Comparison of Space-Plant Versus Sward Plot Selection in Thickspike Wheatgrass (\u3ci\u3eElymus lanceolatus\u3c/i\u3e)

Thickspike wheatgrass (Elymus lanceolatus [Scribn. & J.G. Sm.] Gould) is an important native perennial grass species used for rangeland revegetation in North America. Plant breeding efforts relying on space‐plant evaluations have resulted in limited improvement in this species. The purpose of this study was to characterize the performance of thickspike wheatgrass half‐sib families under space‐plant and sward plot evaluations, estimate the correlation between measured traits in both evaluation settings, and determine the validity of selecting thickspike wheatgrass for rangeland revegetation in the nontarget environment space‐plant plots. The study included 50 thickspike wheatgrass half‐sib families and five commercial cultivars and experimental populations which were evaluated over 3 years in space‐plant and sward plot evaluations at a field site in Box Elder County, Utah, USA. Collected data included stand percentage, flag leaf height, and herbage dry mass. Narrow‐sense heritability estimates were low to moderate (h2 \u3c 0.60) and Spearman and genetic correlation estimates among traits were also generally low to moderate. Overall, there was little evidence to suggest the use space‐plant evaluations in thickspike wheatgrass improvement programmes

Nuclear DNA Content of Perennial Grasses of the Triticeae

Nuclear DNA content was determined by flow cytometry for an array of perennial species of the Triticeae (Poaceae) which characterize the tribe and are representative of the genomes of the Triticeae. The mean nuclear DNA content expressed on a diploid basis (DNA pg/2C) for the diploid genomes (in parentheses) were as follows: Agropyron (PP) 13.9 pg, Pseudoroegneria (StSt) 8.8 pg, Hordeum (HH) 9.5 pg, Psathyrostachys (NsNs) 16.7 pg, and Thinopyrum genomes (EeEe) 14.9 pg and (EeEe) 12.0 pg. The YY genome in Elymus was determined by difference to be 9.3 pg. The unknown or XmXm genome or genomes in Leymus could have DNA contents that range from 2.7 to 7.7 pg/2C. There were significant differences in DNA content of species with similar diploid genomes. There were also significant differences in nuclear DNA content among polyploid species with the same genomes. In general, the nuclear DNA content of the polyploid species of the Triticeae were similar to the expected DNA contents on the basis of previous genomic classifications. However, in some allopolyploid genera such as Thinopyrum and Pascopyrum, the nuclear DNA content of some species was less than expected on the basis of summation of the DNA of constituent genomes. The results indicate that gain or loss of nuclear DNA has occurred during the evolution of the perennial Triticeae and was probably a part of speciation

Braided Rivers and Superconducting Vortex Avalanches

Magnetic vortices intermittently flow through preferred channels when they are forced in or out of a superconductor. We study this behavior using a cellular model, and find that the vortex flow can make braided rivers strikingly similar to aerial photographs of braided fluvial rivers, such as the Brahmaputra. By developing an analysis technique suitable for characterizing a self-affine (multi)fractal, the scaling properties of the braided vortex rivers in the model are compared with those of braided fluvial rivers. We suggest that avalanche dynamics leads to braiding in both cases.Comment: 4 pages, 3 figures. To appear in PR

Atomic and Molecular Carbon as a Tracer of Translucent Clouds

Using archival, high-resolution far-ultraviolet HST/STIS spectra of 34 Galactic O and B stars, we measure CI column densities and compare them with measurements from the literature of CO and H_2 with regard to understanding the presence of translucent clouds along the line-of-sight. We find that the CO/H_2 and CO/CI ratios provide good discriminators for the presence of translucent material, and both increase as a function of molecular fraction, f = 2N(H_2)/N(H). We suggest that sightlines with values below CO/H_2 ~ 1E-6 and CO/CI ~ 1 contain mostly diffuse molecular clouds, while those with values above sample clouds in the transition region between diffuse and dark. These discriminating values are also consistent with the change in slope of the CO v. H_2 correlation near the column density at which CO shielding becomes important, as evidenced by the change in photochemistry regime studied by Sheffer et al. (2008). Based on the lack of correlation of the presence of translucent material with traditional measures of extinction we recommend defining 'translucent clouds' based on the molecular content rather than line-of-sight extinction properties.Comment: 9 pages, accepted for publication in the Astrophysical Journal; new version corrects minor typographical error

