| 1. |
- Abdoullaye, Doukary, et al.
(författare)
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Permanent genetic resources added to molecular ecology resources database 1 August 2009 - 30 September 2009
- 2010
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:1, s. 232-236
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Tidskriftsartikel (refereegranskat)abstract
- This article documents the addition of 238 microsatellite marker loci and 72 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Adelges tsugae, Artemisia tridentata, Astroides calycularis, Azorella selago, Botryllus schlosseri, Botrylloides violaceus, Cardiocrinum cordatum var. glehnii, Campylopterus curvipennis, Colocasia esculenta, Cynomys ludovicianus, Cynomys leucurus, Cynomys gunnisoni, Epinephelus coioides, Eunicella singularis, Gammarus pulex, Homoeosoma nebulella, Hyla squirella, Lateolabrax japonicus, Mastomys erythroleucus, Pararge aegeria, Pardosa sierra, Phoenicopterus ruber ruber and Silene latifolia. These loci were cross-tested on the following species: Adelges abietis, Adelges cooleyi, Adelges piceae, Pineus pini, Pineus strobi, Tubastrea micrantha, three other Tubastrea species, Botrylloides fuscus, Botrylloides simodensis, Campylopterus hemileucurus, Campylopterus rufus, Campylopterus largipennis, Campylopterus villaviscensio, Phaethornis longuemareus, Florisuga mellivora, Lampornis amethystinus, Amazilia cyanocephala, Archilochus colubris, Epinephelus lanceolatus, Epinephelus fuscoguttatus, Symbiodinium temperate-A clade, Gammarus fossarum, Gammarus roeselii, Dikerogammarus villosus and Limnomysis benedeni. This article also documents the addition of 72 sequencing primer pairs and 52 allele specific primers for Neophocaena phocaenoides.
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| 2. |
- Apuli, Rami-Petteri, et al.
(författare)
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Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen (Populus tremula)
- 2020
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Ingår i: G3. - : GENETICS SOCIETY AMERICA. - 2160-1836. ; 10:1, s. 299-309
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Tidskriftsartikel (refereegranskat)abstract
- The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.
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| 3. |
- Apuli, Rami-Petteri, et al.
(författare)
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The genetic basis of adaptation in phenology in an introduced population of Black Cottonwood (Populus trichocarpa, Torr. & Gray)
- 2021
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Ingår i: BMC Plant Biology. - : BioMed Central (BMC). - 1471-2229. ; 21
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Tidskriftsartikel (refereegranskat)abstract
- Background: Entering and exiting winter dormancy present important trade-offs between growth and survival at northern latitudes. Many forest trees display local adaptation across latitude in traits associated with these phenology transitions. Transfers of a species outside its native range introduce the species to novel combinations of environmental conditions potentially requiring different combinations of alleles to optimize growth and survival. In this study, we performed genome wide association analyses and a selection scan in a P. trichocarpa mapping population derived from crossings between clones collected across the native range and introduced into Sweden. GWAS analyses were performed using phenotypic data collected across two field seasons and in a controlled phytotron experiment.Results: We uncovered 584 putative candidate genes associated with spring and autumn phenology traits as well as with growth. Many regions harboring variation significantly associated with the initiation of leaf shed and leaf autumn coloring appeared to have been evolving under positive selection in the native environments of P. trichocarpa. A comparison between the candidate genes identified with results from earlier GWAS analyses performed in the native environment found a smaller overlap for spring phenology traits than for autumn phenology traits, aligning well with earlier observations that spring phenology transitions have a more complex genetic basis than autumn phenology transitions.Conclusions: In a small and structured introduced population of P. trichocarpa, we find complex genetic architectures underlying all phenology and growth traits, and identify multiple putative candidate genes despite the limitations of the study population.
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| 4. |
- Bachmann, Jörg Alexander, 1989-
(författare)
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Evolutionary consequences of dominance at the Brassicaceae self-incompatibility locus
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Self-incompatibility (SI) is a genetic mechanism that allows plants to enforce outcrossing by rejecting self-pollen and pollen from close relatives. In the Brassicaceae, SI is sporophytic and controlled by the self-incompatibility locus (S-locus). The S-locus harbors two tightly linked genes SRK and SCR, which encode the female and male SI specificity determinants, respectively. S-locus heterozygotes often only express the S-specificity of the more dominant allele, and at the pollen level such dominance relationships are mediated by small RNAs (sRNAs). The S-locus is thus an example of a locus under strong balancing selection, where dominance modifiers have evolved.In this thesis, I investigate the consequences of S-locus dominance for plant mating system evolution and allopolyploid speciation. I further investigate evolutionary conservation and sequence-level effects of dominance relationships among S-alleles. For this purpose, I used the crucifer genus Capsella as a model system.First, I demonstrated that targeted long-read sequencing results in structurally accurate assemblies of full-length S-haplotype sequences, and that indel errors in such assemblies can be corrected using short reads. Second, I investigated the genetic basis of loss of SI, the first step in the evolution of self-fertilisation, in the self-compatible (SC) Capsella orientalis. I found that loss of SI was dominant and mapped to the S-locus, where C. orientalis harbored a fixed coding frameshift deletion in SCR that is likely to lead to loss of male specificity. I further identified a sRNA-based dominance modifier that is associated with dominant suppression of recessive SCR alleles. Taken together, these results suggest that loss of SI in C. orientalis involved a dominant S-haplotype, suggesting that dominant haplotypes may be favored under conditions that select for loss of SI. Third, I show that a dominant S-haplotype may also have contributed to the shift to SC in the widespread allotetraploid Capsella bursa-pastoris. Fourth, I showed that dominance relationships at the S-locus are largely conserved between the SI outcrossing species C. grandiflora and Arabidopsis halleri which diverged ~8 Mya. I also found that dominant S-haplotypes accumulate more transposable elements than recessive S-haplotypes, in line with expected sequence-level consequences of S-locus dominance. In sum, this thesis provides new insights into the broad conservation of dominance hierarchies at the Brassicaceae S-locus, and the role of dominant S-alleles in allopolyploid speciation and plant mating system shifts.
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| 5. |
- Baison, John, et al.
(författare)
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Genome-Wide Association Study (GWAS) identified novel candidate loci affecting wood formation in Norway spruce
- 2019
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Ingår i: The Plant Journal. - : Wiley. - 0960-7412 .- 1365-313X. ; 100:1, s. 83-100
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Tidskriftsartikel (refereegranskat)abstract
- Norway spruce is a boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics underlying important wood quality traits in the species. We performed a functional Genome-Wide Association Study (GWAS) of 17 wood traits in Norway spruce using 178101 single-nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood traits were defined using functional modelling of wood properties across annual growth rings.We applied a LASSO based association mapping method using a functional multi-locus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis provided 52 significant SNPs from 39 candidate genes, including genes previously implicated in wood formation and tree growth in spruce and other species. Our study represents a multi-locus GWAS for complex wood traits in Norway spruce. The results advance our understanding of the genetics influencing wood traits and identifies candidate genes for future functional studies.
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| 6. |
- Baison, John, et al.
(författare)
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Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce
- 2019
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Ingår i: The Plant Journal. - : John Wiley & Sons. - 0960-7412 .- 1365-313X. ; 100:1, s. 83-100
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Tidskriftsartikel (refereegranskat)abstract
- Norway spruce is a boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics underlying important wood quality traits in the species. We performed a functional genome-wide association study (GWAS) of 17 wood traits in Norway spruce using 178 101 single nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood traits were defined using functional modelling of wood properties across annual growth rings. We applied a Least Absolute Shrinkage and Selection Operator (LASSO-based) association mapping method using a functional multilocus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine a significant quantitative trait locus. The analysis provided 52 significant SNPs from 39 candidate genes, including genes previously implicated in wood formation and tree growth in spruce and other species. Our study represents a multilocus GWAS for complex wood traits in Norway spruce. The results advance our understanding of the genetics influencing wood traits and identifies candidate genes for future functional studies.
