The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

  • Pavy N
  • Namroud M
  • Gagnon F
 et al. 
  • 43

    Readers

    Mendeley users who have this article in their library.
  • 30

    Citations

    Citations of this article.

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.

Author-supplied keywords

  • Picea
  • demography
  • linkage disequilibrium
  • nucleotide diversity
  • selection signatures
  • spruce

Get free article suggestions today

Mendeley saves you time finding and organizing research

Sign up here
Already have an account ?Sign in

Find this document

Authors

  • N. Pavy

  • M. C. Namroud

  • F. Gagnon

  • N. Isabel

  • J. Bousquet

Cite this document

Choose a citation style from the tabs below

Save time finding and organizing research with Mendeley

Sign up for free