Abstract
The use of single-nucleotide polymorphisms (SNPs) as molecular markers in plant studies has become increasingly common. With the development of these markers, there is an interest in determining levels of variation in natural populations. Here, we identify and characterize levels of SNPs in wild populations of aspen (Populus tremuloides Michx.). Four populations were sampled from Alberta and British Columbia in Western Canada. A total of 35 gene regions were selected for analysis. The loci selected are mainly involved in wood formation and include regions from genes for lignin biosynthesis, cellulose biosynthesis, and other cell wall compounds and a number of transcription factors. Other genes included those coding for growth hormones, disease resistance, and light responses. Primers were developed from conserved regions in multi-species EST alignments. Regions were PCR amplified, and products (approximately 500 to 1,000 bp) were assessed for levels of SNPs using Ecotilling. From a total of approximately 25 kb 462 SNPs were identified, over 18 SNPs/kb. Thus, SNPs are an abundant and potentially useful molecular marker in aspen. Gene diversity (heterozygosity) varied in the gene regions, with an overall average of H T = 0.18. Although gene diversity was considerable, genetic differentiation was low with the overall F ST value being 0.004. A surrogate measure of linkage disequilibrium (LD) was calculated, and overall, the LD was shown to decay relatively rapidly with distance along the gene region. The results obtained from the wood formation genes in this study will enable further targeting of regions for association studies on lignin and cellulose variation in aspen and other Populus species.
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Acknowledgments
This work was undertaken as part of the Genome BC-funded Treenomix project. Funding for AJC and ALPQ was under the Science Foundation Ireland Ureka program. Thanks to Par Ingvarsson for advice on estimating the LD decay.
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Communicated by P. Ingvarsson
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Summary of the Ecotilling data showing the length of the gene region, the number of SNPs detected, the polymorphism rate per kilobase, and the gene diversity and genetic differentiation averaged across each gene region (DOC 64 kb)
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Graphs showing the extent of LD in the different genes. The lengths analyzed were small, but the decay is still evident across all regions (PDF 84 kb)
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Kelleher, C.T., Wilkin, J., Zhuang, J. et al. SNP discovery, gene diversity, and linkage disequilibrium in wild populations of Populus tremuloides . Tree Genetics & Genomes 8, 821–829 (2012). https://doi.org/10.1007/s11295-012-0467-x
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DOI: https://doi.org/10.1007/s11295-012-0467-x