ArticlePloS one2019
Criteria for evaluating molecular markers: Comprehensive quality metrics to improve marker-assisted selection.
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 33 papers.
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Who cites it
33 citing papers in PubMed, 89 citations in OpenAlex.
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- Validation of SNP Markers for Diversity Analysis, Quality Control, and Trait Selection in a Biofortified Cassava Population.Plants (Basel, Switzerland) · 2024Article
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- Combination of GWAS and FMolecular genetics and genomics : MGG · 2023Article
- Breeding and Genomic Approaches towards Development of Fusarium Wilt Resistance in Chickpea.Life (Basel, Switzerland) · 2023Review
- Climate change challenges, plant science solutions.The Plant cell · 2023Article
- Genomic selection to improve husk tightness based on genomic molecular markers in maize.Frontiers in plant science · 2023Article
- Genome-based prediction of agronomic traits in spring wheat under conventional and organic management systems.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Advances in Crop Breeding Through Precision Genome Editing.Frontiers in genetics · 2022Review
- Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content.Frontiers in plant science · 2022Article
- High Resolution Genome Wide Association Studies Reveal Rich Genetic Architectures of Grain Zinc and Iron in Common Wheat (Frontiers in plant science · 2022Article
- Identification of an Elite Core Panel as a Key Breeding Resource to Accelerate the Rate of Genetic Improvement for Irrigated Rice.Rice (New York, N.Y.) · 2021Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite strong interest over many years, the usage of quantitative trait loci in plant breeding has often failed to live up to expectations. A key weak point in the utilisation of QTLs is the "quality" of markers used during marker-assisted selection (MAS): unreliable markers result in variable outcomes, leading to a perception that MAS products fail to achieve reliable improvement. Most reports of markers used for MAS focus on markers derived from the mapping population. There are very few studies that examine the reliability of these markers in other genetic backgrounds, and critically, no metrics exist to describe and quantify this reliability. To improve the MAS process, this work proposes five core metrics that fully describe the reliability of a marker. These metrics give a comprehensive and quantitative measure of the ability of a marker to correctly classify germplasm as QTL[+]/[-], particularly against a background of high allelic diversity. Markers that score well on these metrics will have far higher reliability in breeding, and deficiencies in specific metrics give information on circumstances under which a marker may not be reliable. The metrics are applicable across different marker types and platforms, allowing an objective comparison of the performance of different markers irrespective of the platform. Evaluating markers using these metrics demonstrates that trait-specific markers consistently out-perform markers designed for other purposes. These metrics also provide a superb set of criteria for designing superior marker systems for a target QTL, enabling the selection of an optimal marker set before committing to design.
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