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PCR Allele Competitive Extension (PACE) Workflow for Genotyping by SNP Identification
Anthony Torres1, Jason Argyris2,3, Reginald Gaudino1,4
1Cannabis Research Institute, Discovery Partners Institute, University of Illinois System, Chicago, IL, USA.
Methods in Molecular Biology (Clifton, N.J.)
|June 28, 2025
Summary
This study introduces a simplified Polymerase Chain Reaction Allele Competitive Extension (PACE) method for high-throughput SNP genotyping in plants. This advanced technique accurately identifies specific genetic variations from DNA, aiding in trait selection.
Area of Science:
- Plant Science
- Molecular Biology
- Genetics
Background:
- Advanced genotyping is crucial for plant breeding and genetic research.
- DNA extraction from various plant tissues, including FTA cards and leaf samples, is a common starting point.
- Single Nucleotide Polymorphisms (SNPs) are key genetic markers for identifying desirable traits.
Purpose of the Study:
- To present a simplified and efficient protocol for high-throughput SNP genotyping in plants.
- To demonstrate the application of Polymerase Chain Reaction Allele Competitive Extension (PACE) for genetic analysis.
- To detect specific SNPs in target genes of a dioecious plant.
Main Methods:
- Utilizing DNA extracted from FTA samples and leaf tissue.
- Employing Polymerase Chain Reaction Allele Competitive Extension (PACE) with allele-specific primers.
- Using a PACE master mix for selective primer extension and fluorescent labeling.
- Analyzing results to identify SNP genotypes.
Main Results:
- Achieved high-throughput SNP genotyping with remarkable accuracy.
- Successfully differentiated between two alleles of interest for targeted SNP detection.
- Demonstrated a simplified workflow for efficient SNP genotyping.
- Identified specific genetic variations in target genes of a dioecious plant.
Conclusions:
- The PACE method offers a valuable tool for precise and efficient SNP genotyping in plant science.
- This protocol facilitates the detection of targeted genetic variations linked to desired plant traits.
- The simplified workflow enhances the accessibility of advanced genotyping techniques for plant genetic analysis.
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