Abstract
• In this study, 148 428 simple sequence repeat (SSR) primer pairs were designed
from the unambiguously mapped sequence scaffolds of the Nisqually-1 genome.
The physical position of the priming sites were identified along each of the 19 Populus
chromosomes, and it was specified whether the priming sequences belong to
intronic, intergenic, exonic or UTR regions.
• A subset of 150 SSR loci were amplified and a high amplification success rate (72%)
was obtained in P. tremuloides, which belongs to a divergent subgenus of Populus
relative to Nisqually-1. PCR reactions showed that the amplification success rate of
exonic primer pairs was much higher than that of the intronic/intergenic primer pairs.
• Applying ANOVA and regression analyses to the flanking sequences of microsatellites,
the repeat lengths, the GC contents of the repeats, the repeat motif numbers,
the repeat motif length and the base composition of the repeat motif, it was determined
that only the base composition of the repeat motif and the repeat motif
length significantly affect the microsatellite variability in P. tremuloides samples.
• The SSR primer resource developed in this study provides a database for selecting
highly transferable SSR markers with known physical position in the Populus
genome and provides a comprehensive genetic tool to extend the genome sequence
of Nisqually-1 to genetic studies in different Populus species.
