ArticleScientific reports2021
Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Genome-wide association mapping of distinctness, uniformity and stability traits and varietal identification in rice (Oryza sativa L.).Journal of the science of food and agriculture · 2026Article
- Enhancing hybridization potential through standardizing emasculation techniques and molecular marker integration in finger millet (Eleusine coracana L.).Plant methods · 2026Article
- Application of SNV Detection Methods for Market Control of Food Products from New Genomic Techniques.International journal of molecular sciences · 2026Review
- Development and validation of a minimal SNP genotyping panel for the differentiation of Cannabis sativa cultivars.BMC genomics · 2025Article
- Thousands of trait-specific KASP markers designed for diverse breeding applications in rice (Oryza sativa).G3 (Bethesda, Md.) · 2025Article
- Genetic diversity and population structure studies of West African sweetpotato [Ipomoea batatas (L.) Lam] collection using DArTseq.PloS one · 2025Article
- Validation of sorghum quality control (QC) markers across African breeding lines.The plant genome · 2024Article
- Fine mapping and candidate gene analysis ofFrontiers in plant science · 2024Article
- Assessing the Genetic Diversity of Daylily Germplasm Using SSR Markers: Implications for Daylily Breeding.Plants (Basel, Switzerland) · 2023Article
- DNA-Based Tools to Certify Authenticity of Rice Varieties-An Overview.Foods (Basel, Switzerland) · 2022Review
- Development and Validation of Diagnostic KASP Markers for Brown Planthopper Resistance in Rice.Frontiers in genetics · 2022Article
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7 authors.
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Abstract
Morphological identification of closely related rice species, particularly those in the Oryza AA genome group, presents major challenges and often results in cases of misidentification. Recent work by this group identified diagnostic single nucleotide polymorphic (SNP) markers specific for several rice species and subspecies based on DArTseq next-generation sequencing technology ("DArTseq"). These SNPs can be used for quality control (QC) analysis in rice breeding and germplasm maintenance programs. Here, we present the DArTseq-based diagnostic SNPs converted into Kompetitive allele-specific PCR (KASPar or KASP) assays and validation data for a subset of them; these can be used for low-cost routine genotyping quality control (QC) analysis. Of the 224 species/subspecies' diagnostic SNPs tested, 158 of them produced working KASP assays, a conversion success rate of 70%. Two validation experiments were run with 87 of the 158 SNP markers to ensure that the assays amplified, were polymorphic, and distinguished the five species/subspecies tested. Based on these validation test results, we recommend a panel of 36 SNP markers that clearly delineate O. barthii, O. glaberrima, O. longistaminata, O. sativa spp. indica and japonica. The KASP assays provide a flexible, rapid turnaround and cost-effective tool to facilitate germplasm curation and management of these four Oryza AA genome species across multiple genebanks.
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