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At least 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci

Abstract Wild and weedy relatives of domesticated crops harbor genetic variants that can advance agricultural biotechnology. Here we provide a genome resource for the wild plant green millet ( Setaria viridis ), a model species for studies of C 4 grasses, and use the resource to probe domestication genes in the close crop relative foxtail millet ( Setaria italica ). We produced a platinum-quality genome assembly of S. viridis and de novo assemblies for 598 wild accessions and exploited these assemblies to identify loci underlying three traits: response to climate, a ‘loss of shattering’ trait that permits mechanical harvest and leaf angle, a predictor of yield in many grass crops. With CRISPR–Cas9 genome editing, we validated Less Shattering1 ( SvLes1 ) as a gene whose product controls seed shattering. In S. italica , this gene was rendered nonfunctional by a retrotransposon insertion in the domesticated loss-of-shattering allele SiLes1-TE (transposable element). This resource will enhance the utility of S. viridis for dissection of complex traits and biotechnological improvement of panicoid crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Nth-plant scenario for forest resources and short rotation woody crops: Biorefineries and depots in the contiguous US

Estimating the US potential of woody material is of vital importance to ensure cost-effective supply logistics and develop a sustainable bioenergy and bioproducts industry. We analyzed a mature conversion technology for woody resources for the contiguous US that takes advantage of economies of scale: the nth-plant. Here, we developed a database to quantify the total accessible woody biomass within a distributed network of preprocessing depots and biorefineries considering both quality specifications for conversion and a target cost to compete with fossil fuels. We considered two categories of woody biomass: 1) forest residues from trees, tops and limbs produced from conventional thinning and timber harvesting operations as well as non-timber tree removal; and 2) short rotation woody crops such as poplar, willow, pine, and eucalyptus. A mixed integer linear programming model was developed to analyze scenarios with woody feedstock blends at variable biomass ash contents and cost targets at the biorefinery. When considering a target cost of 85.51 dollars/dry ton (2016$) at the biorefinery, the maximum accessible biomass from forest residues in 2040 remained constant at 106 million dry tons regardless of ash targets. Including short rotation woody crops as part of the blend increased the total accessible biomass to 153 and 195 million dry tons at ash targets of 1% and 1.75%, respectively. We concluded from our analysis that woody resources could address about 55% of EPA’s (Environmental Protection Agency) target of 16 billion gallons of cellulosic biofuel.

09 BIOMASS FUELS↗
NASA NTRS1986

Radar signature determination: Trends and limitations

Modelling studies, as means for assessing what could be called radar signatures, are a part of two radar remote sensing research programs with which the author is affiliated. First, at the University of New South Wales, assessment of SIR-B data is being undertaken for a number of purposes including its value in arid land geomorphological and geological studies, forest and crop assessment, and mapping. A number of early results have been reported, however modelling aspects are still at an early stage. Secondly, the author recently spent 6 months working on SIR-B invertible forest canopy modelling in the Department of Geography at the University of California, Santa Barbara. Results from this work are outlined.

Richards, J. A.↗
DOE OSTI2026

Life cycle analysis of dedicated energy crops for fuel production in the United States

Dedicated energy crops are promising feedstocks to make biofuels including jet fuels. This study applies life cycle analysis (LCA) to estimate direct well-to-wake (WTW) greenhouse gas (GHG) emissions (g CO 2 e/MJ) for jet fuel derived from five energy crops-biomass sorghum, miscanthus, switchgrass, poplar, and willow-via Fischer-Tropsch-to-Jet (FTJ) and Ethanol-to-Jet (ETJ) pathways. The WTW boundary includes direct emissions from biomass production, fuel production, and fuel combustion. The R&D GREET model is expanded to conduct the LCA, using national average biomass yields and farming inputs from the 2023 Billion-Ton Study. In addition, this study estimates emissions from market-mediated effects, including induced land-use change, induced other crop (non-feedstock) production changes, and induced livestock production changes using global economic and emissions factor models. On a per-dry U.S. ton basis, cultivation and harvest emissions are lowest for willow (51,565 g CO 2 e) and highest for biomass sorghum (104,488 g CO 2 e). Per-acre results show similarly high emissions for sorghum and lowest values for poplar and willow. Direct WTW emissions are substantially lower for FTJ (biomass sorghum: 5.5; miscanthus: 10.3; switchgrass: 11.7; poplar: 11.9; and willow: 8.7 g CO 2 e/MJ) than ETJ (33.2; 33.8; 34.8; 36.2; and 31.7 g CO 2 e/MJ, respectively). When market-mediated emissions are included, miscanthus exhibits the lowest total emissions across energy crop pathways. Although results are sensitive to modeling assumptions, they indicate that high-yielding perennial and woody crops, particularly when planted on marginal land, could significantly reduce WTW emissions for bio-jet fuels by combining low direct emissions with soil carbon gains and favorable market-mediated effects.

