ArticlePlant methods2010
Protocol: a simple gel-free method for SNP genotyping using allele-specific primers in rice and other plant species.
Article in Plant methods, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- PCR Conditions for the Detection of Molecular Markers Associated with Blackleg (International journal of molecular sciences · 2026Article
- Phytochemical, Morphological and Genetic Characterisation ofMolecules (Basel, Switzerland) · 2023Article
- Development of new mutant alleles and markers forFrontiers in plant science · 2023Article
- Designed and validated novel allele-specific primer to differentiate Kernel Row Number (KRN) in tropical field corn.PloS one · 2023Article
- Molecular Identification ofAnimals : an open access journal from MDPI · 2022Article
- Development of Single Nucleotide Polymorphism (SNP)-Based Triplex PCR Marker for Serotype-specificPathogens (Basel, Switzerland) · 2022Article
- Modified "Allele-Specific qPCR" Method for SNP Genotyping Based on FRET.Frontiers in plant science · 2021Article
- The development of a novel SNP genotyping assay to differentiate cacao clones.Scientific reports · 2019Article
- Heterologous Hsp90 promotes phenotypic diversity through network evolution.PLoS biology · 2018Article
- Partial loss-of-function of NAL1 alters canopy photosynthesis by changing the contribution of upper and lower canopy leaves in rice.Scientific reports · 2017Article
- Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass.BMC genomics · 2016Article
- Long-Read Single Molecule Real-Time Full Gene Sequencing of Cytochrome P450-2D6.Human mutation · 2016Article
- Allele frequency distribution of CYP2C19*2 allelic variants associated with clopidogrel resistance in cardiac patients.Experimental and therapeutic medicine · 2015Article
- An improved allele-specific PCR primer design method for SNP marker analysis and its application.Plant methods · 2012Article
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Authors and funding
5 authors.
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Abstract
backgroundGenotype analysis using multiple single nucleotide polymorphisms (SNPs) is a useful but labor-intensive or high-cost procedure in plant research. Here we describe an alternative genotyping method that is suited to multi-sample or multi-locus SNP genotyping and does not require electrophoresis or specialized equipment.
resultsWe have developed a simple method for multi-sample or multi-locus SNP genotyping using allele-specific primers (ASP). More specifically, we (1) improved the design of allele-specific primers, (2) established a method to detect PCR products optically without electrophoresis, and (3) standardized PCR conditions for parallel genomic assay using various allele-specific primers. As an illustration of multi-sample SNP genotyping using ASP, we mapped the locus for lodging resistance in a typhoon (lrt5). Additionally, we successfully tested multi-locus ASP-PCR analysis using 96 SNPs located throughout the genomes of rice (Oryza sativa) cultivars 'Koshihikari' and 'Kasalath', and demonstrated its applicability to other diverse cultivars/subspecies, including wild rice (O. rufipogon).
conclusionOur ASP methodology allows characterization of SNPs genotypes without electrophoresis, expensive probes or specialized equipment, and is highly versatile due to the flexibility in the design of primers. The method could be established easily in any molecular biology laboratory, and is applicable to diverse organisms.
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