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

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.

Students, Participatory Design, and Serious Games in a Response to: 'No Algorithmization without Representation: Pilot Study on Regulatory Experiments in an Exploratory Sandbox'.

No Algorithmization without Representation tracked a cohort of 'Lithopy' crypto-government sandbox participants in a longitudinal study looking at COVID-19 contact tracing app acceptance. These survey responses extended experiences with theoretical blockchain town governance by also tracking reasons for and against compliance with contact tracing apps. They found that the expressed opinions of students were incoherent and demanded technical or policy responses outside of the students' direct experiences. In this response to that paper, I leverage the paper's (commendable) open data to suggest that the sandbox's claims of 'No Algorithmization without Representation' is a rediscovery of participatory design within the context of the serious games movement. While Role-Playing Games and War Games are excellent pedagogic tools xor planning tools-using undergraduate students' participation in them as the basis of a claim for increased representation in technology policy is a bold claim. This claim is not fully substantiated by the paper's data. Nevertheless, there is a need for better decision-making and public representation within technology design and policy-making spaces-making the claim for serious games as a meaningful public policy contribution not without merit.

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

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 H2 = 0.56 based on py-MBMS ions known to derive from lignin. Heritability of lignin monomeric syringyl/guaiacyl ratio (S/G) was H2 = 0.81. Broad-sense heritability was also high (up to H2 = 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.

Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa.

BACKGROUND: Populus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to growth, phenology, ecophysiology and wood chemistry. Those traits are influenced by both polygenic control and environmental effects, and their genome architecture and regulation are only partially understood. Genome wide association studies (GWAS) represent an approach to advance that aim using thousands of single nucleotide polymorphisms (SNPs). Genotyping using exome capture methodologies represent an efficient approach to identify specific functional regions of genomes underlying phenotypic variation. RESULTS: We identified 813 K SNPs, which were utilized for genotyping 461 P. trichocarpa clones, representing 101 provenances collected from Oregon and Washington, and established in California. A GWAS performed on 20 traits, considering single SNP-marker tests identified a variable number of significant SNPs (p-value < 6.1479E-8) in association with diameter, height, leaf carbon and nitrogen contents, and δ15N. The number of significant SNPs ranged from 2 to 220 per trait. Additionally, multiple-marker analyses by sliding-windows tests detected between 6 and 192 significant windows for the analyzed traits. The significant SNPs resided within genes that encode proteins belonging to different functional classes as such protein synthesis, energy/metabolism and DNA/RNA metabolism, among others. CONCLUSIONS: SNP-markers within genes associated with traits of importance for biomass production were detected. They contribute to characterize the genomic architecture of P. trichocarpa biomass required to support the development and application of marker breeding technologies.

Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar.

Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output-input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed-based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass-scale deployment of PBCs.

Innovative Method for the Analysis of Dexpanthenol in Hair Care Products.

Background: Dexpanthenol is a widely used humectant in hair care products, especially anti-hairfall products. The hair care industry is highly regulated in East Asia and treats products containing the combination of dexpanthenol, zinc pyrithione, and nicotinamide (vitamin B3) as quasi-drugs. Objective: Because dexpanthenol lacks a UV chromophore, existing methodologies for analysis in finished products include pretreatments and/or HPLC-UV analysis at low wavelengths at which poor signal-to-noise is observed. These time-consuming methods lack the robustness needed for routine use in quality laboratories. This has resulted in the need for a simple, fast, accurate, and robust UHPLC-MS method to quantify dexpanthenol in hair care products that could be easily adapted in quality laboratories. Methods: The MS detection was performed in positive ion mode with data acquired in single-ion recording for dexpanthenol (206.14 m/z), dexpanthenol-d6 (212.29 m/z), and Leucine Enkephalin acetate salt (556.28 m/z). Quantitation was performed using peak area ratio of dexpanthenol to the internal standard. Results: The resulting linear curve R² was 0.9998 with sample precision RSDs <2.5%. The accuracy recoveries were within 2% and the robustness results were within 3% of the nominal conditions. Conclusions: The resulting method for the quantitation of dexpanthenol is fast, accurate, and robust in the range of 170.24-1024.5 ng/mL in shampoo and conditioner, which is easily adaptable in quality laboratories. Highlights: This study determined optimal sample preparation and UHPLC-MS conditions to quantify dexpanthenol in finished hair care products.

Liquid Chromatography Method for the Simultaneous Quantification of Biotin and Vitamin B12 in Vitamin B Supplements.

