Genomic evaluation for breeding and genetic management in Cordia africana, a multipurpose tropical tree species.

BACKGROUND: Planting tested forest reproductive material is crucial to ensure the increased resilience of intensively managed productive stands for timber and wood product markets under climate change scenarios. Single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) analysis is a cost-effective option for using genomic tools to enhance the accuracy of predicted breeding values and genetic parameter estimation in forest tree species. Here, we tested the efficiency of ssGBLUP in a tropical multipurpose tree species, Cordia africana, by partial population genotyping. A total of 8070 trees from three breeding seedling orchards (BSOs) were phenotyped for height. We genotyped 6.1% of the phenotyped individuals with 4373 single nucleotide polymorphisms. The results of ssGBLUP were compared with pedigree-based best linear unbiased prediction (ABLUP) and genomic best linear unbiased prediction (GBLUP), based on genetic parameters, theoretical accuracy of breeding values, selection candidate ranking, genetic gain, and predictive accuracy and prediction bias. RESULTS: Genotyping a subset of the study population provided insights into the level of relatedness in BSOs, allowing better genetic management. Due to the inbreeding detected within the genotyped provenances, we estimated genetic parameters both with and without accounting for inbreeding. The ssGBLUP model showed improved performance in terms of additive genetic variance and theoretical breeding value accuracy. Similarly, ssGBLUP showed improved predictive accuracy and lower bias than the pedigree-based relationship matrix (ABLUP). CONCLUSIONS: This study of C. africana, a species in decline due to deforestation and selective logging, revealed inbreeding depression. The provenance exhibiting the highest level of inbreeding had the poorest overall performance. The use of different relationship matrices and accounting for inbreeding did not substantially affect the ranking of candidate individuals. This is the first study of this approach in a tropical multipurpose tree species, and the analysed BSOs represent the primary effort to breed C. africana.

Identification and high-throughput genotyping of single nucleotide polymorphism markers in a non-model conifer (Abies nordmanniana (Steven) Spach).

Single nucleotide polymorphism (SNP) markers are powerful tools for investigating population structures, linkage analysis, and genome-wide association studies, as well as for breeding and population management. The availability of SNP markers has been limited to the most commercially important timber species, primarily due to the cost of genome sequencing required for SNP discovery. In this study, a combination of reference-based and reference-free approaches were used to identify SNPs in Nordmann fir (Abies nordmanniana), a species previously lacking genomic sequence information. Using a combination of a genome assembly of the closely related Silver fir (Abies alba) species and a de novo assembly of low-copy regions of the Nordmann fir genome, we identified a high density of reliable SNPs. Reference-based approaches identified two million SNPs in common between the Silver fir genome and low-copy regions of Nordmann fir. A combination of one reference-free and two reference-based approaches identified 250 shared SNPs. A subset of 200 SNPs were used to genotype 342 individuals and thereby tested and validated in the context of identity analysis and/or clone identification. The tested SNPs successfully identified all ramets per clone and five mislabeled individuals via identity and genomic relatedness analysis. The identified SNPs will be used in ad hoc breeding of Nordmann fir in Denmark.

Pacemaker implantation after congenital heart surgery: risk and prognosis in a population-based follow-up study.

OBJECTIVE: Although earlier a feared complication of congenital cardiac surgery, the incidence of heart-block and sinus node dysfunction has been lowered to 1-4% due to improved surgical techniques and better anatomical understanding of the cardiac conduction system. Development of feasible pacemaker technologies has further lowered mortality and morbidity. However, pacemaker implantation in paediatric patients is in itself associated with significant morbidity due to pacemaker system failure and replacement. The aim of the present study was to examine prognostic factors of mortality, failure of systems and timing of implantation after surgery in post-surgical pacemaker patients. METHODS: We carried out a historical prospective follow-up analysis of all patients (age less than 18 years) who underwent pacemaker implantation due to post-surgical heart-block or sinus node dysfunction in the period 1981-2002 at our institution. Data was extracted from the Danish Pacemaker Register and hospital records. Kaplan-Meier survival time estimates and Cox proportional hazards analysis (Relative Risk, RR) were used to identify prognostic factors. RESULTS: High RACHS score (RR, 16.57), low age at implantation (RR, 0.22), low age at operation (RR, 0.06) and epicardial lead (RR, 0.18) were significant predictors for early mortality. Similarly, high RACHS score (RR, 4.84), low age at implantation (RR, 0.32), low age operation (RR, 0.38) and epicardial lead (RR, 0.40) were significant predictors failure of 1st pacemaker system. CONCLUSIONS: We identified a number of prognostic factors of patient mortality and failure of systems. One factor, high RACHS score, was previously shown to predict mortality and length of ICU stay in paediatric cardiac surgery; however, this study is the first to show a correlation between RACHS score and mortality as well as failure of pacemaker systems. This may have future implications for preoperative risk stratification of patients and counselling of parents to patients with congenital heart disease.

Effect of modified ultrafiltration on the inflammatory response in paediatric open-heart surgery: a prospective, randomized study.

Modified ultrafiltration (MUF) is often used in conjunction with paediatric cardiac surgery with cardiopulmonary bypass (CPB) and is thought to improve clinical outcome. It is unclear whether these improvements (if any) are due to the removal of inflammatory mediators. In this prospective study, 18 children aged 12-24 months undergoing uncomplicated cardiac surgery with methylprednisolone added in the pump prime were randomized to receive CPB with (n = 10) and without (n = 8) MUF. Cytokines (TNFalpha, IL-6, IL-1beta, IL-10, IL-1ra), complement split products (C3d, C4d) and coagulation system activation (F1 + 2, ATIII) were measured pre-, peri- and up to 48 h postoperatively. For clinical outcome, the alveolar-arterial oxygen (A-a) gradient, transfusion requirement, drain loss, mean blood pressure and requirement for inotropic support were registered up to 24 h postoperatively. Our results show an improvement in postoperative oxygenation as well as a tendency towards decreased drain loss and improved haemodynamics in the MUF group. There were no intergroup differences detectable for TNFalpha, IL-1beta, IL-1ra, complement and coagulation markers. We conclude that MUF in itself does not significantly influence TNFalpha, IL-1beta, IL-1ra and the complement and coagulation profiles in children undergoing cardiac surgery with CPB. Despite this, there was some evidence for improved clinical outcome. Our results do not support that MUF improves postoperative organ function by modulation of the measured markers of inflammation.