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At least 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

Long-term climate change and periodic environmental extremes threaten food and fuel security and global crop productivity. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation—knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass ( Panicum virgatum ). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate–gene–biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene–trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.

09 BIOMASS FUELS↗
DOE OSTI2024

The complex polyploid genome architecture of sugarcane

Sugarcane, the world’s most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype (‘monoploid’) representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Generation, analysis, and transformation of macro-chloroplast Potato (Solanum tuberosum) lines for chloroplast biotechnology

Abstract Chloroplast biotechnology is a route for novel crop metabolic engineering. The potential bio-confinement of transgenes, the high protein expression and the possibility to organize genes into operons represent considerable advantages that make chloroplasts valuable targets in agricultural biotechnology. In the last 3 decades, chloroplast genomes from a few economically important crops have been successfully transformed. The main bottlenecks that prevent efficient transformation in a greater number of crops include the dearth of proven selectable marker gene-selection combinations and tissue culture methods for efficient regeneration of transplastomic plants. The prospects of increasing organelle size are attractive from several perspectives, including an increase in the surface area of potential targets. As a proof-of-concept, we generated Solanum tuberosum (potato) macro-chloroplast lines overexpressing the tubulin-like GTPase protein gene FtsZ1 from Arabidopsis thaliana . Macro-chloroplast lines exhibited delayed growth at anthesis; however, at the time of harvest there was no significant difference in height between macro-chloroplast and wild-type lines. Macro-chloroplasts were successfully transformed by biolistic DNA-delivery and efficiently regenerated into homoplasmic transplastomic lines. We also demonstrated that macro-chloroplasts accumulate the same amount of heterologous protein than wild-type organelles, confirming efficient usage in plastid engineering. Advantages and limitations of using enlarge compartments in chloroplast biotechnology are discussed.

Occhialini, Alessandro (ORCID:000000021162798X)↗
DOE OSTI2023

Tripogon loliiformis tolerates rapid desiccation after metabolic and transcriptional priming during initial drying

Abstract Crop plants and undomesticated resilient species employ different strategies to regulate their energy resources and growth. Most crop species are sensitive to stress and prioritise rapid growth to maximise yield or biomass production. In contrast, resilient plants grow slowly, are small, and allocate their resources for survival in challenging environments. One small group of plants, termed resurrection plants, survive desiccation of their vegetative tissue and regain full metabolic activity upon watering. However, the precise molecular mechanisms underlying this extreme tolerance remain unknown. In this study, we employed a transcriptomics and metabolomics approach, to investigate the mechanisms of desiccation tolerance in Tripogon loliiformis , a modified desiccation-tolerant plant, that survives gradual but not rapid drying. We show that T. loliiformis can survive rapid desiccation if it is gradually dried to 60% relative water content (RWC). Furthermore, the gene expression data showed that T. loliiformis is genetically predisposed for desiccation in the hydrated state, as evidenced by the accumulation of MYB, NAC, bZIP, WRKY transcription factors along with the phytohormones, abscisic acid, salicylic acid, amino acids (e.g., proline) and TCA cycle sugars during initial drying. Through network analysis of co-expressed genes, we observed differential responses to desiccation between T. loliiformis shoots and roots. Dehydrating shoots displayed global transcriptional changes across broad functional categories, although no enrichment was observed during drying. In contrast, dehydrating roots showed distinct network changes with the most significant differences occurring at 40% RWC. The cumulative effects of the early stress responses may indicate the minimum requirements of desiccation tolerance and enable T. loliiformis to survive rapid drying. These findings potentially hold promise for identifying biotechnological solutions aimed at developing drought-tolerant crops without growth and yield penalties.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Case study on climate change effects and food security in Southeast Asia

