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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Capturing in-field root system dynamics with RootTracker

Abstract Optimizing root system architecture offers a promising approach to developing stress tolerant cultivars in the face of climate change, as root systems are critical for water and nutrient uptake as well as mechanical stability. However, breeding for optimal root system architecture has been hindered by the difficulty in measuring root growth in the field. Here, we describe the RootTracker, a technology that employs impedance touch sensors to monitor in-field root growth over time. Configured in a cylindrical, window shutter-like fashion around a planted seed, 264 electrodes are individually charged multiple times over the course of an experiment. Signature changes in the measured capacitance and resistance readings indicate when a root has touched or grown close to an electrode. Using the RootTracker, we have measured root system dynamics of commercial maize (Zea mays) hybrids growing in both typical Midwest field conditions and under different irrigation regimes. We observed rapid responses of root growth to water deficits and found evidence for a “priming response” in which an early water deficit causes more and deeper roots to grow at later time periods. Genotypic variation among hybrid maize lines in their root growth in response to drought indicated a potential to breed for root systems adapted for different environments. Thus, the RootTracker is able to capture changes in root growth over time in response to environmental perturbations.

Aguilar, Jeffrey J.↗
DOE OSTI2024

A maize semi-dwarf mutant reveals a GRAS transcription factor involved in brassinosteroid signaling

Brassinosteroids (BR) and gibberellins (GA) regulate plant height and leaf angle in maize (Zea mays). Mutants with defects in BR or GA biosynthesis or signaling identify components of these pathways and enhance our knowledge about plant growth and development. In this study, we characterized three recessive mutant alleles of GRAS transcription factor 42 (gras42) in maize, a GRAS transcription factor gene orthologous to the DWARF AND LOW TILLERING (DLT) gene of rice (Oryza sativa). These maize mutants exhibited semi-dwarf stature, shorter and wider leaves, and more upright leaf angle. Transcriptome analysis revealed a role for GRAS42 as a determinant of BR signaling. Analysis of the expression consequences from loss of GRAS42 in the gras42-mu1021149 mutant indicated a weak loss of BR signaling in the mutant, consistent with its previously demonstrated role in BR signaling in rice. Loss of BR signaling was also evident by the enhancement of weak BR biosynthetic mutant alleles in double mutants of nana plant1-1 and gras42-mu1021149. The gras42-mu1021149 mutant had little effect on GA-regulated gene expression, suggesting that GRAS42 is not a regulator of core GA signaling genes in maize. Single-cell expression data identified gras42 expressed among cells in the G2/M phase of the cell cycle consistent with its previously demonstrated role in cell cycle gene expression in Arabidopsis (Arabidopsis thaliana). Cis-acting natural variation controlling GRAS42 transcript accumulation was identified by expression genome-wide association study (eGWAS) in maize. Our results demonstrate a conserved role for GRAS42/SCARECROW-LIKE 28 (SCL28)/DLT in BR signaling, clarify the role of this gene in GA signaling, and suggest mechanisms of tillering and leaf angle control by BR.

54 ENVIRONMENTAL SCIENCES↗
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 OSTI2025

Stomata in-sight: Integrating live confocal microscopy with leaf gas exchange and environmental control

Stomatal anatomy (aperture area, length, and width) influences leaf-level physiology traits including conductance to water vapor. Stomatal anatomy can be visualized in situ by microscopy, but the difficulty of regulating the atmospheric environment of a microscope stage means that the conditions under which imaging is done are rarely physiologically relevant. Alternatively, leaf gas exchange instruments that measure gas fluxes reflect stomatal anatomical characteristics in aggregate, but the relative strengths of anatomical traits to control water use (e.g. size vs density) cannot be firmly established. To reconcile the microscopic stomatal characteristics with leaf-level gas exchange, we describe a tool that combines laser scanning confocal microscopy, gas exchange instruments, and machine-learning image analysis to simultaneously observe anatomical characteristics of many (>40) stomata alongside leaf-level traits like photosynthesis, transpiration, and stomatal conductance. We demonstrate how the tool has the resolution capable of quantifying aperture sizes and variability in maize (Zea mays) leaves under 5 steady-state light/pCO 2 treatments while tightly controlling other environmental variables like relative humidity and temperature. A model used to calculate stomatal conductance from measured apertures and stomatal density accurately matched stomatal conductance measured by gas exchange. This technical advancement will provide insight on how stomatal anatomy and function trade off to influence stomatal conductance and leaf-level water use efficiency.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Quantitative Resistance Loci to Southern Rust Mapped in a Temperate Maize Diversity Panel

