Cloned microsatellite repeats differ between 4-base restriction endonucleases

Simple sequence repeat (SSR) loci are an important marker type for populati on genetic studies despite the limitation that development of novel loci re quires construction and screening of genomic DNA libraries. The common prac tice of size fractioning genomic DNA before cloning could lead to different ial representation of SSR loci within genomic libraries. In addition, linka ge mapping studies have shown that small numbers of SSR markers are not ran domly distributed within the genomes from which they are isolated. From att empts to clone five SSR repeat sequences in two wild plant species we show that the numbers and repeat type of potential SSR markers depend on the res triction endonuclease used to sample the genome when constructing DNA libra ries. This observation is consistent with unequal sampling of the genome by different restriction enzymes. However, as a group the five SSR repeal seq uences are not associated with a given restriction enzyme, suggesting they are not clumped within the genome. Use of multiple restriction enzymes to c onstruct DNA libraries may help ensure that cloned SSR loci are drawn from diverse locations in the genome, helping to meet the assumption of randomly located marker loci required for population genetic inferences.