Breeding CWG-R crested wheatgrass for reduced-maintenance turf

Using reduced-maintenance turfgrass as an alternative to current high-maintenance turfgrass species would conserve resources, labor, and potentially reduce pollutants in the environment. CWG-R is an experimental population of crested wheatgrass [Agropyron cristatum (L.) Gaertn.] from Iran that has shown potential as a low-maintenance turf. The objective of this research was to estimate the genetic variation for turf traits within the CWG-R population when evaluated under a reduced-maintenance regimen. Ninety CWG-R clonal lines were established in 1998 near Logan, UT, as spaced-plant plots in a RCB design with four replicates. Maintenance of 50% ET0 replacement, 97.74 kg of nitrogen ha1yr1, and mowing at 7.62 cm was approximately 40% lower than typical for high-input Kentucky bluegrass (Poa pratensis L.) turf. Critical turf traits, including spring regrowth, season-long (March–October) and mid-summer (June–July) turf quality, color, and rhizomatous spread were evaluated in 1999 and 2000. Significant genetic variation among clonal lines was evident with broad-sense heritabilities of 0.65, 0.76, 0.45, and 0.76 for spring regrowth, season-long turf quality, color, and rhizomatous spread, respectively. Several clonal lines remained green throughout the summer months and maintained acceptable turf quality and color ratings during the critical mid-summer period. The high broad-sense heritability estimates within this population indicate potential for successful improvement of critical turf traits by phenotypic selection. These results indicate that that CWG-R could be an important low-maintenance turf-type crested wheatgrass germplasm

RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting

RNA-Seq is increasingly being used to measure human RNA expression on a genome-wide scale. Expression profiles can be interrogated to identify and functionally characterize treatment-responsive genes. Ultimately, such controlled studies promise to reveal insights into molecular mechanisms of treatment effects, identify biomarkers, and realize personalized medicine. RNA-Seq Reports (RSEQREP) is a new open-source cloud-enabled framework that allows users to execute start-to-end gene-level RNA-Seq analysis on a preconfigured RSEQREP Amazon Virtual Machine Image (AMI) hosted by AWS or on their own Ubuntu Linux machine. The framework works with unstranded, stranded, and paired-end sequence FASTQ files stored locally, on Amazon Simple Storage Service (S3), or at the Sequence Read Archive (SRA). RSEQREP automatically executes a series of customizable steps including reference alignment, CRAM compression, reference alignment QC, data normalization, multivariate data visualization, identification of differentially expressed genes, heatmaps, co-expressed gene clusters, enriched pathways, and a series of custom visualizations. The framework outputs a file collection that includes a dynamically generated PDF report using R, knitr, and LaTeX, as well as publication-ready table and figure files. A user-friendly configuration file handles sample metadata entry, processing, analysis, and reporting options. The configuration supports time series RNA-Seq experimental designs with at least one pre- and one post-treatment sample for each subject, as well as multiple treatment groups and specimen types. All RSEQREP analyses components are built using open-source R code and R/Bioconductor packages allowing for further customization. As a use case, we provide RSEQREP results for a trivalent influenza vaccine (TIV) RNA-Seq study that collected 1 pre-TIV and 10 post-TIV vaccination samples (days 1-10) for 5 subjects and two specimen types (peripheral blood mononuclear cells and B-cells)

Proceedings of the 2nd International Triticeae Symposium

At the First International Triticeae Symposium, Helsingborg, Sweden, July 29-August 2, 1991, the participants decided that subsequent meetings will be held every three years. Thus, the Second International Triticeae Symposium was held in Logan, Utah, U.S.A, June 20-24, 1994, with USDA Agricultural Research Service\u27s Forage and Range Research Laboratory and Utah State University as hosts. The purposes of the second symposium were: (I) to exchange the latest scientific information and advancements related to annual and perennial Triticeae species; (2) to promote the exchange of ideas for developing coordinated collaborative research; and (3) to provide an opportunity to see the biodiversity in the Triticeae by visiting the USDA Living Collection of Perennial Triticeae near Logan. In addition to the above scientific goals, the participants also paid tributes to the late Dr. Douglas Dewey at the symposium banquet by presenting a plaque to Mrs. Lois Dewey and a slide show featuring Doug\u27s activities and his many colleaques and associates. Due to various reasons, some contributors of papers were unable to attend the symposium. Nevertheless, their manuscripts are included in the proceedings to benefit all Triticeae workers. Conference support and travel grants from the USDA-CSRS Competitive Grant Program and the International Science Foundation enabled several speakers from China, former Soviet Union countries, and Estonia to attend the symposium. Cooperation and assistance from our colleagues at the USDA-ARS Forage and Range Research Laboratory and the Location Administrative Office (Logan, Utah), the USDA Small Grain Collection (Aberdeen, Idaho), Utah State University and Utah Agricultural Experiment Station , and the Conference and Institute Division and the Student Services of Utah State University (Logan, Utah) made the symposium successful. We also thank many participants for reviewing manuscripts for the symposium proceedings. Most important are the contributions of the conference participants who presented the scientific information and ideas during and after the Second International Triticeae Symposium. For the production of this publication, we thank all authors\u27 patience, peer reviewers\u27 effort, and the Publication Design & Production of Utah State University\u27s excellent job