Southern rust is a severe foliar disease of maize (Zea mays) resulting from infection with the obligate biotrophic fungus Puccinia polysora. This disease reduces photosynthetic productivity, which in turn reduces yields, with the greatest yield losses (up to 50%) associated with earlier onset infections. P. polysora urediniospores overwinter only in tropical and subtropical regions but cause outbreaks when environmental conditions favor initial infection. Increased temperatures and humidity during the growing season combined with an increased frequency of moderate winters are likely to increase the frequency of severe southern rust outbreaks in the U.S. Corn Belt. In summer 2020, a severe outbreak of southern rust was observed in eastern Nebraska, United States. We scored a replicated maize association panel planted in Lincoln, NE for disease severity and found that disease incidence and severity showed significant variation among maize genotypes. Genome-wide association studies identified four loci associated with significant quantitative variation in disease severity. These loci were associated with candidate genes with plausible links to quantitative disease resistance. A transcriptome-wide association study identified additional genes associated with disease severity. Together, these results indicate that substantial diversity in resistance to southern rust exists among current temperate-adapted maize germplasm, including several candidate loci that may explain the observed variation in resistance to southern rust. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Plant Sciences↗
DOE OSTI2021

A new open‐path eddy covariance method for nitrous oxide and other trace gases that minimizes temperature corrections

Abstract Low‐power, open‐path gas sensors enable eddy covariance (EC) flux measurements in remote areas without line power. However, open‐path flux measurements are sensitive to fluctuations in air temperature, pressure, and humidity. Laser‐based, open‐path sensors with the needed sensitivity for trace gases like methane (CH 4 ) and nitrous oxide (N 2 O) are impacted by additional spectroscopic effects. Corrections for these effects, especially those related to temperature fluctuations, often exceed the flux of gases, leading to large uncertainties in the associated fluxes. For example, the density and spectroscopic corrections arising from temperature fluctuations can be one or two orders of magnitude greater than background N 2 O fluxes. Consequently, measuring background fluxes with laser‐based, open‐path sensors is extremely challenging, particularly for N 2 O and gases with similar high‐precision requirements. We demonstrate a new laser‐based, open‐path N 2 O sensor and a general approach applicable to other gases that minimizes temperature‐related corrections for EC flux measurements. The method identifies absorption lines with spectroscopic effects in the opposite direction of density effects from temperature and, thus, density and spectroscopic effects nearly cancel one another. The new open‐path N 2 O sensor was tested at a corn ( Zea mays L.) field in Southwestern Michigan, United States. The sensor had an optimal precision of 0.1 ppbv at 10 Hz and power consumption of 50 W. Field trials showed that temperature‐related corrections were 6% of density corrections, reducing EC random errors by 20‐fold compared to previously examined lines. Measured open‐path N 2 O EC fluxes showed excellent agreement with those made with static chambers ( m = 1.0 ± 0.3; r 2 = .96). More generally, we identified absorption lines for CO 2 and CH 4 flux measurements that can reduce the temperature‐related corrections by 10–100 times compared to existing open‐path sensors. The proposed method provides a new direction for future open‐path sensors, facilitating the expansion of accurate EC flux measurements.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Corn stover harvest reduces soil CO 2 fluxes but increases overall C losses