Billion-Ton Study↗
NASA NTRS2020

Modeling Uncertainty in Large Natural Resource Allocation Problems

The productivity of the world's natural resources is critically dependent on a variety of highly uncertain factors, which obscure individual investors and governments that seek to make long-term, sometimes irreversible investments in their exploration and utilization. These dynamic considerations are poorly represented in disaggregated resource models, as incorporating uncertainty into large-dimensional problems presents a challenging computational task. This study introduces a novel numerical method to solve large-scale dynamic stochastic natural resource allocation problems that cannot be addressed by conventional methods. The method is illustrated with an application focusing on the allocation of global land resource use under stochastic crop yields due to adverse climate impacts and limits on further technological progress. For the same model parameters, the range of land conversion is considerably smaller for the dynamic stochastic model as compared to deterministic scenario analysis. The scenario analysis can thus significantly overstate the magnitude of expected land conversion under uncertain crop yields.

Cai, Yongyang↗
DOE OSTI2024

Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar

Peanut (Arachis hypogaea L.) is a globally important oil and food crop frequently grown in arid, semi-arid, or dryland environments. Improving drought tolerance is a key goal for peanut crop improvement efforts. Here, we present the genome assembly and gene model annotation for “Line8,” a peanut genotype bred from drought-tolerant cultivars. Our assembly and annotation are the most contiguous and complete peanut genome resources currently available. The high contiguity of the Line8 assembly allowed us to explore structural variation both between peanut genotypes and subgenomes. We detect several large inversions between Line8 and other peanut genome assemblies, and there is a trend for the inversions between more genetically diverged genotypes to have higher gene content. We also relate patterns of subgenome exchange to structural variation between Line8 homeologous chromosomes. Unexpectedly, we discover that Line8 harbors an introgression from A.cardenasii, a diploid peanut relative and important donor of disease resistance alleles to peanut breeding populations. The fully resolved sequences of both haplotypes in this introgression provide the first in situ characterization of A.cardenasii candidate alleles that can be leveraged for future targeted improvement efforts. The completeness of our genome will support peanut biotechnology and broader research into the evolution of hybridization and polyploidy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

A Chromosome-Scale Genome Assembly of the Flax Rust Fungus Reveals the Two Unusually Large Effector Proteins, AvrM3 and AvrN

Rust fungi comprise thousands of species, many of which cause disease on important crop plants. The flax rust fungus Melampsora lini has been a model species for the genetic dissection of plant immunity since the 1940s; however, the highly fragmented and incomplete reference genome has so far hindered progress in effector gene discovery. Here, we generated a fully phased, chromosome-scale assembly of the two nuclear genomes of M. lini strain CH5, resolving an additional 320 Mbp of the sequence. The 482-Mbp dikaryotic genome is at least 79% repetitive, with a large proportion (approximately 40%) of the genome comprising young, highly similar transposable elements. The assembly resolves the known effector gene loci, some of which carry complex duplications that were collapsed in the previous assembly. Using a genetic map followed by manual correction of gene models, we identified the AvrM3 and AvrN genes, which encode unusually large fungal effector proteins and trigger defense responses when co-expressed with the corresponding resistance genes. We located the genes linked to the tetrapolar mating system on chromosomes 4 and 9, but in contrast to the cereal rusts that have one pheromone receptor gene per haplotype, in flax rust, three pheromone receptor genes were found, with two of them closely linked on one haplotype. Taken together, we show that a high-quality assembly is crucial for resolving complex gene loci, and given the increasing number of fungal effectors of large size, the commonly applied criterion for effector candidates of being small proteins needs to be reconsidered.

