Search NASA⌕ Search

SEARCH · Search NASA

Results for “Resource Characterization”

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

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

At least 1,045 records · Page 58
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The Demand for a Domestic Offshore Wind Energy Supply Chain

In March of 2021, the Biden-Harris Administration established a National Offshore Wind Target to install 30 GW by 2030. This ambitious goal was not only intended to help reduce dependencies on fossil fuels, but also represents an opportunity to establish a new and sustainable industry in the United States. The announcement referenced the potential benefits of establishing a domestic supply chain, including the opportunity for existing suppliers to produce thousands of components while creating tens of thousands of jobs over the course of the decade. This vision by the Biden-Harris Administration aligns with the perspective of the offshore wind industry. At a Leadership 100 event hosted by the Business Network for Offshore wind in 2019, offshore wind developers and manufacturers identified the need for a roadmap outlining a pathway to a domestic supply chain as the top priority facing the industry. Building up domestic manufacturing capabilities will not only energize local industries but can potentially de-risk individual project by reducing reliance on importing resources from European or Asian markets. Although establishing a domestic supply chain will require significant investment, it has the potential to create substantial benefits throughout the industry and, by extension, on the decarbonization goals of the United States. This study characterizes the challenges and opportunities facing the growth of a domestic supply chain industry and evaluates the potential benefits that could be achieved through the creation of the supply chain. This report is the first of a two-part series which will describe the full supply chain roadmap and the associated benefits; the current report focuses on the high-level deployment, workforce, and component requirements that need to be met to achieve the National Offshore Wind Target. We will present: 1. A deployment pipeline that demonstrates the pathway to 30 GW, the associated demand for major fixed-bottom and floating offshore wind components (turbines, foundations, cables, substations), and the vessel and port requirements to support these installation activities. 2. A series of sensitivity analyses showing how the demand for components, ports, and vessels changes for different technology pathways and availability of the global supply chain. 3. An estimate of the total number of jobs that would be required to support these deployment scenarios under varying levels of assumed domestic content. 4. A comprehensive list of the Tier 1, 2, and 3 components (finished components, subassemblies, and subcomponents) required to construct fixed-bottom and floating offshore wind projects. 5. A discussion of critical path components that represent a significant challenge, bottleneck, or risk for a future domestic supply chain.

17 WIND ENERGY↗
DOE OSTI2024

Multi-scale Simulation, Calibration, and Optimization of Calcium Carbonate Precipitation in Microbial Communities

Ensuring the efficient engineering of microbially induced calcium carbonate precipitation (MICP) is crucial for a variety of environmental and civil engineering applications, such as soil stabilization and carbon sequestration. Addressing this need, we present a comprehensive multi-scale workflow that begins with the isolation of calcium carbonate-producing microbes from soil samples, followed by metagenomic sequencing and metabolic reconstruction. We then characterize microbial growth phenotypes under diverse nutrient conditions, compare observed growth with metabolic model predictions, and apply the Consistent Reproduction of Phenotype (CROP) algorithm to refine these models. Furthermore, we analyze metabolite consumption and production, and develop a consumer-resource model that is calibrated using time-series measurements of growth rates, pH levels, and calcium carbonate precipitation. The primary benefit of our approach lies in its ability to predict and control MICP outcomes, facilitated by a Bayesian methodology that incorporates priors on initial conditions and parameters. This allows us to compute posteriors by integrating experimental data, and to solve a risk optimization problem under uncertainty to identify nutrient conditions that maximize calcium carbonate production. In contrast to non-Bayesian methods, which fail to quantify uncertainty accurately, our approach provides a more reliable pathway to optimizing nutrient conditions, enhancing the likelihood of achieving desired MICP outcomes. This positions our method as a superior alternative in the quest to improve MICP through engineered microbial consortia.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Quantum Simulation of Field Theories Without State Preparation

We propose an algorithm for computing real-time observables using a quantum processor while avoiding the need to prepare the full quantum state. This reduction in quantum resources is achieved by classically sampling configurations in imaginary-time using standard lattice field theory. These configurations can then be passed to quantum processor for time-evolution. This method encounters a signal-to-noise problem which we characterize, and we demonstrate the application of standard lattice QCD methods to mitigate it.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Cyber Physical Grid-Interactive Distributed Energy Resources Control for VPP Dispatch and Regulation: Preprint

