Characterization of microsatellites revealed by genomic sequencing of Populus trichocarpa

Microsatellites or simple sequence repeats (SSRs) are highly polymorphic, codominant markers that have great value for the construction of genetic maps, comparative mapping, population genetic surveys, and paternity analyses. Here, we report the development and testing of a set of SSR markers derived from shotgun sequencing from Populus trichocarpa Torr. & A. Gray, a nonenriched genomic DNA library, and bacterial artificial chromosomes. Approximately 23% of the 1536 genomic clones and 48% of the 768 bacterial artificial chromosome subclones contained an SSR. Of the sequences containing an SSR, 72.4% contained a dinucleotide, 19.5% a trinucleotide, and 8.1% a tetranucleotide repeat unit; 26.6% of the sequences contained multiple SSR motifs in a complex or compound repeat structures. A survey of the genome sequence database revealed very similar proportional distribution, indicating that our limited rapid, shallow sequencing effort is representative of genome-wide patterns. In total, 492 primer pairs were designed and these yielded 77 markers that were mapped in an F-2 pedigree, including 26 that were sufficiently informative to be included in a Populus framework map. SSRs with GC-rich motifs mapped at a significantly higher frequency than expected, although AT-rich SSRs accounted for the majority of mapped markers due to their higher representation in the genome. SSR markers developed from P. trichocarpa showed high utility throughout the genus, with amplification rates in excess of 70% for all Populus species tested. Finally, at least 30% of the markers amplified in several willow species, suggesting that some of these SSRs will be transferable across genera.