Assessing high-resolution melt curve analysis for accurate detection of DNA polymorphisms in the chloroplast gene accD of Crucifer species

To discover chloroplast genome (cpDNA) variations, we performed an assessment of high-resolution melt curve (HRM) analysis for DNA variation within the cp gene accD (acetyl-COA carboxylase gene beta-subunit) at different taxa level of Crucifer. Five short regions of the target gene with sufficient diversity were selected. The results showed that the detection efficiency varied at highly and low polymorphic loci. Amplicons with only one or multiple SNPs were distinguished perfectly. At the intraspecific level, at least 80% variations can be detected, although a few false positives (FPs) existed; however, complex amplicons with multiple SNPs and INDELs coexistence at intertribal level were analysed with more false negatives (FNs). In brief, HRM is an ideal tool when used on rare variance identification within large populations. Further advances in HRM analysis should make it a useful tool for basic and applied studies of plant genetics.