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Fusarium wilt, caused by Fusarium oxysporum f. sp. niveum (Fon), is a soilborne disease that significantly limits yield in watermelon ( Citrullus lanatus) and occasionally causes the loss of an entire year's harvest. Reference-quality de novo genomic assemblies of pathogenic and nonpathogenic strains were generated using a combination of next-generation and third-generation sequencing technologies. Chromosomal-level genomes were produced with representatives from three Fon races, facilitating comparative genomic analysis and the identification of chromosomal structural variation. Syntenic analysis between isolates allowed for differentiation of the core and lineage-specific portions of their genomes. This research will support future efforts to refine the scientific understanding of the molecular and genetic factors underpinning the Fon host range, develop diagnostic assays for each of the four races, and decipher the evolutionary history of race 3. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

The establishment of commercial tree plantations in Malaysian Borneo began with a progression of various species, including Pinus caribea, Acacia mangium, Gmelina arborea, Falcataria moluccana (for...

Single-step GBLUP (HBLUP) efficiently combines genomic, pedigree, and phenotypic information for holistic genetic analyses of disjunct breeding populations. We combined data from two independent multigenerational Eucalyptus globulus breeding populations to provide direct comparisons across the programs and indirect predictions in environments where pedigreed families had not been evaluated. Despite few known pedigree connections between the programs, genomic relationships provided the connectivity required to create a unified relationship matrix, H, which was used to compare pedigree-based and HBLUP models. Stem volume data from 48 sites spread across three regions of southern Australia and wood quality data across 20 sites provided comparisons of model accuracy. Genotyping proved valuable for correcting pedigree errors and HBLUP more precisely defines relationships within and among populations, with relationships among the genotyped individuals used to connect the pedigrees of the two programs. Cryptic relationships among the native range populations provided evidence of population structure and evidence of the origin of landrace populations. HBLUP across programs improved the prediction accuracy of parents and genotyped individuals and enabled breeding value predictions to be directly compared and inferred in regions where little to no testing has been undertaken. The impact of incorporating genetic groups in the estimation of H will further align traditional genetic evaluation pipelines with approaches that incorporate marker-derived relationships into prediction models.

Inoculations of two Acacia populations were used to estimate the level of genetic control for tolerance to Ceratocystis canker and wilt disease following inoculation with the causal pathogen, Ceratocystis manginecans. The first screening utilised a range of clones commonly established in Vietnam along with new candidate clones and provided evidence that variation in wilt symptoms is under a moderate level of genetic control in current deployment populations. Subsequent assessments of tolerance in a pedigreed Acacia auriculiformis progeny trial indicated that internal lesion length assessments were less influenced by seedling height and produced higher heritability estimates than external lesion length assessments. Heritability estimates for damage to detached phyllodes following inoculation increased from 2 to 4 weeks, at which point many leaves were entirely damaged. Assessments of phyllode damage were more heritable than assessments of stem damage, and positive genetic correlations between stems and phyllode damage indicate that families will rank similarly for both traits. If validation trials confirm the results of this study in larger trees, screening as described herein may be used to develop acacia breeds with greater disease tolerance.

Here, we announce the draft genome sequences of three Fusarium circinatum isolates that were used to inoculate slash pines (Pinus elliottii) at the U.S. Forest Service Resistance Screening Center in Asheville, North Carolina. The genomes of these isolates were similar to other publicly available genomes, with average nucleotide identity values of >0.98.

The extent to which spatial structuring of host resistance in wild plant populations reflects direct pathogen imposed selection is a subject of debate. To examine this issue, genetic susceptibility to an exotic and co-evolved native fungal pathogen were compared using two Australian host tree species. Damage to common host germplasm of Corymbia citriodora subsp. variegata (CCV) and Eucalyptus globulus, caused by recently introduced (Austropuccinia psidii) and native (Quambalaria pitereka and Teratosphaeria sp.) pathogens was evaluated in common-garden experiments. There was significant additive genetic variation within host species for susceptibility to both the exotic and native pathogens. However, susceptibility to A. psidii was not genetically correlated with susceptibility to either native pathogen, providing support for pathogen specific rather than general mechanisms of resistance. Population differentiation (QST ) for susceptibility to the native pathogens was greater than neutral expectations (molecular FST ), arguing for divergent selection. Coupled with lower native, but not exotic, pathogen susceptibility in host populations from areas climatically more prone to fungal proliferation, these findings suggest that pathogen imposed selection has directly contributed to a geographic mosaic of host resistance to native pathogens. This article is protected by copyright. All rights reserved.