Melampsora↗
DOE OSTI2020

Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing in Setaria viridis

Previously, Setaria viridis has been developed as a model plant to better understand the C4 photosynthetic pathway in major crops. With the increasing availability of genomic resources for S. viridis research, highly efficient genome editing technologies are needed to create genetic variation resources for functional genomics. In this paper, we developed a protoplast assay to rapidly optimize the multiplexed CRISPR/Cas9 system in S. viridis. Targeted mutagenesis efficiency was further improved by an average of 1.4-fold with the exonuclease, Trex2. Distinctive mutation profiles were found in the Cas9_Trex2 samples with 94% of deletions larger than 10bp, and less than 1% of mutations being insertions. Further analyses indicated that 52.2% of deletions induced by Cas9_Trex2, as opposed to 3.5% by Cas9 alone, were repaired through microhomology-mediated end joining (MMEJ) rather than the canonical NHEJ DNA repair pathway. Combined with the robust agrobacterium-mediated transformation method with more than 90% efficiency, the multiplex CRISPR/Cas9_Trex2 system was demonstrated to induce targeted mutations in two tightly linked genes, svDrm1a and svDrm1b, at the frequency ranging from 73% to 100% in T0 plants. These mutations were transmitted to at least 60% of the transgene-free T1 plants with 33% of them containing bi-allelic or homozygous mutations in both genes. This highly efficient multiplex CRISPR/Cas9_Trex2 system makes it possible to create a large mutant resource for S. viridis in a rapid and high throughput manner, and has the potential to be widely applicable in achieving more predictable MMEJ-mediated mutations in many plant species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Yield and Survival of 19 Cultivars of Willow (Salix spp.) Biomass Crops over Eight Rotations

This study reveals patterns of yield and survival of short-rotation coppice (SRC) willow cultivars over eight rotations (1993–2019). Cultivars fell into four broad categories: commercial, released, stable, and decline. SV1, the singular cultivar that advanced to commercial deployments, had first-rotation yields of 8.9 Mg ha−1 a−1, peaking at 15.2 Mg ha−1 a−1 by the fourth. Mean yields from rotations 2–8 were still 36% above first-rotation yields, confirming the commercial potential for this cultivar over 26 years. The released group (four cultivars) had stable yields over six rotations (approximately 3 to 7 Mg ha−1 a−1), rising to match commercial yields (10 Mg ha−1 a−1) between the sixth and eighth rotation. Most of the cultivars were in the stable group that had relatively consistent yields over time. First-rotation yields in this group were approximately 5 Mg ha−1 a−1, and average yield increased by 23% for rotations 2–8. The two cultivars in the decline group were impacted by disease and browsing that lowered survival and growth. These findings are crucial for understanding willow systems’ potential over their full lifespan as a bioenergy crop, which is a crucial input into yield, economic, and environmental models.

Santucci, Shane↗
DOE OSTI2021

Variation in Gene Expression between Two Sorghum bicolor Lines Differing in Innate Immunity Response

Microbe associated molecular pattern (MAMPs) triggered immunity (MTI) is a key component of the plant innate immunity response to microbial recognition. However, most of our current knowledge of MTI comes from model plants (i.e., Arabidopsis thaliana) with comparatively less work done using crop plants. In this work, we studied the MAMP triggered oxidative burst (ROS) and the transcriptional response in two Sorghum bicolor genotypes, BTx623 and SC155-14E. SC155-14E is a line that shows high anthracnose resistance and the line BTx623 is susceptible to anthracnose. Our results revealed a clear variation in gene expression and ROS in response to either flagellin (flg22) or chitin elicitation between the two lines. While the transcriptional response to each MAMP and in each line was unique there was a considerable degree of overlap, and we were able to define a core set of genes associated with the sorghum MAMP transcriptional response. The GO term and KEGG pathway enrichment analysis discovered more immunity and pathogen resistance related DEGs in MAMP treated SC155-14E samples than in BTx623 with the same treatment. The results provide a baseline for future studies to investigate innate immunity pathways in sorghum, including efforts to enhance disease resistance.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1983

Frost Forecasting for Fruitgrowers

Progress in forecasting from satellite data reviewed. University study found data from satellites displayed in color and used to predict frost are valuable aid to agriculture. Study evaluated scheme to use Earth-temperature data from Geostationary Operational Environmental Satellite in computer model that determines when and where freezing temperatures endanger developing fruit crops, such as apples, peaches and cherries in spring and citrus crops in winter.

