developing resistance to the toxins, thereby rendering the in will increase as well. This result would negate the effectiveness of the PIP corn traits and could reduce production of a US field corn crop valued at $33 billion dollars in 2006 and place US food and now energy security at risk. Concerns over insect pest resistance development to PIP traits have led the USEPA to team with NASA and the Institute for Technology Development (ITD) to develop geo-spatial technologies designed to proactively monitor the corn production landscape for insect pest infestation and possible resistance development. USEPA resistance management simulation models are combined with NASA remote sensi ng products to monitor the corn landscape for resistance development. The two agencies have entered into an agreement which could potentially lead to the development of next generation NASA sensors that will more specifically address the requirements of the USEPA's resistance development strategy and offer opportunities to study the ever changing ecosystem complexities. The USEPA/NASA/ITD team has developed a broad research project entitled CERES (Crop Evaluation Research for Environmental Strategies). CERES is a research effort leading to decision support system tools that are designed to integrate multi-resolution NASA remote sensing data products and USEPA geo -spatial models to monitor the potential for insect pest resistance development from the regional to the landscape and then to the field level.

Casas, Joseph C.↗
DOE OSTI2026

Correlational selection and genetic architecture shape the evolution of the leaf economics spectrum in a perennial grass

The generality of the worldwide leaf economics spectrum (LES) has made it a pillar of trait-based ecological research. Yet, few studies have examined the processes shaping the evolution of the LES within species, in part, because most species occupy only a small portion of the LES. Here, to address this gap, we took advantage of the distinct leaf economics strategies present in different ecotypes of the phenotypically diverse perennial grass Panicum virgatum (switchgrass) to generate a genetic mapping population, which we planted in common gardens at three sites spanning 12 degrees of latitude in the central United States. With this genetic mapping population, we evaluated two potentially interacting causes of LES evolution: 1) genetic architecture, where multiple traits are influenced by either the same gene (pleiotropy) or by genes in close physical proximity (genetic linkage), and 2) correlational selection, where selection acts on traits in combination rather than in isolation. We found that shared genetic architecture influenced covariation between photosynthetic rate (A MASS ) and leaf nitrogen (N MASS ) and between A MASS and leaf mass per area (LMA). We also found that correlational selection favored the trait combinations predicted by the LES (e.g., high LMA with low N MASS or low LMA with high N MASS ) and disfavored other, mismatched trait combinations at two of the three sites. Together, these results demonstrate how the evolution of an integrated LES within species can arise from multiple evolutionary causes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The response of stomatal conductance to seasonal drought in tropical forests

Stomata regulate CO2 uptake for photosynthesis and water loss through transpiration. The approaches used to represent stomatal conductance (gs) in models vary. In particular, current understanding of drivers of the variation in a key parameter in those models, the slope parameter (i.e. a measure of intrinsic plant water-use-efficiency), is still limited, particularly in the tropics. Here we collected diurnal measurements of leaf gas exchange and water potential (?leaf), and a suite of plant traits from the upper canopy of 15 tropical trees in two contrasting Panamanian forests throughout the dry season of the 2016 El Niño. The plant traits included wood density, leaf-mass-per-area (LMA), leaf carboxylation capacity (Vc,max25), leaf water content, the degree of isohydry, and predawn ?leaf. We first investigated how the choice of four commonly used leaf-level gs models with and without the inclusion of ?leaf as an additional predictor variable influence the ability to predict gs, and then explored the abiotic (i.e. month, site-month interaction) and biotic (i.e. tree-species-specific characteristics) drivers of slope parameter variation. Our results show that the inclusion of ?leaf did not improve model performance and that the models that represent the response of gs to vapor pressure deficit performed better than corresponding models that respond to relative humidity. Within each gs model, we found large variation in the slope parameter, and this variation was attributable to the biotic driver, rather than abiotic drivers. We further investigated potential relationships between the slope parameter and the six available plant traits mentioned above, and found that only one trait, LMA, had a significant correlation with the slope parameter (R2=0.66, n=15), highlighting a potential path towards improved model parameterization. This study advances understanding of gs dynamics over seasonal drought, and identifies a practical, trait-based approach to improve modeling of carbon and water exchange in tropical forests.

carbon and water exchange, stomatal conductance mo↗
DOE OSTI2024

Exploring the role of biotic factors in regulating the spatial variability in land surface phenology across four temperate forest sites

Here, land surface phenology (LSP), the characterization of plant phenology with satellite data, is essential for understanding the effects of climate change on ecosystem functions. Considerable LSP variation is observed within local landscapes, and the role of biotic factors in regulating such variation remains underexplored. In this study, we selected four National Ecological Observatory Network terrestrial sites with minor topographic relief to investigate how biotic factors regulate intra-site LSP variability. We utilized plant functional type (PFT) maps, functional traits, and LSP data to assess the explanatory power of biotic factors for the start and end of season (SOS and EOS) variability. Our results indicate that PFTs alone explain only 0.8–23.4% of intra-site SOS and EOS variation, whereas including functional traits significantly improves explanatory power, with cross-validation correlations ranging from 0.50 to 0.85. While functional traits exhibited diverse effects on SOS and EOS across different sites, traits related to competitive ability and productivity were important for explaining both SOS and EOS variation at these sites. These findings reveal that plants exhibit diverse phenological responses to comparable environmental conditions, and functional traits significantly contribute to intra-site LSP variability, highlighting the importance of intrinsic biotic properties in regulating plant phenology.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution. (Model and code can be found at imageomics.github.io/phylo-diffusion)

