ArticleBMC genomics2020
An Axiom SNP genotyping array for Douglas-fir.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 32 citations in OpenAlex.
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- Low-input breeding potential in stone pine, a multipurpose forest tree with low genome diversity.G3 (Bethesda, Md.) · 2025Article
- Accurate Detection ofEcology and evolution · 2024Article
- Needle and Branch Trait Variation Analysis and Associated SNP Loci Mining inInternational journal of molecular sciences · 2024Article
- Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection inFrontiers in genetics · 2024Article
- A multiplexed plant-animal SNP array for selective breeding and species conservation applications.G3 (Bethesda, Md.) · 2023Article
- A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir).G3 (Bethesda, Md.) · 2023Article
- Lignin engineering in forest trees: From gene discovery to field trials.Plant communications · 2022Review
- Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research.The Plant journal : for cell and molecular biology · 2022Article
- Genetic architecture behind developmental and seasonal control of tree growth and wood properties in Norway spruce.Frontiers in plant science · 2022Article
- Genomic Prediction of Complex Traits in Perennial Plants: A Case for Forest Trees.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing.International journal of molecular sciences · 2021Review
- Toward genomic selection inApplications in plant sciences · 2021Article
- 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.Molecular ecology resources · 2021Article
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11 authors at 5 institutions in 1 country.
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Abstract
backgroundIn 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.
resultsWe 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.
conclusionsBased 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.
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