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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Identification of pleiotropic loci mediating structural and non-structural carbohydrate accumulation within the sorghum bioenergy association panel using high-throughput markers

Molecular characterization of diverse germplasm can contribute to breeding programs by increasing genetic gain for sorghum [ Sorghum bicolor (L.) Moench] improvement. Identifying novel marker-trait associations and candidate genes enriches the existing genomic resources and can improve bioenergy-related traits using genomic-assisted breeding. In the current scenario, identifying the genetic loci underlying biomass and carbon partitioning is vital for ongoing efforts to maximize each carbon sink’s yield for bioenergy production. Here, we have processed a high-density genomic marker (22 466 550) data based on whole-genome sequencing (WGS) using a set of 365 accessions from the bioenergy association panel (BAP), which includes ~19.7 million (19 744 726) single nucleotide polymorphism (SNPs) and 2.7 million (~2 721 824) insertion deletions (indels). A set of high-quality filtered SNP (~5.48 million) derived markers facilitated the assessment of population structure, genetic diversity, and genome-wide association studies (GWAS) for various traits related to biomass and its composition using the BAP. The phenotypic traits for GWAS included seed color (SC), plant height (PH), days to harvest (DTH), fresh weight (FW), dry weight (DW), brix content % (BRX), neutral detergent fiber (NDF), acid detergent fiber (ADF), non-fibrous carbohydrate (NFC), and lignin content. Several novel loci and candidate genes were identified for bioenergy-related traits, and some well-characterized genes for plant height ( Dw1 and Dw2 ) and the YELLOW SEED1 locus ( Y1 ) were validated. We further performed a multi-variate adaptive shrinkage analysis to identify pleiotropic QTL, which resulted in several shared marker-trait associations among bioenergy and compositional traits. Significant marker-trait associations with pleiotropic effects can be used to develop molecular markers for trait improvement using a marker-assisted breeding approach. Significant nucleotide diversity and heterozygosity were observed between photoperiod-sensitive and insensitive individuals of the panel. This diverse bioenergy panel with genomic resources will provide an excellent opportunity for further genetic studies, including selecting parental lines for superior hybrid development to improve biomass-related traits in sorghum.

bioenergy association panel↗
DOE OSTI2025

Combining biotechnology with sustainability: feasibility of bioenergy sorghum in generating high-value bioproducts

Biofuels generated through fermentation of plant-derived lignocellulosic biomass are currently not competitive with fossil fuels. Here, a framework is described for the engineering of valuable coproducts to improve the economic feasibility of biofuel production. To accomplish this goal, the desirable traits of the bioenergy crop Sorghum bicolor are harnessed via modern engineering approaches. A robust analysis is provided to highlight the scientific basis, costs, regulatory challenges, and lucrative nature of coproduct development. Sustainable biofuel production could also have far-reaching societal impacts, especially in the context of our rapidly changing global climate. This perspective suggests that the path to profitable biofuel production is attainable and encourages consideration of similar approaches by the biotechnology industry.

09 BIOMASS FUELS↗
DOE OSTI2025

Microbial O 2 consumption as a function of pore structure in soils of sorghum, switchgrass, and prairie vegetation systems

Abstract Microscale O 2 availability in soil, a main factor influencing microbial processing of soil carbon and nitrogen, is a function of O 2 diffusion and microbial O 2 consumption. While O 2 diffusivity is widely studied, it is difficult to quantify the rate of microbial O 2 consumption ( MO ). In this study, we quantified the MO using O 2 microsensor profiling to compare MO in different soils and vegetation systems while manipulating the soil pore structure. Soil samples were collected from three bioenergy vegetation systems, sorghum ( Sorghum bicolor L. Moench), switchgrass ( Panicum virgatum L.), and prairie, at an experimental site in Southeast Michigan, and from switchgrass and prairie systems at two sites in South and North Wisconsin. We prepared soil cores with two contrasting pore structures, that is, large (>30 µm Ø) pore‐dominated soil (LP) and small (<10 µm Ø) pore‐dominated soil (SP), from the same 1‐ to 2‐mm soil size fraction. We quantified MO (nmol O 2 cm −3 s −1 ) using a microprofiler with an oxygen (OX‐100 µm) microsensor (Unisense) pre‐ and post‐38‐day incubation. Across all studied systems, there was a trend for a decrease in SP MO post‐incubation, suggesting a change in microbial metabolism to lower O 2 utilization. However, sizeable microbial O 2 consumption continued in the LP soils, further corroborated by a positive correlation between the C‐CO 2 emission rate and the post‐incubation MO , highlighting that LP provided a better physical microenvironment for the soil microbes.