Martsolf, J. D.↗
NASA NTRS2002

Effect of hydraulic retention time on inorganic nutrient recovery and biodegradable organics removal in a biofilm reactor treating plant biomass leachate

A fixed-film (biofilm) reactor was designed and its performance was determined at various retention times. The goal was to find the optimal retention time for recycling plant nutrients in an advanced life support system, to minimize the size, mass, and volume (hold-up) of a production model. The prototype reactor was tested with aqueous leachate from wheat crop residue at 24, 12, 6, and 3 h hydraulic retention times (HRTs). Biochemical oxygen demand (BOD), nitrates and other plant nutrients, carbohydrates, total phenolics, and microbial counts were monitored to characterize reactor performance. BOD removal decreased significantly from 92% at the 24 h HRT to 73% at 3 h. Removal of phenolics was 62% at the 24 h retention time, but 37% at 3 h. Dissolved oxygen concentrations, nitric acid consumption, and calcium and magnesium removals were also affected by HRT. Carbohydrate removals, carbon dioxide (CO2) productions, denitrification, potassium concentrations, and microbial counts were not affected by different retention times. A 6 h HRT will be used in future studies to determine the suitability of the bioreactor effluent for hydroponic plant production.

NASA Center KSC↗
NASA NTRS2015

Integrated Assessments of the Impact of Climate Change on Agriculture: An Overview of AgMIP Regional Research in South Asia

South Asia encompasses a wide and highly varied geographic region, and includes climate zones ranging from the mountainous Himalayan territory to the tropical lowland and coastal zones along alluvial floodplains. The region's climate is dominated by a monsoonal circulation that heralds the arrival of seasonal rainfall, upon which much of the regional agriculture relies. The spatial and temporal distribution of this rainfall is, however, not uniform over the region. Northern South Asia, central India, and the west coast receive much of their rainfall during the southwest monsoon season, between June and September. These rains partly result from the moisture transport accompanying the monsoonal winds, which move in the southwesterly direction from the equatorial Indian Ocean. Regions further south, such as south/southeast India and Sri Lanka, may receive rains from both the southwest monsoon, and also during the northeast monsoon season between October and December (with northeasterly monsoon wind flow and moisture flux), which results in a bi- or multi-modal rainfall distribution. In addition, rainfall across South Asia displays a large amount of intraseasonal and interannual variability. Interannual variability is influenced by many drivers, both natural (e.g., El Ni-Southern Oscillation; ENSO) and man-made (e.g., rising temperatures due to increasing greenhouse gas concentrations), and it is challenging to obtaining accurate time-series of annual rainfall, even amongst various observed data products, which display inconsistencies amongst themselves. These climatic and rainfall variations can further complicate South Asia's agricultural and water management. Agriculture employs at least 65 of the workforce in most South Asian countries, and nearly 80 of South Asia's poor inhabit rural areas. Understanding the response of current agricultural production to climate variability and future climate change is of utmost importance in securing food and livelihoods for South Asia's growing population. In order to assess the future of food and livelihood security across South Asia, the Agricultural Model Intercomparison and Improvement Project (AgMIP) has undertaken integrated climate-crop-economic assessments of the impact of climate change on food security and poverty in South Asia, encompassing Bangladesh, India, Nepal, Pakistan, and Sri Lanka. AgMIP has funded, on a competitive basis, four South Asian regional research teams (RRTs) and one South Asian coordination team (CT) to undertake climate-crop-economic integrated assessments of food security for many districts in each of these countries, with the goal of characterizing the state of food security and poverty across the region, and projecting how these are subject to change under future climate change conditions.

mountains↗
NASA NTRS2016

Detection of Chlorophyll and Leaf Area Index Dynamics from Sub-weekly Hyperspectral Imagery

Temporally rich hyperspectral time-series can provide unique time critical information on within-field variations in vegetation health and distribution needed by farmers to effectively optimize crop production. In this study, a dense time series of images were acquired from the Earth Observing-1 (EO-1) Hyperion sensor over an intensive farming area in the center of Saudi Arabia. After correction for atmospheric effects, optimal links between carefully selected explanatory hyperspectral vegetation indices and target vegetation characteristics were established using a machine learning approach. A dataset of in-situ measured leaf chlorophyll (Chll) and leaf area index (LAI), collected during five intensive field campaigns over a variety of crop types, were used to train the rule-based predictive models. The ability of the narrow-band hyperspectral reflectance information to robustly assess and discriminate dynamics in foliar biochemistry and biomass through empirical relationships were investigated. This also involved evaluations of the generalization and reproducibility of the predictions beyond the conditions of the training dataset. The very high temporal resolution of the satellite retrievals constituted a specifically intriguing feature that facilitated detection of total canopy Chl and LAI dynamics down to sub-weekly intervals. The study advocates the benefits associated with the availability of optimum spectral and temporal resolution spaceborne observations for agricultural management purposes.

