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Background The aminoglycoside apramycin has been proposed as a drug candidate for the treatment of critical Gram-negative systemic infections. However, the potential of apramycin in the treatment of drug-resistant bloodstream infections (BSIs) has not yet been assessed. Methods The resistance gene annotations of 40 888 blood-culture isolates were analysed. In vitro profiling of apramycin comprised cell-free translation assays, broth microdilution, and frequency of resistance determination. The efficacy of apramycin was studied in a mouse peritonitis model for a total of nine Escherichia coli and Klebsiella pneumoniae isolates. Results Genotypic aminoglycoside resistance was identified in 87.8% of all 6973 carbapenem-resistant Enterobacterales blood-culture isolates, colistin resistance was shown in 46.4% and apramycin in 2.1%. Apramycin activity against methylated ribosomes was > 100-fold higher than that for other aminoglycosides. Frequencies of resistance were < 10-9 at 8 × minimum inhibitory concentration (MIC). Tentative epidemiological cut-offs (TECOFFs) were determined as 8 µg/mL for E. coli and 4 µg/mL for K. pneumoniae. A single dose of 5 to 13 mg/kg resulted in a 1-log colony-forming unit (CFU) reduction in the blood and peritoneum. Two doses of 80 mg/kg resulted in an exposure that resembles the AUC observed for a single 30 mg/kg dose in humans and led to complete eradication of carbapenem- and aminoglycoside-resistant bacteraemia. Conclusion Encouraging coverage and potent in vivo efficacy against a selection of highly drug-resistant Enterobacterales isolates in the mouse peritonitis model warrants the conduct of clinical studies to validate apramycin as a drug candidate for the prophylaxis and treatment of BSI., Niels Frimodt-Møller, Diarmaid Hughes, Carina Vingsbo Lundberg and Sven N. Hobbie share senior authorship

In-field data were collected in Costa Rica between 2018–2021 on newly planted grafted and non-grafted coffee plants grown under artificial shade nets and across an elevation gradient (1050, 1250 and 1450 m.a.s.l). The coffee plants consisted of Coffea arabica F1 hybrid plants (‘H3 i.e. Caturra cv. X Ethiopian 531’), which were derived from a somatic embryogenesis clonal propagation process, an American C. arabica pure line (‘Villa Sarchi’) and C. canephora ‘Nemaya’ (the latter two both being produced by seed). Data from eight different coffee types (including these three genotypes) and different grafting combinations (including reverse and auto-grafting) were collected. Data concerned plant traits such as grafting compatibility (plant collar diameters above and below graft union), agronomic characteristics (aerial and root traits), leaf ecophysiology (leaf gas-exchange and chlorophyll fluorescence), yield and quality attributes (bean size, peaberry percentage, WB100 and SCA note). Climate data were also included for comparison on the farm plots along the elevation gradient. Linear mixed models were used to test for effects of elevation (test sites), coffee types (grafted or non-grafted combinations) and interaction between coffee types and elevations. Least square mean estimates were calculated for significant fixed effects and Tukey tests applied for pairwise tests. A tangential hyperbola curve was used to analyse leaf gas-exchange data. These datasets and R scripts can be re-used as a guide for future analyses concerning coffee agronomy or eco-physiological interactions for other plant species. Other potential re-uses could be meta-analyses aimed at comparing coffee yield, quality, or other agronomic traits across different environmental conditions (such as under shade of an agroforestry system or across different elevation sites).

Ageing plantations, poor genetic material, soil degradation, pests and diseases are, among other factors, limiting cacao production. To meet the increasing demand for cacao in the absence of productivity gains, forests are cleared and the use of external inputs is generalised, with severe negative impacts on biodiversity and GHG emissions. The use of improved plant genetic material should support a sustainable increase of production. In this study, we evaluate and compare the yield performance of four locally-selected clones with those of four widely-used international clones in South America and four full-sib families (crosses of the same international clones). The research was conducted in a long-term trial in Bolivia with different production systems, including monocultures and agroforestry systems under organic and conventional farming and a successional agroforestry system without external inputs. Their cacao yields and the factors determining productivity (pod index, flowering intensity, pod load, pod losses, aboveground biomass, harvesting period) were assessed during 5 years. The cacao trees grown in the two monocultures had higher yields than those in the agroforestry systems. This was the result of higher aboveground biomass, flowering intensity and pod load, and similar pod losses due to cherelle wilt and fungal diseases in the former when compared with the latter. No differences between conventional and organic management were observed. We did not identify any genotypes performing better in a specific production system. On average, the local clones had twofold and five times higher yields than the international ones and the full-sib families, respectively. This was related to their higher total pod load, bigger pods and higher yield efficiency, i.e., higher yield per unit of tree biomass. However, the local clones had less flowering intensity, more cherelle wilt and similar losses due to fungal diseases to those of the international clones. This study cl

Breeding seed orchards (BSOs) or seedling seed orchards (SSOs) comprise seedlings from selected trees in different provenances, but could also include seed lots from provenances. A family from a selected tree is known as an open pollinated family (OP-family). BSOs aim to provide improved germplasm after selection, but also serve as test sites of different seed sources. It is not only important to avoid inbreeding depressions, but one should also seek to retain sufficient genetic diversity in BSOs in order to achieve continued genetic gains in the next breeding generations through recombination (see Ericsson et al. 2013). This issue is addressed in Part II: Analysis and selections in BSOs. This first part presents guidelines on data collection, selection of traits to be measured and methods used to assess the traits of interest.