Chakraborty, Poulamee [Department of Plant Soil an↗
DOE OSTI2024

Computer vision models enable mixed linear modeling to predict arbuscular mycorrhizal fungal colonization using fungal morphology

Abstract The presence of Arbuscular Mycorrhizal Fungi (AMF) in vascular land plant roots is one of the most ancient of symbioses supporting nitrogen and phosphorus exchange for photosynthetically derived carbon. Here we provide a multi-scale modeling approach to predict AMF colonization of a worldwide crop from a Recombinant Inbred Line (RIL) population derived from Sorghum bicolor and S. propinquum . The high-throughput phenotyping methods of fungal structures here rely on a Mask Region-based Convolutional Neural Network (Mask R-CNN) in computer vision for pixel-wise fungal structure segmentations and mixed linear models to explore the relations of AMF colonization, root niche, and fungal structure allocation. Models proposed capture over 95% of the variation in AMF colonization as a function of root niche and relative abundance of fungal structures in each plant. Arbuscule allocation is a significant predictor of AMF colonization among sibling plants. Arbuscules and extraradical hyphae implicated in nutrient exchange predict highest AMF colonization in the top root section. Our work demonstrates that deep learning can be used by the community for the high-throughput phenotyping of AMF in plant roots. Mixed linear modeling provides a framework for testing hypotheses about AMF colonization phenotypes as a function of root niche and fungal structure allocations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Three founding ancestral genomes involved in the origin of sugarcane

Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12 = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum. To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus. The diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered. This evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

MINE: a new way to design genetics experiments for discovery

Abstract The Maximally Informative Next Experiment or MINE is a new experimental design approach for experiments, such as those in omics, in which the number of effects or parameters p greatly exceeds the number of samples n (p > n). Classical experimental design presumes n > p for inference about parameters and its application to p > n can lead to over-fitting. To overcome p > n, MINE is an ensemble method, which makes predictions about future experiments from an existing ensemble of models consistent with available data in order to select the most informative next experiment. Its advantages are in exploration of the data for new relationships with n < p and being able to integrate smaller and more tractable experiments to replace adaptively one large classic experiment as discoveries are made. Thus, using MINE is model-guided and adaptive over time in a large omics study. Here, MINE is illustrated in two distinct multiyear experiments, one involving genetic networks in Neurospora crassa and a second one involving a genome-wide association study in Sorghum bicolor as a comparison to classic experimental design in an agricultural setting.

Biochemistry & Molecular Biology↗
DOE OSTI2021

DCT4 —A New Member of the Dicarboxylate Transporter Family in C 4 Grasses

Malate transport shuttles atmospheric carbon into the Calvin–Benson cycle during NADP-ME C 4 photosynthesis. Previous characterizations of several plant dicarboxylate transporters (DCT) showed that they efficiently exchange malate across membranes. Here, we identify and characterize a previously unknown member of the DCT family, DCT4, in Sorghum bicolor. We show that SbDCT4 exchanges malate across membranes and its expression pattern is consistent with a role in malate transport during C 4 photosynthesis. SbDCT4 is not syntenic to the characterized photosynthetic gene ZmDCT2, and an ortholog is not detectable in the maize reference genome. We found that the expression patterns of DCT family genes in the leaves of Zea mays, and S. bicolor varied by cell type. Our results suggest that subfunctionalization, of members of the DCT family, for the transport of malate into the bundle sheath plastids, occurred during the process of independent recurrent evolution of C 4 photosynthesis in grasses of the PACMAD clade. We also show that this subfunctionalization is lineage independent. Our results challenge the dogma that key C 4 genes must be orthologues of one another among C 4 species, and shed new light on the evolution of C 4 photosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Greater aperture counteracts effects of reduced stomatal density on WUE: a case study on sugarcane and meta-analysis

