| 1. |
- Capador-Barreto, Hernán Dario, et al.
(författare)
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Genetic evidence for sexual reproduction and multiple infections of Norway spruce cones by the rust fungus Thekopsora areolata
- 2020
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 10, s. 7389-7403
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Tidskriftsartikel (refereegranskat)abstract
- Rust fungi are obligate parasites, of plants, with complex and in many cases poorly known life cycles which may include host alteration and up to five spore types with haploid, diploid, and dikaryotic nuclear stages. This study supports thatThekopasora areolata, the causal agent of cherry-spruce rust in Norway spruce, is a macrocyclic heteroecious fungus with all five spore stages which uses two host plantsPrunus padusandPicea abiesto complete its life cycle. High genotypic diversity without population structure was found, which suggests predominantly sexual reproduction, random mating and a high gene flow within and between the populations in Fennoscandia. There was no evidence for an autoecious life cycle resulting from aeciospore infection of pistillate cones that would explain the previously reported rust epidemics without the alternate host. However, within cones and scales identical multilocus genotypes were repeatedly sampled which can be explained by vegetative growth of the fertilized mycelia or repeated mating of mycelium by spermatia of the same genotype. The high genotypic diversity within cones and haplotype inference show that each pistillate cone is infected by several basidiospores. This study provides genetic evidence for high gene flow, sexual reproduction, and multiple infections of Norway spruce cone by the rust fungusT. areolatawhich expands the general understanding of the biology of rust fungi.
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| 2. |
- Castaño Soler, Carles, et al.
(författare)
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Optimized metabarcoding with Pacific biosciences enables semi-quantitative analysis of fungal communities
- 2020
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 228, s. 1149-1158
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies have questioned the use of high-throughput sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region to derive a semi-quantitative representation of fungal community composition. However, comprehensive studies that quantify biases occurring during PCR and sequencing of ITS amplicons are still lacking. We used artificially assembled communities consisting of 10 ITS-like fragments of varying lengths and guanine-cytosine (GC) contents to evaluate and quantify biases during PCR and sequencing with Illumina MiSeq, PacBio RS II and PacBio Sequel I technologies. Fragment length variation was the main source of bias in observed community composition relative to the template, with longer fragments generally being under-represented for all sequencing platforms. This bias was three times higher for Illumina MiSeq than for PacBio RS II and Sequel I. All 10 fragments in the artificial community were recovered when sequenced with PacBio technologies, whereas the three longest fragments (> 447 bases) were lost when sequenced with Illumina MiSeq. Fragment length bias also increased linearly with increasing number of PCR cycles but could be mitigated by optimization of the PCR setup. No significant biases related to GC content were observed. Despite lower sequencing output, PacBio sequencing was better able to reflect the community composition of the template than Illumina MiSeq sequencing.
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| 3. |
- Coignard, J, et al.
(författare)
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A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers
- 2021
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1, s. 1078-
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Tidskriftsartikel (refereegranskat)abstract
- Breast cancer (BC) risk for BRCA1 and BRCA2 mutation carriers varies by genetic and familial factors. About 50 common variants have been shown to modify BC risk for mutation carriers. All but three, were identified in general population studies. Other mutation carrier-specific susceptibility variants may exist but studies of mutation carriers have so far been underpowered. We conduct a novel case-only genome-wide association study comparing genotype frequencies between 60,212 general population BC cases and 13,007 cases with BRCA1 or BRCA2 mutations. We identify robust novel associations for 2 variants with BC for BRCA1 and 3 for BRCA2 mutation carriers, P < 10−8, at 5 loci, which are not associated with risk in the general population. They include rs60882887 at 11p11.2 where MADD, SP11 and EIF1, genes previously implicated in BC biology, are predicted as potential targets. These findings will contribute towards customising BC polygenic risk scores for BRCA1 and BRCA2 mutation carriers.
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| 4. |
- Davydenko, Kateryna, et al.