This guide provides a manual for analysis of data from breeding seed orchards in the statistical program R mainly based on BreedR (Muñoz and Sanchez 2020) aiming at the highest possible genetic gains while considering genetic diversity and providing knowledge on provenances as well. The guide gives some of the theoretical backgrounds for quantitative genetic analysis at the start. However, it is possible to go directly to the chapter on “Data files” and continue from there and modify the R program made for a Cordia africana case to obtain tables with breeding values, which can be used to make the thinning decisions for the BSOs. It is recommended to print out the tables and figures attached at the end of this guide, and at the same time copy the program and paste it into a text editor like “Context” or the Windows editor making it possible to search for the references made in this guide to program steps in the R-program

Ageing plantations, poor genetic material, soil degradation, pests and diseases are, among other factors, limiting cacao production. To meet the increasing demand for cacao in the absence of productivity gains, forests are cleared and the use of external inputs is generalised, with severe negative impacts on biodiversity and GHG emissions. The use of improved plant genetic material should support a sustainable increase of production. In this study, we evaluate and compare the yield performance of four locally-selected clones with those of four widely-used international clones in South America and four full-sib families (crosses of the same international clones). The research was conducted in a long-term trial in Bolivia with different production systems, including monocultures and agroforestry systems under organic and conventional farming and a successional agroforestry system without external inputs. Their cacao yields and the factors determining productivity (pod index, flowering intensity, pod load, pod losses, aboveground biomass, harvesting period) were assessed during 5 years. The cacao trees grown in the two monocultures had higher yields than those in the agroforestry systems. This was the result of higher aboveground biomass, flowering intensity and pod load, and similar pod losses due to cherelle wilt and fungal diseases in the former when compared with the latter. No differences between conventional and organic management were observed. We did not identify any genotypes performing better in a specific production system. On average, the local clones had twofold and five times higher yields than the international ones and the full-sib families, respectively. This was related to their higher total pod load, bigger pods and higher yield efficiency, i.e., higher yield per unit of tree biomass. However, the local clones had less flowering intensity, more cherelle wilt and similar losses due to fungal diseases to those of the international clones. This study

Ash dieback (ADB) has become a major problem across European ash forests. The disease is caused by the invasive pathogenic fungus Hymenoscyphus fraxineus that results in sever crown damage, and especially in young ash trees often rapid mortality. Fortunately, several studies have found that a fraction of F. excelsior trees remain healthy with only few symptoms. Heritability and additive genetic variance in tolerance have been estimated from progeny trials to be moderate to high, with limited genotype x environment (GxE) interaction. High levels of infection pressure are often present in forest areas with newly planted trees revealing their level of tolerance within few years. These features make ADB tolerance suitable for phenotypic selection and led to the hypothesis that strong forward phenotypic selection can create a new generation of ash trees with substantial reduced susceptibility to the disease. As a coordinated effort, this approach is tested by establishing selection trials in Norway, Sweden, Denmark and Lithuania. The joint efforts include sharing of genetic material to estimate GxE, but the program is based on development of tolerant ash trees from local genetic resources. Here we present the concept, challenges, activities and some preliminary results from the field trials.

During the last century, several forest calamities has been caused by host shifts where an introduced fungus has become a severe pathogen on a native species that lacked co-evolutionary history with the new pathogen. This is considered to be the case for the European ash (Fraxinus excelsior) that in recent decades has become severely damaged throughout most of its natural distribution area by the introduced Asian ascomycete Hymenoscyphus fraxineus. Fortunately, genetic variation in resistance against the novel pathogen in Europe was identified early in the epidemic, and a substantial body of research has since focused on understanding the genetics of this resistance with the vision to promote resilience of ash forest based on wise genetic management practices. Here, we review knowledge obtained from common garden trials, inoculation tests, in situ field studies of mature ash forests, analysis of microbiomes, genomes, transcriptomes and analysis in relation to survival and reproductive fitness. Based on present the knowledge, we discuss how genetic considerations can be integrated into the management of natural and planted ash forests to enhance and protect their resistance and evolutionary resilience.

In addition to valuable renewable wood resources, oak forests are essential ecosystems hosting a large amount of biodiversity. Although oaks are predicted to be less affected by a shift in climatic conditions, including more frequent and severe drought spells, compared to other forest tree species, they will have to adapt fast to future climatic changes. Here we use classical landscape genomics to locate genes with a potential adaptive role in drought-resistance among pan-European provenances of sessile oak (Quercus petraea). We ask if an enrichment with alleles beneficial for dry conditions from southern provenances often subjected to drought – be it by natural dispersal, gene flow or human plantings – can enhance the adaptive potential of the native Danish Q. petraea populations to a future drier climate. We find numerous genetic loci (single nucleotide polymorphisms; SNPs) associated with bioclimatic variables describing local precipitation. While many of the associated SNPs are found in inter-genic regions, some are indeed located in, or close to genes, known to be involved in drought stress responses. Thus, beneficial alleles have the potential to spread across the landscape. We will present detailed analyses of these beneficial alleles in order to determine whether they are absent in the local Danish gene pool, or if they are already present at low frequency, and thus enabling adaptation to a drier climate based on standing genetic variation. In conclusion, beneficial alleles found among southern populations of sessile oak is a valuable source for future enrichment of northern oak seed sources and natural populations to ensure their robustness under future climate.