PCR Analysis of SSR Polymorphisms in Plants Using Agarose Gels

Abstract

The alleles of microsatellite (SSR) loci are identified by PCR amplifications of genomic DNA using primer pairs which flank the microsatellite repeats (see also Chapter 11.1. We try to use a single set of amplification and reaction conditions for all the primer pairs, without any optimization of these conditions. This is a necessity when large numbers of primers have to be screened and used. A single locus is normally amplified. More than one locus may be amplified if the genome is polyploid or if non-specific annealing occurs due to bad primer design, poor sequence data or homology of the primers with repeated sequence elements. The fragments obtained from the PCR amplification must be separated from one another to identify polymorphisms in SSRs.