A dramatic rise in the incidence of a serious canker and wilt disease of Acacia mangium has led to the replacement of thousands of hectares of plantation forests in eastern Sabah. A disease screening program was initiated to evaluate levels of disease resistance and tolerance to the causative fungus, Ceratocystis acaciivora, in an A. mangium breeding population. Resistance was evaluated as the presence or absence of external symptoms in two open-pollinated progeny trials. In addition, tolerance was evaluated in one of these trials by measuring the size of lesions produced following a controlled inoculation with C. acaciivora. Heritability estimates were low to moderate for growth traits but were close to zero for the range of traits used to evaluate Ceratocystis resistance and tolerance. Nevertheless, significant differences were found among the three sources (families from the local land race, Queensland and Papua New Guinea origins, all selected in progeny trials in Sabah) and among populations within t...

Disease screening to determine the threat Puccinia psidii poses to plantation and native eucalypts in Australia was undertaken in half-sib families of two contrasting eucalypt species, Eucalyptus cloeziana and E. argophloia. Artificial inoculation with a single-lesion isolate of P. psidii was used to screen these species for resistance to the biotype of P. psidii established in Australia. The objective was to characterize resistance to P. psidii within these two distinct species: E. argophloia, a vulnerable species with a narrow distribution, and E. cloeziana, a species with a broad and extensive distribution in Queensland. Results for E. cloeziana indicate that inland provenances are more resistant to P. psidii infection than provenances from coastal regions. Heritability estimates for the two assessment systems used (resistance on a 1-to-5 ordinal scale verses resistance on a 0-to-1 binomial scale) were low to high (0.24 to 0.63) for E. argophloia and moderate to high (0.4 to 0.91) for E. cloeziana, indicating a significant level of additive genetic variance for rust resistance within the populations. This study demonstrates the potential to select resistant families within the tested populations and indicates that P. psidii could detrimentally affect these species in native forests, nurseries, and plantations. Disease screening to determine the threat Puccinia psidii poses to plantation and native eucalypts in Australia was undertaken in half-sib families of two contrasting eucalypt species, Eucalyptus cloeziana and E. argophloia. Artificial inoculation with a single-lesion isolate of P. psidii was used to screen these species for resistance to the biotype of P. psidii established in Australia. The objective was to characterize resistance to P. psidii within these two distinct species: E. argophloia, a vulnerable species with a narrow distribution, and E. cloeziana, a species with a broad and extensive distribution in Queensland. Results for E. cloeziana indicate that inland provenances are more resistant to P. psidii infection than provenances from coastal regions. Heritability estimates for the two assessment systems used (resistance on a 1-to-5 ordinal scale verses resistance on a 0-to-1 binomial scale) were low to high (0.24 to 0.63) for E. argophloia and moderate to high (0.4 to 0.91) for E. cloeziana, indicating a significant level of additive genetic variance for rust resistance within the populations. This study demonstrates the potential to select resistant families within the tested populations and indicates that P. psidii could detrimentally affect these species in native forests, nurseries, and plantations.