Khurana, Mridul↗
DOE OSTI2025

Multi-site Milling Strategy Reveals Significant Variation in Biomass Composition of Switchgrass ( Panicum virgatum ) Grown at Ten Locations

Cell wall composition influences biomass use as a forage and as a feedstock for biofuel and chemical conversion. To examine the influence of environment on composition of switchgrass (Panicum virgatum L.), we utilized a multi-environment experiment consisting of clones of switchgrass genotypes grown at up to ten locations in the continental US. We tested the influence of different milling treatments on biomass composition trait predictions via near-infrared reflectance spectroscopy (NIRS). We found that most compositional trait predictions (29/34) were significantly different (P < 0.05) when a single lot of biomass was subjected to disparate milling treatments, i.e., knife milling vs. knife milling with an additional cyclone milling. Further, depending on the plant material tested, three to eight compositional trait predictions vary (P < 0.05) when identical biomass was knife milled at different sites followed by cyclone milling at a single site, including for traits such as Klason lignin, nitrogen, and carbon. In some cases, variation due to milling site exceeded environmentally induced compositional variation of a single switchgrass genotype grown at different sites. From these observations, we recommend a protocol with two sequential millings that decouples growth environment from a particular mill. Utilizing this approach, we found that 46/46 biomass composition traits from the warm season herbaceous forage and switchgrass bioethanol NIRS equations vary significantly (P < 0.001) in clones of a switchgrass genotype (WBC) grown at ten sites, with the growth site representing the largest average source of variation (41%). This multi-site milling approach can be used to examine environmental and gene-by-environment influences on composition with the goal of optimizing cell wall composition in different environments for biomass utilization.

09 BIOMASS FUELS↗
DOE OSTI2022

Whole-plant phenotypic engineering: moving beyond ratios for multi-objective optimization of nutrient use efficiency

Nutrient use efficiency (NUE) is typically measured as the ratio of yield to soil nutrient availability but ignores contributions of underlying plant traits. Relevant plant traits can be grouped as root acquisition efficiency, shoot radiation use efficiency, and plant metabolic efficiency. The intentional integration of these traits will lead to synergistic improvements of NUE. Recent progress in trait-focused research includes phenotyping root nutrient uptake rates and respiration, engineering reduced photorespiration, and identification of nutrient assimilation pathways. Traits need to be conceptualized in agricultural systems contexts to improve synchrony of plant demand and soil supply of nutrients, including consideration of crop mixtures. Use of simulation modeling and multi-objective optimization will allow accelerating NUE gains beyond selection for a single ratio.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Increasing Functional Diversity in a Global Land Surface Model Illustrates Uncertainties Related to Parameter Simplification

Abstract Simulations of the land surface carbon cycle typically compress functional diversity into a small set of plant functional types (PFT), with parameters defined by the average value of measurements of functional traits. In most earth system models, all wild plant life is represented by between five and 14 PFTs and a typical grid cell (≈100 × 100 km) may contain a single PFT. Model logic applied to this coarse representation of ecological functional diversity provides a reasonable proxy for the carbon cycle, but does not capture the non‐linear influence of functional traits on productivity. Here we show through simulations using the Energy Exascale Land Surface Model in 15 diverse terrestrial landscapes, that better accounting for functional diversity markedly alters predicted total carbon uptake. The shift in carbon uptake is as great as 30% and 10% in boreal and tropical regions, respectively, when compared to a single PFT parameterized with the trait means. The traits that best predict gross primary production vary based on vegetation phenology, which broadly determines where traits fall within the global distribution. Carbon uptake is more closely associated with specific leaf area for evergreen PFTs and the leaf carbon to nitrogen ratio in deciduous PFTs.

58 GEOSCIENCES↗
DOE OSTI2022

Intra-Specific Variability in Plant Hydraulic Parameters Inferred From Model Inversion of Sap Flux Data

Understanding plant hydraulic regulation is critical for predicting plant and ecosystem responses to projected increases in drought stress. Plant hydraulic regulation is controlled by observable, diverse plant hydraulic traits that can vary as much across individuals of the same species as they do across different species. Direct measurements of plant hydraulic traits from a range of ecosystems remain limited in comparison to other, more readily measured traits (e.g., specific leaf area). Furthermore, plant hydraulic trait measurements, often made at leaf or branch levels, are not easily scaled to whole-plant values that are typically used to predict plant and ecosystem fluxes. In this study, multiple whole-plant hydraulic parameters are inferred from observations of plant water use (i.e., sap flow), soil properties, and meteorological data. We use a Markov Chain Monte Carlo model inversion approach to obtain the best estimates and uncertainty of plant hydraulic parameters that capture whole-plant effective embolism resistance and stomatal sensitivity to decreasing plant water potential. We then use the inferred values in the model to estimate whole-tree water use and isohydricity. This approach reliably infers whole-plant parameter values with enough specificity to resolve inter- and intra-specific differences, and thus supplements time- and labor-intensive direct measurements of traits.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