Abstract Harvesting corn ( Zea mays L.) stover for use as bioenergy feedstock may provide short‐term economic benefits and perhaps improve grain yield in continuous corn systems, but excessive stover removal may lead to long‐term depletion of soil C stocks. To better quantify the impacts of stover harvest on the soil C balance, we investigated CO 2 fluxes under three harvest treatments (none, moderate, and high) in three continuous corn systems: (a) no tillage and no biochar applications, (b) chisel plowing with biochar amendments, and (c) chisel plowing without biochar amendments were quantified. We sampled static chambers 14, 13, and 15 times in 2010, 2011, and 2012, respectively, and the measurements were used to calibrate the Agricultural Production Systems sIMulator model. Although CO 2 ‐C emissions did not differ among the three systems, both moderate (approximately 30%) and high (approximately 60%) stover removal rates reduced simulated CO 2 ‐C emissions by nearly 10% and more than 22%, respectively. Despite these reductions in CO 2 flux, the sum of CO 2 ‐C and stover C exceeded CO 2 ‐C losses in those plots without stover removal. This finding suggested soil C depletion was occurring for the soil and crop management practices used, even though depletion was not evident after 3 years. Application of biochar increased soil C levels, suggesting it may be able to offset some C losses. We conclude that for sustainable, highly productive agroecosystems that include stover harvest, all agronomic practices must be optimized to minimize C losses and maintain soil quality.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Long‐term yields in annual and perennial bioenergy crops in the Midwestern United States

Abstract Many yield predictions in perennial bioenergy species have been made based on data collected during the establishment phase of growth or a limited number of long‐term studies. Few studies compare multiple perennial crops with the dominant agricultural vegetation of the landscape over long time periods. Here, we present the results of 11 years of perennial crop management on fertile agricultural soils in central Illinois, compared with conventional row crop maize/soybean ( Zea mays L., Glycine max L.) production. We examined the long‐term productivity and drought susceptibility of Miscanthus x giganteus Greef et. Deu. ex. Hodkinson et Renvoize (miscanthus), Panicum virgatum L., Cave‐in‐Rock cultivar (switchgrass), and a native prairie mix, in contrast to annual maize/soybean agriculture. Long‐term yields for miscanthus and switchgrass failed to reach initial predictions made during the establishment phase; however, in miscanthus, the 11 th year of production shows little progressive yield loss with age, exceeding the modeled limit for the onset of age‐related decline. Harvest timing and differences in yields from hand and machine harvests in perennial crops likely contribute to overestimates of potential yields. Application of fertilizer to mature miscanthus resulted in significant increases in yield after a severe drought, though modeled effects of management and drought in miscanthus point to a more complex mechanism for yield response.

09 BIOMASS FUELS↗
DOE OSTI2022

Agroecosystem model simulations reveal spatial variability in relative productivity in biomass sorghum and maize in Iowa, USA

Biomass sorghum (Sorghum bicolor L. Moench) is an annual C 4 grass that has emerged as a candidate bioenergy crop but has not been widely grown in the United States. Corn (Zea mays L.), another annual C 4 grass, has been produced on a large scale in the United States for biofuels. Iowa leads the nation in both corn and ethanol production. The high productivity of corn in Iowa creates the research question: could biomass sorghum be as or more productive than corn in the state in terms of bioenergy? Efforts to use crop models to fill the gaps left by field experimentation on biomass sorghum have also been limited thus far. To address our research question, we collected biophysical data on biomass sorghum grown in Iowa for two growing seasons, used them to develop a biomass sorghum module in an agroecosystem model (Agro-IBIS), and predict the potential performance of biomass sorghum across Iowa compared to maize. Despite dry conditions in 2019 and 2020, average biomass sorghum yields were 17.20 Mg ha –1 . By comparison, average corn aboveground biomass was higher in 2020 (22.02 Mg ha –1 ). Soil cores indicated average belowground biomass of 1.46 Mg ha –1 , with roots concentrated near the surface (73% of biomass above 50 cm in a 1 m core). When biomass sorghum model parameters were calibrated with measured values, model output was in close agreement with measured biomass (slope = 0.932, R 2 = 0.91) and evapotranspiration (slope = 0.757, R 2 = 0.64). Subsequent regional simulations revealed a notable latitudinal gradient in biomass sorghum yield, with a strong linear relationship between yield and seasonal growing degree-days (R 2 = 0.89). When these yields were compared to simulated corn aboveground biomass yields, only 3.4% of the state had biomass sorghum yields that were significantly higher than corn. This number was reduced to 0.3% when comparing the crops in terms of energy ethanol yield. Thus, we conclude biomass sorghum must be improved to be competitive with corn as an annual biofuel crop in Iowa. This study provides a baseline against which to compare advancements in sorghum breeding for biomass and stress tolerance in Iowa.

