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At least 19 records

Retracted: Monitoring Hatchery Broodstock Composition and Genetic Variation of Spring/Summer Chinook Salmon in the Columbia River Basin with Multigeneration Pedigrees

Abstract Hatchery production of Chinook Salmon Oncorhynchus tshawytscha in the Columbia River basin comprises most of the anadromous salmonid production in this region. Hatchery facilities and programs serve to mitigate for impacts to salmonids due to the construction and operation of hydropower dams and habitat impacts from development in addition to the conservation and restoration of natural populations. A genetic method referred to as parentage-based tagging (PBT) enables highly reliable detection of hatchery-origin fish and inference of multigeneration pedigrees. This study compiles 11 years of PBT data from nearly 125,000 interior stream-type Chinook Salmon from 24 spawning hatcheries located in tributaries of the mid- and upper Columbia River as well as the Salmon, Clearwater, and Grande Ronde River subbasins. Multigenerational pedigrees allowed investigation of the proportion of natural- and hatchery-origin broodstock (pNOB and pHOB, respectively) for each hatchery and enumeration of the scale of production between segregated and integrated programs. We then compared how pHOB and the scale of production influenced the number of stray fish observed, genetic diversity, relatedness, and age-class compositions within broodstocks. Over 91.0% of hatchery broodstock could be assigned back to their parents, and there was an overall rate of less than 1.0% of broodstock that were unintentionally incorporated into nonnatal hatchery programs. We evaluated 14 segregated programs with 0.0–10.0% pNOB, 7 intermediate programs (10.1–50.0% pNOB), and 3 integrated programs (>50.0% pNOB). There was no correlation between the scale of production or pNOB with the level of genetic diversity, but as production size increased, so did the effective number of breeders. This study demonstrates the utility of PBT as a monitoring tool for hatchery broodstocks, and results suggest that segregated and integrated programs have tradeoffs that generally align with their intended broodstock management purpose of providing fish for harvest and/or fish for supplementation or reintroduction.

Horn, Rebekah L.↗

Multigeneration Pedigrees to Monitor Hatchery Broodstock Composition and Genetic Variation of Spring/Summer Chinook Salmon in the Columbia River Basin

Abstract Hatchery production of Chinook Salmon Oncorhynchus tshawytscha in the Columbia River basin comprises most of the anadromous salmonid production in this region. Hatchery facilities and programs serve to mitigate for impacts to salmonids due to the construction and operation of hydropower dams and habitat impacts from development in addition to the conservation and restoration of natural populations. A genetic method referred to as parentage-based tagging (PBT) enables highly reliable detection of hatchery-origin fish and inference of multigeneration pedigrees. This study compiles 11 years of PBT data from nearly 125,000 interior stream-type Chinook Salmon from 24 spawning hatcheries located on tributaries of the mid- and upper Columbia River and in the Salmon, Clearwater, and Grande Ronde River subbasins. Multigenerational pedigrees allowed for investigation of the proportions of natural- and hatchery-origin broodstock (pNOB and pHOB, respectively) for each hatchery and enumeration of the scale of production between segregated and integrated programs. We then compared how pHOB and the scale of production influenced the number of stray fish observed, genetic diversity, relatedness, and age-class compositions within broodstocks. Over 91.0% of hatchery broodstock could be assigned back to their parents, and overall less than 1.0% of broodstock consisted of fish that were unintentionally incorporated into nonnatal hatchery programs. We evaluated 11 segregated programs with 0.0–10.0% pNOB, 9 intermediate programs (10.1–50.0% pNOB), and 3 integrated programs (>50.0% pNOB). There was no correlation between the scale of production or pNOB with the level of genetic diversity, but as production size increased, so did the effective number of breeders. This study demonstrates the utility of PBT as a monitoring tool for hatchery broodstocks, and results suggest that segregated and integrated programs have tradeoffs that generally align with their intended broodstock management purpose of providing fish for harvest and/or fish for supplementation or reintroduction.