This paper presents a cyber-physical algorithm for grid interactive DER control to enable two features of Virtual Power Plants (VPPs) dispatch and grid voltage regulation, considering the communication and security impacts. We first formulate the DER dispatch problem as a real-time, iterative, and grid-interactive DER control problem. Thereafter, we consider a probabilistic traffic model to characterize packet delays and loss in a communication network, and study how the delays enter the process of information exchange among the grid measurement units, local DER controllers and the grid control center that coordinately execute this dispatch algorithm. Finally, we propose a cyber-physical grid-interactive DER control algorithm using the previous message strategy. The tracking and regulation capabilities of this proposed algorithm can be made immune to the asynchrony resulting from the communications network traffic. We carry out simulations to show possible numerical instabilities and sensitivities of the tracking and regulation capabilities on the proposed strategy. Our results exhibit that the uncertainties of the underlying communications infrastructure must be considered in the control algorithm for the VPP tracking and regulation capabilities of any DER in a generic Cyber-Physical System (CPS).

co-simulation↗
DOE OSTI2015

Temporal Characterization of Hydrates System Dynamics beneath Seafloor Mounds. Integrating Time-Lapse Electrical Resistivity Methods and In Situ Observations of Multiple Oceanographic Parameters

This study was designed to investigate temporal variations in hydrate system dynamics by measuring changes in volumes of hydrate beneath hydrate-bearing mounds on the continental slope of the northern Gulf of Mexico, the landward extreme of hydrate occurrence in this region. Direct Current Resistivity (DCR) measurements were made contemporaneously with measurements of oceanographic parameters at Woolsey Mound, a carbonate-hydrate complex on the mid-continental slope, where formation and dissociation of hydrates are most vulnerable to variations in oceanographic parameters affected by climate change, and where changes in hydrate stability can readily translate to loss of seafloor stability, impacts to benthic ecosystems, and venting of greenhouse gases to the water-column, and eventually, the atmosphere. We focused our study on hydrate within seafloor mounds because the structurally-focused methane flux at these sites likely causes hydrate formation and dissociation processes to occur at higher rates than at sites where the methane flux is less concentrated and we wanted to maximize our chances of witnessing association/dissociation of hydrates. We selected a particularly well-studied hydrate-bearing seafloor mound near the landward extent of the hydrate stability zone, Woolsey Mound (MC118). This mid-slope site has been studied extensively and the project was able to leverage considerable resources from the team’s research experience at MC118. The site exhibits seafloor features associated with gas expulsion, hydrates have been documented at the seafloor, and changes in the outcropping hydrates have been documented, photographically, to have occurred over a period of months. We conducted observatory-based, in situ measurements to 1) characterize, geophysically, the sub-bottom distribution of hydrate and its temporal variability, and 2) contemporaneously record relevant environmental parameters (temperature, pressure, salinity, turbidity, bottom currents) to detect short-term changes within the hydrates system, identify relationships/impacts of local oceanographic parameters on the hydrates system, and improve our understanding of how seafloor instability is affected by hydrates-driven changes. A 2009 DCR survey of MC118 demonstrated that we could image resistivity anomalies to a depth of 75m below the seafloor in water depths of 1km. We reconfigured this system to operate autonomously on the seafloor in a pre-programmed mode, for periods of months. We designed and built a novel seafloor lander and deployment capability that would allow us to investigate the seafloor at potential deployment sites and deploy instruments only when conditions met our criteria. This lander held the DCR system, controlling computers, and battery power supply, as well as instruments to record oceanographic parameters. During the first of two cruises to the study site, we conducted resistivity surveying, selected a monitoring site, and deployed the instrumented lander and DCR, centered on what appeared to be the most active locations within the site, programmed to collect a DCR profile, weekly. After a 4.5-month residence on the seafloor, the team recovered all equipment. Unfortunately, several equipment failures occurred prior to recovery of the instrument packages. Prior to the failures, however, two resistivity profiles were collected together with oceanographic data. Results show, unequivocally, that significant changes can occur in both hydrate volume and distribution during time periods as brief as one week. Occurrences appear to be controlled by both deep and near-surface structure. Results have been integrated with seismic data from the area and show correspondence in space of hydrate and structures, including faults and gas chimneys.