Agriculture, a cornerstone of human civilization, faces rising challenges from climate change, resource limitations, and stagnating yields. Precise crop production forecasts are crucial for shaping trade policies, development strategies, and humanitarian initiatives. This study introduces a comprehensive machine learning framework designed to predict crop production. We leverage CMIP5 climate projections under a moderate carbon emission scenario to evaluate the future suitability of agricultural lands and incorporate climatic data, historical agricultural trends, and fertilizer usage to project yield changes. Our integrated approach forecasts significant regional variations in crop production across Southeast Asia by 2028, identifying potential cropland utilization. Specifically, the cropland area in Indonesia, Malaysia, Philippines, and Viet Nam is projected to decline by more than 10% if no action is taken, and there is potential to mitigate that loss. Moreover, rice production is projected to decline by 19% in Viet Nam and 7% in Thailand, while the Philippines may see a 5% increase compared to 2021 levels. Our findings underscore the critical impacts of climate change and human activities on agricultural productivity, offering essential insights for policy-making and fostering international cooperation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Soil erosion and lateral carbon fluxes from corn stover-derived biofuel

Abstract Crop residues hold promise to alleviate food vs. fuel competition and contribute to biofuel production. However, the impacts of lateral sediment and carbon fluxes caused by residue removal are not fully understood. Here we employ agroecosystem modeling to conservatively estimate lateral sediment and carbon fluxes resulting from partial corn stover removal in the U.S. Midwest. Results show substantial increases in soil erosion resulting from corn stover removal. For example, the area of continuous corn and corn soybean cropping systems exceeding soil erosion tolerance threshold could increase from 1.1 to 13.3% because of 66% corn stover removal. Depending on removal intensity, conservation, and crop rotation, the stover removal-induced increases in eroded soil organic carbon is equivalent to 3.9–12.5 gCO 2 e MJ −1 , which is comparable to other components of the life cycle impacts of corn stover-derived biofuel. Our findings highlight the need to consider the soil erosion and lateral carbon fluxes impacts of corn stover removal in designing supply chains for cellulosic biofuel production.

Science & Technology - Other Topics↗
DOE OSTI2025

Available land for cellulosic biofuel production: a supply chain centered comparison

The land that is potentially available to produce dedicated cellulosic bioenergy crops, often referred to as 'marginal' land, depends heavily on the underlying assumptions used to classify and identify it. In this study we compare three definitions and types of marginal land to identify the interactions between the bioenergy landscape and the logistics networks needed for the biofuel supply chain. Typical studies of the scale, cost, and greenhouse gas (GHG) mitigation potential of cellulosic biofuel take a land-centered approach which may neglect to account for the trade-offs between establishing bioenergy crops and the supply chain design decisions needed to allow those crops to be converted to liquid fuel. A mathematical programming approach is used to minimize the total annualized cost of a large-scale field-to-product system producing bioethanol in the USA midwest. Results show that a high concentration of marginal land leads to efficient systems and that the bioenergy landscape design becomes increasingly important with a higher emphasis on GHG mitigation. Additionally, targeted landscape design (including fertilization) with a focus on fields with high soil carbon sequestration potential can greatly reduce the system-wide GHG emissions for only a small increase in the unit cost of biofuel.

09 BIOMASS FUELS↗
DOE OSTI2025

Predicting weather impacts on corn production in a data-limited region using a transfer learning approach

The stability of food supply and prices may depend more on annual changes in yields from year-to-year variability in weather than on longer-term average changes from changing climatic conditions. However, the absence of high-quality data on crop yields at fine spatial resolutions in many regions of the world makes it challenging to statistically model their response to interannual variability in weather patterns. Therefore, there is a need for empirical methods that can project annual crop yield changes even in limited data regions. Here, we propose a transfer learning algorithm that uses high spatial resolution data from one region to project yields in another region with more limited data. The goal of our work is to understand what data types can be beneficial for transferring learning from a source region to a very different target region with more limited data. We utilize Long Short-Term Memory to develop a transfer learning model that is trained on historical county-level corn yield in the United States and predicts district-level corn yield variations in India. Even using smaller amounts of data in India, simulating a data-scarce region, we achieve an average root mean square error of 0.48 bu acre−1 in predicting interannual yield variations. Using Shapley values to interpret results, we explore the contribution of the different weather parameters to interannual yield variability and find a larger influence of precipitation-related variables. Our study demonstrates the usefulness of this method for transferring models of weather impacts on crop yields trained on a data-rich country to one with more limited data. It suggests the potential of applying the transfer learning model to mitigate the need for extensive raw data globally.