Horn, Rebekah L.↗

Abundance of Major Cell Wall Components in Natural Variants and Pedigrees of Populus trichocarpa

The rapid analysis of biopolymers including lignin and sugars in lignocellulosic biomass cell walls is essential for the analysis of the large sample populations needed for identifying heritable genetic variation in biomass feedstocks for biofuels and bioproducts. In this study, we reported the analysis of cell wall lignin content, syringyl/guaiacyl (S/G) ratio, as well as glucose and xylose content by high-throughput pyrolysis-molecular beam mass spectrometry (py-MBMS) for >3,600 samples derived from hundreds of accessions of Populus trichocarpa from natural populations, as well as pedigrees constructed from 14 parents (7 × 7). Partial Least Squares (PLS) regression models were built from the samples of known sugar composition previously determined by hydrolysis followed by nuclear magnetic resonance (NMR) analysis. Key spectral features positively correlated with glucose content consisted of m/z 126, 98, and 69, among others, deriving from pyrolyzates such as hydroxymethylfurfural, maltol, and other sugar-derived species. Xylose content positively correlated primarily with many lignin-derived ions and to a lesser degree with m/z 114, deriving from a lactone produced from xylose pyrolysis. Models were capable of predicting glucose and xylose contents with an average error of less than 4%, and accuracy was significantly improved over previously used methods. The differences in the models constructed from the two sample sets varied in training sample number, but the genetic and compositional uniformity of the pedigree set could be a potential driver in the slightly better performance of that model in comparison with the natural variants. Broad-sense heritability of glucose and xylose composition using these data was 0.32 and 0.34, respectively. In summary, we have demonstrated the use of a single high-throughput method to predict sugar and lignin composition in thousands of poplar samples to estimate the heritability and phenotypic plasticity of traits necessary to develop optimized feedstocks for bioenergy applications.

09 BIOMASS FUELS↗

Genetic architecture of leaf morphological and physiological traits in a Populus deltoides ‘Danhong’ × P. simonii ‘Tongliao1’ pedigree revealed by quantitative trait locus analysis

Understanding the genetic architecture of leaf morphological and physiological traits will help plant breeders develop high biomass poplar genotypes. Quantitative trait locus (QTL) studies combining next-generation sequencing techniques can advance our understanding of the genetic basis of complex traits. In this study, we measured 13 leaf morphological and physiological traits and identified quantitative trait loci (QTLs) in a Populus deltoides ‘Danhong’ × P. simonii ‘Tongliao1’ F1 population (500 progenies) using a high-density genetic map constructed by whole genome re-sequencing. This linkage map consisted of 5796 single nucleotide polymorphism (SNP) markers assigned to 19 linkage groups (LGs), spanning 2683.80 centimorgans (cM) of genetic length, with an average marker density of 0.46 cM. We identified 109 QTLs on 18 LGs for leaf morphological traits and 55 QTLs on 14 LGs for leaf physiological traits. One-hundred eight putative candidate genes were identified within the candidate genomic region. Co-expression network and gene ontology enrichment analyses suggested that these candidate genes were involved in the photosynthetic process. The differential expression patterns of the CYCLIN (Potri.015G112200) and RED CHLOROPHYLL REDUCTASE (Potri.007G043600) genes between two parents indicated their potential roles in leaf morphological and physiological traits. These findings decipher the genetic architecture of leaf morphological and physiological traits in the P. deltoides ‘Danhong’ × P. simonii ‘Tongliao1’ pedigree and provide candidate genes for future poplar genetic improvement.

59 BASIC BIOLOGICAL SCIENCES↗

Accurate determination of genotypic variance of cell wall characteristics of a Populus trichocarpa pedigree using high-throughput pyrolysis-molecular beam mass spectrometry