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| 7. |
- 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. - : John Wiley & Sons. - 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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| 8. |
- Barker, Hilary L., et al.
(författare)
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Linking plant genes to insect communities : Identifying the genetic bases of plant traits and community composition
- 2019
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 28:19, s. 4404-4421
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Tidskriftsartikel (refereegranskat)abstract
- Community genetics aims to understand the effects of intraspecific genetic variation on community composition and diversity, thereby connecting community ecology with evolutionary biology. Thus far, research has shown that plant genetics can underlie variation in the composition of associated communities (e.g., insects, lichen and endophytes), and those communities can therefore be considered as extended phenotypes. This work, however, has been conducted primarily at the plant genotype level and has not identified the key underlying genes. To address this gap, we used genome‐wide association mapping with a population of 445 aspen (Populus tremuloides) genets to identify the genes governing variation in plant traits (defence chemistry, bud phenology, leaf morphology, growth) and insect community composition. We found 49 significant SNP associations in 13 Populus genes that are correlated with chemical defence compounds and insect community traits. Most notably, we identified an early nodulin‐like protein that was associated with insect community diversity and the abundance of interacting foundation species (ants and aphids). These findings support the concept that particular plant traits are the mechanistic link between plant genes and the composition of associated insect communities. In putting the “genes” into “genes to ecosystems ecology”, this work enhances understanding of the molecular genetic mechanisms that underlie plant–insect associations and the consequences thereof for the structure of ecological communities.
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| 9. |
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| 10. |
- Berglund, Åsa, 1978-, et al.
(författare)
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Lead exposure and biological effects in pied flycatchers (Ficedula hypoleuca) before and after the closure of a lead mine in northern Sweden.
- 2010
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Ingår i: Environmental Pollution. - : Elsevier Ltd. - 0269-7491 .- 1873-6424. ; 158:5, s. 1368-75
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Tidskriftsartikel (refereegranskat)abstract
- Mining activities affect the surrounding environment by increasing exposure to metals. In this study, metal accumulation and its effects on reproduction and health of pied flycatcher (Ficedula hypoleuca) nestlings were monitored before and up to five years after a lead mine and enrichment plant closed down. The lead concentration in moss, nestling blood, liver and feces all indicated decreased lead exposure by at least 31% after closure, although only blood lead decreased significantly. Although the birds responded fairly well to the changed atmospheric deposition (based on moss samples), concentrations were still higher compared with birds in a reference area, and breeding was affected at the mine (smaller clutches and higher mortality). Surviving nestlings suffered from lower hemoglobin levels, mean cell hemoglobin concentrations and inhibited delta-aminolevulinic acid dehydratase activity. Lead poisoning contributed to poor health and adverse reproductive effects, but other factors (e.g. increased parasitic load) probably also affected the birds.
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| 11. |
- Bernhardsson, Carolina, et al.
(författare)
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An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)
- 2019
-
Ingår i: G3. - : Genetics Society of America. - 2160-1836. ; 9:5, s. 1623-1632
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Tidskriftsartikel (refereegranskat)abstract
- Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (similar to 20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.
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| 12. |
- Bernhardsson, Carolina, et al.
(författare)
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Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species
- 2021
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Ingår i: Molecular Ecology Resources. - : John Wiley & Sons. - 1755-098X .- 1755-0998. ; 21:3, s. 880-896
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Tidskriftsartikel (refereegranskat)abstract
- Norway spruce (Picea abies L. Karst) is one of the most important forest tree species with significant economic and ecological impact in Europe. For decades, genomic and genetic studies on Norway spruce have been challenging due to the large and repetitive genome (19.6 Gb with more than 70% being repetitive). To accelerate genomic studies, including population genetics, genome-wide association studies (GWAS) and genomic selection (GS), in Norway spruce and related species, we here report on the design and performance of a 50K single nucleotide polymorphism (SNP) genotyping array for Norway spruce. The array is developed based on whole genome resequencing (WGS), making it the first WGS-based SNP array in any conifer species so far. After identifying SNPs using genome resequencing data from 29 trees collected in northern Europe, we adopted a two-step approach to design the array. First, we built a 450K screening array and used this to genotype a population of 480 trees sampled from both natural and breeding populations across the Norway spruce distribution range. These samples were then used to select high-confidence probes that were put on the final 50K array. The SNPs selected are distributed over 45,552 scaffolds from the P. abies version 1.0 genome assembly and target 19,954 unique gene models with an even coverage of the 12 linkage groups in Norway spruce. We show that the array has a 99.5% probe specificity, >98% Mendelian allelic inheritance concordance, an average sample call rate of 96.30% and an SNP call rate of 98.90% in family trios and haploid tissues. We also observed that 23,797 probes (50%) could be identified with high confidence in three other spruce species (white spruce [Picea glauca], black spruce [P. mariana] and Sitka spruce [P. sitchensis]). The high-quality genotyping array will be a valuable resource for genetic and genomic studies in Norway spruce as well as in other conifer species of the same genus.
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| 13. |
- Bernhardsson, Carolina, et al.
(författare)
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Geographic structure and adaptive population differentiation in herbivore defence genes in European aspen (Populus tremula L., Salicaceae)
- 2012
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Ingår i: Molecular Ecology. - : Blackwell Publishing. - 0962-1083 .- 1365-294X. ; 21:9, s. 2197-2207
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Tidskriftsartikel (refereegranskat)abstract
- When a phenotypic trait is subjected to spatially variable selection and local adaptation, the underlying genes controlling the trait are also expected to show strong patterns of genetic differentiation since alternative alleles are favored in different geographical locations. Here we study 71 SNPs from seven genes associated with inducible defense responses in a sample of P. tremula collected from across Sweden. Four of these genes (PPO2, TI2, TI4 and TI5) show substantial population differentiation and a PCA conducted on the defense SNPs divides the Swedish population into three distinct clusters. Several defense SNPs show latitudinal clines, although these were not robust to multiple testing. However, five SNPs (located within TI4 and TI5) show strong longitudinal clines that remain significant after multiple test correction. Genetic geographical variation, supporting local adaptation, has earlier been confirmed in genes involved in the photoperiod pathway in P. tremula, but this is, to our knowledge, one of the first times that geographic variation has been found in genes involved in plant defense against antagonists.
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| 14. |
- Bernhardsson, Carolina, et al.
(författare)
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Geographic structure in metabolome and herbivore community co-occurs with genetic structure in plant defence genes
- 2013
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Ingår i: Ecology Letters. - Hoboken : Wiley-Blackwell. - 1461-023X .- 1461-0248. ; 16:6, s. 791-798
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Tidskriftsartikel (refereegranskat)abstract
- Plantherbivore interactions vary across the landscape and have been hypothesised to promote local adaption in plants to the prevailing herbivore regime. Herbivores that feed on European aspen (Populus tremula) change across regional scales and selection on host defence genes may thus change at comparable scales. We have previously observed strong population differentiation in a set of inducible defence genes in Swedish P. tremula. Here, we study the geographic patterns of abundance and diversity of herbivorous insects, the untargeted metabolome of the foliage and genetic variation in a set of wound-induced genes and show that the geographic structure co-occurs in all three data sets. In response to this structure, we observe local maladaptation of herbivores, with fewer herbivores on local trees than on trees originated from more distant localities. Finally, we also identify 28 significant associations between single nucleotide polymorphisms SNPs from defence genes and a number of the herbivore traits and metabolic profiles.