International audience; AbstractKey messageEucalyptus pellitademonstrated good growth and wood quality traits in this study, with young plantation grown timber being suitable for both solid and pulp wood products. All traits examined were under moderate levels of genetic control with little genotype by environment interaction when grown on two contrasting sites in Vietnam.ContextEucalyptus pellita currently has a significant role in reforestation in the tropics. Research to support expanded of use of this species is needed: particularly, research to better understand the genetic control of key traits will facilitate the development of genetically improved planting stock.AimsThis study aimed to provide estimates of the heritability of diameter at breast height over bark, wood basic density, Kraft pulp yield, modulus of elasticity and microfibril angle, and the genetic correlations among these traits, and understand the importance of genotype by environment interactions in Vietnam.MethodsData for diameter and wood properties were collected from two 10-year-old, open-pollinated progeny trials of E. pellita in Vietnam that evaluated 104 families from six native range and three orchard sources. Wood properties were estimated from wood samples using near-infrared (NIR) spectroscopy. Data were analysed using mixed linear models to estimate genetic parameters (heritability, proportion of variance between seed sources and genetic correlations).ResultsVariation among the nine sources was small compared to additive variance. Narrow-sense heritability and genetic correlation estimates indicated that simultaneous improvements in most traits could be achieved from selection among and within families as the genetic correlations among traits were either favourable or close to zero. Type B genetic correlations approached one for all traits suggesting that genotype by environment interactions were of little importance. These results support a breeding strategy utilizing a single breeding population advanced by selecting the best individuals across all seed sources.ConclusionBoth growth and wood properties have been evaluated. Multi-trait selection for growth and wood property traits will lead to more productive populations of E. pellita both with improved productivity and improved timber and pulp properties.

A network of 92 pedigreed ex situ conservation plantings of Pinus tecunumanii, established as replicated progeny within provenance trials, is used to present a principal components-based analysis that illustrates the climatic preferences of 23 populations from the species’ native range. This meta-analysis quantifies changes in the relative productivity, assessed as individual-tree volume, of populations across climatic gradients and associates the preference of a population with increased volume production along the climatic gradient. Clustering and ordination on the matrix containing estimates of change in productivity for each population summarise differentials in productivity associated with climatic gradients. The preference of populations along principal components therefore reflects the adaptive profiles of populations, which may be used with breeding-value estimates from routine genetic evaluations to assist with the development of deployment populations targeting different environments. As well, the approach may be used to test whether the preference of a population, estimated as population loadings for growth differentials, is affected by the climate in the native range of the population. This relationship may be interpreted as an estimate of how much local climate shapes the adaptive profiles of populations. The amount and seasonality of precipitation most clearly differentiate the adaptive profiles of populations, with less variation in the population responses explained by temperature differentiation. As expected from type-B correlation estimates, most populations exhibited small changes in relative productivity across climatic gradients. However, patterns of similarities in adaptive profiles among populations were evident using spatial orientation to display population responses to the climatic variables experienced in the provenance trials. Clustering and ordination of population responses derived from empirical data served to identify populations that responded positively or negatively to climatic variables; this information may help guide conservation genetics efforts, direct the deployment of germplasm, or identify seed sources that are sensitive to changes in climatic variables. Linking response patterns to the climatic data from the native range of each population indicated little effect of local climate shaping adaptive profiles.

Near infrared (NIR) spectra from foliage of the tropical pine species Pinus caribaea var. hondurensis, P. elliottii var. elliottii and their hybrids have been used to classify the extent of hybridisation for the F1 and backcross progeny. Comparison of results for F1 hybrids with simulated hybrids, made from admixtures of pure parent foliage samples, showed increased variation in the NIR spectra of the F1 hybrids as evidenced by greater scatter in the principal component analysis scores plot. Both partial least-squares–discriminant analysis and soft independent modelling of class analogy using the foliage spectra provide identification of the hybrid individuals from the parent taxa. In addition, it is possible to visualise the extent of genetic additive effect in hybrid-parent backcrosses. NIR spectra from foliage samples of P. radiata, a temperate pine species, were clearly discriminated from P. elliottii and P. caribaea. Near infrared spectroscopy has the potential to confirm and assess the extent of hybridisation in softwood species. In extreme situations whereby trial records are lost or trial plot labelling is missing, it might be possible to use NIR spectra from foliage to recover taxon information of seedlings.