Background: The determination of cyanocobalamin (vitamin B12) and biotin has always been challenging because of the lack of a chromophore for biotin and trace level input for vitamin B12 in supplements. Microbiological assay methods are currently used for quantitation. However, these methods are time consuming, may lack specificity, and have high imprecision. Objective: Our laboratory developed and validated an LC method for the simultaneous quantitation of vitamin B12 and biotin. Methods: This LC method uses a single quadruple mass analyzer to detect biotin and vitamin B12 at m/z 245.10 and m/z 678.29, respectively. Results: The mass analyzer allows for low limits of quantitation (biotin: 1 ng/mL; vitamin B12: 4 ng/mL). Precision results showed that injections are repeatable without the use of an internal standard (RSD < 5%). Single analyst (n = 5: RSD < 3%), within lab (n = 10: RSD < 8%), and multilab (n = 20: RSD < 13%) precision results were also much better than those reported by microbiological assay methods. Linearity was evaluated between 92.00 ng/mL and 9200 ng/mL (R² 09916) for biotin and between 4.846 ng/mL and 484.6 ng/mL (R² 0.9999) for vitamin B12. The method is accurate between 20 ng/mL and 60 ng/mL for vitamin B12 and between 400 ng/mL and 1200 ng/mL for biotin. Conclusions: The results show a simple, accurate, and precise method for the quantitation of vitamin B12 and biotin. Highlights: This work demonstrates that single quadrupole mass analyzers can be successfully used to quantify trace level analytes in quality control laboratories.

Security Fatigue.

Security fatigue has been used to describe experiences with online security. This study identifies the affective manifestations resulting from decision fatigue and the role it plays in users' security decisions.

Association genetics of chemical wood properties in black poplar (Populus nigra).

Black poplar (Populus nigra) is a potential feedstock for cellulosic ethanol production, although breeding for this specific end use is required. Our goal was to identify associations between single nucleotide polymorphism (SNP) markers within candidate genes encoding cellulose and lignin biosynthetic enzymes, with chemical wood property phenotypic traits, toward the aim of developing genomics-based breeding technologies for bioethanol production. Pyrolysis molecular beam mass spectrometry was used to determine contents of five- and six-carbon sugars, lignin, and syringyl : guaiacyl ratio. The association population included 599 clones from 17 half-sib families, which were successfully genotyped using 433 SNPs from 39 candidate genes. Statistical analyses were performed to estimate genetic parameters, linkage disequilibrium (LD), and single marker and haplotype-based associations. A moderate to high heritability was observed for all traits. The LD, across all candidate genes, showed a rapid decay with physical distance. Analysis of single marker-phenotype associations identified six significant marker-trait pairs, whereas nearly 280 haplotypes were associated with phenotypic traits, in both an individual and multiple trait-specific manner. The rapid decay of LD within candidate genes in this population and the genetic associations identified suggest a close relationship between the associated SNPs and the causative polymorphisms underlying the genetic variation of lignocellulosic traits in black poplar.

Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem.

• An association genetics approach was used to examine individual genes and alleles at the loci responsible for complex traits controlling lignocellulosic biosynthesis in black cottonwood (Populus trichocarpa). Recent interest in poplars as a source of renewable energy, combined with the vast genomic resources available, has enabled further examination of their genetic diversity. • Forty candidate genes were resequenced in a panel of 15 unrelated individuals to identify single nucleotide polymorphisms (SNPs). Eight hundred and seventy-six SNPs were successfully genotyped in a clonally replicated population (448 clones). The association population (average of 2.4 ramets per clone) was phenotyped using pyrolysis molecular beam mass spectrometry. Both single-marker and haplotype-based association tests were implemented to identify associations for composite traits representing lignin content, syringyl : guaiacyl ratio and C6 sugars. • Twenty-seven highly significant, unique, single-marker associations (false discovery rate Q < 0.10) were identified across 40 candidate genes in three composite traits. Twenty-three significant haplotypes within 11 genes were discovered in two composite traits. • Given the rapid decay of within-gene linkage disequilibrium and the high coverage of amplicons across each gene, it is likely that the numerous polymorphisms identified are in close proximity to the causative SNPs and the haplotype associations reflect information present in the associations between markers.

Predictors of course completion for the U.S. Army pharmacy specialist course.

The purpose of this study was to determine predictors of successful completion of the U.S. Army Medical Department pharmacy specialist (91Q) training program. The sample consisted of 143 students from four course iterations, and only students enrolled in the course for the first time were included for analysis. The relationship between 16 predictor variables and successful completion was assessed. Five variables, the ranks of private (E1) and specialist (E4), cross-trainee status, gender, and Armed Services Vocational Aptitude Battery (ASVAB) general technical (GT) score, were found to be significant predictors using simple linear regression. Using hierarchical multiple linear regression analysis, three variables, service component, gender, and ASVAB GT score, were found to have a significant unique shared variance with success. The results of this study indicate that ASVAB GT scores are predictive of success (p < 0.01) in the 91Q training program. Using these predictors, the selection process may be modified to improve the likelihood of student success in the course.