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| 15. |
- Bernhardsson, Carolina, et al.
(författare)
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Molecular population genetics of elicitor-induced resistance genes in European aspen (Populus tremula L., Salicaceae)
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 6:9, s. e24867-
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Tidskriftsartikel (refereegranskat)abstract
- Owing to their long life span and ecological dominance in many communities, forest trees are subject to attack from a diverse array of herbivores throughout their range, and have therefore developed a large number of both constitutive and inducible defenses. We used molecular population genetics methods to examine the evolution of eight genes in European aspen, Populus tremula, that are all associated with defensive responses against pests and/or pathogens, and have earlier been shown to become strongly up-regulated in poplars as a response to wounding and insect herbivory. Our results show that the majority of these defense genes show patterns of intraspecific polymorphism and site-frequency spectra that are consistent with a neutral model of evolution. However, two of the genes, both belonging to a small gene family of polyphenol oxidases, show multiple deviations from the neutral model. The gene PPO1 has a 600 bp region with a highly elevated K(A)/K(S) ratio and reduced synonymous diversity. PPO1 also shows a skew toward intermediate frequency variants in the SFS, and a pronounced fixation of non-synonymous mutations, all pointing to the fact that PPO1 has been subjected to recurrent selective sweeps. The gene PPO2 shows a marked excess of high frequency, derived variants and shows many of the same trends as PPO1 does, even though the pattern is less pronounced, suggesting that PPO2 might have been the target of a recent selective sweep. Our results supports data from both Populus and other species which have found that the the majority of defense-associated genes show few signs of selection but that a number of genes involved in mediating defense against herbivores show signs of adaptive evolution.
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| 16. |
- Bernhardsson, Carolina, et al.
(författare)
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Population differentiation in arthropod community structure and phenotypic association with inducible defense genes in European Aspen (Populus tremula L., salicaceae)
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Plant-herbivore interactions are known to vary across a landscape due to both variation in abiotic and biotic factors. Such spatial variation tends to promoting local adaption of plants to the prevailing herbivore regime. Here we use data from a common garden to look for patterns across populations in the abundance and diversity of herbivorous insects. We also screen for variation in the untargeted metabolome of the foliage of a subset of the same trees. We also search for phenotypic associations between genetic variation in a number of wound-induced genes and phenotypic variation in herbivore abundance, diversity and in metabolomes. We observe significant genetic variation in a number of herbivore-related traits but low correlations between traits. We do observe substantial genetic structure in both herbivore community structure and in metabolic profiles and this structure is aligned with genetic structure we have previously documented for a set of defense genes. We also identify a number of significant associations between SNPs from wound-induced defense genes and a number of the herbivore traits and metabolic profiles. However, these associations are likely not causal, but are rather caused by the underlying population structure we observe. These results highlight to the importance of historical processes and the need to better understand both the current-day geographic distribution of different herbivore species as well as the post-glacial colonization history of both plants and herbivores.
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| 17. |
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| 18. |
- Bernhardsson, Carolina, et al.
(författare)
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Variant Calling Using Whole Genome Resequencing and Sequence Capture for Population and Evolutionary Genomic Inferences in Norway Spruce (Picea Abies)
- 2020
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Ingår i: The Spruce Genome. - Switzerland : Springer Nature. - 9783030210014 - 9783030210007 ; , s. 9-36
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Bokkapitel (refereegranskat)abstract
- Advances in next-generation sequencing methods and the development of new statistical and computational methods have opened up possibilities for large-scale, high-quality genotyping in most organisms. Conifer genomes are large and are known to contain a high fraction of repetitive elements and this complex genome structure has bearings for approaches that aim to use next-generation sequencing methods for genotyping. In this chapter, we provide a detailed description of a workflow for variant calling using next-generation sequencing in Norway spruce (Picea abies). The workflow starts with raw sequencing reads and proceeds through read mapping to variant calling and variant filtering. We illustrate the pipeline using data derived from both whole-genome resequencing data and reduced representation sequencing. We highlight possible problems and pitfalls of using next-generation sequencing data for genotyping stemming from the complex genome structure of conifers and how those issues can be mitigated or eliminated.
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| 19. |
- Bos, Antoine, 1975-
(författare)
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Natural variation in cold adaptation and freezing tolerance in Arabidopsis thaliana
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Plants have spread to almost everywhere in the world. As they disperse, they meet many different environments to which they may be able to adapt. For a plant species to adapt to a new environment, genetic variation is needed. The individuals differ from each other in their genetic composition, which often means differences in phenotypes. Those individuals that manage to reproduce will form the next generation. With different conditions in different environments, it will not be the same phenotypes that reproduce everywhere. In that way, plant species will form into a mosaic of locally adapted populations varying genetically as the species disperses. After the last ice age plants have started to disperse away from the equators. With increasing latitudes come increasing challenges to migrating plants. As plant species disperse northwards along this gradient of varying conditions individuals are selected for cold adaptive traits like flowering time and freezing tolerance, acquired by cold acclimation. In this way, genetic variation from the original populations for these traits becomes sorted out along a latitudinal cline. The aim of this thesis was to understand how selection along a latitudinal gradient has shaped natural variation in cold adaptive traits in plants dispersing northwards, and specifically, to investigate what variation can be observed in phenotypes for these traits and how these traits correlate with genetic variation in genes known to be involved in cold acclimation. In this study significant variation was found in a sample of the model plan Arabidopsis thaliana accessions in cold adaptive traits flowering time and freezing tolerance. A clear latitudinal cline in the cold adaptive traits freezing tolerance for A. thaliana was observed. Analysis of nucleotide polymorphism for the cold responsive ICE1 (inducer of CBF expression 1) transcription factor revealed a haplotype structure with two allelic clades as well as unusually high levels of synonymous polymorphism. Nucleotide polymorphism analysis for the transcription factors CBF1, CBF2 and CBF3 (C-repeat binding factors) that play a key role in regulating the expression of a group of target genes known as the “CBF regulon” showed a distinct geographical haplotype structure. One haplotype was dominant in southern accessions while in the other northern accessions overrepresented. There was a significant effect of CBF haplotype on both freezing tolerance and flowering time even after correcting for latitude. Significant differences in CBF expression levels were found between the different CBF genes as well as between different accessions. Sequence variation at CBF was shown to have a significant effect on expression levels of CBF2. No clear correlations were found between CBF gene expression and freezing tolerance or temperature sensitivity for any of the accessions used in the study. This highlights the complex relationship between sequence variation in candidate genes and gene expression, and the problems associated with unraveling the genetic basis of ecologically important traits.
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| 20. |
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| 21. |
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| 22. |
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| 23. |
- Capador‐Barreto, Hernán D., et al.
(författare)
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Killing two enemies with one stone? : Genomics of resistance to two sympatric pathogens in Norway spruce
- 2021
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 30:18, s. 4433-4447
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Tidskriftsartikel (refereegranskat)abstract
- Trees must cope with the attack of multiple pathogens, often simultaneously during their long lifespan. Ironically, the genetic and molecular mechanisms controlling this process are poorly understood. The objective of this study was to compare the genetic component of resistance in Norway spruce to Heterobasidion annosum s.s. and its sympatric congener Heterobasidion parviporum. Heterobasidion root- and stem-rot is a major disease of Norway spruce caused by members of the Heterobasidion annosum species complex. Resistance to both pathogens was measured using artificial inoculations in half-sib families of Norway spruce trees originating from central to northern Europe. The genetic component of resistance was analysed using 63,760 genome-wide exome-capture sequenced SNPs and multitrait genome-wide associations. No correlation was found for resistance to the two pathogens; however, associations were found between genomic variants and resistance traits with synergic or antagonist pleiotropic effects to both pathogens. Additionally, a latitudinal cline in resistance in the bark to H. annosum s.s. was found; trees from southern latitudes, with a later bud-set and thicker stem diameter, allowed longer lesions, but this was not the case for H. parviporum. In summary, this study detects genomic variants with pleiotropic effects which explain multiple disease resistance from a genic level and could be useful for selection of resistant trees to both pathogens. Furthermore, it highlights the need for additional research to understand the evolution of resistance traits to multiple pathogens in trees.
