HIGH RESOLUTION MELTING DETECTS SEQUENCE POLYMORPHISM IN RUBUS OCCIDENTALIS MONOMORPHIC MICROSATELLITE MARKERS
Microsatellite, or simple sequence repeat (SSR), markers are valuable as co-dominant genetic markers with a variety of applications such as DNA fingerprinting, linkage mapping, and population structure analysis. However, primer pairs designed from the regions that flank SSRs often generate fragments with no size polymorphism. High resolution melting (HRM) technology provides a new method of identifying sequence variations in these amplified fragments. In this study, we used HRM to identify polymorphism in SSR PCR products that were monomorphic for size in a black raspberry (Rubus occidentalis subgenus Idaeobatus) population. When HRM revealed polymorphism between the parents of a mapping population, the seedlings were genotyped and scored. The HRM markers segregated in a Mendelian fashion. Comparison of DNA sequences of the parents revealed the presence of single nucleotide polymorphisms (SNP) in the amplicons. HRM can be a valuable tool for detecting polymorphism in PCR amplicons using existing primer pairs that would otherwise be of little use.
Dossett, M., Bassil, N.V. and Finn, C.E. (2012). HIGH RESOLUTION MELTING DETECTS SEQUENCE POLYMORPHISM IN RUBUS OCCIDENTALIS MONOMORPHIC MICROSATELLITE MARKERS. Acta Hortic. 926, 91-95
SSR, single nucleotide polymorphism, HRM, black raspberry