The exotic rust pathogen Puccinia psidii is now widespread along the east coast of Australia from temperate Victoria to tropical far north Queensland, with a current host range exceeding 200 species from 37 myrtaceous genera. To determine the threat P. psidii poses to plantation and native eucalypts, artificial inoculation was used to screen germplasm of spotted gum (Corymbia spp.) for resistance to the biotype of P. psidii that has become established in Australia. The objective was to characterize resistance to P. psidii within the Corymbia species complex so that management strategies for the deployment of germplasm from existing breeding programmes of these spotted gum species could be developed. Symptom development initiated 7 days after inoculation, with resistant and susceptible seedlings identified within all species, provenances and families. Inter- and intraspecific variability in rust resistance was observed among spotted gum species. There was no apparent relationship between climatic conditions at the provenance origin and disease resistance. The heritability estimates for all assessments are moderate to high and indicate a significant level of additive genetic variance for rust resistance within the populations. The results of this study clearly identify potential to select for resistance at the family level within the tested populations. While the potential for P. psidii to detrimentally impact upon Corymbia in the nursery and in young plantations was demonstrated, estimations of the heritability of resistance suggest that efforts to enhance this trait through breeding have reasonable prospects for success.

A novel methodology for describing genotype by environment interactions estimated from multi-environment field trials is described and an empirical example using an extensive trial network of eucalypts is presented. The network of experiments containing 65 eucalypts was established in 38 replicated field trials across the tropics and subtropics of eastern Australia, with a selection of well-tested species used to provide a more detailed examination of productivity differentials across environmental gradients. By focusing on changes in species’ productivity across environmental gradients, the results are applicable for all species established across the range of environments evaluated in the trial network and simultaneously classify species and environments so that results may be applied across the landscape. The methodology developed was able to explain most (93 %) of the variation in the selected species relative changes in productivity across the various environmental variables examined. Responses were primarily regulated by changes in variables related to water availability and secondarily by temperature related variables. Clustering and ordination can identify groups of species with similar physiological responses to environment and may also guide the parameterisation and calibration of process based models of plant growth. Ordination was particularly useful in the identification of species with distinct environmental response patterns that would be useful as probes for extracting more information from future trials.

Evaluation of a series of spotted gum (Corymbia citirodora) progeny trials, established in the subtropical region of Queensland, Australia, was undertaken to provide information for the development of advanced-generation breeding populations suitable for pulp production. Measurements of growth at two ages were combined with assessments of wood density and pulp yield from a selected sample of provenances to provide comparisons between provenances, to generate genetic parameter estimates and to predict genetic gain potential. Although growth at this age was moderate relative to other eucalypts, the near-infrared predictions of average wood density of 756 kg m(-3) and pulp yield of 55% indicate the species has considerable potential as a pulpwood crop. A pulp productivity breeding objective was used to identify production populations using a range of selection trait weightings to determine potential genetic gain for pulp productivity. Genetic parameters indicated (1) levels of genetic control were moderate for all traits and higher for wood property traits, (2) genetic improvements could be achieved by selection among and within provenances with greater levels of improvement available from selection within populations, (3) genotype by environment interactions were negligible, (4) genetic correlations between traits were favourable, and (5) selection of volume production alone would maximise improvements in pulp productivity.

The fungal pathogen Quambalaria pitereka can cause significant damage to spotted gum (Corymbia sp.) plantations in Australia. A series of seven progeny trials, involving seed from a range-wide collection from 527 individuals within 25 native populations of Corymbia citriodora sub-species variegata, were assessed for height growth and damage from Quambalaria around 1 year after planting. Infection at this young age has been found to detrimentally impact growth, form, and wood quality for many years. Genetic variance was found to be significant at both the provenance and family level. However, selection of families within provenances should lead to greater levels of genetic gain than what can be realized from selecting among provenances as estimates of additive genetic variance were consistently greater than estimates of variance among populations. Strong relationships between height and Quambalaria shoot blight (QSB) damage assessments in these trials were evidenced by very high genetic correlations between the traits; therefore, selection for any of these traits could be used to identify more productive and QSB-tolerant populations. While both provenances and families were found to interact with the trial environments at a similar level across traits, genetic correlations indicated that rankings for growth were be less stable than rankings for QSB tolerance across environments. Genetic parameter estimates derived from general and generalized linear models were very similar and either analytical method could be used to evaluate fungal damage.