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| 24. |
- Cole, Christopher T., et al.
(författare)
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Pathway position constrains the evolution of an ecologically important pathway in aspens (Populus tremula L.)
- 2018
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Ingår i: Molecular Ecology. - : Wiley-Blackwell. - 0962-1083 .- 1365-294X. ; 27:16, s. 3317-3330
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Tidskriftsartikel (refereegranskat)abstract
- Many ecological interactions of aspens and their relatives (Populus spp.) are affected by products of the phenylpropanoid pathway synthesizing condensed tannins (CTs), whose production involves trade-offs with other ecologically important compounds and with growth. Genes of this pathway are candidates for investigating the role of selection on ecologically important, polygenic traits. We analysed sequences from 25 genes representing 10 steps of the CT synthesis pathway, which produces CTs used in defence and lignins used for growth, in 12 individuals of European aspen (Populus tremula). We compared these to homologs from P.trichocarpa, to a control set of 77 P. tremula genes, to genome-wide resequencing data and to RNA-seq expression levels, in order to identify signatures of selection distinct from those of demography. In Populus, pathway position exerts a strong influence on the evolution of these genes. Nonsynonymous diversity, divergence and allele frequency shifts (Tajima's D) were much lower than for synonymous measures. Expression levels were higher, and the direction of selection more negative, for upstream genes than for those downstream. Selective constraints act with increasing intensity on upstream genes, despite the presence of multiple paralogs in most gene families. Pleiotropy, expression level, flux control and codon bias appear to interact in determining levels and patterns of variation in genes of this pathway, whose products mediate a wide array of ecological interactions for this widely distributed species.
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| 25. |
- de Carvalho, Dulcineia, et al.
(författare)
-
Admixture facilitates adaptation from standing variation in the European aspen (P. tremula L.), a widespread forest tree
- 2010
-
Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 19:8, s. 1638-1650
-
Tidskriftsartikel (refereegranskat)abstract
- Adaptation to new environments can start from new mutations or from standing variation already present in natural populations. Whether admixture constrains or facilitates adaptation from standing variation is largely unknown, especially in ecological keystone or foundation species. We examined patterns of neutral and adaptive population divergence in Populus tremula L., a widespread forest tree, using mapped molecular genetic markers. We detected the genetic signature of postglacial admixture between a Western and an Eastern lineage of P. tremula in Scandinavia, an area suspected to represent a zone of postglacial contact for many species of animals and plants. Stringent divergence-based neutrality tests provided clear indications for locally varying selection at the European scale. Six of 12 polymorphisms under selection were located less than 1 kb away from the nearest gene predicted by the Populus trichocarpa genome sequence. Few of these loci exhibited a signature of 'selective sweeps' in diversity-based tests, which is to be expected if adaptation occurs primarily from standing variation. In Scandinavia, admixture explained genomic patterns of ancestry and the nature of clinal variation and strength of selection for bud set, a phenological trait of great adaptive significance in temperate trees, measured in a common garden trial. Our data provide a hitherto missing direct link between past range shifts because of climatic oscillations, and levels of standing variation currently available for selection and adaptation in a terrestrial foundation species.
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| 26. |
- De La Torre, Amanda, 1976-, et al.
(författare)
-
Genetic architecture and genomic patterns of gene flow between hybridizing species of Picea
- 2015
-
Ingår i: Heredity. - : Nature Publishing Group. - 0018-067X .- 1365-2540. ; 115:2, s. 153-164
-
Tidskriftsartikel (refereegranskat)abstract
- Hybrid zones provide an opportunity to study the effects of selection and gene flow in natural settings. We employed nuclear microsatellites (single sequence repeat (SSR)) and candidate gene single-nucleotide polymorphism markers (SNPs) to characterize the genetic architecture and patterns of interspecific gene flow in the Picea glauca x P. engelmannii hybrid zone across a broad latitudinal (40-60 degrees) and elevational (350-3500 m) range in western North America. Our results revealed a wide and complex hybrid zone with broad ancestry levels and low interspecific heterozygosity, shaped by asymmetric advanced-generation introgression, and low reproductive barriers between parental species. The clinal variation based on geographic variables, lack of concordance in clines among loci and the width of the hybrid zone points towards the maintenance of species integrity through environmental selection. Congruency between geographic and genomic clines suggests that loci with narrow clines are under strong selection, favoring either one parental species (directional selection) or their hybrids (overdominance) as a result of strong associations with climatic variables such as precipitation as snow and mean annual temperature. Cline movement due to past demographic events (evidenced by allelic richness and heterozygosity shifts from the average cline center) may explain the asymmetry in introgression and predominance of P. engelmannii found in this study. These results provide insights into the genetic architecture and fine-scale patterns of admixture, and identify loci that may be involved in reproductive barriers between the species.
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| 27. |
- de La Torre, Amanda R., et al.
(författare)
-
Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants
- 2017
-
Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 34:6, s. 1363-1377
-
Tidskriftsartikel (refereegranskat)abstract
- The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained. Although some attention has been given to flowering plants, reports of molecular evolutionary rates for their sister plant clade (gymnosperms) are scarce, and to our knowledge differences in molecular evolution among seed plant clades have never been tested in a phylogenetic framework. Angiosperms and gymnosperms differ in a number of features, of which contrasting reproductive biology, life spans, and population sizes are the most prominent. The highly conserved morphology of gymnosperms evidenced by similarity of extant species to fossil records and the high levels of macrosynteny at the genomic level have led scientists to believe that gymnosperms are slow-evolving plants, although some studies have offered contradictory results. Here, we used 31,968 nucleotide sites obtained from orthologous genes across a wide taxonomic sampling that includes representatives of most conifers, cycads, ginkgo, and many angiosperms with a sequenced genome. Our results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species. Longer generation times and larger genome sizes are some of the factors explaining the slow rates of molecular evolution found in gymnosperms. In contrast to their slow rates of molecular evolution, gymnosperms possess higher substitution rate ratios than angiosperm taxa. Finally, our study suggests stronger and more efficient purifying and diversifying selection in gymnosperm than in angiosperm species, probably in relation to larger effective population sizes.
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| 28. |
- De La Torre, Amanda R, et al.
(författare)
-
Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in Picea gene families
- 2015
-
Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 7:4, s. 1002-1015
-
Tidskriftsartikel (refereegranskat)abstract
- The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (> 50,000 expressed genes) to study the relationship between gene expression, codon bias, rates of sequence divergence, protein length, and gene duplication. We found that gene expression is correlated with rates of sequence divergence and codon bias, suggesting that natural selection is acting on Picea protein-coding genes for translational efficiency. Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families. Tissue-specific patterns of gene expression were more common in large gene families with large gene expression divergence than in single-copy families. Recent family expansions combined with large gene expression variation in paralogs and increased rates of sequence evolution suggest that some Picea gene families are rapidly evolving to cope with biotic and abiotic stress. Our study highlights the importance of gene expression and natural selection in shaping the evolution of protein-coding genes in Picea species, and sets the ground for further studies investigating the evolution of individual gene families in gymnosperms.
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| 29. |
- de La Torre, Amanda R, et al.
