Characterization of microsatellites revealed by genomic sequencing ofPopulus trichocarpa

We report the development and testing of a set of simple sequence repeat markers derived from shotgun sequencing from Populus trichocarpa Torr. & A

Gerald A Tuskan; Lee E Gunter; Zamin K Yang; TongMing Yin; Mitchell M Sewell; Stephen P DiFazio

2004

Scholarcy highlights

  • Microsatellite or simple sequence repeat markers represent a rich set of abundant, highly polymorphic codominant markers that can be used in genetic fingerprinting and clonal fidelity applications, genetic mapping and marker-aided selection procedures, and assessments of genetic diversity and phylogeny
  • SSRs appear to be abundant in the Populus genome and can be efficiently isolated via random shotgun sequencing
  • Our results from the ORNL bacterial artificial chromosome fragments suggest that targeting regions known to contain expressed sequences may increase the efficiency of SSR isolation, in keeping with observations that SSRs tend to be associated with low-copy DNA and coding regions in other species
  • The relatively small-scale shotgun sequencing effort yielded results that were highly concordant with those obtained with comprehensive shotgun sequencing of the entire genome, suggesting that the microsatellite contents of other species could be well characterized with very shallow shotgun sequencing
  • The frequency of amplification of the discovered markers across other Populus species suggests that they will prove useful across the genus as well as among species from other closely related genera
  • The priming sites are often unique and highly conserved sequence tags, boding well for comparative mapping. These SSR markers should serve as the primary bridge connecting the genome sequence of P. trichocarpa to genetic improvement programs of many other tree species
  • These simple sequence repeat markers should serve as the primary bridge connecting the genome sequence of P. trichocarpa to genetic improvement programs of many other tree species

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