Dataset Information

Microsatellite loci for an old rare species, Pseudotaxus chienii, and transferability in Taxus wallichiana var. mairei (Taxaceae).

ABSTRACT: UNLABELLED: PREMISE OF THE STUDY:Microsatellite loci were developed for Pseudotaxus chienii, an old rare species endemic to China, and which provided a useful tool for investigating the patterns of population genetic structure, phylogeography, evolutionary history, and adaptive potential. Transferability was assayed in the related species, Taxus wallichiana var. mairei. • METHODS AND RESULTS:A total of 15 microsatellite loci were targeted in P. chienii using the Fast Isolation by AFLP of Sequences COntaining Repeats (FIASCO) protocol. Polymorphism was evaluated in five populations of P. chienii and five populations of T. wallichiana var. mairei. Of these loci, 13 were polymorphic in P. chienii, whereas 15 were polymorphic in T. wallichiana var. mairei. • CONCLUSIONS:The 15 microsatellite loci developed lay a solid foundation for further studies on population genetic variability and investigations of local adaptation. Additionally, cross-species amplification in T. wallichiana var. mairei showed that these loci may also have potential utility in other genera of Taxaceae.

SUBMITTER: Deng Q

PROVIDER: S-EPMC4105040 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

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Microsatellite loci for an old rare species, Pseudotaxus chienii, and transferability in Taxus wallichiana var. mairei (Taxaceae).

Deng Qi Q Su Ying-Juan YJ Wang Ting T

Applications in plant sciences 20130430 5

<h4>Unlabelled</h4><h4>Premise of the study</h4>Microsatellite loci were developed for Pseudotaxus chienii, an old rare species endemic to China, and which provided a useful tool for investigating the patterns of population genetic structure, phylogeography, evolutionary history, and adaptive potential. Transferability was assayed in the related species, Taxus wallichiana var. mairei. •<h4>Methods and results</h4>A total of 15 microsatellite loci were targeted in P. chienii using the Fast Isolat ...[more]

PMID: 25202547

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Project description:BackgroundElucidating the effects of geography and selection on genetic variation is critical for understanding the relative importance of adaptation in driving differentiation and identifying the environmental factors underlying its occurrence. Adaptive genetic variation is common in tree species, especially widely distributed long-lived species. Pseudotaxus chienii can occupy diverse habitats with environmental heterogeneity and thus provides an ideal material for investigating the process of population adaptive evolution. Here, we characterize genetic and expression variation patterns and investigate adaptive genetic variation in P. chienii populations.ResultsWe generated population transcriptome data and identified 13,545 single nucleotide polymorphisms (SNPs) in 5037 unigenes across 108 individuals from 10 populations. We observed lower nucleotide diversity (π = 0.000701) among the 10 populations than observed in other gymnosperms. Significant negative correlations between expression diversity and nucleotide diversity in eight populations suggest that when the species adapts to the surrounding environment, gene expression and nucleotide diversity have a reciprocal relationship. Genetic structure analyses indicated that each distribution region contains a distinct genetic group, with high genetic differentiation among them due to geographical isolation and local adaptation. We used FST outlier, redundancy analysis, and latent factor mixed model methods to detect molecular signatures of local adaptation. We identified 244 associations between 164 outlier SNPs and 17 environmental variables. The mean temperature of the coldest quarter, soil Fe and Cu contents, precipitation of the driest month, and altitude were identified as the most important determinants of adaptive genetic variation. Most candidate unigenes with outlier signatures were related to abiotic and biotic stress responses, and the monoterpenoid biosynthesis and ubiquitin-mediated proteolysis KEGG pathways were significantly enriched in certain populations and deserve further attention in other long-lived trees.ConclusionsDespite the strong population structure in P. chienii, genomic data revealed signatures of divergent selection associated with environmental variables. Our research provides SNPs, candidate unigenes, and biological pathways related to environmental variables to facilitate elucidation of the genetic variation in P. chienii in relation to environmental adaptation. Our study provides a promising tool for population genomic analyses and insights into the molecular basis of local adaptation.

Dataset Information

Microsatellite loci for an old rare species, Pseudotaxus chienii, and transferability in Taxus wallichiana var. mairei (Taxaceae).

Publications

Microsatellite loci for an old rare species, Pseudotaxus chienii, and transferability in Taxus wallichiana var. mairei (Taxaceae).

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