Comparisons of protein profiles of beech bark disease resistant and susceptible American beech (Fagus grandifolia)

Linking genotype to phenotype to identify genetic variation relating to host susceptibility in the mountain pine beetle system

Identifying genetic variants responsible for phenotypic variation under selective pressure has the potential to enable productive gains in natural resource conservation and management. Despite this potential, identifying adaptive candidate loci is not trivial, and linking genotype to phenotype is a major challenge in contemporary genetics. Many of the population genetic approaches commonly used to identify adaptive candidates will simultaneously detect false positives, particularly in nonmodel species, where experimental evidence is seldom provided for putative roles of the adaptive candidates identified by outlier approaches. In this study, we use outcomes from population genetics, phenotype association, and gene expression analyses as multiple lines of evidence to validate candidate genes. Using lodgepole and jack pine as our nonmodel study species, we analyzed 17 adaptive candidate loci together with 78 putatively neutral loci at 58 locations across Canada (N > 800) to determine whether relationships could be established between these candidate loci and phenotype related to mountain pine beetle susceptibility. We identified two candidate loci that were significant across all population genetic tests, and demonstrated significant changes in transcript abundance in trees subjected to wounding or inoculation with the mountain pine beetle fungal associate Grosmannia clavigera. Both candidates are involved in central physiological processes that are likely to be invoked in a trees response to stress. One of these two candidate loci showed a significant association with mountain pine beetle attack status in lodgepole pine. The spatial distribution of the attack-associated allele further coincides with other indicators of susceptibility in lodgepole pine. These analyses, in which population genetics was combined with laboratory and field experimental validation approaches, represent first steps toward linking genetic variation to the phenotype of mountain pine beetle susceptibility in lodgepole and jack pine, and provide a roadmap for more comprehensive analyses.

Proteogenomics from a bioinformatics angle: A growing field

Proteogenomics is a research area that combines areas as proteomics and genomics in a multi-omics setup using both mass spectrometry and high-throughput sequencing technologies. Currently, the main goals of the field are to aid genome annotation or to unravel the proteome complexity. Mass spectrometry based identifications of matching or homologues peptides can further refine gene models. Also, the identification of novel proteoforms is also made possible based on detection of novel translation initiation sites (cognate or near-cognate), novel transcript isoforms, sequence variation or novel (small) open reading frames in intergenic or un-translated genic regions by analyzing high-throughput sequencing data from RNAseq or ribosome profiling experiments. Other proteogenomics studies using a combination of proteomics and genomics techniques focus on antibody sequencing, the identification of immunogenic peptides or venom peptides. Over the years, a growing amount of bioinformatics tools and databases became available to help streamlining these cross-omics studies. Some of these solutions only help in specific steps of the proteogenomics studies, e.g. building custom sequence databases (based on next generation sequencing output) for mass spectrometry fragmentation spectrum matching. Over the last few years a handful integrative tools also became available that can execute complete proteogenomics analyses. Some of these are presented as stand-alone solutions, whereas others are implemented in a web-based framework such as Galaxy. In this review we aimed at sketching a comprehensive overview of all the bioinformatics solutions that are available for this growing research area. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:584-599, 2017.

Genome-wide association study identifies a major gene for beech bark disease resistance in American beech (Fagus grandifolia Ehrh.)

BACKGROUND

The American Beech tree (Fagus grandifolia Ehrh.), native to eastern North America, is ecologically important and provides high quality wood products. This species is susceptible to beech bark disease (BBD) and is facing high rates of mortality in North America. The disease occurs from an interaction between the woolly beech scale insect (Cryptococcus fagisuga), one of two species of the fungus Neonectria (N. faginata or N. ditissima), and American Beech trees.

METHODS

In this case-control genome-wide association study (GWAS), we tested 16 K high quality SNPs using the Affymetrix Axiom 1.5 K - 50 K assay to genotype an association population of 514 individuals. We also conducted linkage analysis in a full-sib family of 115 individuals. Fisher's exact test and logistic regression tests were performed to test associations between SNPs and phenotypes.

RESULTS

Association tests revealed four highly significant SNPs on chromosome (Chr) 5 for a single gene (Mt), which encodes a mRNA for metallothionein-like protein (metal ion binding) in Fagus sylvatica. Metallothioneins represent Cys-rich metal chelators able to coordinate metal atoms and may play an important role in the resistance mechanisms against beech scale insect.

CONCLUSION

The GWAS study has identified a single locus of major effect contributing to beech bark disease resistance. Knowledge of this genetic locus contributing to resistance might be used in applied breeding, conservation and restoration programs.

