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Open Access Highly Accessed Research article

A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation

Glenn T Howe1*, Jianbin Yu12, Brian Knaus3, Richard Cronn3, Scott Kolpak1, Peter Dolan4, W Walter Lorenz5 and Jeffrey FD Dean5

Author affiliations

1 Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon, 97331, USA

2 Current address, DuPont Pioneer International, Willmar, Minnesota, 56201, USA

3 Pacific Northwest Research Station, USDA Forest Service, Corvallis, Oregon, 97331, USA

4 Department of Mathematics, University of Minnesota, Morris, MN, USA

5 Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, 30602, USA

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Citation and License

BMC Genomics 2013, 14:137  doi:10.1186/1471-2164-14-137

Published: 28 February 2013

Abstract

Background

Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauca) are native to North America, the coastal variety is also widely planted for timber production in Europe, New Zealand, Australia, and Chile. Our main goal was to develop a SNP resource large enough to facilitate genomic selection in Douglas-fir breeding programs. To accomplish this, we developed a 454-based reference transcriptome for coastal Douglas-fir, annotated and evaluated the quality of the reference, identified putative SNPs, and then validated a sample of those SNPs using the Illumina Infinium genotyping platform.

Results

We assembled a reference transcriptome consisting of 25,002 isogroups (unique gene models) and 102,623 singletons from 2.76 million 454 and Sanger cDNA sequences from coastal Douglas-fir. We identified 278,979 unique SNPs by mapping the 454 and Sanger sequences to the reference, and by mapping four datasets of Illumina cDNA sequences from multiple seed sources, genotypes, and tissues. The Illumina datasets represented coastal Douglas-fir (64.00 and 13.41 million reads), interior Douglas-fir (80.45 million reads), and a Yakima population similar to interior Douglas-fir (8.99 million reads). We assayed 8067 SNPs on 260 trees using an Illumina Infinium SNP genotyping array. Of these SNPs, 5847 (72.5%) were called successfully and were polymorphic.

Conclusions

Based on our validation efficiency, our SNP database may contain as many as ~200,000 true SNPs, and as many as ~69,000 SNPs that could be genotyped at ~20,000 gene loci using an Infinium II array—more SNPs than are needed to use genomic selection in tree breeding programs. Ultimately, these genomic resources will enhance Douglas-fir breeding and allow us to better understand landscape-scale patterns of genetic variation and potential responses to climate change.