To investigate genotype by environment interaction (G×E) for clones of radiata pine (Pinus radiata), clonal stability was evaluated for growth and form traits from three trials in New Zealand and three trials in Australia. There were 215–245 clones in common between pairs of New Zealand trials, 17–26 clones in common among Australian trials, while 32–52 clones were in common between New Zealand and Australian sites. Clonal repeatability $$ \left( {\hat{H}^{2} } \right) $$ and type-B genetic correlations were estimated. The general trend across the six trials for clonal repeatability was that $$ \hat{H}^{2} $$ was greatest for height (HGT) followed by diameter at breast height (DBH), stem straightness (STR), and branch quality score (BRQ). Within New Zealand trials, there was little evidence of G×E for growth traits, but more for form traits. For DBH the average type-B genetic correlation within New Zealand was 0.82; and for HGT, the average type-B genetic correlation within New Zealand was 0.76. Within Australia, there was only one statistically significant type-B genetic correlation for DBH and this estimate was high indicating that clonal ranks were similar on these two trials. Additionally, within Australia and between regions type-B genetic correlations were generally high for form traits, at least for STR. One Australian trial (Trial 5) showed relatively high clonal stability with the three trials in New Zealand indicating that the ranks of these clones were relatively stable in both regions. From a clonal testing standpoint, these results suggest that stable clones can be identified that perform well in both New Zealand and Australia. Improvements in both growth and form traits can be expected when radiata pine clones are transferred between Australia and New Zealand within regions similar to those sampled in this trial series.

The expansion of red mahogany (Eucalyptus pellita) plantations in the wet tropics of northern Australia has increased interest in the domestication of the species. A review of an overseas breeding population was undertaken to enhance our current understanding of genetic parameters for E. pellita, which are essential for the development of advanced-generation breeding programs. The large genetic differences between and within provenances, as well as the moderate heritability estimates for growth and form traits, imply that tree breeding can create improved breeds and reduce variability in plantation forests. Our analysis suggests that breeding value predictions of parents tested in first-generation provenance-progeny trials are less indicative of an individual's genetic merit than breeding values generated from second-generation trials. The low heritability estimate in the first generation relative to the second generation and the reduced inter-generational correlations will influence the level of genetic gain that can be realised. The implications of these findings for the management of E. pellita breeding populations and the production of improved seed for plantation forestry in the tropics are discussed.

A new breeding strategy is presented for the Radiata Pine Breeding Company, a New Zealand based research consortium, that drives the breeding program for Pinus radiata for both the New Zealand and New South Wales based Australian forest plantation industry. The new strategy builds on the existing base for P. radiata, and on the last strategy review in 2000. The new strategy comprises a large open-pollinated (OP) Main Population (MP) with 500 female parents and two sublines (250 female parents per subline). The MP will be tested using alpha designs, single-tree plots and incomplete blocks to maximise efficiency. Each subline will be tested on four sites, geographically distant from the other subline. The MP will be managed in discrete generations. Selection of the next generation will be using a combination of backward and forward selection, but the strict control of inbreeding with identified lineage will rely on the development of parental reconstruction for OP progeny. There are alternatives to this, however, such as estimating the group coancestry and accepting some additional increase in inbreeding. This is a new and significant departure from previous breeding strategies for P. radiata in New Zealand. There will also be a single, small Elite Population (EP), tested 50% as progeny and 50% as clones. Twenty four parents will be tested each year as clones and 24 as seedling progeny with some overlap between the two. It is expected that the clonal population will capture the greatest gains in traits with low heritabilities, and the half-sib progeny will capture the greatest gains in traits with high heritabilities. The two sublines will be maintained in the EP, and breeding will be managed as a rolling front with trials established every year, while trials of the MP will be established every 10 years.

Eighty six full-sib Corymbia F1 hybrid families (crosses between C. torelliana and four spotted gum taxa: C. citriodora subsp. variegata, C. citriodora subsp. citriodora, C. henryi and C. maculata), were planted in six trials across six disparate sites in south-eastern Queensland to evaluate their productivity and determine their potential utility for plantation forestry. In each trial, the best-growing 20% of hybrid families grew significantly faster (P = 0.05) than open-pollinated seedlots of the parent species Corymbia citriodora subsp. variegata, ranging from 107% to 181% and 127% to 287% of the height and diameter respectively. Relative performance of hybrid families growing on more than one site displayed consistency in ranking for growth across sites and analysis showed low genotype-by-environment interaction. Heritability estimates based on female and male parents across two sites at age six years for height and diameter at breast height, were high (0.62 ± 0.28 to 0.64 ± 0.35 and 0.31 ± 0.21 to 0.69 ± 0.37 respectively), and low to moderate (0.03 ± 0.04 to 0.33 ± 0.22) for stem straightness, branch size, incidence of ramicorns, and frost and disease resistance traits at ages one to three years. The proportion of dominance variance for height and diameter had reduced to zero by age six years. Based on these promising results, further breeding and pilot-scale family forestry and clonal forestry deployment is being undertaken. These results have also provided insights regarding the choice of a future hybrid breeding strategy.

