ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2020
Overcoming polyploidy pitfalls: a user guide for effective SNP conversion into KASP markers in wheat.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 75 citations in OpenAlex.
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- Identification of KASP markers and putative genes for herbicide (metribuzin) tolerance in common wheat (Triticum aestivum L.).BMC plant biology · 2026Article
- High resolution mapping and development of diagnostic KASP markers for FHB resistance QTL on chromosome 1B in an elite soft red winter wheat cultivar 'Jamestown'.Molecular breeding : new strategies in plant improvement · 2026Article
- Genome-wide exploration of bacterial leaf blight resistance and fine mapping of major resistance gene (Bb13) in upland cotton (Gossypium hirsutum L.).The plant genome · 2026Article
- Identification of stripe rust adult plant resistance genes in the hard winter wheat cultivar Baker's Ann.The plant genome · 2026Article
- Dissecting the genetics of forage quality traits in soft red winter wheat in the U.S. southeast region.Frontiers in plant science · 2026Article
- Genetic diversity study and molecular marker development for economic traits in Korean pine based on RAD-Seq.Frontiers in plant science · 2026Article
- Genetic Dissection of Frost Tolerance in Winter Durum Wheat: Three Validated KASP Markers for Marker-Assisted Selection.Plants (Basel, Switzerland) · 2025Article
- Genetic dissection of plant architecture reveals haplotypes controlling sink-related traits in oilseed rape under limited nitrogen fertilization.BMC plant biology · 2025Article
- New crops on the block: effective strategies to broaden our food, fibre, and fuel repertoire in the face of increasingly volatile agricultural systems.Journal of experimental botany · 2025Review
- Mapping quantitative trait loci for seminal root angle in a selected durum wheat population.The plant genome · 2025Article
- Thousands of trait-specific KASP markers designed for diverse breeding applications in rice (Oryza sativa).G3 (Bethesda, Md.) · 2025Article
- Multiple copy number variants ofFrontiers in plant science · 2025Article
- SNP loci identification and KASP marker development system for genetic diversity, population structure, and fingerprinting in sweetpotato (Ipomoea batatas L.).BMC genomics · 2024Article
- 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
- Dissecting the genetic basis of resistance to Soil-borne cereal mosaic virus (SBCMV) in durum wheat by bi-parental mapping and GWAS.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- GenoBaits®WheatplusEE: a targeted capture sequencing panel for quick and accurate identification of wheat-Thinopyrum derivatives.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Reviewing the essential roles of remote phenotyping, GWAS and explainable AI in practical marker-assisted selection for drought-tolerant winter wheat breeding.Frontiers in plant science · 2024Review
- Development of an SNP marker set for marker-assisted backcrossing using genotyping-by-sequencing in tetraploid perilla.Molecular genetics and genomics : MGG · 2023Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
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Abstract
key messageConversion of SNP chip assays into locus-specific KASP markers requires adapted strategies in polyploid species with high genome homeology. Procedures are exemplified by QTL-associated SNPs in hexaploid wheat. Kompetitive allele-specific PCR (KASP) markers are commonly used in marker-assisted commercial plant breeding due to their cost-effectiveness and throughput for high sample volumes. However, conversion of trait-linked SNP markers from array-based SNP detection technologies into KASP markers is particularly challenging in polyploid crop species, due to the presence of highly similar homeologous and paralogous genome sequences. We evaluated strategies and identified key requirements for successful conversion of Illumina Infinium assays from the wheat 90 K SNP array into robust locus-specific KASP markers. Numerous examples showed that commonly used software for semiautomated KASP primer design frequently fails to achieve locus-specificity of KASP assays in wheat. Instead, alignment of SNP probes with multiple reference genomes and Sanger sequencing of relevant genotypes, followed by visual KASP primer placement, was critical for locus-specificity. To identify KASP assays resulting in false calling of heterozygous individuals, validation of KASP assays using extended reference genotype sets including heterozygous genotypes is strongly advised for polyploid crop species. Applying this strategy, we developed highly reproducible, stable KASP assays that are predictive for root biomass QTL haplotypes from highly homoeologous wheat chromosome regions. Due to their locus-specificity, these assays predicted root biomass considerably better than the original trait-associated markers from the Illumina array.
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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.