ArticleFrontiers in plant science2020
Suitability of Single-Nucleotide Polymorphism Arrays Versus Genotyping-By-Sequencing for Genebank Genomics in Wheat.
Article in Frontiers in plant science, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it, 50 citations in OpenAlex.
- Optimizing Genomic-Enabled Prediction in Small-Scale Maize Hybrid Breeding Programs: A Roadmap Review.Frontiers in plant science · 2021Pooled it
- Individual plant genetics reveal the control of local adaptation in European maize landraces.BMC biology · 2025Article
- Wheat improvement through advances in single nucleotide polymorphism (SNP) detection and genotyping with a special emphasis on rust resistance.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Review
- On the usefulness of mock genomes to define heterotic pools, testers, and hybrid predictions in orphan crops.Frontiers in plant science · 2023Article
- Large-scale genotyping and phenotyping of a worldwide winter wheat genebank for its use in pre-breeding.Scientific data · 2022Article
- QTL Analysis for Bread Wheat Seed Size, Shape and Color Characteristics Estimated by Digital Image Processing.Plants (Basel, Switzerland) · 2022Article
- Genomic prediction of preliminary yield trials in chickpea: Effect of functional annotation of SNPs and environment.The plant genome · 2022Article
- Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies.Molecular breeding : new strategies in plant improvement · 2022Review
- Exploring the diversity and genetic structure of the U.S. National Cultivated Strawberry Collection.Horticulture research · 2022Article
- Population-tailored mock genome enables genomic studies in species without a reference genome.Molecular genetics and genomics : MGG · 2022Article
- Exploring the legacy of Central European historical winter wheat landraces.Scientific reports · 2021Article
- GWAS identifies an ortholog of the rice D11 gene as a candidate gene for grain size in an international collection of hexaploid wheat.Scientific reports · 2021Article
- Single-trait, multi-locus and multi-trait GWAS using four different models for yield traits in bread wheat.Molecular breeding : new strategies in plant improvement · 2021Article
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- Article
- Marker-Assisted Introgression and Stacking of Major QTLs Controlling Grain Number (Plants (Basel, Switzerland) · 2021Article
- K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology.Plant methods · 2021Article
- Building pan-genome infrastructures for crop plants and their use in association genetics.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Review
- The History of Lentil (Frontiers in plant science · 2021Article
- Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (PeerJ · 2021Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genebank genomics promises to unlock valuable diversity for plant breeding but first, one key question is which marker system is most suitable to fingerprint entire genebank collections. Using wheat as model species, we tested for the presence of an ascertainment bias and investigated its impact on estimates of genetic diversity and prediction ability obtained using three marker platforms: simple sequence repeat (SSR), genotyping-by-sequencing (GBS), and array-based SNP markers. We used a panel of 378 winter wheat genotypes including 190 elite lines and 188 plant genetic resources (PGR), which were phenotyped in multi-environmental trials for grain yield and plant height. We observed an ascertainment bias for the array-based SNP markers, which led to an underestimation of the molecular diversity within the population of PGR. In contrast, the marker system played only a minor role for the overall picture of the population structure and precision of genome-wide predictions. Interestingly, we found that rare markers contributed substantially to the prediction ability. This combined with the expectation that valuable novel diversity is most likely rare suggests that markers with minor allele frequency deserve careful consideration in the design of a pre-breeding program.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.