Elevated frequency of SNPs flanking GA microsatellites in rice

DNA microsatellites have long been used as a marker for genetic comparison between individuals and closely related species. This is due to their rapid generation of polymorphism and relative ease of analysis. There are however limitations in using microsatellites for very high throughput analysis and concerns over accuracy due to the effect of homoplasy and potential for bias during analysis. Single nucleotide polymorphisms (SNP’s) are becoming increasingly popular as an alternative to microsatellites as they are able to identifying individuals for the purposes of varietal identification with high throughput, low cost and relative accuracy. We set out to look at regions of the genome that may contain a higher abundance of SNP’s by investigating the flanking regions of microsatellites as a region of known genetic instability. A combination of direct sequencing and database analysis was used to generate a measure of SNP frequency in rice microsatellite flanking regions. Our data indicates that SNP’s are significantly more abundant in the flanks of the di-nucleotide repeat GA than in the tri-nucleotide repeat GAA or in the region surrounding the microsatellites. This suggests that targeting the flanking regions of di-nucleotide microsatellites may be a useful strategy in identifying SNP’s in closely related individuals.