| 1. |
- Kastally, Chedly, et al.
(författare)
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Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research
- 2022
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Ingår i: The Plant Journal. - : John Wiley & Sons. - 0960-7412 .- 1365-313X. ; 109:5, s. 1337-1350
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Tidskriftsartikel (refereegranskat)abstract
- Pinus sylvestris (Scots pine) is the most widespread coniferous tree in the boreal forests of Eurasia, with major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies, genetic mapping and genomic selection. We present a new 50K single-nucleotide polymorphism (SNP) genotyping array for Scots pine research, breeding and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array and identified 47 712 high-quality SNPs for the final array (called 'PiSy50k'). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissue-specific expression patterns and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.9%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the level of Mendelian error was negligible. In addition, array genotypes successfully discriminate between Scots pine populations of Finnish and Scottish origins. The PiSy50k SNP array will be a valuable tool for a wide variety of future genetic studies and forestry applications.
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| 2. |
- Palmé, Anna, 1973-, et al.
(författare)
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Selection on Nuclear Genes in a Pinus Phylogeny
- 2009
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 26:4, s. 893-905
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Tidskriftsartikel (refereegranskat)abstract
- In this study, we investigate natural selection in a pine phylogeny. DNA sequences from 18 nuclear genes were used toconstruct a very well-supported species tree including 10 pine species. This tree is in complete agreement witha previously reported supertree constructed from morphological and molecular data, but there are discrepancies withprevious chloroplast phylogenies within the section Pinus. A significant difference in evolutionary rate between Piceaand Pinus was found, which could potentially indicate a lower mutation rate in Picea, but other scenarios are alsopossible. Several approaches were used to study selection patterns in a set of 21 nuclear genes in pines and in some casesin Picea and Pseudotsuga. The overall pattern suggests efficient purifying selection resulting in low branch-specific dn/dsratios with an average of 0.22, which is similar to other higher plants. Evidence for purifying selection was common andfound on at least 55% of the branches. Evidence of positive selection at several sites was found in a phytocyanin homologand significant differences in dn/ds among the branches in the gene tree in dehydrin 1. Several genes suitable for furtherphylogenetic analysis at various levels of divergence were identified.
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| 3. |
- Savolainen, Outi, et al.
(författare)
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Adaptation of forest trees to climate change
- 2007
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Ingår i: Climate change and forest genetic diversity. - Rome : Bioversity International. - 9789290437499 ; , s. 19-30
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Konferensbidrag (refereegranskat)
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| 4. |
- Wachowiak, Witold, et al.
(författare)
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Speciation history of three closely related pines Pinus mugo (T.), P. uliginosa (N.) and P. sylvestris (L.)
- 2011
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 20:8, s. 1729-1743
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Tidskriftsartikel (refereegranskat)abstract
- Nucleotide polymorphisms at genomic regions including 17 nuclear loci, two chloroplast and one mitochondrial DNA fragments were used to study the speciation history of three pine species: dwarf mountain pine (Pinus mugo), peat-bog pine (P. uliginosa) and Scots pine (P. sylvestris). We set out to investigate three specific speciation scenarios: (I) P. uliginosa is a homoploid hybrid between the other two, (II) the species have evolved without gene flow after divergence and (III) there has been substantial gene flow between the species since their divergence. Overall, the genetic data suggest that P. mugo and P. uliginosa share the same gene pool (average net divergence of 0.0001) and that the phenotypic differences (e.g. growth form) are most likely due to very limited areas of the genome. P. mugo and P. uliginosa are more diverged from P. sylvestris than from each other (average net divergence of 0.0027 and 0.0026, respectively). The nucleotide patterns can best be explained by the divergence with migration speciation scenario, although the hybrid speciation scenario with small genomic contribution from P. sylvestris cannot be completely ruled out. We suggest that the large amount of shared polymorphisms between the pine taxa and the lack of monophyly at all loci studied between P. sylvestris and P. mugo-P. uliginosa can largely be explained by relatively recent speciation history and large effective population sizes but also by interspecific gene flow. These closely related pine taxa form an excellent system for searching for loci involved in adaptive variation as they are differentiated in phenotype and ecology but have very similar genetic background.
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