| 1. |
- Barcala, Maximiliano Estravis, et al.
(författare)
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Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species
- 2024
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Ingår i: The Plant Journal. - 0960-7412 .- 1365-313X. ; 117:3, s. 944-955
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Tidskriftsartikel (refereegranskat)abstract
- Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.
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| 2. |
- Chaudhary, Rajiv, et al.
(författare)
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Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in 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
- The Heterobasidion annosum s.l species complex comprises the most damaging forest pathogens to Norway spruce. We revisited previously identified Quantitative Trait Loci (QTLs) related to Heterobasidion-resistance in Norway spruce to identify candidate genes associated with these QTLs. We identified 329 candidate genes associated with the resistance QTLs using a gene-based composite map for Pinaceae. To evaluate the transcriptional responses of these candidate genes to H. parviporum, we inoculated Norway spruce plants and sequenced the transcriptome of the interaction at 3 and 7 days post inoculation. Out of 298 expressed candidate genes 124 were differentially expressed between inoculation and wounding control treatment. Interestingly, PaNAC04 and two of its paralogs in the subgroup III-3 of the NAC family transcription factors were found to be associated with one of the QTLs and was also highly induced in response to H. parviporum. These genes are possibly involved in the regulation of biosynthesis of flavonoid compounds. Furthermore, several of the differentially expressed candidate genes were associated with the phenylpropanoid pathway including a phenylalanine ammonia-lyase, a cinnamoyl-CoA reductase, a caffeoyl-CoA O-methyltransferase and a PgMYB11-like transcription factor gene. Combining transcriptome and genetic linkage analyses can help identifying candidate genes for functional studies and molecular breeding in non-model species.
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| 3. |
- Chaudhary, Rajiv
(författare)
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Identification of molecular markers associated with fungal resistance in Norway spruce and common ash
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Trees are giants of the forests, possessing nutrient-rich tissues that make them natural targets for pathogens. In Europe, the fungal pathogens Heterobasidion annosum s.l. and Hymenoscyphus fraxineus are associated with Norway spruce and common ash, respectively. H. annosum s.l. causes stem and root-rot and, in economic terms, is a major pathogen of Norway spruce. H. fraxineus, which causes ash dieback disease, results in severe mortality of common ash, which leads to adverse ecological losses. The aim of this thesis was to use modern molecular methods to identify markers for fungal resistance in Norway spruce and common ash for early selection of superior genotypes for resistance tree breeding. By combining genetic map-based information and transcriptome analyses, differentially expressed genes were identified that associate with resistance to Heterobasidion parviporum in Norway spruce. Among the candidate genes were PaNAC04 and two of its paralogues in subgroup III-3 in the NAC family of transcription factors, a transcription factor gene PgMYB11, and a number of genes encoding enzyme in the biosynthesis of phenylpropanoids. Eleven Norway spruce markers that correlated with variation in resistance to H. parviporum were identified in an association genetics study. Laccase PaLAC5 was associated with the control of lesion length development and is likely to be involved in induced defence in close proximity to the H. parviporum infection site. PaLAC5 may be associated with lignosuberized boundary zone formation in spruce inner bark. Finally, one non-synonymous SNP associated with disease severity in common ash was identified in a gene encoding a subtilisin-related peptidase S8/S53 domain. The Hi-Plex-PCR amplification method demonstrated an inexpensive, time-effective method for generating data with potential for use in future tree breeding programmes. Low population differentiation between genotypes selected for disease resistance and the wild population susceptible to ash dieback indicated opportunities for further selection without significantly losing genetic diversity in the ash population.
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| 4. |
- Chaudhary, Rajiv, et al.
(författare)
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Marker-Trait Associations for Tolerance to Ash Dieback in Common Ash (Fraxinus excelsior L.)
- 2020
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Ingår i: Forests. - : MDPI. - 1999-4907. ; 11:10
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Tidskriftsartikel (refereegranskat)abstract
- Common ash (Fraxinus excelsior L.) is a tree species of significant ecological and economic importance that has suffered a devastating decline since the 1990s in Europe. Native ash species are being threatened by the alien invasive fungus Hymenoscyphus fraxineus, which causes ash dieback. The main goal of the study was to develop markers for traits related to tolerance to ash dieback and to investigate whether genotypes selected for tolerance were genetically different from susceptible wild populations. We phenotyped 326 ash trees from Sweden for disease severity and genotyped them using 63 amplicon-derived single-nucleotide polymorphism (SNP) markers derived from genes in 40 scaffolds spanning 8 MB in total, which represents approximately 1% of the ash genome. We used a mixed linear model to test for an association between genotypic variation at these loci and disease severity of ash. In total, two SNPs were found to have significant associations. One non-synonymous SNP associated with the disease severity of ash was found in a gene predicted to encode a subtilisin-related peptidase S8/S53 domain. A second marginally significant marker was associated with an LRR gene. Our results demonstrate an inexpensive time-effective method for generating genomic data that could have potential for use in future tree breeding programs and provide information for marker-assisted selection. Our study also showed a low differentiation between genotypes selected for disease tolerance and the wild population of ash representing a range of susceptibilities to ash dieback, indicating opportunities for further selection without significantly losing genetic diversity in the ash population.
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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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