Oaks (Quercus spp.) are widespread hardwood trees in the Northern Hemisphere and of high ecological, economic, and social values. Optimal experimental design of genetic trials is essential for ...accurate estimates of genetic parameters and improving the genetic merit of breeding stock. Here, we evaluate the use of post hoc row-column factors combined with spatial adjustment to improve genetic analyses of parents and individual trees in field progeny tests of plantation hardwoods, using cherrybark oak (Quercus pagoda Raf.) as an example. For tree height, post hoc incomplete blocking reduced ~14% more of the within-block environmental variance compared to the randomized complete block design (RCBD) model. Incomplete blocking also improved the heritability estimates for height by 7% to 14% compared to the original RCBD model. No clinal trend for growth breeding values was identified due to provenances. Our approach warrants the initial selection for height as early as age ~10 based on its moderate narrow-sense heritability of 0.2; however, diameter and volume need longer evaluation times. The post hoc incomplete blocking is more efficient and promising to improve the genetic analysis of Q. pagoda to minimize the environmental heterogeneity influences. Adjusting competition and spatial effects, including the distance principal components and autoregressive residual structure notably improves the model fit based on the observed reductions in AICs and BICs. Employing our approach is promising for hardwood genetic improvement in the southern USA.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
•We propose a novel method to guide seed deployment and assisted migration decisions.•The method assesses the probability of family performance under altered climate conditions.•The approach can be ...applied to categorical data which covers many environmental metrics.•The approach accounts for both genetic and environmental effects.•The developed models can be readily implemented in Decision Support Systems.
Climate change is impacting distributions of both fauna and flora, including many crops. In order to ensure the health and vigor of the species we depend upon for food and fiber, assisted migration strategies may need to be implemented. This is especially true for long-lived forest trees. Multinomial logit regression was used to develop a Categorical Universal Response Function (CURF) to delineate deployment zones for loblolly pine (Pinus taeda L.) using 15-year measurements from the Western Gulf Forest Tree Improvement Program (WGFTIP) Geographic Seed Source Study (GSSS). The CURF uses performance categories for the response variable, and the model assigns the probabilities with which the performance for a given seed source will fall into these various categories. First and second powers of minimum temperature of the coldest month, summer precipitation, and variation measures of these two metrics at both the seed source site of origin and the test location were used as independent variables. Planted tree volume, accounting for both survival and growth, was used as the response variable. Model performance was good, with the AUC score ranging from 0.785 to 0.808, depending on (1) whether or not the variable interactions were included and (2) the variable selection criterion used (AIC or BIC). Resulting models were then applied to historic weather patterns to illustrate inferred deployment zones for three seed sources. The projected performance generally agreed with the current consensus on loblolly pine seed movement guidelines. The models developed here can be readily implemented in a Decision Support System as they (1) suggest sets of adapted loblolly pine families from which foresters can choose based on local knowledge, (2) can be easily expanded to include other variables, and (3) can be applied to outputs from projected climate scenarios to extrapolate into the future.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Deployment of improved loblolly pine (
Pinus taeda L.) genotypes across the southern United States is a standard silvicultural practice. Most planting is conducted using open-pollinated (OP) families ...from first- or second-generation seed orchards, and these OP families typically display remarkable rank stability for productivity and quality traits across a range of site characteristics, climates, and silvicultural systems. With only a few exceptions, families are generally stable in performance across all sites within a climatic zone. As tree improvement and nursery programs progress towards deployment of more intensively selected genotypes and less genetically diverse full-sib families or clones, there may be a greater likelihood that genotype by environment (G
×
E) interactions will become important, particularly as the level of silvicultural treatment intensity increases. We present evidence from numerous trials with full-sib families and clones demonstrating that G
×
E for growth and other traits is no more significant than for OP families. At present and for the foreseeable future, G
×
E does not appear to be a major concern for the majority of deployed genetic sources under most silvicultural systems.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
First-generation selection (FGS) and second-generation selection (SGS) breeding populations of loblolly pine from east Texas were studied to estimate the genetic diversity, population structure, ...linkage disequilibrium (LD), signatures of selection and association of breeding traits with a genome-wide panel of 4,264 single nucleotide polymorphisms (SNPs). Relatively high levels of observed (H ₒ = 0.178–0.198) and expected (H ₑ = 0.180–0.198) heterozygosities were observed in all populations. The amount of inbreeding was very low with many populations exhibiting a slight excess of heterozygotes. The population structure was weak, but F ST indicated more pronounced differentiation in the SGS populations. As expected for outcrossing natural populations, the genome-wide LD was low, but marker density was insufficient to deduce the decay rate. Numerous associations were found between various phenotypic traits and SNPs, but only a few remained significant after false positive correction. Signatures of diversifying and balancing selection were found in markers representing important biological functions. These results present the first step in the application of marker-assisted selection (MAS) to the Western Gulf Forest Tree Improvement Program (WGFTIP) for loblolly pine and will contribute to the knowledgebase necessary for genomic selection technology.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
We present the results of the three-month above-ground commissioning run of the Large Underground Xenon (LUX) experiment at the Sanford Underground Research Facility located in Lead, South Dakota, ...USA. LUX is a 370kg liquid xenon detector that will search for cold dark matter in the form of Weakly Interacting Massive Particles (WIMPs). The commissioning run, conducted with the detector immersed in a water tank, validated the integration of the various sub-systems in preparation for the underground deployment. Using the data collected, we report excellent light collection properties, achieving 8.4 photoelectrons per keV for 662keV electron recoils without an applied electric field, measured in the center of the WIMP target. We also find good energy and position resolution in relatively high-energy interactions from a variety of internal and external sources. Finally, we have used the commissioning data to tune the optical properties of our simulation and report updated sensitivity projections for spin-independent WIMP-nucleon scattering.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Invasive plants decrease biodiversity, modify vegetation structure, and inhibit growth and reproduction of native species. Japanese honeysuckle (Lonicera japonica Thunb.) is the most prevalent ...invasive vine in the forestlands of eastern Texas. Hence, we aimed to identify potential factors influencing the distribution of the species, quantify the relative importance of each factor, and test possible management strategies. We analyzed an extensive dataset collected as part of the Forest Inventory and Analysis Program of the United States Department of Agriculture (USDA) Forest Service to quantify the range expansion of Japanese honeysuckle in the forestlands of eastern Texas from 2006 to 2011. We then identified potential factors influencing the likelihood of presence of Japanese honeysuckle using boosted regression trees. Our results indicated that the presence of Japanese honeysuckle on sampled plots almost doubled during this period (from 352 to 616 plots), spreading extensively, geographically. The probability of invasion was correlated with variables representing landscape conditions, climatic conditions, forest features, disturbance factors, and forest management activities. Habitats most at risk to invasion under current conditions occurred primarily in northeastern Texas, with a few invasion hotspots in the south. Estimated probabilities of invasion were reduced most by artificial site regeneration, with habitats most at risk again occurring primarily in northeastern Texas.
