# A simple and flexible approach for detecting small numbers of SNPs

## TL;DR

This paper introduces a simple and cost-effective method for detecting small numbers of SNPs using T-C mismatch, achieving 83.3% efficiency in bitter gourd.

## Contribution

A novel, flexible SNP detection method based on T-C mismatch and gel electrophoresis for low-cost, small-scale SNP analysis.

## Key findings

- The method achieved 83.3% detection efficiency for twelve SNPs in bitter gourd.
- The approach is simple, flexible, and suitable for molecular marker-assisted breeding.
- It can be applied to improve stress resistance and agricultural productivity.

## Abstract

SNP markers represent the most extensively distributed and abundant type of polymorphic markers. Although researchers have developed high-throughput detection methods for SNP markers, there remains a lack of simple, flexible, and cost-effective approaches for detecting small numbers of SNPs. To address this need, this study proposes a method for detecting SNPs based on T-C mismatch. Specifically, two upstream primers were designed with a single base difference at the 3’ end. Additionally, a T-C mismatch was introduced within 5 bp upstream of the 3’ end to distinguish SNPs. Detection was achieved through PCR amplification and subsequent gel electrophoresis analysis. In this study, twelve random SNPs from bitter gourd were selected, and the detection efficiency was found to be 83.3%. The proposed SNP detection method is characterized by its simplicity and flexibility, offering an effective tool for molecular marker-assisted selection breeding in applications such as stress resistance improvement and agricultural productivity enhancement.