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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.

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.

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.

Background 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. Results 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. Conclusions 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.

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.

The Majorana Demonstrator is a planned 40 kg array of Germanium detectors intended to demonstrate the feasibility of constructing a tonne-scale experiment that will seek neutrinoless double beta decay (0νββ) in 76Ge. Such an experiment would require backgrounds of less than 1 count tonne-year in the 4 keV region of interest around the 2039 keV Q-value of the ββ decay. Designing low-noise electronics, which must be placed in close proximity to the detectors, presents a challenge to reaching this background target. This paper will discuss the Majorana collaboration's solutions to some of these challenges.

Neutrinoless double-beta (0νββ) decay is a hypothesized process where in some even-even nuclei it might be possible for two neutrons to simultaneously decay into two protons and two electrons without emitting neutrinos. This is possible only if neutrinos are Majorana particles, i.e. fermions that are their own antiparticles. Neutrinos being Majorana particles would explicitly violate lepton number conservation, and might play a role in the matter-antimatter asymmetry in the universe. The observation of neutrinoless double-beta decay would also provide complementary information related to neutrino masses. The Majorana Collaboration is constructing the MAJORANA DEMONSTRATOR, with a total of 40-kg Germanium detectors, to search for the 0νββ decay of 76Ge and to demonstrate a background rate at or below 3 counts/(ROI·t·y) in the 4 keV region of interest (ROI) around the 2039 keV Q-value for 76Ge 0νββ decay. In this paper, we discuss the physics of neutrinoless double beta decay and then focus on the MAJORANA DEMONSTRATOR, including its design and approach to achieve ultra-low backgrounds and the status of the experiment.

The accession number for the sequence submitted to NCBI Sequence Read Archive (SRA) listed in the original article [1] is incorrect; SRP075763 should be SRP075363.

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.

A meta-analysis of 520 parents and 51,439 individuals was used to develop two equations for predicting age-age genetic correlations in Pinus taeda L. Genetic and phenotypic family mean correlations and heritabilities were estimated for ages ranging from 2 to 25 years on 31 sites in the southern U.S. and Zimbabwe. Equations for predicting age-age correlations based on P. taeda populations from west and east of the Mississippi River proved statistically different. Both predictive equations proved conservative for validation datasets consisting of younger tests in the U.S. and Zimbabwe. Age-dependent log-linear predictive equations were favored over growth-dependent equations. All P. taeda predictive equations based on genetic correlations favored earlier selection when compared to a generalized conifer predictive equation based on phenotypic correlations. The age-age correlations structure showed stability independent of planting density and across a wide range of family sizes.