Characterization of Testing Locations for Developing Cool-Season Grass Species

The identification of best testing locations facilitates the allocation of resources in a breeding program, allowing emphasis to be placed at the sites best suited for identifying superior plant materials for the target environment. The objective of this study was the identification of best locations for the evaluation and testing of cool-season grass species within the Northern Great Plains and Intermountain regions of the USA. This study also sought to subdivide the locations into meaningful environmental groupings based on similar entry performance. The study characterized initial stand frequency and forage production (over a 3-yr period) of crested wheatgrass [Agropyron cristatum (L.) Gaertn.; A. desertorum (Fisch. ex Link) Schultes; A. fragile (Roth) Candargy], intermediate wheatgrass [Thinopyrum intermedium (Host) Barkworth & D.R. Dewey], and smooth bromegrass (Bromus inermis Leyss.) at six locations within these regions. Results suggested the existence of best testing locations and environmental groupings for each of the species. For example, the Ithaca, NE, location was consistently a good location for testing forage production. Although there were some consistencies, generally, the best testing locations and environmental groupings were species and trait specific. Thus, the targeted use of locations appeared to be most useful on an individual species basis, rather than considered across the cool-season grass species

Overcoming High Energy Backgrounds at Pulsed Spallation Sources

Instrument backgrounds at neutron scattering facilities directly affect the quality and the efficiency of the scientific measurements that users perform. Part of the background at pulsed spallation neutron sources is caused by, and time-correlated with, the emission of high energy particles when the proton beam strikes the spallation target. This prompt pulse ultimately produces a signal, which can be highly problematic for a subset of instruments and measurements due to the time-correlated properties, and different to that from reactor sources. Measurements of this background have been made at both SNS (ORNL, Oak Ridge, TN, USA) and SINQ (PSI, Villigen, Switzerland). The background levels were generally found to be low compared to natural background. However, very low intensities of high-energy particles have been found to be detrimental to instrument performance in some conditions. Given that instrument performance is typically characterised by S/N, improvements in backgrounds can both improve instrument performance whilst at the same time delivering significant cost savings. A systematic holistic approach is suggested in this contribution to increase the effectiveness of this. Instrument performance should subsequently benefit.Comment: 12 pages, 8 figures. Proceedings of ICANS XXI (International Collaboration on Advanced Neutron Sources), Mito, Japan. 201

Quantitative Trait Loci (QTL) for Forage Traits in Intermediate Wheatgrass When Grown as Spaced-Plants versus Monoculture and Polyculture Swards

It has been hypothesized that the genetic control of forage traits, especially biomass, for grass plants growing as spaced-plants versus swards is different. Likewise, the genetic control of compatibility in grass–legume polyculture mixtures is assumed to be different than for forage production in a grass monoculture. However, these hypotheses are largely unvalidated, especially at the DNA level. This study used an intermediate wheatgrass mapping population to examine the effect of three competition environments (spaced-plants, polyculture, and monoculture) on classical quantitative genetic parameters and quantitative trait loci (QTL) identification for biomass, morphology, and forage nutritive value. Moderate to high heritable variation was observed for biomass, morphological traits, and nutritive value within all three environments (H ranged from 0.50 to 0.87). Genetic correlations (rG) among environments for morphology and nutritive value were predominantly high, however, were moderately-low (0.30 to 0.48) for biomass. Six biomass QTL were identified, including three on linkage groups (LG) 1, 6, and 15 that were only expressed in the monoculture environment. Moreover, three biomass QTL on LG 10, 14, and 15 exhibited significant QTL by environment interactions. This study verified that the genetic control of grass biomass in a monoculture versus a grass–legume mixture is only partially the same, with additional genes expressed in monoculture, and that biomass in widely spaced-plants versus swards is predominantly under different genetic control. These results indicate that selection for improved grass biomass will be most successful when conducted within the targeted monoculture or polyculture sward environment per se