Stomata regulate CO 2 and water vapor exchange between leaves and the atmosphere. Stomata are a target for engineering to improve crop intrinsic water use efficiency (iWUE). One example is by expressing genes that lower stomatal density (SD) and reduce stomatal conductance (g sw ). However, the quantitative relationship between reduced SD, g sw , and the mechanisms underlying it is poorly understood. We addressed this knowledge gap using low-SD sugarcane (Saccharum spp. hybrid) as a case study alongside a meta-analysis of data from 10 species. Transgenic expression of EPIDERMAL PATTERNING FACTOR 2 from Sorghum bicolor (SbEFP2) in sugarcane reduced SD by 26-38% but did not affect gsw compared to wildtype. Further, no changes occurred in stomatal complex size or proxies for photosynthetic capacity. Measurements of gas exchange at low CO 2 concentrations that promote complete stomatal opening to normalize aperture size between genotypes were combined with modeling of maximum gsw from anatomical data. These data suggest that increased stomatal aperture is the only possible explanation for maintaining gsw when SD is reduced. Meta-analysis across C 3 dicots, C 3 monocots, and C 4 monocots revealed engineered reductions in SD are strongly correlated with lower gsw (r 2 =0.60-0.98), but this response is damped relative to the change in anatomy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes

Abstract Stomata allow CO2 uptake by leaves for photosynthetic assimilation at the cost of water vapor loss to the atmosphere. The opening and closing of stomata in response to fluctuations in light intensity regulate CO2 and water fluxes and are essential for maintaining water-use efficiency (WUE). However, a little is known about the genetic basis for natural variation in stomatal movement, especially in C4 crops. This is partly because the stomatal response to a change in light intensity is difficult to measure at the scale required for association studies. Here, we used high-throughput thermal imaging to bypass the phenotyping bottleneck and assess 10 traits describing stomatal conductance (gs) before, during and after a stepwise decrease in light intensity for a diversity panel of 659 sorghum (Sorghum bicolor) accessions. Results from thermal imaging significantly correlated with photosynthetic gas exchange measurements. gs traits varied substantially across the population and were moderately heritable (h2 up to 0.72). An integrated genome-wide and transcriptome-wide association study identified candidate genes putatively driving variation in stomatal conductance traits. Of the 239 unique candidate genes identified with the greatest confidence, 77 were putative orthologs of Arabidopsis (Arabidopsis thaliana) genes related to functions implicated in WUE, including stomatal opening/closing (24 genes), stomatal/epidermal cell development (35 genes), leaf/vasculature development (12 genes), or chlorophyll metabolism/photosynthesis (8 genes). These findings demonstrate an approach to finding genotype-to-phenotype relationships for a challenging trait as well as candidate genes for further investigation of the genetic basis of WUE in a model C4 grass for bioenergy, food, and forage production.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Identification and characterization of a set of monocot BAHD monolignol transferases

Plant BAHD acyltransferases perform a wide range of enzymatic tasks in primary and secondary metabolism. Acyl-CoA monolignol transferases, which couple a CoA substrate to a monolignol creating an ester linkage, represent a more recent class of such acyltransferases. The resulting conjugates may be used for plant defense but are also deployed as important “monomers” for lignification, in which they are incorporated into the growing lignin polymer chain. p-Coumaroyl-CoA monolignol transferases (PMTs) increase the production of monolignol p-coumarates, and feruloyl-CoA monolignol transferases (FMTs) catalyze the production of monolignol ferulate conjugates. We identified putative FMT and PMT enzymes in sorghum (Sorghum bicolor) and switchgrass (Panicum virgatum) and have compared their activities to those of known monolignol transferases. The putative FMT enzymes produced both monolignol ferulate and monolignol p-coumarate conjugates, whereas the putative PMT enzymes produced monolignol p-coumarate conjugates. Enzyme activity measurements revealed that the putative FMT enzymes are not as efficient as the rice (Oryza sativa) control OsFMT enzyme under the conditions tested, but the SbPMT enzyme is as active as the control OsPMT enzyme. These putative FMTs and PMTs were transformed into Arabidopsis (Arabidopsis thaliana) to test their activities and abilities to biosynthesize monolignol conjugates for lignification in planta. The presence of ferulates and p-coumarates on the lignin of these transformants indicated that the putative FMTs and PMTs act as functional feruloyl-CoA and p-coumaroyl-CoA monolignol transferases within plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A sorghum ascorbate peroxidase with four binding sites has activity against ascorbate and phenylpropanoids

