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

Abstract

BackgroundDouglas-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.ResultsWe 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.ConclusionsBased 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.

Detection of SNPs based on DNA specific-locus amplified fragment sequencing in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook)

“…Genome-wide SNP-based dendrogram analysis definitely provided an efficient and accuracy tool to address the genetic relationship of the germplasms and it will help us to select more divergent parents to improve the diversity of the seed orchard, as well as to better protect and manage them in the future. For conifer SNP genotyping, whole genome sequencing remained unattainable, but flexible methods such as population RNA-seq, EST re-sequencing approach and specific SNP array seemed to be rather feasible (Uchiyama et al, 2012;Howe et al, 2013;Liu et al, 2014;Plomion et al, 2014;Heer et al, 2016). In this study, we demonstrated that SLAF-seq is also an efficient method for the population SNP genotyping in conifer (Chinese fir).…”

Insights into Conifer Giga-Genomes

“…Sequencing of cDNAs, genomes, and transcriptomes accelerated the discovery of SNPs and the development of large SNP databases for several conifers (Howe et al, 2013;Pavy et al, 2013a;Canales et al, 2014;Pinosio et al, 2014). The landscape of nucleotide diversity showed that the frequency of nucleotide polymorphisms varied significantly across gene families as a function of genes that appear to be specific to conifers and the breadth of expression patterns (Pavy et al, 2013a).…”

“…The landscape of nucleotide diversity showed that the frequency of nucleotide polymorphisms varied significantly across gene families as a function of genes that appear to be specific to conifers and the breadth of expression patterns (Pavy et al, 2013a). SNPs have been used to design high-throughput genotyping chips of broad coverage in species of spruce and pine as well as Douglas fir (Pseudotsuga menziesii) and other conifer species (Chancerel et al, 2011(Chancerel et al, , 2013Pavy et al, 2012Pavy et al, , 2013bHowe et al, 2013). They have been used to conduct various structural and population genome scans for genetic linkage mapping (see below) and for large-scale association studies with phenotypic and environmental variation in spruces, pines, and Douglas fir (Eckert et al, 2012;Prunier et al, 2013;De La Torre et al, 2014b).…”

Source identification of western Oregon Douglas‐fir wood cores using mass spectrometry and random forest classification

“…Due to the dominance of Douglas-fir across a wide array of environments and heterogeneous landscapes in western Oregon (Hermann and Lavender, 1990; Ohmann and Spies, 1998) and its characteristic high levels of phenotypic and genetic variability (St. Clair et al, 2005; Eckert et al, 2009; Krutovsky et al, 2009; Howe et al, 2013), a relationship between geography and molecular composition and abundance is possible, regardless of whether genetics or environmental conditions are responsible for wood chemical variation.…”