Comparative sequencing of a microsatellite locus reveals size homoplasy within and between European oak species (Quercus spp.)

Microsatellites (simple sequence repeats [SSRs]) are highly variable molecular markers that are a rich and readily assayed source of variation for population. genetic studies. Cross-amplification between closely related species is possible when there are no (or few) sequence differences in the primer binding sites. The occurrence of nonhomologous fragments of the same size (size homoplasy) is a constraint of microsatellites. Size homoplasy can be caused by insertions/deletions (indels) in SSR flanking regions. We found that size variation in locus ssrQZAG9 is due to different repeat numbers of the SSR motifs but also to indels in SSR flanking regions. Indels were found within species belonging to sections Robur and Cerris of genus Quercus and also between species of the 2 sections. In section Robur (Quercis robur L., Quercus petraea [Matt.] Liebl., Quercus pubescens Willd.), we detected rare alleles with an indel of 57 bp or 62 bp followed by a smaller indel of 12 bp in the SSR flanking regions. These alleles show a size range overlapping with that of alleles amplified in Quercus cerris L. (section Cerris). Multiple alignments with sequences of section Robur revealed the same SSR repeat motif but multiple indels in SSR flanking regions in Q. cerris. We discuss the effects of size homoplasy of SSR loci for the study of interspecific gene flow and on estimates of population differentiation.