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Ingvarsson, Pär K.
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Publications (10 of 70) Show all publications
Bernhardsson, C., Vidalis, A., Wang, X., Scofield, D., Schiffthaler, B., Baison, J., . . . Ingvarsson, P. K. (2019). An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies). G3: Genes, Genomes, Genetics, 9(5), 1623-1632
Open this publication in new window or tab >>An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)
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2019 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 9, no 5, p. 1623-1632Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Genetics Society of America, 2019
Keywords
genetic map, Norway spruce, Picea abies, sequence capture, genome assembly
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-159871 (URN)10.1534/g3.118.200840 (DOI)000467271400031 ()30898899 (PubMedID)
Projects
Bio4Energy
Funder
Knut and Alice Wallenberg Foundation
Available from: 2019-06-10 Created: 2019-06-10 Last updated: 2019-09-06Bibliographically approved
Baison, J., Vidalis, A., Zhou, L., Chen, Z.-Q., Li, Z., Sillanpaeae, M. J., . . . Garcia-Gil, M. R. (2019). Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce. The Plant Journal
Open this publication in new window or tab >>Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce
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2019 (English)In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313XArticle in journal (Refereed) Epub ahead of print
Abstract [en]

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.

Place, publisher, year, edition, pages
WILEY, 2019
Keywords
candidate genes, functional trait mapping, genome-wide association mapping, Norway spruce, quence capture, single nucleotide polymorphisms
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-162327 (URN)10.1111/tpj.14429 (DOI)000478331500001 ()31166032 (PubMedID)
Available from: 2019-08-20 Created: 2019-08-20 Last updated: 2019-08-20
Ingvarsson, P. K. & Dahlberg, H. (2019). The effects of clonal forestry on genetic diversity in wild and domesticated stands of forest trees. Scandinavian Journal of Forest Research, 34(5), 370-379
Open this publication in new window or tab >>The effects of clonal forestry on genetic diversity in wild and domesticated stands of forest trees
2019 (English)In: Scandinavian Journal of Forest Research, ISSN 0282-7581, E-ISSN 1651-1891, Vol. 34, no 5, p. 370-379Article in journal (Refereed) Published
Abstract [en]

The level of genetic diversity maintained in a population is determined by the combined action of mutation, gene flow, genetic drift and selection. Forest tree breeding is a relatively recent phenomenon compared to most crop species and the material that is being deployed is, genetically, often very similar to wild-growing populations. The introduction of vegetative propagation has been hailed as a more efficient and flexible method than seed orchards to rapidly realize breeding progress and to adapt material to future climate change. What remains unclear is how a large deployment of vegetatively propagated material may affect the patterns of genetic diversity within and among forest stands. Here we review what is currently known about genetic diversity in managed and natural forest stands and specifically address the impacts of clonal forestry. To assess this we develop a quantitative model to describe the consequences of clone deployment on genetic and genotypic diversity in Swedish forests. We conclude with some remarks specific to Swedish conditions, likely scenarios for clonal deployment and finally some suggestions for future research priorities.

Place, publisher, year, edition, pages
Taylor & Francis, 2019
Keywords
Clones, forestry, genetic diversity, genotypic diversity
National Category
Forest Science
Identifiers
urn:nbn:se:umu:diva-160272 (URN)10.1080/02827581.2018.1469665 (DOI)000469520300006 ()
Funder
Swedish Foundation for Strategic Research
Available from: 2019-06-18 Created: 2019-06-18 Last updated: 2019-06-18Bibliographically approved
Rosvall, O., Bradshaw, R. H. W., Egertsdotter, U., Ingvarsson, P. K., Mullin, T. J. & Wu, H. (2019). Using Norway spruce clones in Swedish forestry: implications of clones for management. Scandinavian Journal of Forest Research, 34(5), 390-404
Open this publication in new window or tab >>Using Norway spruce clones in Swedish forestry: implications of clones for management
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2019 (English)In: Scandinavian Journal of Forest Research, ISSN 0282-7581, E-ISSN 1651-1891, Vol. 34, no 5, p. 390-404Article, review/survey (Refereed) Published
Abstract [en]

This final paper of the series discusses implications of various aspects of using clones in forestry. Benefits from using clones are considerable. A large benefit arises from the ability to deploy genetic gain much sooner than is possible through conventional seed orchards. This benefit applies even to the use of clones to implement family forestry, even though the clones themselves are not tested. The requirement for genetic diversity at both the stand and landscape levels requires active management to ensure that diversity is conserved. This is achieved partly through the management of breeding populations, as well as by managing the genetic diversity and number of genotypes deployed in clone mixtures. A numerical example is given comparing diversity of clone and seed orchard deployment over time. Many aspects of managing concerns about using clones are about communication to clarify public perceptions and establishing a code of practice.