(författare)
-
Insights into conifer giga-genomes
- 2014
-
Ingår i: Plant Physiology. - : American Society of Plant Biologists. - 0032-0889 .- 1532-2548. ; 166:4, s. 1724-1732
-
Tidskriftsartikel (refereegranskat)abstract
- Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world's forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20-30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes.
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| 30. |
- Du, Qingzhang, et al.
(författare)
-
Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in Populus tomentosa
- 2015
-
Ingår i: DNA research. - : Oxford University Press. - 1340-2838 .- 1756-1663. ; 22:1, s. 53-67
-
Tidskriftsartikel (refereegranskat)abstract
- Economically important traits in many species generally show polygenic, quantitative inheritance. The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined. Here, we investigated 11 full-length genes in cellulose biosynthesis, on 10 growth and wood-property traits, within a population of 460 unrelated Populus tomentosa individuals, via multi-gene association. To validate positive associations, we conducted single-marker analysis in a linkage population of 1,200 individuals. We identified 118, 121, and 43 associations (P < 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R-2). Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume. Single-marker analysis validated 61 associations (false discovery rate, Q <= 0.10), representing 38 SNPs from nine genes, and its average effect (R-2 = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants. Moreover, a structural gene-gene network based on tissue-specific transcript abundances provides a better understanding of the multi-gene pathway affecting tree growth and lignocellulose biosynthesis. Our study highlights the importance of pathway-based multiple gene associations to uncover the nature of genetic variance for quantitative traits and may drive novel progress in molecular breeding.
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| 31. |
- Du, Shuhui, et al.
(författare)
-
Multilocus analysis of nucleotide variation and speciation in three closely related Populus (Salicaceae) species
- 2015
-
Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 24:19, s. 4994-5005
-
Tidskriftsartikel (refereegranskat)abstract
- Historical tectonism and climate oscillations can isolate and contract the geographical distributions of many plant species, and they are even known to trigger species divergence and ultimately speciation. Here, we estimated the nucleotide variation and speciation in three closely related Populus species, Populus tremuloides, P.tremula and P.davidiana, distributed in North America and Eurasia. We analysed the sequence variation in six single-copy nuclear loci and three chloroplast (cpDNA) fragments in 497 individuals sampled from 33 populations of these three species across their geographic distributions. These three Populus species harboured relatively high levels of nucleotide diversity and showed high levels of nucleotide differentiation. Phylogenetic analysis revealed that P.tremuloides diverged earlier than the other two species. The cpDNA haplotype network result clearly illustrated the dispersal route from North America to eastern Asia and then into Europe. Molecular dating results confirmed that the divergence of these three species coincided with the sundering of the Bering land bridge in the late Miocene and a rapid uplift of the Qinghai-Tibetan Plateau around the Miocene/Pliocene boundary. Vicariance-driven successful allopatric speciation resulting from historical tectonism and climate oscillations most likely played roles inthe formation of the disjunct distributions and divergence of these three Populus species.
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| 32. |
- Eklöf, Helena, et al.
(författare)
-
Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies
- 2020
-
Ingår i: Forests. - : MDPI. - 1999-4907. ; 11:11
-
Tidskriftsartikel (refereegranskat)abstract
- Conifer genomes are characterized by their large size and high abundance of repetitive material, making large-scale genotyping in conifers complicated and expensive. One of the consequences of this is that it has been difficult to generate data on genome-wide levels of genetic variation. To date, researchers have mainly employed various complexity reduction techniques to assess genetic variation across the genome in different conifer species. These methods tend to capture variation in a relatively small subset of a typical conifer genome and it is currently not clear how representative such results are. Here we take advantage of data generated in the first large-scale re-sequencing effort in Norway spruce and assess how well two commonly used complexity reduction methods, targeted capture probes and genotyping by sequencing perform in capturing genome-wide variation in Norway spruce. Our results suggest that both methods perform reasonably well for assessing genetic diversity and population structure in Norway spruce (Picea abies (L.) H. Karst.). Targeted capture probes were slightly more effective than GBS, likely due to them targeting known genomic regions whereas the GBS data contains a substantially greater fraction of repetitive regions, which sometimes can be problematic for assessing genetic diversity. In conclusion, both methods are useful for genotyping large numbers of samples and they greatly reduce the cost involved with genotyping a species with such a complex genome as Norway spruce.
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| 33. |
- Eklöf, Helena, et al.
(författare)
-
Do modern forestry practices impact the genetic diversity of planted stands of Norway spruce (Picea abies)
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Norway spruce (Picea abies) is an important tree species in Sweden, making up almost 40% of standing forest on productive forest land. It is presently unclear if and in what way current forestry practices in Sweden, where the majority of new forest stands are derived from planting genetically improved seeds, affects the distribution of genetic diversity in newly planted stands. Earlier studies comparing managed and natural forests have found little difference in genetic diversity but they have all relied on a small number of genetic markers and have therefore had limited statistical power. Here we use a PoolSeq based genotyping by sequencing strategy to generate a data set consisting of circa 40k SNPs that we use assess the amount and distribution of genetic diversity in Norway spruce. For our comparisons we sampled 15 old stands that had not been logged for at least 150 years in the Västerbotten and Västernorrland counties, northern Sweden. In the vicinity of each old forest stands, we also sampled trees from two young stands that had been re-planted following clear-cutting within the last 20 years. For each of the 45 populations (15 old and 30 planted), we pooled 30 trees and genotyped them using GBS in order to be able to assess stand-based allele frequencies. We found no obvious correspondence between the population structure estimated from the SNP data and the geography of sampling sites. The mean values for a number of common diversity and differentiation statistics did not differ significantly between old and planted stands. However, we observe that variation in these statistics were consistently larger among the planted stands and significantly so for mean allele frequency (p=0.036) and pairwise FST values (p=1.66e-05). Our results suggest that re-forestation using planting has not affected the overall genetic diversity in the planted stands. However, the larger variation we observe among the planted stands for most summary statistics suggest that the re-forestation practices might have long-term effects of how this genetic diversity is partitioned among different stands.
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| 34. |
- Eklöf, Helena, 1989-
(författare)
-
Genetic diversity and differentiation in natural and managed stands of Norway spruce (Picea abies)
- 2021
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Being one of Sweden’s most important tree species, both as a keystone species and for the forest industry, it is important that we keep our stands of Norway spruce (Picea abies (L.) Karst.) as healthy as possible. With an unclear starting point of existing genetic diversity in natural forests we need to both evaluate what levels of natural diversity we have to begin with and how modern forestry practices might affect this. Previous studies have used relatively few markers to study this or similar situation before. We proved that both capture probes and genotyping by sequencing (GBS) show similar results in common diversity measurements and offers many SNPs, although capture probes showed slightly more diversity in the results, we choose to use PoolSeq and GBS together to examine a large number of planted and natural stands of Norwegian spruce in northern Sweden. In line with previous results on the subject we did not find any large differences between our young, planted forests and our old forests, suggesting that today’s re-planting methods have not affected the general diversity in different stands. However, we did find a difference in the variance of our summary statistics on a stand level between planted and old stands, an indicator that there is a possibility that forestry can cause long-term effects. This becomes even more important in the light of possible clonal deployment of Norway spruce. I believe that more research is needed over both larger geographical areas and with a focus on within stand variation. Using mitochondrial and chloroplast DNA to discern finer details of spatial distribution within stands and looking closer at the genotypic diversity within natural and planted stands. An effort should also be put into examine how these possible differences are affecting the rest of the ecosystem, living with and among Norway spruce.
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| 35. |
- Fataftah, Nazeer, et al.
