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Publications (10 of 38) Show all publications
diva2:1327167
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.

Keywords
genetic map, Norway spruce, Picea abies, sequence capture, genome assembly
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-386179 (URN)10.1534/g3.118.200840 (DOI)000467271400031 ()30898899 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC)
Available from: 2019-06-19 Created: 2019-06-19 Last updated: 2019-06-19Bibliographically approved
diva2:1366759
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 1365-313X, Vol. 100, no 1, p. 83-100Article in journal (Refereed) Published
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, sequence capture, single nucleotide polymorphisms
National Category
Forest Science
Identifiers
urn:nbn:se:uu:diva-396127 (URN)10.1111/tpj.14429 (DOI)000478331500001 ()31166032 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationThe Kempe Foundations
Available from: 2019-06-05 Created: 2019-10-30 Last updated: 2019-11-04Bibliographically approved
diva2:1313996
Open this publication in new window or tab >>Summer comes to the Southern Ocean: How phytoplankton shape bacterioplankton communities far into the deep dark sea
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2019 (English)In: Ecosphere, ISSN 2150-8925, E-ISSN 2150-8925, Vol. 10, no 3, article id e02641Article in journal (Refereed) Published
National Category
Ecology
Identifiers
urn:nbn:se:uu:diva-382662 (URN)10.1002/ecs2.2641 (DOI)000463977000027 ()
Available from: 2019-03-12 Created: 2019-05-07 Last updated: 2019-05-07Bibliographically approved