Agro-IBIS↗
DOE OSTI2022

Soil phosphorus drawdown by perennial bioenergy cropping systems in the Midwestern US

Abstract Without fertilization, harvest of perennial bioenergy cropping systems diminishes soil nutrient stocks, yet the time course of nutrient drawdown has not often been investigated. We analyzed phosphorus (P) inputs (fertilization and atmospheric deposition) and outputs (harvest and leaching losses) over 7 years in three representative biomass crops—switchgrass ( Panicum virgatum L.), miscanthus ( Miscanthus × giganteus ) and hybrid poplar trees ( Populus nigra × P. maximowiczii )—as well as in no‐till corn (maize; Zea mays L.) for comparison, all planted on former cropland in SW Michigan, USA. Only corn received P fertilizer. Corn (grain and stover), switchgrass, and miscanthus were harvested annually, while poplar was harvested after 6 years. Soil test P (STP; Bray‐1 method) was measured in the upper 25 cm of soil annually. Harvest P removal was calculated from tissue P concentration and harvest yield (or annual woody biomass accrual in poplar). Leaching was estimated as total dissolved P concentration in soil solutions sampled beneath the rooting depth (1.25 m), combined with hydrological modeling. Fertilization and harvest were by far the dominant P budget terms for corn, and harvest P removal dominated the P budgets in switchgrass, miscanthus, and poplar, while atmospheric deposition and leaching losses were comparatively insignificant. Because of significant P removal by harvest, the P balances of switchgrass, miscanthus, and poplar were negative and corresponded with decreasing STP, whereas P fertilization compensated for the harvest P removal in corn, resulting in a positive P balance. Results indicate that perennial crop harvest without P fertilization removed legacy P from soils, and continued harvest will soon draw P down to limiting levels, even in soils once heavily P‐fertilized. Widespread cultivation of bioenergy crops may, therefore, alter P balances in agricultural landscapes, eventually requiring P fertilization, which could be supplied by P recovery from harvested biomass.

09 BIOMASS FUELS↗
DOE OSTI2026

Corn and Switchgrass Derived Sustainable Aviation Fuel Carbon Intensity

The production and use of sustainable aviation fuel (SAF) could lower aviation's carbon footprint. Feedstock agricultural management can optimize—or potentially determine—SAF sustainability and profitability, but long-term SAF feedstock comparisons are limited. Life cycle assessments (LCA) are commonly used to estimate the carbon intensity of producing SAF from emerging feedstocks due to the limited availability of long-term, primary field data. We quantified the agricultural phase and well-to-wake (WTWa) carbon intensities of producing SAF from no-till, continuous corn (Zea mays L.) under 120 kg N ha−1 year−1 (120 N corn) and switchgrass (Panicum virgatum L.) under 60 or 120 kg N ha−1 year−1 (60 N and 120 N SWG, respectively) via LCAs based on measured data from a long-term (1998-present) field experiment on marginally productive cropland located in Eastern NE, USA. Measured data included crop productivity, long-term changes in soil organic carbon (SOC) stocks (0–150 cm), annual soil N2O emissions, and field management practices. Both 120 N corn (2078 L ha−1) and 120 N SWG (1752 L ha−1) produced more SAF than 60 N SWG (1229 L ha−1) (p < 0.0001). However, making SAF from corn had greater life cycle GHG emissions (i.e., WTWa carbon intensity) than making SAF from 120 N and 60 N SWG (61.5 > −14.5 and −27.5 g CO2e MJ−1 SAF, respectively; p = 0.0007), primarily due to SOC accrual during crop production. Here, we demonstrate that agricultural management (e.g., crop type, fertilizer use) can determine the sustainably and productivity of producing SAF by using long-term, measured field data in LCAs.