Abstract Background Pyrolysis-molecular beam mass spectrometry (py-MBMS) analysis of a pedigree of Populus trichocarpa was performed to study the phenotypic plasticity and heritability of lignin content and lignin monomer composition. Instrumental and microspatial environmental variability were observed in the spectral features and corrected to reveal underlying genetic variance of biomass composition. Results Lignin-derived ions (including m/z 124, 154, 168, 194, 210 and others) were highly impacted by microspatial environmental variation which demonstrates phenotypic plasticity of lignin composition in Populus trichocarpa biomass. Broad-sense heritability of lignin composition after correcting for microspatial and instrumental variation was determined to be H 2 = 0.56 based on py-MBMS ions known to derive from lignin. Heritability of lignin monomeric syringyl/guaiacyl ratio ( S / G ) was H 2 = 0.81. Broad-sense heritability was also high (up to H 2 = 0.79) for ions derived from other components of the biomass including phenolics (e.g., salicylates) and C5 sugars (e.g., xylose). Lignin and phenolic ion abundances were primarily driven by maternal effects, and paternal effects were either similar or stronger for the most heritable carbohydrate-derived ions. Conclusions We have shown that many biopolymer-derived ions from py-MBMS show substantial phenotypic plasticity in response to microenvironmental variation in plantations. Nevertheless, broad-sense heritability for biomass composition can be quite high after correcting for spatial environmental variation. This work outlines the importance in accounting for instrumental and microspatial environmental variation in biomass composition data for applications in heritability measurements and genomic selection for breeding poplar for renewable fuels and materials.

09 BIOMASS FUELS↗

Describing patterns of familial cancer risk in subfertile men using population pedigree data

STUDY QUESTION Can we simultaneously assess risk for multiple cancers to identify familial multicancer patterns in families of azoospermic and severely oligozoospermic men? SUMMARY ANSWER Here, distinct familial cancer patterns were observed in the azoospermia and severe oligozoospermia cohorts, suggesting heterogeneity in familial cancer risk by both type of subfertility and within subfertility type. WHAT IS KNOWN ALREADY Subfertile men and their relatives show increased risk for certain cancers including testicular, thyroid, and pediatric. STUDY DESIGN, SIZE, DURATION A retrospective cohort of subfertile men (N = 786) was identified and matched to fertile population controls (N = 5674). Family members out to third-degree relatives were identified for both subfertile men and fertile population controls (N = 337 754). The study period was 1966–2017. Individuals were censored at death or loss to follow-up, loss to follow-up occurred if they left Utah during the study period. PARTICIPANTS/MATERIALS, SETTING, METHODS Azoospermic (0 × 10 6 /mL) and severely oligozoospermic (<1.5 × 10 6 /mL) men were identified in the Subfertility Health and Assisted Reproduction and the Environment cohort (SHARE). Subfertile men were age- and sex-matched 5:1 to fertile population controls and family members out to third-degree relatives were identified using the Utah Population Database (UPDB). Cancer diagnoses were identified through the Utah Cancer Registry. Families containing ≥10 members with ≥1 year of follow-up 1966–2017 were included (azoospermic: N = 426 families, 21 361 individuals; oligozoospermic: N = 360 families, 18 818 individuals). Unsupervised clustering based on standardized incidence ratios for 34 cancer phenotypes in the families was used to identify familial multicancer patterns; azoospermia and severe oligospermia families were assessed separately. MAIN RESULTS AND THE ROLE OF CHANCE Compared to control families, significant increases in cancer risks were observed in the azoospermia cohort for five cancer types: bone and joint cancers hazard ratio (HR) = 2.56 (95% CI = 1.48–4.42), soft tissue cancers HR = 1.56 (95% CI = 1.01–2.39), uterine cancers HR = 1.27 (95% CI = 1.03–1.56), Hodgkin lymphomas HR = 1.60 (95% CI = 1.07–2.39), and thyroid cancer HR = 1.54 (95% CI = 1.21–1.97). Among severe oligozoospermia families, increased risk was seen for three cancer types: colon cancer HR = 1.16 (95% CI = 1.01–1.32), bone and joint cancers HR = 2.43 (95% CI = 1.30–4.54), and testis cancer HR = 2.34 (95% CI = 1.60–3.42) along with a significant decrease in esophageal cancer risk HR = 0.39 (95% CI = 0.16–0.97). Thirteen clusters of familial multicancer patterns were identified in families of azoospermic men, 66% of families in the azoospermia cohort showed population-level cancer risks, however, the remaining 12 clusters showed elevated risk for 2-7 cancer types. Several of the clusters with elevated cancer risks also showed increased odds of cancer diagnoses at young ages with six clusters showing increased odds of adolescent and young adult (AYA) diagnosis [odds ratio (OR) = 1.96–2.88] and two clusters showing increased odds of pediatric cancer diagnosis (OR = 3.64–12.63). Within the severe oligozoospermia cohort, 12 distinct familial multicancer clusters were identified. All 12 clusters showed elevated risk for 1–3 cancer types. An increase in odds of cancer diagnoses at young ages was also seen in five of the severe oligozoospermia familial multicancer clusters, three clusters showed increased odds of AYA diagnosis (OR = 2.19–2.78) with an additional two clusters showing increased odds of a pediatric diagnosis (OR = 3.84–9.32). LIMITATIONS, REASONS FOR CAUTION Although this study has many strengths, including population data for family structure, cancer diagnoses and subfertility, there are limitations. First, semen measures are not available for the sample of fertile men. Second, there is no information on medical comorbidities or lifestyle risk factors such as smoking status, BMI, or environmental exposures. Third, all of the subfertile men included in this study were seen at a fertility clinic for evaluation. These men were therefore a subset of the overall population experiencing fertility problems and likely represent those with the socioeconomic means for evaluation by a physician. WIDER IMPLICATIONS OF THE FINDINGS This analysis leveraged unique population-level data resources, SHARE and the UPDB, to describe novel multicancer clusters among the families of azoospermic and severely oligozoospermic men. Distinct overall multicancer risk and familial multicancer patterns were observed in the azoospermia and severe oligozoospermia cohorts, suggesting heterogeneity in cancer risk by type of subfertility and within subfertility type. Describing families with similar cancer risk patterns provides a new avenue to increase homogeneity for focused gene discovery and environmental risk factor studies. Such discoveries will lead to more accurate risk predictions and improved counseling for patients and their families. STUDY FUNDING/COMPETING INTEREST(S) This work was funded by GEMS: Genomic approach to connecting Elevated germline Mutation rates with male infertility and Somatic health (Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD): R01 HD106112). The authors have no conflicts of interest relevant to this work.