(författare)
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Invasion of Emerald Ash Borer Agrilus planipennis and Ash Dieback Pathogen Hymenoscyphus fraxineus in Ukraine-A Concerted Action
- 2022
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Ingår i: Forests. - : MDPI AG. - 1999-4907. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Emerald Ash Borer (EAB), Agrilus planipennis, is a beetle that originates from East Asia. Upon invasion to North America in the early 2000s, it killed untold millions of ash trees. In European Russia, EAB was first detected in Moscow in 2003 and proved to have the potential to also kill native European ash (Fraxinus excelsior). The beetle has since spread in all geographic directions, establishing itself in eastern Ukraine by 2019 and possessing potential for further westward spread towards the EU. Apart from the approaching EAB, F. excelsior is currently threatened by the dieback disease (ADB) caused by the invasive ascomycete fungus Hymenoscyphus fraxineus. The infestation by EAB combined with ADB infection is expected to be more lethal than either of them alone, yet the potential consequences are unknown. To date, eastern Ukraine represents the geographic area in which both invasions overlap, thus providing the opportunity for related investigations. The aims of the study were to investigate: (i) the EAB expansion range in Ukraine, (ii) the relative susceptibility of F. excelsior and American ash (Fraxinus pennsylvanica) to EAB and ADB, and (iii) the combined effect/impact on ash condition imposed by both the pest and disease in the area subjected to the invasion. The results have demonstrated that (i) the invasion of EAB is currently expanding both in terms of newly infested trees and invaded geographic area; (ii) F. excelsior is more resistant to EAB than F. pennsylvanica, while F. excelsior is more susceptible to ADB than F. pennsylvanica; and (iii) the infection by ADB is likely to predispose F. excelsior to the infestation by EAB. It was concluded that inventory and mapping of surviving F. excelsior, affected by both ADB and EAB, is necessary to acquire genetic resources for the work on strategic, long-term restoration of F. excelsior in devastated areas, thereby tackling a possible invasion of EAB to the EU.
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| 5. |
- Elfstrand, Malin, et al.
(författare)
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Association genetics identifies a specifically regulated Norway spruce laccase gene, PaLAC5, linked to Heterobasidion parviporum resistance
- 2020
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Ingår i: Plant, Cell and Environment. - : Wiley. - 0140-7791 .- 1365-3040. ; 43, s. 1779-1791
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Tidskriftsartikel (refereegranskat)abstract
- It is important to improve the understanding of the interactions between the trees and pathogens and integrate this knowledge about disease resistance into tree breeding programs. The conifer Norway spruce (Picea abies) is an important species for the forest industry in Europe. Its major pathogen is Heterobasidion parviporum, causing stem and root rot.In this study, we identified 11 Norway spruce QTLs (Quantitative trait loci) that correlate with variation in resistance to H. parviporum in a population of 466 trees by association genetics. Individual QTLs explained between 2.1 and 5.2% of the phenotypic variance. The expression of candidate genes associated with the QTLs was analysed in silico and in response to H. parviporum hypothesizing that (a) candidate genes linked to control of fungal sapwood growth are more commonly expressed in sapwood, and; (b) candidate genes associated with induced defences are respond to H. parviporum inoculation. The Norway spruce laccase PaLAC5 associated with control of lesion length development is likely to be involved in the induced defences. Expression analyses showed that PaLAC5 responds specifically and strongly in close proximity to the H. parviporum inoculation. Thus, PaLAC5 may be associated with the lignosuberized boundary zone formation in bark adjacent to the inoculation site.
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| 6. |
- Elfstrand, Malin, et al.
(författare)
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Genotypic variation in Norway spruce correlates to fungal communities in vegetative buds
- 2020
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 29, s. 199-213
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Tidskriftsartikel (refereegranskat)abstract
- The taxonomically diverse phyllosphere fungi inhabit leaves of plants. Thus, apart from the fungi's dispersal capacities and environmental factors, the assembly of the phyllosphere community associated with a given host plant depends on factors encoded by the host's genome. The host genetic factors and their influence on the assembly of phyllosphere communities under natural conditions are poorly understood, especially in trees. Recent work indicates that Norway spruce (Picea abies) vegetative buds harbour active fungal communities, but these are hitherto largely uncharacterized. This study combines internal transcribed spacer sequencing of the fungal communities associated with dormant vegetative buds with a genome-wide association study (GWAS) in 478 unrelated Norway spruce trees. The aim was to detect host loci associated with variation in the fungal communities across the population, and to identify loci correlating with the presence of specific, latent, pathogens. The fungal communities were dominated by known Norway spruce phyllosphere endophytes and pathogens. We identified six quantitative trait loci (QTLs) associated with the relative abundance of the dominating taxa (i.e., top 1% most abundant taxa). Three additional QTLs associated with colonization by the spruce needle cast pathogen Lirula macrospora or the cherry spruce rust (Thekopsora areolata) in asymptomatic tissues were detected. The identification of the nine QTLs shows that the genetic variation in Norway spruce influences the fungal community in dormant buds and that mechanisms underlying the assembly of the communities and the colonization of latent pathogens in trees may be uncovered by combining molecular identification of fungi with GWAS.
