Genetic parameters and improvement strategies for the Pinus elliottii var. elliottii x Pinus caribaea var. hondurensis hybrid in Queensland, Australia

Conventional and novel quantitative genetic methods were used to examine the genetic basis of variation in wood and growth properties in a progeny test of Pinus elliottii var.elliottii(PEE),Pinus caribaea var. hondurensis(PCH) and their F1 and F2 hybrids(PEExPCH). Progeny originated from four NCII mating designs:6x6-parent designs in PEE and PCH,a 12xl2-parent design in the F1 hybrid using the same set of PEE and PCH parents, and an unrelated 6x6-parent design in the F2 hybrid. Wood density and tree basal area at each tree age were measured using x-ray densitometry of radial samples taken at breast height from an 11-year-old trial of the four taxa planted at two sites in South-East Queensland, Australia. Spiral grain angle was measured on a ring-by-ring basis in the F1 hybrid.Based on the results,comparisons were made among candidate hybrid breeding strategies for the genetic improvement of PEExPCH. The PEE population was characterised by a relatively low stem volume and high wood density, and PCH and PEExPCH by the opposite.Economic pressures are leading Queensland plantation managers of PEExPCH to seek to reduce rotation lengths,but this is dependent on maintaining wood quality comparable to current mature plantations. This study found that low wood density and moderate spiral grain angles in the inner growth rings of the F1 hybrid will require improvement in order to meet this quality criterion. Wood density and spiral grain were more strongly heritable than stem volume in PEE, PCH and the F1 hybrid.Economically significant improvements in all three traits could be achieved by family selection, though strong positive genetic correlations between wood density and measures of density variability suggested that the economic significance of the latter should be investigated. Concurrent improvement of wood density and stem volume in PCH is complicated by a strong adverse genetic correlation between these traits (rA=-0.84). A comparison of genetic gains indicated that selection of parents for pure species progeny performance at tree age 12 was nearly as efficient as direct selection of parents for F1 hybrid progeny performance at age 12,for both stem volume and wood density.Given its shorter breeding cycle interval, pure species selection is likely to be an efficient alternative breeding strategy to direct selection in PEExPCH F1 hybrids, for the purpose of improving wood density.However, the pure-hybrid genetic correlation was only moderate in stem volume in PEE, casting doubt on the value of pure species selection for stem volume, despite the high indirect selection efficiency.Under any type of breeding strategy,density and spiral grain at age 12 could be efficiently improved by selection on field screening measurements using the Pilodyn and Bubble Protractor, respectively, and on direct single-ring measurements of these traits from age 4 onwards; tree basal area could be selected from age 6 onwards in the F1 hybrid, and age 4 onwards in PEE and PCH. The genetic basis of F1 hybrid heterosis in stem volume and wood density was investigated using the quantitative genetic model of Li and Wu(1996). Overdominance or pseudo­ overdominance did not contribute to better-parent heterosis in stem volume or to negative mid­ parent heterosis in wood density. Alleles contributed by PEE conferred increased wood density,and alleles contributed by PCH conferred increased stem volume, providing evidence for the genetic basis of "complementarity" in the PEExPCH hybrid.The primary importance of additive gene action in both traits in the F1 hybrid is consistent with results from the genetic gain analysis,but further suggests that direct forward selection in a composite hybrid population may be an efficient alternative to pure species selection, for PEExPCH hybrid improvement;the results hence do not support Shelbourne's hypothesis that interspecific tree hybrids are "genetic dead ends".This study corroborates scattered evidence from previous studies that advanced generation hybridisation may provide a powerful future tool for tree breeders in "complementary" interspecific hybrid tree taxa

A genome-wide SNP genotyping resource for tropical pine tree species

We performed gene and genome targeted SNP discovery towards the development of a genome-wide, multispecies genotyping array for tropical pines. Pooled RNA-seq data from shoots of seedlings from five tropical pine species was used to identify transcript-based SNPs resulting in 1.3 million candidate Affymetrix SNP probe sets. In addition, we used a custom 40 K probe set to perform capture-seq in pooled DNA from 81 provenances representing the natural ranges of six tropical pine species in Mexico and Central America resulting in 563 K candidate SNP probe sets. Altogether, 300 K RNA-seq (72%) and 120 K capture-seq (28%) derived SNP probe sets were tiled on a 420 K screening array that was used to genotype 576 trees representing the 81 provenances and commercial breeding material. Based on the screening array results, 50 K SNPs were selected for commercial SNP array production including 20 K polymorphic SNPs for P. patula, P. tecunumanii, P. oocarpa and P. caribaea, 15 K for P. greggii and P. maximinoi, 13 K for P. elliottii and 8K for P. pseudostrobus. We included 9.7 K ancestry informative SNPs that will be valuable for species and hybrid discrimination. Of the 50 K SNP markers, 25% are polymorphic in only one species, while 75% are shared by two or more species. The Pitro50K SNP chip will be useful for population genomics and molecular breeding in this group of pine species that, together with their hybrids, represent the majority of fast-growing tropical and subtropical pine plantations globally.DATA AVAILABILITY STATEMENT : The pooled targeted capture sequencing data have been made available via NCBI SRA BioProject accession PRJNA742386. RNA-seq data are available via NCBI SRA BioProject accessions PRJNA416697 (P. tecunumanii), PRJNA416698 (P. patula), PRJNA685280 (P. oocarpa), PRJNA685281 (P. greggii) and PRJNA685282 (P. maximinoi). Metadata and probe set sequences used for markers selected for the 50 K commercial array are available as Supporting Information (Table S5). Genotype data set used for PCA and STRUCTURE analysis is available in Supporting Information (Table S6).http://www.wileyonlinelibrary.com/journal/men2022-08-12hj2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