60 APPLIED LIFE SCIENCES↗

Construction of a Code Verification Matrix for Heat Conduction With Finite Element Code Applications

When establishing the pedigree of a simulation tool, code verification is used to ensure that the implemented numerical algorithm is a faithful representation of its underlying mathematical model. During this process, numerical results on various meshes are systematically compared to a reference analytic solution. The selection of analytic solutions can be a laborious process, as it is difficult to establish adequate code confidence without performing redundant work. In this report we address this issue by applying a physics-based process that establishes a set of reference problems. In this process, code simulation options are categorized and systematically tested, which ensures that gaps in testing are easily identified and addressed. The resulting problems are primarily intended for code verification analysis but may also be useful for comparison to other simulation codes, troubleshooting activities, or training exercises. The process is used to select fifteen code verification problems relevant for the one-dimensional steady-state heat conduction equation. These problems are applicable to a wide variety of simulation tools, but, in this work, a demonstration is performed using the finite element-based nuclear fuel performance code BISON. Convergence to the analytic solution at the theoretical rate is quantified for a selection of the problems, which establishes a baseline pedigree for the code. Not only can this standard set of conduction solutions be used for verification of other codes, but also the physics-based process for selecting problems can be utilized to quantify and expand testing for any simulation tool.

42 ENGINEERING↗

Data for Identifying the best high-biomass sorghum hybrids based on biomass yield potential and feedstock quality affected by nitrogen fertility management under various environments

Data were collected from agronomy fields in Urbana and Ewing, IL, during the 2022 and 2023 growing seasons. The dataset includes dry biomass yield, nitrogen, phosphorus, and potassium concentrations and removals, and chemical composition elements (cellulose, hemicellulose, lignin, and soluble fractions) for 13 high-biomass sorghum hybrids. data_sharing.xlsx contains 20 columns and 104 rows. Below is the explanation of all variables in the file: Year: 2022; 2023 Location: Urbana, IL; Ewing, IL N rate (kg-N/ha): 0; 112 Hybrid #: H1-H13 Pedigree: Pedigree for 13 hybrids Dry biomass yield (Mg/ha): Aboveground dry biomass yield N (g/kg): Nitrogen concentration in plant tissue P (g/kg): Phosphorus concentration in plant tissue K (g/kg): Potassium concentration in plant tissue N (kg/ha): Nitrogen removal by aboveground biomass P (kg/ha): Phosphorus removal by aboveground biomass K (kg/ha): Potassium removal by aboveground biomass Cellulose (g/kg): Cellulose concentration in plant tissue Hemicellulose (g/kg): Hemicellulose concentration in plant tissue Lignin (g/kg): Lignin concentration in plant tissue Soluble (g/kg): Soluble concentration in plant tissue Cellulose (Mg/ha): Cellulose content in aboveground biomass Hemicellulose (Mg/ha): Hemicellulose content in aboveground biomass Lignin (Mg/ha): Lignin content in aboveground biomass Soluble (Mg/ha): Soluble content in aboveground biomass