Houborg, Rasmus↗
DOE OSTI2023

Analysis of Vertical Bifacial Photovoltaic Array Performance

Agrivoltaics is a developing technology where solar panels are installed within farm fields to get a dual-use out of the same plot of land. There is still much engineering work to do to maximize the electrical output of these arrays without sacrificing too much space or impeding the growth of crops. Vertical bifacial modules have potential for this purpose, and our model examines how much power can be generated with different configurations.

14 SOLAR ENERGY↗
NASA NTRS2014

Global and Time-Resolved Monitoring of Crop Photosynthesis with Chlorophyll Fluorescence

Photosynthesis is the process by which plants harvest sunlight to produce sugars from carbon dioxide and water. It is the primary source of energy for all life on Earth; hence it is important to understand how this process responds to climate change and human impact. However, model-based estimates of gross primary production (GPP, output from photosynthesis) are highly uncertain, in particular over heavily managed agricultural areas. Recent advances in spectroscopy enable the space-based monitoring of sun-induced chlorophyll fluorescence (SIF) from terrestrial plants. Here we demonstrate that spaceborne SIF retrievals provide a direct measure of the GPP of cropland and grassland ecosystems. Such a strong link with crop photosynthesis is not evident for traditional remotely sensed vegetation indices, nor for more complex carbon cycle models. We use SIF observations to provide a global perspective on agricultural productivity. Our SIF-based crop GPP estimates are 50-75% higher than results from state-of-the-art carbon cycle models over, for example, the US Corn Belt and the Indo-Gangetic Plain, implying that current models severely underestimate the role of management. Our results indicate that SIF data can help us improve our global models for more accurate projections of agricultural productivity and climate impact on crop yields. Extension of our approach to other ecosystems, along with increased observational capabilities for SIF in the near future, holds the prospect of reducing uncertainties in the modeling of the current and future carbon cycle.

fluorescence↗
NASA NTRS1999

Growing wheat in Biosphere 2 under elevated CO2: observations and modeling

Spring wheat (Triticum aestivum L., cv. Yecora Rojo) was grown in the intensive agricultural biome (IAB) of Biosphere 2 during the l995-l996 winter/spring season. Environmental conditions were characterized by a day/night temperature regime of 27/17 degrees C, relative humidity (RH) levels around 45%, mean atmospheric CO2 concentration of 450 ppmv, and natural light conditions with mean intensities about half of outside levels. Weekly samples of above-ground plant matter were collected throughout the growing season and phenological events recorded. A computer model, CERES-Wheat, previously tested under both field and controlled conditions, was used to simulate the observed crop growth and to help in data analysis. We found that CERES-Wheat simulated the data collected at Biosphere 2 to within 10% of observed, thus suggesting that wheat growth inside the IAB was comparable to that documented in other environments. The model predicts phenological stages and final dry matter (DM) production within l0% of the observed data. Measured DM production rates, normalized for light absorbed by the crop. suggested photosynthetic efficiencies intermediate between those observed under optimal field conditions and those recorded in NASA-Controlled Ecological Life-Support Systems (CELSS). We suggest that such a difference can be explained primarily in terms of low light levels inside the IAB, with additional effects due to elevated CO2 concentrations and diffuse light fractions.

Non-NASA Center↗
NASA NTRS1982

A statistical model for radar images of agricultural scenes

The presently derived and validated statistical model for radar images containing many different homogeneous fields predicts the probability density functions of radar images of entire agricultural scenes, thereby allowing histograms of large scenes composed of a variety of crops to be described. Seasat-A SAR images of agricultural scenes are accurately predicted by the model on the basis of three assumptions: each field has the same SNR, all target classes cover approximately the same area, and the true reflectivity characterizing each individual target class is a uniformly distributed random variable. The model is expected to be useful in the design of data processing algorithms and for scene analysis using radar images.

Frost, V. S.↗