Abstract In planta, H2O2 is produced as a by-product of enzymatic reactions and during defense responses. Ascorbate peroxidase (APX) is a key enzyme involved in scavenging cytotoxic H2O2. Here, we report the crystal structure of cytosolic APX from sorghum (Sorghum bicolor) (Sobic.001G410200). While the overall structure of SbAPX was similar to that of other APXs, SbAPX uniquely displayed four bound ascorbates rather than one. In addition to the ɣ-heme pocket identified in other APXs, ascorbates were bound at the δ-meso and two solvent-exposed pockets. Consistent with the presence of multiple binding sites, our results indicated that the H2O2-dependent oxidation of ascorbate displayed positive cooperativity. Bound ascorbate at two surface sites established an intricate proton network with ascorbate at the ɣ-heme edge and δ-meso sites. Based on crystal structures, steady-state kinetics, and site-directed mutagenesis results, both ascorbate molecules at the ɣ-heme edge and the one at the surface are expected to participate in the oxidation reaction. We provide evidence that the H2O2-dependent oxidation of ascorbate by APX produces a C2-hydrated bicyclic hemiketal form of dehydroascorbic acid at the ɣ-heme edge, indicating two successive electron transfers from a single-bound ascorbate. In addition, the δ-meso site was shared with several organic compounds, including p-coumaric acid and other phenylpropanoids, for the potential radicalization reaction. Site-directed mutagenesis of the critical residue at the ɣ-heme edge (R172A) only partially reduced polymerization activity. Thus, APX removes stress-generated H2O2 with ascorbates, and also uses this same H2O2 to potentially fortify cell walls via oxidative polymerization of phenylpropanoids in response to stress.

Plant Sciences↗
DOE OSTI2026

Development of male-sterile lines of Setaria viridis to accelerate C 4 model plant genetics

Setaria viridis is a diploid C 4 grass in the Poaceae family, notable for its rapid life cycle of 6–8 weeks from sowing to seed—much shorter than the 4–5 months required by crops such as Zea mays and Sorghum bicolor . This fast growth makes S. viridis a valuable model for C 4 crop research. Genetic crosses are essential for studying gene function, but manual crossing is labor-intensive and time-consuming. Here, to address this, we developed a male-sterile line by targeting the S. viridis ortholog of Setaria italica NO POLLEN 1 ( SiNP1 ), which encodes a glucose–methanol–choline oxidoreductase required for pollen exine formation. Using Cas9 and TREX2 -mediated genome editing, we generated SiNP1 knockouts in both the S. viridis ME034V and A10.1 backgrounds that were fully male-sterile. Backcrossing T 0 male-sterile plants to ME034V wild-type followed by selfing yielded a stable BC 1 F 2 line homozygous for a 59 bp deletion in the S. viridis NO POLLEN 1 gene, easily genotyped by PCR and maintained by heterozygous siblings. Using this line, we developed a simple and efficient crossing protocol that eliminates the need for emasculation. This method enables a single person to perform up to 100 crosses per day—compared to 15 using traditional methods—and yields 20–32 F 1 hybrid seeds per panicle with 100% genetic purity. We also quantified pollen flow and outcrossing frequencies under greenhouse conditions to develop optimal bagging strategies and prevent unintended pollination. This resource accelerates genetic research in S. viridis , enhancing its utility as a premier C 4 model for mapping and functional genomics.

C4 research↗
DOE OSTI2022

The recent evolutionary rescue of a staple crop depended on over half a century of global germplasm exchange

Rapid environmental change can lead to population extinction or evolutionary rescue. The global staple crop sorghum (Sorghum bicolor) has recently been threatened by a global outbreak of an aggressive new biotype of sugarcane aphid (SCA; Melanaphis sacchari). We characterized genomic signatures of adaptation in a Haitian breeding population that had rapidly adapted to SCA infestation, conducting evolutionary population genomics analyses on 296 Haitian lines versus 767 global accessions. Genome scans and geographic analyses suggest that SCA adaptation has been conferred by a globally rare East African allele of RMES1, which spread to breeding programs in Africa, Asia, and the Americas. De novo genome sequencing revealed potential causative variants at RMES1. Markers developed from the RMES1 sweep predicted resistance in eight independent commercial and public breeding programs. These findings demonstrate the value of evolutionary genomics to develop adaptive trait technology and highlight the benefits of global germplasm exchange to facilitate evolutionary rescue.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Draft Genome Sequences of 14 Bacterial Isolates from the Rhizosphere of Bioenergy Sorghum