(författare)
-
GIGANTEA influences leaf senescence in trees in two different ways
- 2021
-
Ingår i: Plant Physiology. - : Oxford University Press. - 0032-0889 .- 1532-2548. ; 187:4, s. 2435-2450
-
Tidskriftsartikel (refereegranskat)abstract
- GIGANTEA (GI) genes have a central role in plant development and influence several processes. Hybrid aspen T89 (Populus tremula x tremuloides) trees with low GI expression engineered through RNAi show severely compromised growth. To study the effect of reduced GI expression on leaf traits with special emphasis on leaf senescence, we grafted GI-RNAi scions onto wild-type rootstocks and successfully restored growth of the scions. The RNAi line had a distorted leaf shape and reduced photosynthesis, probably caused by modulation of phloem or stomatal function, increased starch accumulation, a higher carbon-to-nitrogen ratio, and reduced capacity to withstand moderate light stress. GI-RNAi also induced senescence under long day (LD) and moderate light conditions. Furthermore, the GI-RNAi lines were affected in their capacity to respond to “autumn environmental cues” inducing senescence, a type of leaf senescence that has physiological and biochemical characteristics that differ from those of senescence induced directly by stress under LD conditions. Overexpression of GI delayed senescence under simulated autumn conditions. The two different effects on leaf senescence under LD or simulated autumn conditions were not affected by the expression of FLOWERING LOCUS T. GI expression regulated leaf senescence locally-the phenotype followed the genotype of the branch, independent of its position on the tree-and trees with modified gene expression were affected in a similar way when grown in the field as under controlled conditions. Taken together, GI plays a central role in sensing environmental changes during autumn and determining the appropriate timing for leaf senescence in Populus.
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| 36. |
- Gao, Jie, et al.
(författare)
-
Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau
- 2012
-
Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 21:19, s. 4811-4827
-
Tidskriftsartikel (refereegranskat)abstract
- Pinus densata is an ecologically successful homoploid hybrid that inhabits vast areas of heterogeneous terrain on the south-eastern Tibetan Plateau as a result of multiple waves of colonization. Its region of origin, route of colonization onto the plateau and the directions of introgression with its parental species have previously been defined, but little is known about the isolation and divergence history of its populations. In this study, we surveyed nucleotide polymorphism over eight nuclear loci in 19 representative populations of P. densata and its parental species. Using this information and coalescence simulations, we assessed the historical changes in its population size, gene flow and divergence in time and space. The results indicate a late Miocene origin for P. densata associated with the recent uplift of south-eastern Tibet. The subsequent differentiation between geographical regions of this species began in the late Pliocene and was induced by regional topographical changes and Pleistocene glaciations. The ancestral P. densata population had a large effective population size but the central and western populations were established by limited founders, suggesting that there were severe bottlenecks during the westward migration out of the ancestral hybrid zone. After separating from their ancestral populations, population expansion occurred in all geographical regions especially in the western range. Gene flow in P. densata was restricted to geographically neighbouring populations, resulting in significant differentiation between regional groups. The new information on the divergence and demographic history of P. densata reported herein enhances our understanding of its speciation process on the Tibetan Plateau.
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| 37. |
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| 38. |
- Grimberg, Åsa, et al.
(författare)
-
Storage lipid accumulation is controlled by photoperiodic signal acting via regulators of growth cessation and dormancy in hybrid aspen
- 2018
-
Ingår i: New Phytologist. - : John Wiley & Sons. - 0028-646X .- 1469-8137. ; 219:2, s. 619-630
-
Tidskriftsartikel (refereegranskat)abstract
- The signalling pathways that control seasonal modulation of carbon metabolism in perennial plants are poorly understood. Using genetic, metabolic and natural variation approaches, we identify factors mediating photoperiodic control of storage lipid accumulation in the model tree hybrid aspen (Populus tremula x tremuloides). We characterized lipid accumulation in transgenic hybrid aspen with impaired photoperiodic and hormonal responses. Genome-wide association mapping was performed in Swedish aspen (P.tremula) genotypes to determine genetic loci associated with genotype variation in lipid content. Our data show that the storage lipid triacylglycerol (TAG) accumulates in cambial meristem and pith rays of aspen in response to photoperiodic signal controlling growth cessation and dormancy induction. We show that photoperiodic control of TAG accumulation is mediated by the FLOWERING LOCUS T/CONSTANS module, which also controls the induction of growth cessation. Hormonal and chromatin remodelling pathways also contribute to TAG accumulation by photoperiodic signal. Natural variation exists in lipid accumulation that is controlled by input from multiple loci. Our data shed light on how the control of storage metabolism is temporally coordinated with growth cessation and dormancy by photoperiodic signal, and reveals that storage lipid accumulation between seeds and perennating organs of trees may involve distinct regulatory circuits.
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| 39. |
- Hall, David, 1974-, et al.
(författare)
-
Adaptive evolution of the Populus tremula photoperiod pathway
- 2011
-
Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 20:7, s. 1463-1474
-
Tidskriftsartikel (refereegranskat)abstract
- Environmental cues entrain the circadian clock, a core component of the photoperiod pathway in plants, to daily and seasonal changes. The circadian clock mediates input signals from light and temperature receptors to downstream target genes through feedback loops. Several studies have shown that a correct timing of the circadian system is a fitness advantage and genes in photoperiod network have been implied to evolve in response to the diversifying selection in heterogeneous environment. In an attempt to quantify the extent of the historical patterns of selection on genes in the photoperiod pathway in the widely distributed tree species European aspen (Populus tremula) we obtained sequences for twenty-five of the genes in the network and these genes were compared to patterns of nucleotide diversity in 77 randomly chosen genes from across the genome of P. tremula. We found a significant reduction in synonymous diversity in photoperiod genes while non-synonymous diversity was in line with data from control genes. A substantial fraction of the genes show signs of selection, with eight genes showing signs of rapid protein evolution. In contrast to our expectations, genes closely associated with the core circadian clock show rapid protein evolution despite their central position in the pathway. Furthermore, selection on non-synonymous mutations is negatively correlated with synonymous diversity across all genes, indicating the action of recurrent selective sweeps.
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| 40. |
- Hall, David, 1974-, et al.
(författare)
-
Adaptive population differentiation in phenology across a latitudinal gradient in European aspen (Populus tremula, L.) : a comparison of neutral markers, candidate genes and phenotypic traits
- 2007
-
Ingår i: Evolution. - : Wiley InterScience. - 0014-3820 .- 1558-5646. ; 61, s. 2849-2860
-
Tidskriftsartikel (refereegranskat)abstract
- A correct timing of growth cessation and dormancy induction represents a critical ecological and evolutionary trade-off between survival and growth in most forest trees (Rehfeldt et al. 1999; Horvath et al. 2003; Howe et al. 2003). We have studied the deciduous tree European Aspen (Populus tremula) across a latitudinal gradient and compared genetic differentiation in phenology traits with molecular markers. Trees from 12 different areas covering 10 latitudinal degrees were cloned and planted in two common gardens. Several phenology traits showed strong genetic differentiation and clinal variation across the latitudinal gradient, with QST values generally exceeding 0.5. This is in stark contrast to genetic differentiation at several classes of genetic markers (18 neutral SSRs, 7 SSRs located close to phenology candidate genes and 50 SNPs from five phenology candidate genes) that all showed FST values around 0.015. We thus find strong evidence for adaptive divergence in phenology traits across the latitudinal gradient. However, the strong population structure seen at the quantitative traits is not reflected in underlying candidate genes. This result fit theoretical expectations that suggest that genetic differentiation at candidate loci is better described by FST at neutral loci rather than by QST at the quantitative traits themselves.
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| 41. |
- Hall, David, 1974-, et al.
