ArticleBMC genomics2018
A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies).
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 29 citations in OpenAlex.
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- High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers.G3 (Bethesda, Md.) · 2024Article
- Genomic insights into the genotype-environment mismatch and conservation units of a Qinghai-Tibet Plateau endemic cypress under climate change.Evolutionary applications · 2022Article
- Genetic diversity of Norway spruce ecotypes assessed by GBS-derived SNPs.Scientific reports · 2021Article
- Connecting tree-ring phenotypes, genetic associations and transcriptomics to decipher the genomic architecture of drought adaptation in a widespread conifer.Molecular ecology · 2021Article
- 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
- Host-specific gene expression as a tool for introduction success in Naupactus parthenogenetic weevils.PloS one · 2021Article
- Whole-exome sequencing reveals a long-term decline in effective population size of red spruce (Evolutionary applications · 2020Article
- Article
- An Axiom SNP genotyping array for Douglas-fir.BMC genomics · 2020Article
- Multi-trait genomic selection for weevil resistance, growth, and wood quality in Norway spruce.Evolutionary applications · 2020Article
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNorway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that should sustain the development of genomic tools for the conservation of natural and domesticated genetic diversity resources, and hasten tree breeding efforts in this species.
resultsTargeted sequencing was achieved by capturing P. abies exome with probes previously designed from the sequenced transcriptome of white spruce (Picea glauca (Moench) Voss). Capture efficiency was high (74.5%) given a high level of exome conservation between the two species. Using stringent criteria, we delimited a set of 61,771 high-confidence SNPs across 13,543 genes. To validate SNPs, a high-throughput genotyping array was developed for a subset of 5571 predicted SNPs representing as many different gene loci, and was used to genotype over 1000 trees. The estimated true positive rate of the resource was 84.2%, which was comparable with the genotyping success rate obtained for P. abies control SNPs recycled from previous genotyping efforts. We also analyzed SNP abundance across various gene functional categories. Several GO terms and gene families involved in stress response were found over-represented in highly polymorphic genes.
conclusionThe annotated high-confidence SNP catalog developed herein represents a valuable genomic resource, being representative of over 13 K genes distributed across the P. abies genome. This resource should serve a variety of population genomics and breeding applications in Norway spruce.
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