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

Abstract

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 glauco) 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.

Citation

Howe, Glenn R.; Yu, Jianbin; Knaus, Brian; Cronn, Richard; Kolpak, Scott; Dolan, Peter; Lorenz, W. Walter; Dean, Jeffrey F.D. 2013. A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation. BMC Genomics. 14(Art. 137): 1-22.