Impacts of Beech Bark Disease and Climate Change on American Beech

American beech (Fagus grandifolia Ehrh.) is a dominant component of forest tree cover over a large portion of eastern North America and this deciduous, mast-bearing tree species plays a key role in these forest ecosystems. Beech bark disease (BBD) is a scale insect-fungus complex that has caused the decline and death of afflicted beech trees. This disease has become a common feature in North American forest landscapes. Resistance to BBD is at the level of the beech scale (Cryptococcus fagisuga Lind.). Beech scale attack predisposes the tree to subsequent infection by Neonectria fungi. The impact of this tree disease has been shown to be significant, particularly in beech dominated forests. Scale-free trees (resistant to BBD) have been reported to range from only 1% to 3% in infested stands, with estimates ranging from 80–95% for overall infestation (for all beech within the current North American range). In addition to BBD, overall beech health will be directly impacted by climate change, if one specifically considers the expected fluctuations in precipitation leading to both drought periods and flooding. Beech is particularly sensitive to both extremes and is less resilient than other broad leaf tree species. Although the increase in global temperatures will likely shift the current range of the American beech, milder winters and less snowpack will favor propagation and survival of the beech scale. This review aims to present the current outlook for American beech in light of climate change. The natural history of the American beech and the onslaught of BBD during the last century will be covered, followed by the potential effects of a changing climate on BBD-infested forests. Evidence from models of European beech (Fagus sylvatica) and other host-pathogen systems will supplement data directly gathered to evaluate BBD in American beech. We present the case that although climate change is likely to be a confounding factor in the continued loss of American beech, increasing our understanding of possible mechanisms of resistance and environmental factors that may influence susceptibility of American beech to BBD can inform proactive management strategies.

Relation entre la composition foliaire et la présence de la maladie corticale du hêtre dans les stations du Réseau d’étude et de surveillance des écosystèmes forestiers du Québec

La maladie corticale du hêtre (MCH) est de plus en plus fréquente dans les forêts de l’est de l’Amérique du Nord. Des chercheurs ont avancé l’hypothèse que l’expansion de cette maladie pourrait être en partie liée au statut nutritif des arbres. Pour tester cette hypothèse, nous avons vérifié la relation entre l’apparition de cette maladie et la composition du feuillage du hêtre (Fagus grandifolia Ehrh.) dans les stations du Réseau d’étude et de surveillance des écosystèmes forestiers du Québec. Sur les 14 stations contenant du hêtre, cinq présentaient des symptômes de la maladie entre 2006 et 2012. Les arbres infectés étaient en moyenne de plus grand diamètre que ceux qui ne l’étaient pas. La présence de la MCH était liée en partie à la composition foliaire des arbres (pseudo-R2 : 0,551). L’analyse indique que plus le rapport N/P du feuillage du hêtre est élevé, plus la probabilité d’infection par la MCH est importante; et plus les rapports Zn/Mn et Mg/K du feuillage sont élevés, plus la probabilité d’infection par la MCH est faible. Ces rapports donnent à penser que les conditions d’acidification du sol et de drainage influencent la vigueur des arbres et, conséquemment, leur vulnérabilité à la MCH.

Mature beech trees (Fagus grandifolia; Fagaceae) are persistently clonal in coves and beech gaps in the Great Smoky Mountains

PREMISE OF THE STUDY

Angiosperms frequently have mixed sexual and asexual reproductive strategies, which can have significant consequences for population and community structure. Many tree species respond to disturbance by vegetative sprouting over sexual reproduction, but the ability to do so varies within and among species and is poorly studied. We tested the hypothesis that root sprouting in Fagus grandifolia is more important in high-elevation beech forests (extreme environmental conditions), relative to lower-elevation cove hardwood forests (optimal environmental conditions), in Great Smoky Mountains National Park.

METHODS

Four cove hardwood and two high-elevation beech gap forests were sampled. Fagus grandifolia trees were tagged, mapped, and genotyped at each site using six nuclear microsatellite loci. A subset of trees was cored to determine minimum ages of identified clonal lineages. Relationships between measures of clonal richness, diameter, forest type, and elevation were compared by nonparametric analyses.

KEY RESULTS

Five of six sites were highly dependent on sprouting; one site was entirely dependent on reproduction by seed. Clonal richness did not differ significantly by forest type or elevation, but differed significantly from previously published work. Tree diameter was significant by elevation and significant between the present study and previously published work.

CONCLUSIONS

The results of this study in the context of previously published work suggest that relatively recent recruits may be more likely to reflect both sexual and asexual strategies, whereas mature F. grandifolia may be more likely to be the result of persistent clonal lineages.

Mass Spectrometry and its Applications in Life Sciences

Deciphering the biological and clinical significance of the proteins is investigated by mass spectrometry in a relatively new field, named proteomics. Mass spectrometry is, however, also used in chemistry for many years. In this Research Front we try to show the potential use of mass spectrometry in chemical, environmental and biomedical research and also to illustrate the applications of mass spectrometry in proteomics.