environmental adaptability↗

Commercial Electronic Part Class Definitions

Electronic parts used in Nuclear Security Enterprise (NSE) applications have varying pedigrees. Understanding the differences among these "part classes" will better enable Kansas City National Security Campus (KCNSC) and Sandia National Laboratories (SNL, or Sandia) to effectively manage factors such as risk, effort, cost, etc. across all functional areas which have a shared interest in the definition and acquisition process. Regardless of the pedigree and complexity, all parts are expected to meet necessary quality and reliability requirements. This activity has been conducted as part of the COTS Transformation Initiative (CTI).

42 ENGINEERING↗

Uncertainty in inventories for life cycle assessment: State‐of‐the‐art, challenges, and new technologies

Uncertainty is a critical factor that can hinder the quality and potential applications of life cycle assessment (LCA) results. A prominent source of uncertainty stems from the life cycle inventory (LCI) data. Various methodologies exist to estimate the uncertainty associated with LCI data, primarily based on the widely used structured pedigree matrix approach or the computationally intensive Monte Carlo simulation. This perspective review explores how new technologies (e.g., computational algorithms and data collection methods) from data science and related fields can contribute to identifying, quantifying, and reducing uncertainty in LCI modeling. A brief overview of the sources of uncertainty in LCI modeling and how they are addressed in current LCA practice is provided. Additionally, several new technologies are identified, and the potential benefits of their implementation in reducing uncertainties in LCI modeling are discussed. This perspective review concludes by identifying potential areas that require further development for these technologies.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Genomic variation within the maize stiff-stalk heterotic germplasm pool

The stiff-stalk heterotic group in Maize (Zea mays L.) is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and, to a lesser extent, B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four expired Plant Variety Protection (ex-PVP) lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40, which is a Pioneer Hi-Bred International (PHI) early stiff-stalk type. Sequence was generated using long-read sequencing achieving highly contiguous assemblies of 2.13-2.18 Gbp with N50 scaffold lengths >200 Mbp. Inbred-specific gene annotations were generated using a core five-tissue gene expression atlas, whereas transposable element (TE) annotation was conducted using de novo and homology-directed methodologies. Compared with the reference inbred B73, synteny analyses revealed extensive collinearity across the five stiff-stalk genomes, although unique components of the maize pangenome were detected. Comparison of this set of stiff-stalk inbreds with the original Iowa Stiff Stalk Synthetic breeding population revealed that these inbreds represent only a proportion of variation in the original stiff-stalk pool and there are highly conserved haplotypes in released public and ex-Plant Variety Protection inbreds. Despite the reduction in variation from the original stiff-stalk population, substantial genetic and genomic variation was identified supporting the potential for continued breeding success in this pool. The assemblies described here represent stiff-stalk inbreds that have historical and commercial relevance and provide further insight into the emerging maize pangenome.

59 BASIC BIOLOGICAL SCIENCES↗

Biomass Quality Responses to Selection for Increased Biomass Yield in Perennial Energy Grasses