carbon intensity↗
DOE OSTI2022

Comparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass ( Panicum virgatum )

Summary Switchgrass ( Panicum virgatum ) is a bioenergy model crop valued for its energy efficiency and drought tolerance. The related monocot species rice ( Oryza sativa ) and maize ( Zea mays ) deploy species‐specific, specialized metabolites as core stress defenses. By contrast, specialized chemical defenses in switchgrass are largely unknown. To investigate specialized metabolic drought responses in switchgrass, we integrated tissue‐specific transcriptome and metabolite analyses of the genotypes Alamo and Cave‐in‐Rock that feature different drought tolerance. The more drought‐susceptible Cave‐in‐Rock featured an earlier onset of transcriptomic changes and significantly more differentially expressed genes in response to drought compared to Alamo. Specialized pathways showed moderate differential expression compared to pronounced transcriptomic alterations in carbohydrate and amino acid metabolism. However, diterpenoid‐biosynthetic genes showed drought‐inducible expression in Alamo roots, contrasting largely unaltered triterpenoid and phenylpropanoid pathways. Metabolomic analyses identified common and genotype‐specific flavonoids and terpenoids. Consistent with transcriptomic alterations, several root diterpenoids showed significant drought‐induced accumulation, whereas triterpenoid abundance remained predominantly unchanged. Structural analysis verified select drought‐responsive diterpenoids as oxygenated furanoditerpenoids. Drought‐dependent transcriptome and metabolite profiles provide the foundation to understand the molecular mechanisms underlying switchgrass drought responses. Accumulation of specialized root diterpenoids and corresponding pathway transcripts supports a role in drought stress tolerance.

transcriptomics↗
DOE OSTI2024

Data‐driven identification of environmental variables influencing phenotypic plasticity to facilitate breeding for future climates

Summary Phenotypic plasticity describes a genotype's ability to produce different phenotypes in response to different environments. Breeding crops that exhibit appropriate levels of plasticity for future climates will be crucial to meeting global demand, but knowledge of the critical environmental factors is limited to a handful of well‐studied major crops. Using 727 maize ( Zea mays L.) hybrids phenotyped for grain yield in 45 environments, we investigated the ability of a genetic algorithm and two other methods to identify environmental determinants of grain yield from a large set of candidate environmental variables constructed using minimal assumptions. The genetic algorithm identified pre‐ and postanthesis maximum temperature, mid‐season solar radiation, and whole season net evapotranspiration as the four most important variables from a candidate set of 9150. Importantly, these four variables are supported by previous literature. After calculating reaction norms for each environmental variable, candidate genes were identified and gene annotations investigated to demonstrate how this method can generate insights into phenotypic plasticity. The genetic algorithm successfully identified known environmental determinants of hybrid maize grain yield. This demonstrates that the methodology could be applied to other less well‐studied phenotypes and crops to improve understanding of phenotypic plasticity and facilitate breeding crops for future climates.

