An Axiom SNP genotyping array for Douglas-fir

Abstract

Background: In forest trees, genetic markers have been used to understand the genetic architecture of natural populations, identify quantitative trait loci, infer gene function, and enhance tree breeding. Recently, new, efficient technologies for genotyping thousands to millions of single nucleotide polymorphisms (SNPs) have finally made large-scale use of genetic markers widely available. These methods will be exceedingly valuable for improving tree breeding and understanding the ecological genetics of Douglas-fir, one of the most economically and ecologically important trees in the world. Results: We designed SNP assays for 55,766 potential SNPs that were discovered from previous transcriptome sequencing projects. We tested the array on~2300 related and unrelated coastal Douglas-fir trees (Pseudotsuga menziesii var. menziesii) from Oregon and Washington, and 13 trees of interior Douglas-fir (P. menziesii var. glauca). As many as~28 K SNPs were reliably genotyped and polymorphic, depending on the selected SNP call rate. To increase the number of SNPs and improve genome coverage, we developed protocols to 'rescue' SNPs that did not pass the default Affymetrix quality control criteria (e.g., 97% SNP call rate). Lowering the SNP call rate threshold from 97 to 60% increased the number of successful SNPs from 20,669 to 28,094. We used a subset of 395 unrelated trees to calculate SNP population genetic statistics for coastal Douglas-fir. Over a range of call rate thresholds (97 to 60%), the median call rate for SNPs in Hardy-Weinberg equilibrium ranged from 99.2 to 99.7%, and the median minor allele frequency ranged from 0.198 to 0.233. The successful SNPs also worked well on interior Douglas-fir.Conclusions: Based on the original transcriptome assemblies and comparisons to version 1.0 of the Douglas-fir reference genome, we conclude that these SNPs can be used to genotype about 10 K to 15 K loci. The Axiom genotyping array will serve as an excellent foundation for studying the population genomics of Douglas-fir and for implementing genomic selection. We are currently using the array to construct a linkage map and test genomic selection in a three-generation breeding program for coastal Douglas-fir.

Development of a single nucleotide polymorphism array for population genomic studies in four European pine species

“…The reported conversion rate in some animal species was lower (~60% in shellfish: Lapègue et al, 2014; chicken: Kranis et al, 2013). High‐density SNP arrays developed in other tree species showed similar conversion rates (around 60%–70% in Pinus taeda : Eckert et al, 2009; Pinus pinaster : Plomion et al, 2016; Pseudotsuga menziesii : Howe et al, 2013, 2020; Picea glauca : Pavy et al, 2013) depending on the source of SNPs for assay development and the type of genotyping platform.…”

Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species

“…To increase the marker density for AM in conifer trees, access to a genome‐wide SNP array would enable high‐throughput and relatively cost‐efficient genotyping. SNP arrays have already been developed for a number of spruce species and in other conifers based on transcriptome data (Howe et al., 2020; Perry et al., 2020; Plomion et al., 2016). However, transcriptome‐based approaches, such as RNA sequencing, have thus far yielded relatively small arrays, covering <10,000 SNPs in most cases, and due to the nature of transcriptome data they also generally lack genomic information from intergenic regions (Bartholome et al., 2016; Pavy et al., 2013, 2016).…”

“…Several SNP arrays have recently been developed in conifers for use in genome‐wide association studies (GWAS) and GS. These have mostly been based on candidate gene sequencing but have also utilized data from microarrays or RNA sequencing and are generally limited to a few thousand SNPs (Bartholome et al., 2016; Beaulieu et al., 2014; Resende et al., 2012; Zapata‐Valenzuela et al., 2013) to several tens of thousands of SNPs (Howe et al., 2020; Perry et al., 2020). Two high‐density SNP arrays relying on the Infinium iSelect technology were designed for the conifer species white spruce ( Picea glauca ), containing 7,338 and 9,559 SNPs, respectively, using in silico SNP prediction through the alignment of transcript sequences and candidate genes (Pavy et al., 2013).…”

A 3K Axiom SNP array from a transcriptome-wide SNP resource sheds new light on the genetic diversity and structure of the iconic subtropical conifer tree Araucaria angustifolia (Bert.) Kuntze

“…[ 38 , 40 – 43 ], Cunninghamia spp. [ 44 ], Cryptomeria japonica [ 45 , 46 ] and Pseudotsuga menziesii [ 47 ]. More recently, however, with advances in technology and cost reductions, SNP arrays have become very competitive with alternative sequence based SNP genotyping methods.…”