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Nucleotide diversity and linkage disequilibrium of adaptive significant genes in Larix (Pinaceae)

Abstract

Nucleotide polymorphism in genes potentially responsible for the adaptation to the latitudinal gradient of climate was investigated in the Siberian larch (Larix sibirica). The genes were selected among those previously studied in Douglas fir (Pseudotsuga menziesii), the variability of which indicates the influence of selection or shows the association with phenotypic traits that are important for adaptation to low temperatures and to geographically heterogeneous environment. Nucleotide sequences of eight genes, including coding and noncoding regions, were amplified and sequenced using newly developed primers specific to Larix. The sample size was 123 megagametophytes per locus in L. sibirica and 16.2 in L. occidentalis, which was taken as the outgroup. The length of the sequenced fragments was 246–1700 bp. Nucleotide polymorphism π averaged 0.00536 (0.002–0.008), and haplotype diversity was H d: 0.822 (0.625–0.948). Tajima’s D was negative in all fragments and significant in three, while statistics D* and F* was significant in three and four segments, respectively, and F s was significant in three. This may indicate the presence of purifying selection on these genes or population growth. The HKA test revealed no significant deviations from the neutral model of evolution in all genes. The recombination parameter ρ/θ = 0.28 was close to the value obtained from P. menziesii. To investigate the association of polymorphic sites (factor) in these eight genes to the latitude of investigated individuals (trait), the generalized linear model (GLM) was used taking into account the population structure. After false discovery rate (FDR) correction, no significant associations were found. The age of the split of American and Eurasian Larix lineages based on the nucleotide differences in the eight genes between L. sibirica and L. occidentalis is estimated to be 12 million years, which is much younger than the age of the most ancient Larix fossils.

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Correspondence to V. L. Semerikov.

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Original Russian Text © V.L. Semerikov, S.A. Semerikova, M.A. Polezhaeva, 2013, published in Genetika, 2013, Vol. 49, No. 9, pp. 1055–1064.

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Semerikov, V.L., Semerikova, S.A. & Polezhaeva, M.A. Nucleotide diversity and linkage disequilibrium of adaptive significant genes in Larix (Pinaceae). Russ J Genet 49, 915–923 (2013). https://doi.org/10.1134/S102279541309007X

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  • DOI: https://doi.org/10.1134/S102279541309007X

Keywords

  • Linkage Disequilibrium
  • Nucleotide Diversity
  • Single Nucleotide Polymorphism
  • Siberian Larch
  • Pseudotsuga Menziesii