Place, publisher, year, edition, pages
Taylor & Francis, 2019
Keywords
Clonal forestry, tree breeding, genetic diversity, somatic embryogenesis, forest management, Sweden
National Category
Forest Science
Identifiers
urn:nbn:se:umu:diva-160270 (URN)10.1080/02827581.2019.1590631 (DOI)000469520300008 ()
Available from: 2019-06-18 Created: 2019-06-18 Last updated: 2019-06-18Bibliographically approved
Wang, J., Ding, J., Tan, B., Robinson, K. M., Michelson, I. H., Johansson, A., . . . Ingvarsson, P. K. (2018). A major locus controls local adaptation and adaptive life history variation in a perennial plant. Genome Biology, 19, Article ID 72.
Open this publication in new window or tab >>A major locus controls local adaptation and adaptive life history variation in a perennial plant
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2018 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 19, article id 72Article in journal (Refereed) Published
Abstract [en]

Background: The initiation of growth cessation and dormancy represent critical life history trade offs between survival and growth and have important fitness effects in perennial plants Such adaptive life history traits often show strong local adaptation along environmental gradients but, despite then importance, the genetic architecture of these traits remains poorly understood.

Results: We integrate whole genome re sequencing with environmental and phenotypic data from common garden experiments to investigate the genomic basis of local adaptation across a latitudinal gradient in European aspen (Populus tremula). A single genomic region containing the PtFT2 gene mediates local adaptation in the timing of bud set and explains 65% of the observed genetic variation in bud set This locus is the likely target of a recent selective sweep that originated right before or during colonization of northern Scandinavia following the last glaciation Field and greenhouse experiments confirm that variation in PtFT2 gene expression affects the phenotypic variation in bud set that we observe in wild natural populations.

Conclusions: Our results reveal a major effect locus that determines the timing of bud set and that has facilitated rapid adaptation to shorter growing seasons and colder climates in European aspen. The discovery of a single locus explaining a substantial fraction of the variation in a key life-history trait is remarkable, given that such traits are generally considered to be highly polygenic. These findings provide a dramatic illustration of how loci of large effect for adaptive traits can arise and be maintained over large geographical scales in natural populations.

Place, publisher, year, edition, pages
BioMed Central, 2018
Keywords
Populus tremula, Local adaptation, Genomic basis, PtFT2, Adaptive traits, Selective sweep
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-150175 (URN)10.1186/s13059-018-1444-y (DOI)000434210500001 ()29866176 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Note

Originally included in thesis in manuscript form.

Available from: 2018-07-18 Created: 2018-07-18 Last updated: 2018-08-14Bibliographically approved
Michelson, I. H., Ingvarsson, P. K., Robinson, K. M., Edlund, E., Eriksson, M. E., Nilsson, O. & Jansson, S. (2018). Autumn senescence in aspen is not triggered by day length. Physiologia Plantarum: An International Journal for Plant Biology, 162(1), 123-134
Open this publication in new window or tab >>Autumn senescence in aspen is not triggered by day length
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2018 (English)In: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 162, no 1, p. 123-134Article in journal (Refereed) Published
Abstract [en]

Autumn senescence in mature aspens, grown under natural conditions, is initiated at almost the same date every year. The mechanism of such precise timing is not understood but we have previously shown that the signal must be derived from light. We studied variation in bud set and autumn senescence in a collection of 116 natural Eurasian aspen (Populus tremula) genotypes, from 12 populations in Sweden and planted in one northern and one southern common garden, to test the hypothesis that onset of autumn senescence is triggered by day length. We confirmed that, although bud set seemed to be triggered by a critical photoperiod/day length, other factors may influence it. The data on initiation of autumn senescence, on the other hand, were incompatible with the trigger being the day length per se, hence the trigger must be some other light-dependent factor.

Place, publisher, year, edition, pages
John Wiley & Sons, 2018
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-143636 (URN)10.1111/ppl.12593 (DOI)000418236000008 ()28591431 (PubMedID)
Available from: 2018-01-08 Created: 2018-01-08 Last updated: 2018-06-09Bibliographically approved
Lin, Y.-C., Wang, J., Delhomme, N., Schiffthaler, B., Sundström, G., Zuccolo, A., . . . Street, N. R. (2018). Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. Proceedings of the National Academy of Sciences of the United States of America, 115(46), E10970-E10978
Open this publication in new window or tab >>Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 46, p. E10970-E10978Article in journal (Refereed) Published
Abstract [en]

The Populus genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily Populus trichocarpa (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in Populus, we produced genome assemblies and population genetics resources of two aspen species, Populus tremula L. and Populus tremuloides Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with P. trichocarpa but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (PopGenIE.org).