Loblolly pine (Pinus taeda L.) is one of the most widely planted and commercially important forest tree species in the USA and worldwide, and is an object of intense genomic research. However, whole ...genome resequencing in loblolly pine is hampered by its large size and complexity and a lack of a good reference. As a valid and more feasible alternative, entire exome sequencing was hence employed to identify the gene-associated single nucleotide polymorphisms (SNPs) and to genotype the sampled trees.
The exons were captured in the ADEPT2 association mapping population of 375 clonally-propagated loblolly pine trees using NimbleGen oligonucleotide hybridization probes, and then exome-enriched genomic DNA fragments were sequenced using the Illumina HiSeq 2500 platform. Oligonucleotide probes were designed based on 199,723 exons (≈49 Mbp) partitioned from the loblolly pine reference genome (PineRefSeq v. 1.01). The probes covered 90.2 % of the target regions. Capture efficiency was high; on average, 67 % of the sequence reads generated for each tree could be mapped to the capture target regions, and more than 70 % of the captured target bases had at least 10X sequencing depth per tree. A total of 972,720 high quality SNPs were identified after filtering. Among them, 53 % were located in coding regions (CDS), 5 % in 5' or 3' untranslated regions (UTRs) and 42 % in non-target and non-coding regions, such as introns and adjacent intergenic regions collaterally captured. We found that linkage disequilibrium (LD) decayed very rapidly, with the correlation coefficient (r (2)) between pairs of SNPs linked within single scaffolds decaying to half maximum (r (2) = 0.22) within 55 bp, to r (2) = 0.1 within 192 bp, and to r (2) = 0.05 within 451 bp. Population structure analysis using unlinked SNPs demonstrated the presence of two main distinct clusters representing western and eastern parts of the loblolly pine range included in our sample of trees.
The obtained results demonstrated the efficiency of exome capture for genotyping species such as loblolly pine with a large and complex genome. The highly diverse genetic variation reported in this study will be a valuable resource for future genetic and genomic research in loblolly pine.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
A 2005 survey of practices indicated limited use of three-dimensional (3D) imaging modalities and planning methods in cervix cancer brachytherapy in Australia and New Zealand. However, advancing ...technologies and published recommendations are influencing change. This survey aims to identify both changes in practice and awareness and uptake of Groupe European de Curietherapie of the European Society for Therapeutic Radiology and Oncology (GEC-ESTRO) recommendations.
A survey was emailed to all radiotherapy departments with brachytherapy facilities. Twenty departments practise brachytherapy for cancer of the cervix. The survey consisted of five questions enquiring about use and type of 3D imaging; rate of reimaging and replanning; and contouring, prescribing and reporting practices.
A 100% response rate was obtained. Sixty-five per cent of departments use 3D CT imaging to plan brachytherapy insertions. Thirty per cent of departments use two-dimensional (2D) x-rays. Four departments (20%) use a combination of imaging modalities including CT, ultrasound and MRI. Sixty-five per cent of departments reimage and replan for each insertion. Four departments (20%) contour, prescribe dose and report treatment according to GEC-ESTRO recommendations.
There has been a marked increase in the use of 3D imaging and awareness of GEC-ESTRO recommendations. Implementation and reporting of image-based gynaecological brachytherapy is strongly dependent on local resources and infrastructure.
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BFBNIB, DOBA, FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, SIK, UILJ, UKNU, UL, UM, UPUK
The goal of the Majorana Demonstrator project is to search for 0νββ decay in 76Ge. Of all candidate isotopes for 0νββ, 76Ge has some of the most favorable characteristics. Germanium detectors are a ...well established technology, and in searches for 0νββ, the high purity germanium crystal acts simultaneously as source and detector. Furthermore, p-type germanium detectors provide excellent energy resolution and a specially designed point contact geometry allows for sensitive pulse shape discrimination. This paper will summarize the experiences the MAJORANA collaboration made with enriched germanium detectors manufactured by ORTEC®®. The process from production, to characterization and integration in MAJORANA mounting structure will be described. A summary of the performance of all enriched germanium detectors will be given.
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