Horticulture, Environment, and Biotechnology : HEB

Korean Society of Horticultural Science (한국원예학회)
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Optimization of High Resolution Melting Analysis and Discovery of Single Nucleotide Polymorphism in Capsicum

Park, Soung-Woo;An, Song-Ji;Yang, Hee-Bum;Kwon, Jin-Kyung;Kang, Byoung-Cheorl

  • Published : 20090200
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Abstract

High resolution melting (HRM) analysis is an inexpensive, simple, and rapid detection technology for single nucleotide polymorphism (SNP). In this study, we tested and applied HRM analysis for SNP marker discovery in pepper. To obtain accurate and reproducible HRM results, the PCR conditions were tested first. Factors affecting PCR reactions also affected HRM results. Best HRM results could be obtained with the PCR condition of 1.5 mM of MgCl$_{2}$, 60 mM of KCl, and 2.5 ng.$\mu$l$^{-1}$ of template DNA. With the optimized PCR condition, the usefulness of HRM analysis for SNP detection was evaluated for 60 COSII markers with known SNP information. SNPs were successfully detected by HRM analysis with an average success rate of 65% (39 of 60). SNPs were most successfully (about 90%) detected for amplicons smaller than 250 bp in size. Among the SNPs, single base pair changes were the most successfully detected (79.2%). This study is the first report about on HRM application in pepper which demonstrates that HRM will be a very useful tool for SNP discovery and application in pepper.

Keywords

References

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