Different methods for predicting clonal values were explored for diameter growth (diameter at breast height (DBH)) in a radiata pine clonal forestry program: (1) clones were analyzed with a full model in which the total genetic variation was partitioned into additive, dominance, and epistasis (Clone Only—Full Model); (2) clones were analyzed together with seedling base population data (Clone Plus Seedling (CPS)), and (3) clones were analyzed with a reduced model in which the only genetic term was the total genetic variance (Clone Only—Reduced Model). DBH was assessed at age 5 for clones and between ages 4 to 13 at the seedling trials. Significant additive, dominance, and epistatic genetic effects were estimated for DBH using the CPS model. Nonadditive genetic effects for DBH were 87% as large as additive genetic effects. Narrow-sense (\(\hat h^2 \)) and broad-sense (\(\hat H^2 \)) heritability estimates for DBH using the CPS model were 0.14 ± 0.01 and 0.26 ± 0.01, respectively. Accuracy of predicted clonal values increased 4% by combining the clone and seedling data over using clonal data alone, resulting in greater confidence in the predicted genetic performance of clones. Our results indicate that exploiting nonadditive genetic effects in clonal varieties will generate greater gains than that typically obtainable from conventional family-based forestry of radiata pine. The predicted genetic gain for DBH from deployment of the top 5% of clones was 24.0%—an improvement of more than 100% over family forestry at the same selection intensity. We conclude that it is best practice to predict clonal values by incorporating seedling base population data in the clonal analysis.

Midrotation data from large block plots of resistant and susceptible slash (Pinus elliottii Engelm.) and loblolly pine (Pinus taeda L.) were used in combination with the Georgia pine plantation simulator growth model to provide projected gains per hectare in volume and value generated by resistance to fusiform rust (Cronartium quercum (Berk.) Miyabe ex Shirai f.sp. fusiforme). The difference in the projected volume production between the resistant and susceptible planting stock of slash pine was larger than the difference between resistance levels in loblolly pine. The increases in projected volume and the reductions in percent infection of the resistant stock led to large differences in the value of the resistant and susceptible planting stock. At a 6% real discount rate, plantations of resistant slash pine were on average worth between 40.2 and 89.8% more than plantations of susceptible slash pine. Plantations of resistant loblolly were on average worth between 6.1 and 40.3% more than plantations of susceptible loblolly pine. However, the marginal value of rust resistance in loblolly was not significantly different from zero under the assumption that economic differences are only due to volume losses and not losses due to product degrade.

Wood is an important biological resource which contributes to nutrient and hydrology cycles through ecosystems, and provides structural support at the plant level. Thousands of genes are involved in wood development, yet their effects on phenotype are not well understood. We have exploited the low genomic linkage disequilibrium (LD) and abundant phenotypic variation of forest trees to explore allelic diversity underlying wood traits in an association study. Candidate gene allelic diversity was modelled against quantitative variation to identify SNPs influencing wood properties, growth and disease resistance across three populations of Corymbia citriodora subsp. variegata, a forest tree of eastern Australia. Nine single nucleotide polymorphism (SNP) associations from six genes were identified in a discovery population (833 individuals). Associations were subsequently tested in two smaller populations (130-160 individuals), 'validating' our findings in three cases for actin 7 (ACT7) and COP1 interacting protein 7 (CIP7). The results imply a functional role for these genes in mediating wood chemical composition and growth, respectively. A flip in the effect of ACT7 on pulp yield between populations suggests gene by environment interactions are at play. Existing evidence of gene function lends strength to the observed associations, and in the case of CIP7 supports a role in cortical photosynthesis.