ArticlePloS one2019
A high-density exome capture genotype-by-sequencing panel for forestry breeding in Pinus radiata.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Article
- A public mid-density genotyping platform for pecan [Carya illinoinensis (Wangenh.) K. Koch].The plant genome · 2026Article
- A public mid-density genotyping platform for cultivated cranberry (Vaccinium macrocarpon Aiton).The plant genome · 2025Article
- Pinus radiata genome reveals a downward demographic trajectory and opportunities for genomics-assisted breeding.G3 (Bethesda, Md.) · 2025Article
- Leveraging UAV spectral and thermal traits for the genetic improvement of resistance to Dothistroma needle blight inFrontiers in plant science · 2025Article
- Article
- Identification and high-throughput genotyping of single nucleotide polymorphism markers in a non-model conifer (Abies nordmanniana (Steven) Spach).Scientific reports · 2023Article
- Utilization of Genotyping-by-Sequencing (GBS) for Rice Pre-Breeding and Improvement: A Review.Life (Basel, Switzerland) · 2022Review
- High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata.BMC genomics · 2022Article
- The western redcedar genome reveals low genetic diversity in a self-compatible conifer.Genome research · 2022Article
- Chasing genetic correlation breakers to stimulate population resilience to climate change.Scientific reports · 2022Article
- The long road to bloom in conifers.Forestry research · 2022Review
- Current status and trends in forest genomics.Forestry research · 2022Review
- 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
- Genetic Variation in Drought-Tolerance Traits and Their Relationships to Growth inFrontiers in plant science · 2021Article
- Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine.BMC genomics · 2020Article
- Effect of trait's expression level on single-step genomic evaluation of resistance to Dothistroma needle blight.BMC plant biology · 2020Article
- Marker Selection in Multivariate Genomic Prediction Improves Accuracy of Low Heritability Traits.Frontiers in genetics · 2020Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Development of genome-wide resources for application in genomic selection or genome-wide association studies, in the absence of full reference genomes, present a challenge to the forestry industry, where longer breeding cycles could benefit from the accelerated selection possible through marker-based breeding value predictions. In particular, large conifer megagenomes require a strategy to reduce complexity, whilst ensuring genome-wide coverage is achieved. Using a transcriptome-based reference template, we have successfully developed a high density exome capture genotype-by-sequencing panel for radiata pine (Pinus radiata D.Don), capable of capturing in excess of 80,000 single nucleotide polymorphism (SNP) markers with a minor allele frequency above 0.03 in the population tested. This represents approximately 29,000 gene models from a core set of 48,914 probes. A set of 704 SNP markers capable of pedigree reconstruction and differentiating individual genotypes were tested within two full-sib mapping populations. While as few as 70 markers could reconstruct parentage in almost all cases, the impact of missing genotypes was noticeable in several offspring. Therefore, 60 sets of 110 randomly selected SNP markers were compared for both parentage reconstruction and clone differentiation. The performance in parentage reconstruction showed little variation over 60 iterations. However, there was notable variation in discriminatory power between closely related individuals, indicating a higher density SNP marker panel may be required to elucidate hidden relationships in complex pedigrees.
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