Vishwakarma, Srishti [ORNL] (ORCID:000000031674419↗
DOE OSTI2023

Valuation of pollination services from habitat management: a case study of utility scale solar energy facilities in the United States

Creating and maintaining pollinator habitats following the ecological infrastructure concept in degraded or unutilized land, such as solar energy facilities, is a practical way to synergistically advance the food, energy, and ecology nexus. Given the large land-use requirements for solar farming—the fastest growing renewable energy technology–considerable attention has been focused on strategies to maximize multiple ecosystem services. In this study, we coupled the principles of agronomy and ecology with economics and integrated national-scale data on crops, pollinators, and solar facilities to identify locations for creating pollinator habitats and estimating the economic value of pollination from the habitats. We examined opportunities for pollination services from pollinator-friendly utility-scale solar facilities adjacent to 42 million hectares of pollination-dependent crops in the conterminous United States at high resolution of 1 ha. We used the net income method to estimate the potential economic value of creating habitat in the land adjacent to solar facilities in the eight states with the greatest number of solar installations. Creating pollinator habitats at the 217 utility-scale solar facilities in these states could support adjacent 80,000 hectares of high pollinator dependent crops, which could potentially generate a pollination value of $\$$120 to $\$$264 million USD. The location-specific information and high-resolution maps generated for the United States demonstrate integration of grey and green infrastructure to support the food, energy, and environment nexus.

14 SOLAR ENERGY↗
DOE OSTI2022

A Chromosome-Scale Genome Assembly of a Helicoverpa zea Strain Resistant to Bacillus thuringiensis Cry1Ac Insecticidal Protein

Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. Helicoverpa zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt-resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Exploring genetic diversity, population structure, and subgenome differences in the allopolyploid Camelina sativa : implications for future breeding and research studies

Abstract Camelina (Camelina sativa), an allohexaploid species, is an emerging aviation biofuel crop that has been the focus of resurgent interest in recent decades. To guide future breeding and crop improvement efforts, the community requires a deeper comprehension of subgenome dominance, often noted in allopolyploid species, “alongside an understanding of the genetic diversity” and population structure of material present within breeding programs. We conducted population genetic analyses of a C. sativa diversity panel, leveraging a new genome, to estimate nucleotide diversity and population structure, and analyzed for patterns of subgenome expression dominance among different organs. Our analyses confirm that C. sativa has relatively low genetic diversity and show that the SG3 subgenome has substantially lower genetic diversity compared to the other two subgenomes. Despite the low genetic diversity, our analyses identified 13 distinct subpopulations including two distinct wild populations and others putatively representing founders in existing breeding populations. When analyzing for subgenome composition of long non-coding RNAs, which are known to play important roles in (a)biotic stress tolerance, we found that the SG3 subgenome contained significantly more lincRNAs compared to other subgenomes. Similarly, transcriptome analyses revealed that expression dominance of SG3 is not as strong as previously reported and may not be universal across all organ types. From a global analysis, SG3 “was only significant higher expressed” in flower, flower bud, and fruit organs, which is an important discovery given that the crop yield is associated with these organs. Collectively, these results will be valuable for guiding future breeding efforts in camelina.