58 GEOSCIENCES↗
DOE OSTI2023

Panorama 360 (Final Report)

This is the final technical report for the DOE-funded Panorama 360 project. Panorama 360 provided a resource for the collection, analysis, and sharing of performance data about end-to-end scientific workflows executing on DOE facilities. The work focused on workflows that include experimental data generation at DOE facilities. The main activities of Panorama 360 include the development of: 1. A distributed repository that stores different types of workflow execution data (e.g., point and time series performance traces at fine- and coarse-grained levels); 2. A set of open-source data capture, curation, and publishing tools fully integrated with a state-of-the-art workflow management system that automates data ingestion to the repository and enables users to discover, query, and process data from the repository; 3. A set of analysis algorithms and machine learning based tools to perform analysis and characterization of the gathered data, which can be used to detect anomalous performance or system faults; and 4. Best practices and recommendations for workflow evaluation, analysis, execution, and architectures.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Global Archaeal Diversity Revealed Through Massive Data Integration: Uncovering Just Tip of Iceberg

The domain of Archaea has gathered significant interest for its ecological and biotechnological potential and its role in helping us to understand the evolutionary history of Eukaryotes. In comparison to the bacterial domain, the number of adequately described members in Archaea is relatively low, with less than 1000 species described. It is not clear whether this is solely due to the cultivation difficulty of its members or, indeed, the domain is characterized by evolutionary constraints that keep the number of species relatively low. Based on molecular evidence that bypasses the difficulties of formal cultivation and characterization, several novel clades have been proposed, enabling insights into their metabolism and physiology. Given the extent of global sampling and sequencing efforts, it is now possible and meaningful to question the magnitude of global archaeal diversity based on molecular evidence. To do so, we extracted all sequences classified as Archaea from 500 thousand amplicon samples available in public repositories. After processing through our highly conservative pipeline, we named this comprehensive resource the ‘Global Archaea Diversity’ (GAD), which encompassed nearly 3 million molecular species clusters at 97% similarity, and organized it into over 500 thousand genera and nearly 100 thousand families. Saline environments have contributed the most to the novel taxa of this previously unseen diversity. The majority of those 16S rRNA gene sequence fragments were verified by matches in metagenomic datasets from IMG/M. These findings reveal a vast and previously overlooked diversity within the Archaea, offering insights into their ecological roles and evolutionary importance while establishing a foundation for the future study and characterization of this intriguing domain of life.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Multi-omics data resource: Data package 23 (Pck023)

The data package consists of isolated pancreatic islets from adult male C57BL6/J mice treated with IL-1β + IFNγ, IL-1β + IFNγ + NMMA, or NMMA alone for 18 h and submitted for scRNA-seq. This study focused on the cell-type-specific effects of nitric oxide signaling in islets and characterized the heterogeneity of responses. Data contributors: Jennifer S Stancill & John A Corbett: Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA Data repository: GSE183010 Publication: 10.1093/function/zqab063

Sarkar, Soumyadeep [Pacific Northwest National Lab↗
DOE OSTI2020

High Resolution Ocean Surface Wave Hindcast (US Wave) Data

The development of this dataset was funded by the U.S. Department of Energy, Office of Energy Efficiency & Renewable Energy, Water Power Technologies Office to improve our understanding of the U.S. wave energy resource and to provide critical information for wave energy project development and wave energy converter design. This high resolution publicly available long-term wave hindcast dataset will - when complete - cover the entire U.S. Exclusive Economic Zone (EEZ). Available data includes the Hawaiian Islands, West and Atlantic Coasts, with future additions including the Alaskan coasts, Gulf of Mexico and the Freely associated States. The data can be used to investigate the historical record of wave statistics at any U.S. site. As such, the dataset could also be of value to any entity with marine operations inside the U.S. EEZ. These data are available for download without login credentials through the free and publicly accessible Open Energy Data Initiative (OEDI) data viewer which allows users to browse and download individual or groups of files.

16 TIDAL AND WAVE POWER↗
DOE OSTI2025

Enhancing Streamflow Reanalysis Across the Conterminous US Leveraging Multiple Gridded Precipitation Data Sets

Streamflow observations, essential for various water resource applications, are often unavailable at critical locations in need. Although different models have been proposed to enhance streamflow predictability at ungauged locations, the challenge extends beyond model fidelity. Differences in meteorologic forcing data sets, precipitation in particular, can significantly affect the accuracy of hydrologic predictions. This challenge intensifies across regions characterized by diverse hydro-climatological and geographical conditions, such as in the conterminous US (CONUS) where a single precipitation product struggles to consistently replicate observed hydrographs, particularly peak flow dynamics. To enhance streamflow predictions, we utilize a VIC-RAPID hydrologic modeling framework driven by multiple commonly used meteorological forcing data sets, such as Daymet, PRISM, ST4, AORC, and their hybrids and create multiple sets of 40-year (1980–2019) hourly, daily, and monthly streamflow reanalysis, Dayflow Version 2, for 2.7 million river reaches across the CONUS. Most forcings lead to skillful streamflow performance, except for ST4 in the mountainous west, where severe radar blockage adversely affects the accuracy. The evaluation using over 6,000 hourly stream gauges shows that hourly AORC and ST4 lead to improved annual peak flow performance over Daymet—driven streamflow (Dayflow V1), particularly in smaller basins, highlighting the value of high temporal resolution forcings in hydrologic predictions. Compared with other benchmark data sets like National Water Model V3.0, AORC-driven VIC-RAPID exhibits improved regional streamflow performance, with comparable peak flow representation. We envision that multi-forcing streamflow reanalysis data can inform regions in need of forcing data enhancement, diagnose hydrologic model performance, and benefit diverse water resource applications.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Spatial and Temporal Quantification of Spontaneous Imbibition