Perennial grasses are candidates for biomass cropping systems that are focused on providing a wide range of ecosystem services in addition to sustainable bioenergy production. Switchgrass (Panicum virgatum L.) and big bluestem (Andropogon gerardii Vitman) are two of the dominant grasses of the tallgrass prairie and both are candidates for development of multifunctional diverse production systems. Breeding programs for both species are aimed at increasing biomass yield as a mechanism of improving economic sustainability without increasing production costs. The objective of this study was to determine if long-term selection for increased biomass yield in these two species has had any adverse impacts on biomass quality, or the ability to convert biomass into bioenergy. Check cultivars and improved breeding populations of both species were evaluated for a wide range of biomass quality traits at 13 locations in the North Central and Northeastern USA, and a subset of these populations were also subjected to more intensive and detailed fermentation analyses. In general, lignin and ferulates either remained constant or decreased following selection for increased biomass yield in the various genetic pedigrees. These changes resulted in some increases in predicted ethanol production and in vitro digestibility. Here, the prediction of increased digestibility was confirmed by higher glucose release by pretreatment and deconstruction of an advanced lowland population. However, bioreactor fermentations with two different biofuel-producing microbes showed no differences in ethanol production. Overall, these studies indicated that the improved switchgrass and big bluestem populations had greater biomass yields without significantly reducing biomass quality or conversion efficiency into ethanol, suggesting that selection can achieve increases in biomass productivity while maintaining consistent biomass quality.

09 BIOMASS FUELS↗

SCALE depletion capabilities for molten salt reactors and other liquid-fueled systems

Nuclear reactor systems that use fuel dissolved in a liquid have the potential for enhanced safety characteristics, improved fuel-cycle outcomes, and more efficient isotope-production configurations. In these reactor systems, the fueled liquid may simultaneously undergo irradiation, physical and chemical removal processes, and fueling. The modeling and simulation of this transmutation and decay with material additions and removals is an ongoing research area. An accurate simulation tool is critical to the reactor and fuel-cycle design, reactor deployment, and source-term characterization for these advanced reactor systems. The work described herein involved implementing, testing, and applying the capability to perform reactor physics simulations within the Oak Ridge National Laboratory-developed SCALE suite for nuclear systems analyses and design, leveraging much of its pedigree in quality-assurance and reactor-analysis capabilities. The functionalities to simulate irradiation with material feeds and removals had been added in ORIGEN, and the TRITON reactor physics sequence was extended to calculate the total removed material and track external nonirradiated mixtures to estimate separate processing or waste streams. Results from these capabilities align with analytical expectations obtained from ORIGEN for simplified test cases and with expectations for a molten salt reactor application. This implementation, available with the SCALE 6.3 release, provides for a more efficient and accurate material accountability methodology, allowing for the characterization, design, and analysis of the complete isotopic material inventory of advanced liquid-fueled systems for a variety of applications.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Modeling Ti–6Al–4V using crystal plasticity, calibrated with multi-scale experiments, to understand the effect of the orientation and morphology of the α and β phases on time dependent cyclic loading

Classically, crystal plasticity modeling has used a range of constitutive equations, in which the incorporation of additional physics-based relationships typically results in additional model parameters. These additional parameters need to be reliably calibrated, which often necessitates the use of a range of experimental data acquired at multiple length scales. In this work, a crystal plasticity based finite element (CPFE) model for a dual-phase Titanium alloy, Ti–6Al–4V, is developed. The α and β phases of the microstructure are explicitly modeled. The model is calibrated using a systematic optimization routine and experimental data that consist of macroscopic stress-strain curves coupled with lattice strains on different crystallographic planes for the two phases. These experimental data were obtained from in situ high energy X-ray diffraction experiments for multiple material pedigrees, with varying crystallographic orientation distribution and β volume fractions. Depending on the thermomechanical-processing route and the heat treatment used to manufacture the alloy, Ti–6Al–4V can exist in a wide number of microstructural forms, which often results in the α and β phases either having well aligned slip systems (following the Burgers orientation relationship (BOR)) or possessing no alignment of the slip systems across the interphase boundary (not following the BOR). In this study, the fully-calibrated CPFE model is used to gain a comprehensive understanding of the deformation behavior of Ti–6Al–4V, specifically, the effect of microstructures that follow the BOR (or not) on time-dependent cyclic loading (including the effects of dwell hold times).

36 MATERIALS SCIENCE↗

Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding

Genome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence–absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the ‘Pawnee’ cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence–absence and functional annotation database among genomes and within the two outbred haplotypes of the ‘Lakota’ genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.

