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Search for nucleotide diversity patterns of local adaptation in dehydrins and other cold-related candidate genes in Scots pine (Pinus sylvestris L.)

Abstract

Nucleotide variation at several cold candidate genes including seven members of the dehydrin gene family was surveyed in haplotypes of Scots pine (Pinus sylvestris) sampled in populations showing divergence for cold tolerance in Europe. Patterns of nucleotide diversity, linkage disequilibrium, and frequency spectrum of alleles were compared between north and south populations to search for signs of directional selection potentially underlying adaptation to cold. Significant differentiation between populations in allelic frequency or haplotype structure was detected at dhn1, dhn3, and abaH loci. Allelic dimorphism with no evidence of haplotype clustering by geographical distribution was found at dhn9. An excess of fixed non-synonymous mutations as compared to the outgroup P. pinaster pine species was found at dhn1. Differences in nucleotide polymorphisms were found between the members of the Kn class of dehydrin upregulated during cold acclimation (average πsil = 0.004) as compared to the SKn class (average πsil = 0.024). The multilocus nucleotide diversity at silent sites (θ W = 0.009) was moderate compared to other conifer species, but higher than previous estimates for Scots pine. There was an excess of rare and high frequency derived variants as revealed by significantly negative multilocus value of Tajima’s D (D = −0.72, P < 0.01) and negative mean value of Fay and Wu H statistics (H = −0.50). The level of linkage disequilibrium decayed rapidly with an average expected r 2 of 0.2 at about 200 bp. Overall, there was a positive correlation between polymorphism and divergence at ten loci when outgroup sequence was available. The discovered polymorphism will be used for further evaluation of the adaptive role of genes through association mapping studies.

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Acknowledgments

We thank Katri Kärkkäinen from the Finnish Forest Research Institute for providing seed material, Monique van Wordragen from NSure bv, The Netherlands for sharing some of the Scots pine EST sequences prior to publishing, Timo Knürr from University of Oulu for statistical assistance, and anonymous reviewers for useful suggestions. This work was supported by University of Oulu, EU project TREESNIPS (QLRT-2001-01973), and the Centre for Population Genetic analyses funded by the Academy of Finland.

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Correspondence to Witold Wachowiak.

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Communicated by G. Vendramin

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Table S1

Summary statistics of nucleotide and haplotype variation, neutrality tests, and recombination rate estimates at cold-related genes in the north and south groups of Scots pine (DOC 89.5 KB).

Table S2

Nucleotide variation measured as θ W (Watterson 1975) in a total dataset and in P. sylvestris samples divided into four geographical regions. θ W = median for silent sites (synonymous and non-coding), CI = credibility intervals (97.5%) (DOC 26.5 KB).

Table S3

F ST values and heterozygosity estimates at cold candidate loci used for outliers detection using Beaumont and Nichols (1996) approach (DOC 32.0 KB).

Fig. S1

Posterior densities of multilocus estimates of nucleotide diversity θ w (Watterson 1975) based on silent sites (synonymous and non-coding) for all loci analyzed for P. sylvestris samples from four geographical regions in Europe (see text for details). 95% credibility intervals are given in Supplementary Table S2 (DOC 39.5 KB).

Fig. S2

a, b Scatter plot of the squared correlation of allele frequencies (r 2) as a function of distance in base pairs between pairs of polymorphic sites in north and south groups for dhn1 locus (a) and five loci combined (excluding dhn1) (b). Decline in linkage disequilibrium is shown by non-linear fitting curve of the mutation-recombination-drift model (see “Material and methods” section for details). Recombination rate parameter c (standard error in parentheses) for dhn1 in north group is c = 0.005 (0.001) and in the south group is c = 0.010 (0.001). Recombination rate parameter c for the remaining loci in north group is c = 0.0036 (0.0005) and in south group is c = 0.0029 (standard error 0.0005) (DOC 97.0 KB).

Fig. S3

Distribution of F ST values estimated from 14 cold candidate genes in Scots pine plotted against heterozygosity (see Supplementary Table S3). The quantiles plotted are estimated using Beaumont and Nichols (1996) approach and the infinite allele model with expected mean F ST = 0.014. The outlier indicates abaH locus (DOC 50.0 KB).

Fig. S4

Distribution of F ST values estimated from 99 SNPs and Indels of MAF >10% in Scots pine plotted against total diversity (π). The quantiles plotted are estimated using Beaumont and Nichols (1996) approach and the infinite allele model with expected mean F ST = 0.012. The outliers include polymorphic sites in dhn1, dhn9, abaH locus (see “Results” section) (DOC 34.0 KB).

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Wachowiak, W., Balk, P.A. & Savolainen, O. Search for nucleotide diversity patterns of local adaptation in dehydrins and other cold-related candidate genes in Scots pine (Pinus sylvestris L.). Tree Genetics & Genomes 5, 117 (2009). https://doi.org/10.1007/s11295-008-0188-3

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Keywords

  • Plant adaptation
  • Cold tolerance
  • Gene families
  • Nucleotide diversity
  • Linkage disequilibrium
  • SNPs
  • Pinus sylvestris