We report the draft genomes of a collection of 15 bacteria, isolated from the rhizosphere soil of bioenergy sorghum (Sorghum bicolor (L.) Moench). These isolates belong to the genera, Acidovorax, Nocardioides, Agrobacterium, Peribacillus, Caulobacter, Cupriavidus, Pseudomonas, Rhizobium, Sphingomonas, Priestia, Dyadobacter, Roseomonas, Ideonella, and Bacillus.

Black, Grace S.↗
DOE OSTI2023

Chapter 24: The Compound Middle Lamella as a Target for Improved Deconstruction of Woody Biomass

The compound middle lamella (CML) of woody angiosperm species, such as poplar (Populus spp.), birch (Betula spp.), and alder (Alnus spp.), and gymnosperm species, such as pine (Pinus spp.), Douglas fir (Pseudotsuga menziesii), and spruce (Picea spp.), is an amalgam of lignin, hemicellulosic xylans, and pectic polysaccharides that is the major site of cell-cell adhesion of fibre cells and tracheary elements. In grass species, such as sorghum (Sorghum bicolor), switchgrass (Panicum virgatum), and sugarcane (Saccharum officinarum), a phenylpropanoid network deposited in xylan-rich primary walls extends into the lignified CML. This review traces the early history of discovery of the molecular components of the CML and presents the current state of knowledge on the development of the CML in bioenergy-relevant woody species and grasses. This chapter emphasises the role of the CML in the recalcitrance of biomass to deconstruction by mechanical and enzymatic means for conversion to biofuels and valuable bioproducts. The use of genetic engineering to alter CML composition and structure to facilitate biomass deconstruction and to redesign wood to generate materials with novel properties is discussed.

BIOMASS FUELS↗
DOE OSTI2020

High-throughput screening of Protein-DNA interactions in Sorghum

Drought is the primary abiotic factors negatively affecting agriculture, causing tremendous reductions in yield world-wide. Drought responsive adaptation strategies require complex molecular responses to including hormone signaling and production of osmo-protectants, as well as developmental responses including stomatal closure, changes to leaf morphology, and altered root system architecture. A common strategy to better understand these adaptation mechanisms is to compare plants with differing drought tolerances and has been successful in multiple crop plants including wheat, rice, and maize. To better understand drought adaptation strategies, we compared the cytosolic- and organelle-enriched protein profiles of leaves from two Sorghum bicolor genotypes with differing pre-flowering drought tolerances after 8-weeks of growth under water limitation. In agreement with previous literature findings, we observed significant drought-induced changes in the abundance of multiple heat shock proteins and dehydrins in both genotypes. We also identified unique proteins that might play a role in genotype dependent drought adaptation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

TGCM: (T)rait, (G)ene, and (C)rop Growth (M)odel Directed Targeted Gene Characterization in Sorghum (Final Technical Report)

Understanding which genes control important crop traits could help scientists develop better bioenergy and food crops more efficiently. However, plant genomes contain tens of thousands of genes, and testing each one individually is expensive and time-consuming. This project developed computational tools to predict which genes are most likely to matter, allowing researchers to focus their efforts where they will have the greatest impact. This project developed and validated integrated approaches combining machine learning, quantitative genetics, and crop growth modeling to improve the efficiency of functional gene characterization in sorghum (Sorghum bicolor), a critical bioenergy and food security crop. The research addressed a fundamental challenge in plant biology: the majority of genes in plant genomes lack experimentally validated functions, making it difficult to prioritize which genes to study using resource-intensive reverse genetics approaches.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Biomass sorghum production in Iowa, USA

This dataset includes field measurement and model simulation data from Josh Bendorf's (former MS student with Drs. VanLoocke & Heaton, ISU Dept. of Agronomy) thesis project focusing on the simulation of biomass sorghum ( Sorghum bicolor L. Moench) in the state of Iowa. Measured field data are provided in CSV file format for 2019 & 2020. Model output files are provided as NetCDF file format for the state of Iowa (1998-2007) & the larger US region (1969-2018).

Agricultural production systems simulation↗