ArticleHeredity2012
The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers.
Article in Heredity, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 70 citations in OpenAlex.
- Genomic insights into the improvement of Chinese fir from ancient domestication continuum to modern breeding.Nature communications · 2026Article
- Integrating GWAS-guided markers preselection with genomic selection enhances prediction of pulpwood-related traits in slash pine (Pinus elliottii Englem.).BMC plant biology · 2026Article
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- Ecotypic divergence in Mongolian Scots pine persists via large-effect genetic adaptation and phenotypic plasticity.BMC plant biology · 2025Article
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- Contrasting levels of transcriptome-wide SNP diversity and adaptive molecular variation among conifers.Frontiers in plant science · 2025Article
- The western redcedar genome reveals low genetic diversity in a self-compatible conifer.Genome research · 2022Article
- Finding common ground: Toward comparable indicators of adaptive capacity of tree species to a changing climate.Ecology and evolution · 2021Article
- Connecting tree-ring phenotypes, genetic associations and transcriptomics to decipher the genomic architecture of drought adaptation in a widespread conifer.Molecular ecology · 2021Article
- Genome-wide shifts in climate-related variation underpin responses to selective breeding in a widespread conifer.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Adaptive evolution in a conifer hybrid zone is driven by a mosaic of recently introgressed and background genetic variants.Communications biology · 2021Article
- Genetic control of tracheid properties in Norway spruce wood.Scientific reports · 2020Article
- Whole-exome sequencing reveals a long-term decline in effective population size of red spruce (Evolutionary applications · 2020Article
- 275 years of forestry meets genomics inEvolutionary applications · 2020Review
- Review
- Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as the genotyping platform in Norway spruce.BMC genomics · 2018Article
- A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies).BMC genomics · 2018Article
- Exploring the genetic basis of gene transcript abundance and metabolite levels in loblolly pine (Pinus taeda L.) using association mapping and network construction.BMC genetics · 2018Article
- De novo assembly of English yew (Taxus baccata) transcriptome and its applications for intra- and inter-specific analyses.Plant molecular biology · 2018Article
- Association genetics of phenolic needle compounds in Norway spruce with variable susceptibility to needle bladder rust.Plant molecular biology · 2017Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In plants, knowledge about linkage disequilibrium (LD) is relevant for the design of efficient single-nucleotide polymorphism arrays in relation to their use in population and association genomics studies. Previous studies of conifer genes have shown LD to decay rapidly within gene limits, but exceptions have been reported. To evaluate the extent of heterogeneity of LD among conifer genes and its potential causes, we examined LD in 105 genes of white spruce (Picea glauca) by sequencing a panel of 48 haploid megagametophytes from natural populations and further compared it with LD in other conifer species. The average pairwise r(2) value was 0.19 (s.d.=0.19), and LD dropped quickly with a half-decay being reached at a distance of 65 nucleotides between sites. However, LD was significantly heterogeneous among genes. A first group of 29 genes had stronger LD (mean r(2)=0.28), and a second group of 38 genes had weaker LD (mean r(2)=0.12). While a strong relationship was found with the recombination rate, there was no obvious relationship between LD and functional classification. The level of nucleotide diversity, which was highly heterogeneous across genes, was also not significantly correlated with LD. A search for selection signatures highlighted significant deviations from the standard neutral model, which could be mostly attributed to recent demographic changes. Little evidence was seen for hitchhiking and clear relationships with LD. When compared among conifer species, on average, levels of LD were similar in genes from white spruce, Norway spruce and Scots pine, whereas loblolly pine and Douglas fir genes exhibited a significantly higher LD.
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