(författare)
-
Patterns of selection at the phytochrome A locus in European aspen (Populus tremula)
-
Annan publikation (populärvet., debatt m.m.)abstract
- When a phenotype with a higher fitness arises in the population the underlying alleles are swept through the population until they reach fixation. The area surrounding the locus of the beneficial allele hitchhikes with the allele under selection, and the size of the area affected depends on the strength of selection. In Populus tremula a < 20kb region on linkage group 13 shows great reduction in synonymous diversity and an increase in rare and derived alleles as indicated by low negative values of Tajima's D and Fay and Wu's H. There is also an increase in associations between allleles at SNP sites in this region. We find that the sweep peaks in exon 2 of the phytochrome A gene. PHYA has not only undergone rapid protein evolution, it also show higher divergence in P. tremula than other plants examined, where it is unusually conserved, further pointing to adaptive significance of the increased rate of protein evolution seen in P. tremula.
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| 42. |
- Hall, David, 1974-
(författare)
-
Tracing selection and adaptation along an environmental gradient in Populus tremula
- 2009
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The distribution of the expressed genotype is moved around in the population over time byevolution. Natural selection is one of the forces that act on the phenotype to change the patterns ofnucleotide variation underlying those distributions. How the phenotype changes over aheterogeneous environment describes the type of evolutionary force acting on this trait and thisshould be reflected in the variation at loci underlying this trait. While the variation in phenotypesand at the nucleotide level in a population indicates the same evolutionary force, it does notnecessarily mean that they are connected. In natural populations the continuous shifting of geneticmaterial through recombination events break down possible associations between loci facilitates theexamination of possible causal loci to single base pair differences in DNA-sequences. Connecting thegenotype and the phenotype thus provides an important step in the understanding the geneticarchitecture of complex traits and the forces that shape the observed patterns.This thesis examines the European aspen, Populus tremula, sampled from subpopulations overan extensive latitudinal gradient covering most of Sweden. Results show a clear geneticdifferentiation in the timing of bud set, a measure of the autumnal cessation of growth, betweendifferent parts of Sweden pointing at local adaptation. In the search for candidate genes thatunderlie the local adaptation found, most genes (25) in the photoperiodic gene network wereexamined for signals of selection. Genes in the photoperiodic network show an increase in theheterogeneity of differentiation between sampled subpopulations in Sweden. Almost half (12) of theexamined genes are under some form of selection. Eight of these genes show positive directionalselection on protein evolution and the gene that code for a photoreceptor, responsible for mediatingchanging light conditions to downstream targets in the network, has the hallmarks of a selectivesweep. The negative correlation between positive directional selection and synonymous diversityindicates that the majority of the photoperiod gene network has undergone recurrent selectivesweeps. A phenomenon that likely has occurred when P. tremula has readapted to the northern lightregimes during population expansion following retracting ice between periods of glaciations. Two ofthe genes under selection also have single nucleotide polymorphisms (SNP) that associate with budset, two in the PHYB2 gene and one in the LHY2 gene. Furthermore, there is an additional SNP inLHY1 that explain part of the variation in timing of bud set, despite the lack of a signal of selection atthe LHY1 gene. Together these SNPs explain 10-15% of the variation in the timing of bud set and 20-30% more if accounting for the positive co-variances between SNPs. There is thus rather extensiveevidence that genes in the photoperiod gene network control the timing of bud set, and reflect localadaptation in this trait.
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| 43. |
- Hall, David, et al.
(författare)
-
Using association mapping to dissect the genetic basis of complex traits in plants
- 2010
-
Ingår i: Briefings in Functional Genomics & Proteomics. - : Oxford University Press (OUP). - 1473-9550 .- 1477-4062 .- 2041-2649 .- 2041-2657. ; 9:2, s. 157-165
-
Tidskriftsartikel (refereegranskat)abstract
- Association or linkage disequilibrium mapping has become a very popular method for dissecting the genetic basis of complex traits in plants. The benefits of association mapping, compared with traditional quantitative trait locus mapping, is, for example, a relatively detailed mapping resolution and that it is far less time consuming since no mapping populations need to be generated. The surge of interest in association mapping has been fueled by recent developments in genomics that allows for rapid identification and scoring of genetic markers which has traditionally limited mapping experiments. With the decreasing cost of genotyping future emphasis will likely focus on phenotyping, which can be both costly and time consuming but which is crucial for obtaining reliable results in association mapping studies. In addition, association mapping studies are prone to the identification of false positives, especially if the experimental design is not rigorously controlled. For example, population structure has long been known to induce many false positives and accounting for population structure has become one of the main issues when implementing association mapping in plants. Also, with increasing numbers of genetic markers used, the problem becomes separating true from false positive and this highlights the need for independent validation of identified association. With these caveats in mind, association mapping nevertheless shows great promise for helping us understand the genetic basis of complex traits of both economic and ecological importance.
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| 44. |
- Hallingbäck, Henrik, et al.
(författare)
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Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis
- 2021
-
Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 22
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Tidskriftsartikel (refereegranskat)abstract
- Background Sex chromosomes are in some species largely undifferentiated (homomorphic) with restricted sex determination regions. Homomorphic but different sex chromosomes are found in the closely related genera Populus and Salix indicating flexible sex determination systems, ideal for studies of processes involved in sex chromosome evolution. We have performed genome-wide association studies of sex and analysed sex chromosomes in a population of 265 wild collected Salix viminalis accessions and studied the sex determining locus. Results A total of 19,592 markers were used in association analyses using both Fisher's exact tests and a single-marker mixed linear model, which resulted in 48 and 41 sex-associated (SA) markers respectively. Across all 48 SA markers, females were much more often heterozygous than males, which is expected if females were the heterogametic sex. The majority of the SA markers were, based on positions in the S. purpurea genome, located on chromosome 15, previously demonstrated to be the sex chromosome. Interestingly, when mapping the genotyping-by-sequencing sequence tag harbouring the two SA markers with the highest significance to the S. viminalis genomic scaffolds, five regions of very high similarity were found: three on a scaffold that represents a part of chromosome 15, one on a scaffold that represents a part of chromosome 9 and one on a scaffold not anchored to the genome. Based on segregation differences of the alleles at the two marker positions and on differences in PCR amplification between females and males we conclude that females had multiple copies of this DNA fragment (chromosome 9 and 15), whereas males only had one (chromosome 9). We therefore postulate that the female specific sequences have been copied from chromosome 9 and inserted on chromosome 15, subsequently developing into a hemizygous W chromosome linked region. Conclusions Our results support that sex determination in S. viminalis is controlled by one locus on chromosome 15. The segregation patterns observed at the SA markers furthermore confirm that S. viminalis females are the heterogametic sex. We also identified a translocation from chromosome 9 to the W chromosome.
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| 45. |
- Hu, Jia, et al.
(författare)
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Fumarate reductase drives methane emissions in the genus Oryza through differential regulation of the rhizospheric ecosystem
- 2024
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Ingår i: Environment International. - 0160-4120 .- 1873-6750. ; 190
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Tidskriftsartikel (refereegranskat)abstract
- The emergence of waterlogged Oryza species similar to 15Mya (million years ago) supplied an anoxic warm bed for methane-producing microorganisms, and methane emissions have hence accompanied the entire evolutionary history of the genus Oryza. However, to date no study has addressed how methane emission has been altered during Oryza evolution. In this paper we used a diverse collection of wild and cultivated Oryza species to study the relation between Oryza evolution and methane emissions. Phylogenetic analyses and methane detection identified a co-evolutionary pattern between Oryza and methane emissions, mediated by the diversity of the rhizospheric ecosystems arising from different oxygen levels. Fumarate was identified as an oxygen substitute used to retain the electron transport/energy production in the anoxic rice root, and the contribution of fumarate reductase to Oryza evolution and methane emissions has also been assessed. We confirmed the between-species patterns using genetic dissection of the traits in a cross between a low and high methane-emitting species. Our findings provide novel insights on the evolutionary processes of rice paddy methane emissions: the evolution of wild rice produces different Oryza species with divergent rhizospheric ecosystem attributing to the different oxygen levels and fumarate reductase activities, methane emissions are comprehensively assessed by the rhizospheric environment of diversity Oryza species and result in a co-evolution pattern.