54 ENVIRONMENTAL SCIENCES↗

A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders

Abstract Unsolved Mendelian cases often lack obvious pathogenic coding variants, suggesting potential non-coding etiologies. Here, we present a single cell multi-omic framework integrating embryonic mouse chromatin accessibility, histone modification, and gene expression assays to discover cranial motor neuron (cMN)cis-regulatory elements and subsequently nominate candidate non-coding variants in the congenital cranial dysinnervation disorders (CCDDs), a set of Mendelian disorders altering cMN development. We generate single cell epigenomic profiles for ~86,000 cMNs and related cell types, identifying ~250,000 accessible regulatory elements with cognate gene predictions for ~145,000 putative enhancers. We evaluate enhancer activity for 59 elements using an in vivo transgenic assay and validate 44 (75%), demonstrating that single cell accessibility can be a strong predictor of enhancer activity. Applying our cMN atlas to 899 whole genome sequences from 270 genetically unsolved CCDD pedigrees, we achieve significant reduction in our variant search space and nominate candidate variants predicted to regulate known CCDD disease genesMAFB, PHOX2A, CHN1, andEBF3– as well as candidates in recurrently mutated enhancers through peak- and gene-centric allelic aggregation. This work delivers non-coding variant discoveries of relevance to CCDDs and a generalizable framework for nominating non-coding variants of potentially high functional impact in other Mendelian disorders.

Science & Technology - Other Topics↗

Plutonium isotope ratio measurements by total evaporation-thermal ionization mass spectrometry (TE-TIMS): an evaluation of uncertainties using traceable standards from the New Brunswick Laboratory

The accuracy and precision of isotope amount ratio measurements using thermal ionization mass spectrometry (TIMS) instrumentation are described, and the measurement of Pu materials is emphasized. The mass fractionation observed for Am, Ga, Pu, and U for isotope amount ratio measurements using the total evaporation (TE) technique is compared with theoretical estimates to demonstrate the advantage of the TE methodology and to investigate systematic biases in the major isotope amount ratios of U and Pu certified reference material (CRM) standards from the U.S. provider of CRMs. The quality of the Pu isotopic data generated by TIMS instruments in an analytical laboratory is demonstrated by the application of the double ratio technique to estimate the 241 Pu half-life. Analytical data on traceable Pu CRMs from the New Brunswick Laboratory (NBL), generated as part of routine measurements supporting various programs, are used for this half-life estimation. Although the 241 Pu abundances in CRMs of 136, 137, 138, and 126-A are approximately 200–2000× smaller than those in the 241 Pu material used in the previous Institute for Reference Materials and Measurements (IRMM) evaluation of the 241 Pu half-life, the half-life value estimated in this work shows excellent agreement with the currently accepted value from the IRMM. This agreement also demonstrates the pedigree of the Pu isotopic standards from the NBL and the quality of the isotope amount ratio measurements using TIMS instrumentation. For both the major and minor Pu isotope amount ratios, this report describes the relative importance of the factors affecting the uncertainty of TIMS measurements, which are considered the gold standard in isotope ratio measurements (LA-UR-24-29199).

07 ISOTOPE AND RADIATION SOURCES↗

High-resolution mapping reveals hotspots and sex-biased recombination in Populus trichocarpa

Abstract Fine-scale meiotic recombination is fundamental to the outcome of natural and artificial selection. Here, dense genetic mapping and haplotype reconstruction were used to estimate recombination for a full factorial Populus trichocarpa cross of 7 males and 7 females. Genomes of the resulting 49 full-sib families (N = 829 offspring) were resequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The 14 parental genetic maps contained 1,820 SNP/INDELs on average that covered 376.7 Mb of physical length across 19 chromosomes. Comparison of parental and progeny haplotypes allowed fine-scale demarcation of cross-over regions, where 38,846 cross-over events in 1,658 gametes were observed. Cross-over events were positively associated with gene density and negatively associated with GC content and long-terminal repeats. One of the most striking findings was higher rates of cross-overs in males in 8 out of 19 chromosomes. Regions with elevated male cross-over rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate cross-over hotspots spread throughout the genome. DNA sequence motifs enriched in these regions showed striking similarity to those of maize, Arabidopsis, and wheat. These findings, and recombination estimates, will be useful for ongoing efforts to accelerate domestication of this and other biomass feedstocks, as well as future studies investigating broader questions related to evolutionary history, perennial development, phenology, wood formation, vegetative propagation, and dioecy that cannot be studied using annual plant model systems.

59 BASIC BIOLOGICAL SCIENCES↗