Kusmec, Aaron↗
DOE OSTI2025

Brachypodium SPEECHLESS2 Promoter Drives Expression of a Synthetic EPF to Reduce Stomatal Density in Sugarcane Without Pleiotropic Effects

Stomata are microscopic pores that regulate the exchange of CO 2 and water vapour, making them a major target for engineering plants with improved intrinsic water use efficiency (iWUE). Proof-of-concept studies have demonstrated the potential to increase iWUE by reducing stomatal density (SD) and stomatal conductance (g sw ) by ubiquitously expressing EPIDERMAL PATTERNING FACTOR (EPF) family genes. However, unwanted effects on leaf, stem and reproductive traits are often observed when EPFs are misexpressed in this fashion. We sought to test if these effects result from pleiotropy and to identify a targeted promoter that can circumvent the side effects while retaining the desired reduction in SD. A previously reported synthetic EPF (EPF syn ) was expressed in sugarcane ( Saccharum spp.) using two putatively tissue-specific promoters from Brachypodium distachyon (BdCESA7p and BdSPCH2p) and a ubiquitous control from Zea mays (ZmUBI4p). BdSPCH2p control reduced SD to statistically equivalent levels as ZmUBI4p on the abaxial (23%) and adaxial (23%) leaf surfaces. ZmUB4p and BdCESA7p induce expression in four tissue types often associated with pleiotropic effects in EPF-expressing low SD plants. Transgenic plants carrying either the BdCESA7p or ZmUBI4p EPF syn cassettes displayed leaf chlorosis, reduced leaf nitrogen and chlorophyll content, and altered stem architecture. However, transgenic events harboring the BdSPCH2p EPF syn cassette restricted EPF syn expression to the stomatal development zone and leaf nodal tissues and produced transgenic plants without the associated pleiotropic effects. These results represent an important step toward engineering low-SD crops since they show that targeted gene expression can engineer stomatal patterning without impairing agronomically important traits.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Leaf cell wall properties and stomatal density influence oxygen isotope enrichment of leaf water

Measurements of oxygen isotope enrichment of leaf water above source water (Δ 18 O LW ) can improve our understanding of the interaction between leaf anatomy and physiology on leaf water transport. Models have been developed to predict Δ 18 O LW such as the string-of-lakes model, which describes the mixing of leaf water pools, and the Péclet effect model, which incorporates transpiration rate and the mixing length between unenriched xylem and enriched mesophyll water in the mesophyll (L m ) or veins (L v ). Here, in this work, we compare measurements and models of Δ 18 O LW on two cell wall composition mutants grown under two light intensities and relative humidities to evaluate cell wall properties on leaf water transport. In maize (Zea mays), the compromised ultrastructure of the suberin lamellae in the bundle sheath of the ALIPHATIC SUBERIN FERULOYL TRANSFERASE mutant (Zmasft) reduced barriers to apoplastic water movement, resulting in higher E and, potentially, L v and, consequently, lower Δ 18 O LW . The difference in Δ 18 O LW in cellulose synthase-like F6 (CslF6) mutants and wild-type of rice (Oryza sativa) grown under two light intensities co-varied with stomatal density. These results show that cell wall composition and stomatal density influence Δ 18 O LW and that stable isotopes can facilitate the development of a physiologically and anatomically explicit water transport model.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Characterization of switchgrass ( Panicum virgatum L.) PvKSL1 as a levopimaradiene/abietadiene‐type diterpene synthase

Abstract The diverse class of plant diterpenoid metabolites serves important functions in mediating growth, chemical defence, and ecological adaptation. In major monocot crops, such as maize (Zea mays), rice (Oryza sativa), and barley (Hordeum vulgare), diterpenoids function as core components of biotic and abiotic stress resilience. Switchgrass (Panicum virgatum) is a perennial grass valued as a stress‐resilient biofuel model crop. Previously we identified an unusually large diterpene synthase family that produces both common and species‐specific diterpenoids, several of which accumulate in response to abiotic stress. Here, we report discovery and functional characterization of a previously unrecognized monofunctional class I diterpene synthase (PvKSL1) viain vivoco‐expression assays with different copalyl pyrophosphate (CPP) isomers, structural and mutagenesis studies, as well as genomic and transcriptomic analyses. In particular, PvKSL1 convertsent‐CPP intoent‐abietadiene,ent‐palustradiene,ent‐levopimaradiene, andent‐neoabietadiene via a 13‐hydroxy‐8(14)‐ent‐abietene intermediate. Notably, although featuring a distinctent‐stereochemistry, this product profile is near‐identical to bifunctional (+)‐levopimaradiene/abietadiene synthases occurring in conifer trees. PvKSL1 has three of four active site residues previously shown to control (+)‐levopimaradiene/abietadiene synthase catalytic specificity. However, mutagenesis studies suggest a distinct catalytic mechanism in PvKSL1. Genome localization ofPvKSL1distant from other diterpene synthases, and its phylogenetic distinctiveness from known abietane‐forming diterpene synthases, support an independent evolution of PvKSL1 activity. Albeit at low levels,PvKSL1gene expression predominantly in roots suggests a role of diterpenoid formation in belowground tissue. Together, these findings expand the known chemical and functional space of diterpenoid metabolism in monocot crops.