Spontaneous imbibition–the process of a wetting fluid displacing a non-wetting fluid purely by capillary forces–is a ubiquitous phenomenon in porous and fibrous materials. Here we present a new experimental method for quantification of spontaneous imbibition in geologic materials. This method makes it possible to perform spontaneous imbibition under elevated pressure conditions relevant to environmental and energy resource applications. In this work, computed tomography imaging reveals a new time-independent scaling relationship that describes local imbibition rates as a function of water saturation. Imbibition capillary pressure curves are calculated with this wetting-phase pressure and flowrate characterization, with no assumptions about the functional form, end point behavior, or scaling factors. Calculated end-point capillary pressure is nonzero, in agreement with recent pore-scale measurements of capillary pressure of trapped nonwetting phase. This work provides a new approach and insights into trapping and remobilization of non-wetting fluids in CO 2 storage reservoirs and contaminated groundwater aquifers.

58 GEOSCIENCES↗
DOE OSTI2017

Integrating tools for non-targeted analysis research and chemical safety evaluations at the US EPA

Tens-of-thousands of chemicals are registered in the U.S. for use in countless processes and products. Recent evidence suggests that many of these chemicals are measureable in environmental and/or biological systems, indicating the potential for widespread exposures. Traditional public health research tools, including in vivo studies and targeted analytical chemistry methods, have been unable to meet the needs of screening programs designed to evaluate chemical safety. As such, new tools have been developed to enable rapid assessment of potentially harmful chemical exposures and their attendant biological responses. One group of tools, known as “nontargeted analysis” (NTA) methods, allows the rapid characterization of thousands of never-before-studied compounds in a wide variety of environmental, residential, and biological media. This article discusses current applications of NTA methods, challenges to their effective use in chemical screening studies, and ways in which shared resources (e.g., chemical standards, databases, model predictions, and media measurements) can advance their use in risk-based chemical prioritization. A brief review is provided of resources and projects within EPA’s Office of Research and Development (ORD) that provide benefit to, and receive benefits from, NTA research endeavors. A summary of EPA’s Non-Targeted Analysis Collaborative Trial (ENTACT) is also given, which makes direct use of ORD resources to benefit the global NTA research community. Finally, a research framework is described that shows how NTA methods will bridge chemical prioritization efforts within ORD. This framework exists as a guide for institutions seeking to understand the complexity of chemical exposures, and the impact of these exposures on living systems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Computable and Operationally Meaningful Multipartite Entanglement Measures

Multipartite entanglement is an essential resource for quantum communication, quantum computing, quantum sensing, and quantum networks. The utility of a quantum state |ψ$\rangle$ for these applications is often directly related to the degree or type of entanglement present in |ψ$\rangle$. Therefore, efficiently quantifying and characterizing multipartite entanglement is of paramount importance. Here, in this work, we introduce a family of multipartite entanglement measures, called concentratable entanglements. Several well-known entanglement measures are recovered as special cases of our family of measures, and hence we provide a general framework for quantifying multipartite entanglement. We prove that the entire family does not increase, on average, under local operations and classical communications. We also provide an operational meaning for these measures in terms of probabilistic concentration of entanglement into Bell pairs. Finally, we show that these quantities can be efficiently estimated on a quantum computer by implementing a parallelized SWAP test, opening up a research direction for measuring multipartite entanglement on quantum devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Newborn Screening Quality Assurance Program for CFTR Mutation Detection and Gene Sequencing to Identify Cystic Fibrosis

All newborn screening laboratories in the United States and many worldwide screen for cystic fibrosis. Most laboratories use a second-tier genotyping assay to identify a panel of mutations in the CF transmembrane regulator (CFTR) gene. Centers for Disease Control and Prevention’s Newborn Screening Quality Assurance Program houses a dried blood spot repository of samples containing CFTR mutations to assist newborn screening laboratories and ensure high-quality mutation detection in a high-throughput environment. Recently, CFTR mutation detection has increased in complexity with expanded genotyping panels and gene sequencing. To accommodate the growing quality assurance needs, the repository samples were characterized with several multiplex genotyping methods, Sanger sequencing, and 3 next-generation sequencing assays using a high-throughput, low-concentration DNA extraction method. The samples performed well in all of the assays, providing newborn screening laboratories with a resource for complex CFTR mutation detection and next-generation sequencing as they transition to new methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology

Abstract Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Advanced Simulation and Experiments of Strongly Coupled Geomechanics and Flow for Gas Hydrate Deposits: Validation and Field Application. Final Report

The objectives of the proposed research are (1) to investigate geomechanical responses induced by depressurization experimentally and numerically; (2) to enhance the current numerical simulation technology in order to simulate complex physically coupled processes by depressurization and (3) to perform in-depth numerical analyses of two selected potential production test sites: one based on the deposits observed at the Ulleung basin UBGH2-6 site; and the other based on well-characterized accumulations from the westend Prudhoe Bay. To these ends, the recipient will have the following specific objectives: 1). Information obtained from multi-scale experiments previously conducted at the recipient’s research partner (the Korean Institute of Geoscience and Mineral Resources (KIGAM)) that were designed to represent the most promising known Ulleung Basin gas hydrate deposit as drilled at site UBGH2-6 will be evaluated (Task 2). These findings will be further tested by new experimental studies at Lawrence Berkeley National Laboratory (LBNL) and Texas A&M (TAMU) (Task 3) that are designed capture complex coupled physical processes between flow and geomechanics, such as sand production, capillarity, and formation of secondary hydrates. The findings of Tasks 2 and 3 will be used to further improve numerical codes. 2) Develop (in Tasks 4 through 6) an advanced coupled geomechanics and non-isothermal flow simulator (T+MAM) to account for large deformation and strong capillarity. This new code will be validated using data from the literature, from previous work by the project team, and with the results of the proposed experimental studies. The developed simulator will be applied to both Ulleung Basin and Prudhoe Bay sites, effectively addressing complex geomechanical and petrophysical changes induced by depressurization (e.g., frost-heave, strong capillarity, cryo-suction, induced fracturing, and dynamic permeability).

02 PETROLEUM↗
DOE OSTI2025

Develop a new integrated macro→micro←nano (MMN) multiscale modeling framework to optimize high strength aluminum alloys and processes for vehicle light-weighting​

Bending tests provide a means to study plane strain fracture performance of 6000 series aluminum alloys. Metrics from bending tests have been correlated with self-pierce riveting (SPR) performance of a high strength AA6111 automotive aluminum alloy in previous works. Using the ORNL HPC resources, this project developed an innovative macro→micro←nano (MMN) multiscale microstructure-based finite element (FE) code to further understanding of the relationship between microstructure and fracture properties of high-strength 6000-series alloys. This work started with microstructural characterization in both mesoscale and nanoscale and bending performance characterization of AA6111 HS2-T6 alloy at Ford, the MMN framework was applied to this alloy to simulate 3-point VDA bending. From the results of the macro-modeling of 3-point VDA bending, the critical region of fracture was identified, and the region geometry was used to construct the micro-model. The fracture criterion of micron-scale precipitates and aluminum matrix which contains submicron and nano particles (AL-SMP-NP) in the micro-model was calibrated and validated by comparing simulated and measured bending results. With the AL-SMP-NP fracture strain obtained, the fracture strain of Al-matrix containing nano particles (ALNP) will similarly be determined by a submicron scale-model using an edge-constrained FE modeling approach developed by Hu et al. With the ALNP fracture strain obtained, the fracture strain of Al-matrix containing no particles will similarly be determined by a nano scale-model using an edge-constrained FE modeling approach. After the MMN framework is built and fracture criterion calibrated, nano-model FE simulations with virtual microstructures was performed to obtain a reduced order model (ROM) of the fracture criterion of the ALNP as a function of volume fraction, size, and distribution of the nanoparticle. This nano→submicron→micro modeling part allows exploration of the influence of different material nanostructures from different process conditions on the bending properties within the multiscale bending simulation framework and the ROM of material bendability as a function of nanoparticle size and shape was established. This obtained reduced order model (ROM) could help guide the design and selection of materials to improve existing SPR process models that could replace trial-and-error rivet/die selection and help to design new rivet/die combinations capable of robustly joining new higher strength 6000 5 series alloys in automotive body structures. This would enable lightweighting of Ford vehicles leading to greater fuel efficiency and reduce manufacturing time and energy.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Natural Allelic Variations in Highly Polyploidy Saccharum Complex

Sugarcane ( Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWAmem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. Furthermore, the target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.

59 BASIC BIOLOGICAL SCIENCES↗