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| 7. |
- Elfstrand, Malin, et al.
(författare)
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Root Rot Resistance Locus PaLAR3 Is Delivered by Somatic Embryogenesis (SE) Pipeline in Norway Spruce (Picea abies (L.) Karst.)
- 2021
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Ingår i: Forests. - : MDPI AG. - 1999-4907. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Research Highlights: The Norway spruce somatic embryogenesis (SE) pipeline is suitable for multiplication of material with root rot resistance traits. Background and Objectives: Heterobasidion root rot is the economically most severe forest pathogen in Europe, reducing the benefit of planting elite forest material. In this study, the SE-propagation ability of elite Norway spruce material carrying root rot resistance traits was studied. Materials and Methods: We analyzed the presence of the root rot resistance locus PaLAR3B among 80 Finnish progeny-tested Norway spruce plus-trees used for SE-plant production as well as in 241 SE lines (genotypes) derived from them. Seven full-sib families with lines having either AA, AB, or BB genotype for PaLAR3 locus were further studied for their SE-plant propagation ability. Results: The results indicate that 47.5% of the studied elite trees carry the PaLAR3B allele (45% are heterozygous and 2.5% homozygous). The resistance allele was present among the SE lines as expected based on Mendelian segregation and did not interfere with somatic embryo production capacity. All embryos from PaLAR3 genotypes germinated well and emblings were viable in the end of first growing season. However, in three families, PaLAR3B homo- or heterozygotes had 23.2% to 32.1% lower viability compared to their respective hetero- or PaLAR3A homozygotes. Conclusions: There is no trade-off between root rot resistance locus PaLAR3B and somatic embryo production ability, but the allele may interfere with Norway spruce embling establishment.
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| 8. |
- Finlay, Roger, et al.
(författare)
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Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems
- 2024
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Ingår i: New Phytologist. - 0028-646X .- 1469-8137. ; 242, s. 1676-1690
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Tidskriftsartikel (refereegranskat)abstract
- Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils.We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls.Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling.Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.
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| 9. |
- Hu, Yang, et al.
(författare)
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The conifer root rot pathogens Heterobasidion irregulare and Heterobasidion occidentale employ different strategies to infect Norway spruce
- 2020
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Heterobasidion irregulare and H. occidentale are two closely related conifer root rot pathogens in the H. annosum sensu lato (s.l.) species complex. The two species H. irregulare and H. occidentale have different host preference with pine and non-pine tree species favored, respectively. The comparison of transcriptomes of H. irregulare and H. occidentale growing in Norway spruce bark, a susceptible host non-native to North America, showed large differences in gene expression. Heterobasidion irregulare induced more genes involved in detoxification of host compounds and in production of secondary metabolites, while the transcriptome induced in H. occidentale was more oriented towards carbohydrate degradation. Along with their separated evolutionary history, the difference might be driven by their host preferences as indicated by the differentially expressed genes enriched in particular Gene Ontology terms.
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| 10. |
- Lankinen, Åsa, et al.
(författare)
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Challenges and opportunities for increasing the use of low-risk plant protection products in sustainable production. A review
- 2024
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Ingår i: Agronomy for Sustainable Development. - : Springer. - 1774-0746 .- 1773-0155. ; 44:2
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Forskningsöversikt (refereegranskat)abstract
- Plant production systems worldwide are struggling to meet the diverse and increasing needs of humankind while also facing challenges such as climate change and biodiversity loss. This, combined with the desirable transition from the use of conventional pesticides to more sustainable plant protection solutions, has led to an urgent, and increasing, need for low-risk plant protection products (PPPs) to be developed, applied, and integrated into management practices across all types of plant production systems. Despite a high demand from end users and consumers together with joint political goals at the EU level to replace conventional pesticides, the number of low-risk PPPs on the European market remains low, in comparison to synthetic agrochemicals. In this review, we summarize knowledge about the policy, technical, and administrative issues hampering the process of bringing new low-risk PPPs to the European market. We present an overview of the challenges in using the low-risk PPPs that are currently available within the EU agricultural, horticultural, and forestry sectors. We describe the variation in modes of action and the limitations associated with different application techniques and give concrete examples of problems and solutions from Swedish plant production sectors, in contrast to global perspectives as demonstrated by examples from African agriculture. Finally, we conclude that trans-sectoral, multi-actor approaches are required and provide suggestions on how to address the remaining knowledge gaps related to efficiency, application, and economics of low-risk PPP use in Integrated Pest Management (IPM) solutions for plant protection to improve future food security in Europe.
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