Place, publisher, year, edition, pages
NATL ACAD SCIENCES, 2018
Keywords
genome assembly, natural selection, coexpression, population genetics, Populus
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-154950 (URN)10.1073/pnas.1801437115 (DOI)000449934400020 ()30373829 (PubMedID)2-s2.0-85056516875 (Scopus ID)
Available from: 2019-01-07 Created: 2019-01-07 Last updated: 2019-01-07Bibliographically approved
Cole, C. T. & Ingvarsson, P. K. (2018). Pathway position constrains the evolution of an ecologically important pathway in aspens (Populus tremula L.). Molecular Ecology, 27(16), 3317-3330
Open this publication in new window or tab >>Pathway position constrains the evolution of an ecologically important pathway in aspens (Populus tremula L.)
2018 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 16, p. 3317-3330Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2018
Keywords
condensed tannins, E-R anticorrelation, gene expression, negative selection, pathway pleiotropy, plant defence
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-151564 (URN)10.1111/mec.14785 (DOI)000442219600010 ()29972878 (PubMedID)
Funder
Swedish Research Council
Available from: 2018-09-10 Created: 2018-09-10 Last updated: 2018-09-10Bibliographically approved
de La Torre, A. R., Li, Z., Van de Peer, Y. & Ingvarsson, P. K. (2017). Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants. Molecular biology and evolution, 34(6), 1363-1377
Open this publication in new window or tab >>Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants
2017 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 34, no 6, p. 1363-1377Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Oxford University Press, 2017
Keywords
gymnosperms, angiosperms, substitution rates, selection, mutation, life-history traits
National Category
Evolutionary Biology Genetics Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-135960 (URN)10.1093/molbev/msx069 (DOI)000402061700006 ()28333233 (PubMedID)
Available from: 2017-06-29 Created: 2017-06-29 Last updated: 2018-06-09Bibliographically approved
Tan, B., Grattapaglia, D., Martins, G. S., Ferreira, K. Z., Sundberg, B. & Ingvarsson, P. K. (2017). Evaluating the accuracy of genomic prediction of growth and wood traits in two Eucalyptus species and their F-1 hybrids. BMC Plant Biology, 17, Article ID 110.
Open this publication in new window or tab >>Evaluating the accuracy of genomic prediction of growth and wood traits in two Eucalyptus species and their F-1 hybrids
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2017 (English)In: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 17, article id 110Article in journal (Refereed) Published
Abstract [en]

Background: Genomic prediction is a genomics assisted breeding methodology that can increase genetic gains by accelerating the breeding cycle and potentially improving the accuracy of breeding values. In this study, we use 41,304 informative SNPs genotyped in a Eucalyptus breeding population involving 90 E. grandis and 78 E. urophylla parents and their 949 F-1 hybrids to develop genomic prediction models for eight phenotypic traits-basic density and pulp yield, circumference at breast height and height and tree volume scored at age three and six years. We assessed the impact of different genomic prediction methods, the composition and size of the training and validation set and the number and genomic location of SNPs on the predictive ability (PA). Results: Heritabilities estimated using the realized genomic relationship matrix (GRM) were considerably higher than estimates based on the expected pedigree, mainly due to inconsistencies in the expected pedigree that were readily corrected by the GRM. Moreover, the GRM more precisely capture Mendelian sampling among related individuals, such that the genetic covariance was based on the true proportion of the genome shared between individuals. PA improved considerably when increasing the size of the training set and by enhancing relatedness to the validation set. Prediction models trained on pure species parents could not predict well in F-1 hybrids, indicating that model training has to be carried out in hybrid populations if one is to predict in hybrid selection candidates. The different genomic prediction methods provided similar results for all traits, therefore either GBLUP or rrBLUP represents better compromises between computational time and prediction efficiency. Only slight improvement was observed in PA when more than 5000 SNPs were used for all traits. Using SNPs in intergenic regions provided slightly better PA than using SNPs sampled exclusively in genic regions. Conclusions: The size and composition of the training set and number of SNPs used are the two most important factors for model prediction, compared to the statistical methods and the genomic location of SNPs. Furthermore, training the prediction model based on pure parental species only provide limited ability to predict traits in interspecific hybrids. Our results provide additional promising perspectives for the implementation of genomic prediction in Eucalyptus breeding programs by the selection of interspecific hybrids.

Place, publisher, year, edition, pages
BioMed Central, 2017
Keywords
Genomic relationship, Genomic heritability, Two-generation, Genome annotation, High-density SNP-chip, Bayesian LASSO, GBLUP, rrBLUP
National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:umu:diva-138559 (URN)10.1186/s12870-017-1059-6 (DOI)000404909700001 ()28662679 (PubMedID)
Available from: 2017-09-13 Created: 2017-09-13 Last updated: 2018-06-09Bibliographically approved
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