Agriculture↗
DOE OSTI2024

Propelling sustainable energy: Multi-omics analysis of pennycress FATTY ACID ELONGATION1 knockout for biofuel production

Abstract The aviation industry’s growing interest in renewable jet fuel has encouraged the exploration of alternative oilseed crops. Replacing traditional fossil fuels with a sustainable, domestically sourced crop can substantially reduce carbon emissions, thus mitigating global climate instability. Pennycress (Thlaspi arvense L.) is an emerging oilseed intermediate crop that can be grown during the offseason between maize (Zea mays) and soybean (Glycine max) to produce renewable biofuel. Pennycress is being domesticated through breeding and mutagenesis, providing opportunities for trait enhancement. Here, we employed metabolic engineering strategies to improve seed oil composition and bolster the plant's economic competitiveness. FATTY ACID ELONGATION1 (FAE1) was targeted using CRISPR-Cas 9 gene editing to eliminate very long chain fatty acids (VLCFAs) from pennycress seed oil, thereby enhancing its cold flow properties. Through an integrated multiomics approach, we investigated the impact of eliminating VLCFAs in developing and mature plant embryos. Our findings revealed improved cold-germination efficiency in fae1, with seedling emergence occurring up to 3 d earlier at 10 °C. However, these alterations led to a tradeoff between storage oil content and composition. Additionally, these shifts in lipid biosynthesis were accompanied by broad metabolic changes, such as the accumulation of glucose and ADP-glucose quantities consistent with increased starch production. Furthermore, shifts to shorter FA chains triggered the upregulation of heat shock proteins, underscoring the importance of VLCFAs in stress signaling pathways. Overall, this research provides crucial insights for optimizing pennycress seed oil while preserving essential traits for biofuel applications.

Rasoul, Amira (ORCID:0009000714290175)↗
DOE OSTI2021

Serendipita Fungi Modulate the Switchgrass Root Transcriptome to Circumvent Host Defenses and Establish a Symbiotic Relationship

The fungal family Serendipitaceae encompasses root-associated lineages with endophytic, ericoid, orchid, and ectomycorrhizal lifestyles. Switchgrass is an important bioenergy crop for cellulosic ethanol production owing to high biomass production on marginal soils otherwise unfit for food crop cultivation. The aim of this study was to investigate the host plant responses to Serendipita spp. colonization by characterizing the switchgrass root transcriptome during different stages of symbiosis in vitro. For this, we included a native switchgrass strain, Serendipita bescii, and a related strain, S. vermifera, isolated from Australian orchids. Serendipita colonization progresses from thin hyphae that grow between root cells to, finally, the production of large, bulbous hyphae that fill root cells during the later stages of colonization. We report that switchgrass seems to perceive both fungi prior to physical contact, leading to the activation of chemical and structural defense responses and putative host disease resistance genes. Subsequently, the host defense system appears to be quenched and carbohydrate metabolism adjusted, potentially to accommodate the fungal symbiont. In addition, prior to contact, switchgrass exhibited significant increases in root hair density and root surface area. Furthermore, genes involved in phytohormone metabolism such as gibberellin, jasmonic acid, and salicylic acid were activated during different stages of colonization. Both fungal strains induced plant gene expression in a similar manner, indicating a conserved plant response to members of this fungal order. Understanding plant responsiveness to Serendipita spp. will inform our efforts to integrate them into forages and row crops for optimal plant–microbe functioning, thus facilitating low-input, sustainable agricultural practices.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Community-Driven Metadata Standards for Agricultural Microbiome Research

Accelerating the pace of microbiome science to enhance crop productivity and agroecosystem health will require transdisciplinary studies, comparisons among datasets, and synthetic analyses of research from diverse crop management contexts. However, despite the widespread availability of crop-associated microbiome data, variation in field sampling and laboratory processing methodologies, as well as metadata collection and reporting, significantly constrains the potential for integrative and comparative analyses. Here we discuss the need for agriculture-specific metadata standards for microbiome research, and propose a list of “required” and “desirable” metadata categories and ontologies essential to be included in a future minimum information metadata standards checklist for describing agricultural microbiome studies. We begin by briefly reviewing existing metadata standards relevant to agricultural microbiome research, and describe ongoing efforts to enhance the potential for integration of data across research studies. Our goal is not to delineate a fixed list of metadata requirements. Instead, we hope to advance the field by providing a starting point for discussion, and inspire researchers to adopt standardized procedures for collecting and reporting consistent and well-annotated metadata for agricultural microbiome research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Microbial biotechnology in the effort to end hunger