Genetic parameter estimates informed by a marker-based pedigree: A case study with Eucalyptus cladocalyx in southern Australia

Analysis of stem diameter, height and axis persistence (AP) in a first-generation Eucalyptus cladocalyx breeding population comprising 137 wild and land-race families planted at 11 sites in southern Australia revealed significant genetic variation among subpopulations and among families within subpopulations. Alternative analyses were carried out using individual-tree mixed models that (i) assumed the trees within families were half-siblings (HS) and (ii) used molecular marker-based information to account for highly heterogeneous relatedness and inbreeding depression among families resulting from mixed mating (MM). For certain site and trait combinations, the HS models would not converge, as estimates of additive variance exceeded the total phenotypic variance, demonstrating the fundamental unsuitability of the HS assumption for this breeding population. Where HS models converged, moderate to very high heritability estimates resulted for growth traits. The MM assumption resulted in re-ranking of individual-tree breeding values and markedly lower estimates of narrow-sense heritability for all trait-site combinations. In some cases, however, heritability remained moderate to high, probably reflecting unquantified dominance variance in some highly inbred subpopulations. Genotype-by-environment interaction was significant overall due to reactivity of genotypes on a few sites, with type-B correlations between pairs of sites ranging from 0.06 to 0.99. Generally, families from the Australian land race were found to perform particularly well for both growth and AP traits. Some wild families were found to be vigorous, despite significant inbreeding. The study has demonstrated that traditional models assuming non-relatedness and/or homogeneous inbreeding in first-generation eucalypt breeding populations can be significantly improved upon by flexible mixed models that integrate marker-based data

Inheritance of spiral grain in the juvenile core of Pinus radiata

Spiral grain is the angular arrangement of fibres in a tangential plane with reference to the pith or vertical tree axis. Spiral grain angles exceeding 5° can cause wood to twist, which may result in a considerable amount of waste and degrade. We assess

Endothelial activation, haemostasis and thrombosis biomarkers in Ugandan children with severe malaria participating in a clinical trial

Abstract Background Malaria is a major cause of morbidity and mortality in sub-Saharan Africa, and poor outcomes have been associated with endothelial activation. In this study, biomarkers of endothelial activation, haemostasis, and thrombosis were measured in Ugandan children with severe malaria who participated in a clinical trial, in order to investigate associations between these processes. Methods Serum and plasma were collected from participants at baseline (day 1), and on days 2, 3, 4, and 14. Von Willebrand factor (VWF) antigen was measured in stored plasma samples from all trial participants, and its association with mortality and changes over time were analysed. VWF multimer patterns were evaluated in baseline serum samples by gel electrophoresis followed by Western blotting. Levels of angiopoietins 1 and 2, VWF antigen, total active VWF, ADAMTS13, platelet counts, apolipoprotein A1, and syndecan-1 were measured in stored serum samples from 12 survivors at baseline and day 4. Results VWF antigen levels were associated with mortality, and decreased over time in survivors. Baseline VWF antigen and total active VWF levels were elevated, and very large multimers were present in the baseline serum of several patients. Higher platelet counts were associated with higher angiopoietin-1 and apolipoprotein A1 levels, while lower platelet counts were associated with higher syndecan-1, a marker of endothelial damage. Higher angiopoietin-2 to angiopoietin-1 ratio and higher syndecan-1 levels were correlated with lower apolipoprotein A1 levels. There were no correlations between total active VWF, VWF antigen, or ADAMTS13 levels and the other biomarkers at baseline. Changes in biomarker levels between baseline and day 4 were not correlated. Conclusions These results confirm that severe malaria is associated with endothelial activation, and suggest that endothelial activation contributes to microvascular thrombosis and endothelial damage

Universal Speech Tools: The Cslu Toolkit

A set of freely available, universal speech tools is needed to accelerate progress in the speech technology. The CSLU Toolkit represents an effort to make the core technology and fundamental infrastructure accessible, affordable and easy to use. The CSLU Toolkit has been under development for five years. This paper describes recent improvements, additions and uses of the CSLU Toolkit. 1. INTRODUCTION Since 1993, the Center for Spoken Language Understanding (CSLU) has focused on incorporating state-of-the-art spokenlanguage technology into a portable, comprehensive and easyto -use software environment. The result of these efforts is the CSLU Toolkit. The toolkit integrates learning materials, authoring tools and core technologies such as speech recognition, text-to-speech synthesis, facial animation and speech reading. The toolkit is designed to support basic research, development and education activities related to spoken language systems and human-computer interfaces. What are our ..