The predictive power of phylogeny on growth rates in soil bacterial communities

Abstract Predicting ecosystem function is critical to assess and mitigate the impacts of climate change. Quantitative predictions of microbially mediated ecosystem processes are typically uninformed by microbial biodiversity. Yet new tools allow the measurement of taxon-specific traits within natural microbial communities. There is mounting evidence of a phylogenetic signal in these traits, which may support prediction and microbiome management frameworks. We investigated phylogeny-based trait prediction using bacterial growth rates from soil communities in Arctic, boreal, temperate, and tropical ecosystems. Here we show that phylogeny predicts growth rates of soil bacteria, explaining an average of 31%, and up to 58%, of the variation within ecosystems. Despite limited overlap in community composition across these ecosystems, shared nodes in the phylogeny enabled ancestral trait reconstruction and cross-ecosystem predictions. Phylogenetic relationships could explain up to 38% (averaging 14%) of the variation in growth rates across the highly disparate ecosystems studied. Our results suggest that shared evolutionary history contributes to similarity in the relative growth rates of related bacteria in the wild, allowing phylogeny-based predictions to explain a substantial amount of the variation in taxon-specific functional traits, within and across ecosystems.

Walkup, Jeth (ORCID:0000000279082963)↗
DOE OSTI2022

Genetic mapping and prediction of flowering time and plant height in a maize Stiff Stalk MAGIC population

Abstract The Stiff Stalk heterotic pool is a foundation of US maize seed parent germplasm and has been heavily utilized by both public and private maize breeders since its inception in the 1930s. Flowering time and plant height are critical characteristics for both inbred parents and their test crossed hybrid progeny. To study these traits, a 6-parent multiparent advanced generation intercross population was developed including maize inbred lines B73, B84, PHB47 (B37 type), LH145 (B14 type), PHJ40 (novel early Stiff Stalk), and NKH8431 (B73/B14 type). A set of 779 doubled haploid lines were evaluated for flowering time and plant height in 2 field replicates in 2016 and 2017, and a subset of 689 and 561 doubled haploid lines were crossed to 2 testers, respectively, and evaluated as hybrids in 2 locations in 2018 and 2019 using an incomplete block design. Markers were derived from a practical haplotype graph built from the founder whole genome assemblies and genotype-by-sequencing and exome capture-based sequencing of the population. Genetic mapping utilizing an update to R/qtl2 revealed differing profiles of significant loci for both traits between 635 of the DH lines and 2 sets of 570 and 471 derived hybrids. Genomic prediction was used to test the feasibility of predicting hybrid phenotypes based on the per se data. Predictive abilities were highest on direct models trained using the data they would predict (0.55–0.63), and indirect models trained using per se data to predict hybrid traits had slightly lower predictive abilities (0.49–0.55). Overall, this finding is consistent with the overlapping and nonoverlapping significant quantitative trait loci found within the per se and hybrid populations and suggests that selections for phenology traits can be made effectively on doubled haploid lines before hybrid data is available.

Genetics & Heredity↗
DOE OSTI2021

DIRT/3D: 3D root phenotyping for field-grown maize ( Zea mays )

The development of crops with deeper roots holds substantial promise to mitigate the consequences of climate change. Deeper roots are an essential factor to improve water uptake as a way to enhance crop resilience to drought, to increase nitrogen capture, to reduce fertilizer inputs, and to increase carbon sequestration from the atmosphere to improve soil organic fertility. A major bottleneck to achieving these improvements is high-throughput phenotyping to quantify root phenotypes of field-grown roots. We address this bottleneck with Digital Imaging of Root Traits (DIRT)/3D, an image-based 3D root phenotyping platform, which measures 18 architecture traits from mature field-grown maize (Zea mays) root crowns (RCs) excavated with the Shovelomics technique. DIRT/3D reliably computed all 18 traits, including distance between whorls and the number, angles, and diameters of nodal roots, on a test panel of 12 contrasting maize genotypes. The computed results were validated through comparison with manual measurements. Overall, we observed a coefficient of determination of r 2 > 0.84 and a high broad-sense heritability of H$_{mean}^{2}$ < 0.6 for all but one trait. The average values of the 18 traits and a developed descriptor to characterize complete root architecture distinguished all genotypes. DIRT/3D is a step toward automated quantification of highly occluded maize RCs. Therefore, DIRT/3D supports breeders and root biologists in improving carbon sequestration and food security in the face of the adverse effects of climate change.

59 BASIC BIOLOGICAL SCIENCES↗