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| 46. |
- Ingvarsson, Pär
(författare)
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Adaptive signals of flowering time pathways in wild barley from Israel over 28 generations
- 2020
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Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 124, s. 62-76
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Tidskriftsartikel (refereegranskat)abstract
- Flowering time is one of the most critical traits for plants' life cycles, which is influenced by various environment changes, such as global warming. Previous studies have suggested that to guarantee reproductive success, plants have shifted flowering times to adapt to global warming. Although many studies focused on the molecular mechanisms of early flowering, little was supported by the repeated sampling at different time points through the changing climate. To fully dissect the temporal and spatial evolutionary genetics of flowering time, we investigated nucleotide variation in ten flowering time candidate genes and nine reference genes for the same ten wild-barley populations sampled 28 years apart (1980-2008). The overall genetic differentiation was significantly greater in the descendant populations (2008) compared with the ancestral populations (1980); however, local adaptation tests failed to detect any single-nucleotide polymorphism (SNP)/indel under spatial-diversifying selection at either time point. By contrast, the WFABC (Wright-Fisher ABC-based approach) that detected 54 SNPs/indels was under strong selection during the past 28 generations. Moreover, all these 54 alleles were segregated in the ancestral populations, but fixed in the descendent populations. Among the top ten SNPs/indels, seven were located in genes of FT1 (FLOWERING TIME LOCUS T1), CO1 (CONSTANS-LIKE PROTEIN 1), and VRN-H2 (VERNALIZATION-H2), which have been documented to be associated with flowering time regulation in barley cultivars. This study might suggest that all ten populations have undergone parallel evolution over the past few decades in response to global warming, and even an overwhelming local adaptation and ecological differentiation.
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| 47. |
- Ingvarsson, Pär
(författare)
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Applying an artificial neural network approach for drought tolerance screening among Iranian wheat landraces and cultivars grown under well-watered and rain-fed conditions
- 2019
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Ingår i: Acta Physiologiae Plantarum. - : Springer Science and Business Media LLC. - 0137-5881 .- 1861-1664. ; 41
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Tidskriftsartikel (refereegranskat)abstract
- In the current study, an alpha-lattice design was used to investigate 320 Iranian bread wheat cultivars and landraces under non-stressed and rain-fed conditions, according to phenological, morphological and physiological parameters. An artificial neural network (ANN) was trained to evaluate the relative importance of different drought tolerance indices (DTIs) using a multilayer perceptron model. Our findings suggest that the Iranian wheat germplasm harbors large genetic diversity for all the studied traits. Correlation analyses highlighted the important role of seed number per spike, thousand kernel weight, leaf greenness and canopy temperature in predicting grain yield under both non-stressed and rain-fed conditions. Moreover, correlations between stressed-yield (Y-s) and yield index (Y-I, r = 1**), harmonic mean (HM, r = 0.94**), geometric mean productivity (GMP, r = 0.86**), and stress tolerance index (STI, r = 0.86**) were all large, which was further confirmed by the results of ANN and a principal component analysis. A hierarchical clustering, visualized using a heatmap plot, classified cultivars and landraces into four separate groups, where high-yielding and drought-tolerant genotypes clustered in the same group. The result of ANN indicated that MP and YI had the highest relative importance for screening compatible genotypes for well-watered and rain-fed conditions, respectively. Overall, the selection of genotypes according to agronomic and physiological traits in association with an appropriate DTI can identify favorable wheat genotypes in a field trial to breed for well-watered and water-limited environments. Furthermore, the ANN successfully evaluated the relative importance of different DTIs in wheat.
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| 48. |
- Ingvarsson, Pär, 1969-, et al.
(författare)
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Clinal variation in phyB2, a candidate gene for day-length-induced growth cessation and bud set, across a latitudinal gradient in European aspen (Populus tremula).
- 2006
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Ingår i: Genetics. - Pittsburgh, Pennsylvania, USA : the Genetics Society of America. - 0016-6731 .- 1943-2631. ; 172:3, s. 1845-53
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Tidskriftsartikel (refereegranskat)abstract
- The initiation of growth cessation and dormancy represents a critical ecological and evolutionary trade-off between survival and growth in most forest trees. The most important environmental cue regulating the initiation of dormancy is a shortening of the photoperiod and phytochrome genes have been implicated in short-day-induced bud set and growth cessation in Populus. We characterized patterns of DNA sequence variation at the putative candidate gene phyB2 in 4 populations of European aspen (Populus tremula) and scored single-nucleotide polymorphisms in an additional 12 populations collected along a latitudinal gradient in Sweden. We also measured bud set from a subset of these trees in a growth chamber experiment. Buds set showed significant clinal variation with latitude, explaining ~90% of the population variation in bud set. A sliding-window scan of phyB2 identified six putative regions with enhanced population differentiation and four SNPs showed significant clinal variation. The clinal variation at individual SNPs is suggestive of an adaptive response in phyB2 to local photoperiodic conditions. Three of four SNPs showing clinal variation were located in regions with excessive genetic differentiation, demonstrating that searching for regions of high genetic differentiation can be useful for identifying sites putatively involved in local adaptation.
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| 49. |
- Ingvarsson, Pär
(författare)
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Evolution of strong reproductive isolation in plants: broad-scale patterns and lessons from a perennial model group
- 2020
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Ingår i: Philosophical Transactions B: Biological Sciences. - : The Royal Society. - 0962-8436 .- 1471-2970. ; 375
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Tidskriftsartikel (refereegranskat)abstract
- Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the 'escape' of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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| 50. |
- Ingvarsson, Pär
(författare)
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Evolutionary Origins of Pseudogenes and Their Association with Regulatory Sequences in Plants
- 2019
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Ingår i: Plant Cell. - : Oxford University Press (OUP). - 1040-4651 .- 1532-298X. ; 31, s. 563-578
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Tidskriftsartikel (refereegranskat)abstract
- Pseudogenes (Psi s), nonfunctional relatives of functional genes, form by duplication or retrotransposition, and loss of gene function by disabling mutations. Evolutionary analysis provides clues to Psi origins and effects on gene regulation. However, few systematic studies of plant Psi s have been conducted, hampering comparative analyses. Here, we examined the origin, evolution, and expression patterns of Psi s and their relationships with noncoding sequences in seven angiosperm plants. We identified similar to 250,000 Psi s, most of which are more lineage specific than protein-coding genes. The distribution of Psi s on the chromosome indicates that genome recombination may contribute to Psi elimination. Most Psi s evolve rapidly in terms of sequence and expression levels, showing tissue- or stage-specific expression patterns. We found that a surprisingly large fraction of nontransposable element regulatory noncoding RNAs (microRNAs and long noncoding RNAs) originate from transcription of Psi proximal upstream regions. We also found that transcription factor binding sites preferentially occur in putative Psi proximal upstream regions compared with random intergenic regions, suggesting that Psi s have conditioned genome evolution by providing transcription factor binding sites that serve as promoters and enhancers. We therefore propose that rapid rewiring of Psi transcriptional regulatory regions is a major mechanism driving the origin of novel regulatory modules.
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