The UN has set a series of goals with the aim of fostering sustainability on our planet. Among these goals, Sustainable Development Goal (SDG) 2 aims to END HUNGER by 2030. However, under the current global conditions, this will be difficult to achieve without significant efforts by governments and other stakeholders. It is imperative that we prioritize the increase of agricultural production while simultaneously exploring sustainable resources for crop production (Sessitsch et al., 2018). Technologies such as precision agriculture, genetic engineering of crops and the use of bioinoculants and biopesticides hold tremendous potential to enhance crop production.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2020

Biomass Production with Conservation Practices for Two Iowa Watersheds

Hydrologic modeling was used to estimate potential changes in nutrients, suspended sediment, and streamflow in various biomass production scenarios with conservation practices under different landscape designs. Two major corn and soybean croplands were selected for study: the South Fork of the Iowa River watershed and the headwater of the Raccoon River watershed. A physically based model, the Soil and Water Assessment Tool, was used to simulate hydrology and water quality under different scenarios with conservation practices and biomass production. Scenarios are based on conservation practices and biomass production; riparian buffer (RB), saturated buffer, and grassed waterways; various stover harvest rates of 30%, 45%, and 70% with and without winter cover crops; and conversion of marginal land to switchgrass. Conservation practices and landscape design with different biomass feedstocks were shown to significantly improve water quality while supporting sustainable biomass production. Model results for nitrogen, phosphorus, and suspended sediments were analyzed temporally at spatial scales that varied from hydrologic response units to the entire watershed. With conservation practices, water quality could potentially improve by reducing nitrogen loads by up to 20%–30% (stover harvest with cover crop), phosphorus loads by 20%–40% (RB), and sediment loads by 30%–70% (stover harvest with cover crop and RB).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

How do drought and heat affect the response of soybean seed yield to elevated O 3 ? An analysis of 15 seasons of free–air O 3 concentration enrichment studies

The coincidence of rising ozone concentrations ([O 3 ]), increasing global temperatures, and drought episodes is expected to become more intense and frequent in the future. A better understanding of the responses of crop yield to elevated [O 3 ] under different levels of drought and high temperature stress is, therefore, critical for projecting future food production potential. Using a 15-year open-air field experiment in central Illinois, we assessed the impacts of elevated [O 3 ] coupled with variation in growing season temperature and water availability on soybean seed yield. Thirteen soybean cultivars were exposed to a wide range of season-long elevated [O 3 ] in the field using free-air O 3 concentration enrichment. Elevated [O3] treatments reduced soybean seed yield from as little as 5.3% in 2005 to 35.2% in 2010. Although cultivars differed in yield response to elevated [O 3 ] (R), ranging from 17.5% to –76.4%, there was a significant negative correlation between R and O 3 dosage. Soybean cultivars showed greater seed yield losses to elevated [O 3 ] when grown at drier or hotter conditions compared to wetter or cooler years, because the hotter and drier conditions were associated with greater O 3 treatment. However, year-to-year variation in weather conditions did not influence the sensitivity of soybean seed yield to a given increase in [O 3 ]. Collectively, this study quantitatively demonstrates that, although drought conditions or warmer temperatures led to greater O 3 treatment concentrations and O 3 -induced seed yield reduction, drought and temperature stress did not alter soybean's sensitivity to O 3 . Our results have important implications for modeling the effects of rising O 3 pollution on crops and suggest that altering irrigation practices to mitigate O 3 stress may not be effective in reducing crop sensitivity to O 3 .

60 APPLIED LIFE SCIENCES↗