Plant Sciences↗
DOE OSTI2020

Single‐parent expression drives dynamic gene expression complementation in maize hybrids

SUMMARY Single‐parent expression (SPE) is defined as gene expression in only one of the two parents. SPE can arise from differential expression between parental alleles, termed non‐presence/absence (non‐PAV) SPE, or from the physical absence of a gene in one parent, termed PAV SPE. We used transcriptome data of diverse Zea mays (maize) inbreds and hybrids, including 401 samples from five different tissues, to test for differences between these types of SPE genes. Although commonly observed, SPE is highly genotype and tissue specific. A positive correlation was observed between the genetic distance of the two inbred parents and the number of SPE genes identified. Regulatory analysis showed that PAV SPE and non‐PAV SPE genes are mainly regulated by cis effects, with a small fraction under trans regulation. Polymorphic transposable element insertions in promoter sequences contributed to the high level of cis regulation for PAV SPE and non‐PAV SPE genes. PAV SPE genes were more frequently expressed in hybrids than non‐PAV SPE genes. The expression of parentally silent alleles in hybrids of non‐PAV SPE genes was relatively rare but occurred in most hybrids. Non‐PAV SPE genes with expression of the silent allele in hybrids are more likely to exhibit above high parent expression level than hybrids that do not express the silent allele, leading to non‐additive expression. This study provides a comprehensive understanding of the nature of non‐PAV SPE and PAV SPE genes and their roles in gene expression complementation in maize hybrids.

Li, Zhi↗
DOE OSTI2020

A temporal hierarchy underpins the transcription factor–DNA interactome of the maize UPR

Adverse environmental conditions reduce crop productivity and often increase the load of unfolded or misfolded proteins in the endoplasmic reticulum (ER). This potentially lethal condition, known as ER stress, is buffered by the unfolded protein response (UPR), a set of signaling pathways designed to either recover ER functionality or ignite programmed cell death. Despite the biological significance of the UPR to the life of the organism, the regulatory transcriptional landscape underpinning ER stress management is largely unmapped, especially in crops. To fill this significant knowledge gap, we performed a large–scale systems–level analysis of the protein–DNA interaction (PDI) network in maize (Zea mays). Using 23 promoter fragments of six UPR marker genes in a high–throughput enhanced yeast one–hybrid assay, we identified a highly interconnected network of 262 transcription factors (TFs) associated with significant biological traits and 831 PDIs underlying the UPR. We established a temporal hierarchy of TF binding to gene promoters within the same family as well as across different families of TFs. Cistrome analysis revealed the dynamic activities of a variety of cis–regulatory elements (CREs) in ER stress–responsive gene promoters. By integrating the cistrome results into a TF network analysis, we mapped a subnetwork of TFs associated with a CRE that may contribute to UPR management. Lastly, we validated the role of a predicted network hub gene using the Arabidopsis system. The PDIs, TF networks, and CREs identified in our work are foundational resources for understanding transcription–regulatory mechanisms in the stress responses and crop improvement.

59 BASIC BIOLOGICAL SCIENCES↗