Characterization of microsatellites revealed by genomic sequencing ofPopulus trichocarpa

Abstract

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 F2 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.

Geographical barriers and climate influence demographic history in narrowleaf cottonwoods

“…We chose 24 SSR loci (Supplementary Table 1) from a publically available list identified by the Populus trichocarpa Genome Project (Tuskan et al, 2004; http://www.ornl.gov/sci/ipgc/ssr_resource.htm). These loci have reliable repeat motifs, most are tri-or tetranucleotide repeats, are easily amplified, and are distributed throughout the genome.…”

Sex-specific pattern of spatial genetic structure in dioecious and clonal tree species, Populus alba L.

“…A set of 16 nuclear microsatellite markers (nSSRs) developed by van der Schoot et al (2000) and Tuskan et al (2004) and available at http://web.ornl.gov/sci/ipgc/ssr_resource.htm was used in the genotyping procedure as described in Dering et al (2015) ( Table 2). INEst 1.0 (Chybicki and Burczyk 2009) was used to estimate genetic diversity parameters at the genet level in both sexes: expected (H e ) and observed heterozygosity (H o ), number of alleles per locus (A), inbreeding coefficient of Weir and Cockerham (1984) (F IS ), and frequency of null alleles.…”

Genetic and physical mapping of Melampsora rust resistance genes in Populus and characterization of linkage disequilibrium and flanking genomic sequence

“…We required that primers have an 80% or greater match over 70% of their length, and that they be correctly oriented and separated by the distance expected, based on the size of the products amplified. (Stirling et al, 2001) and SSR ( Tuskan et al, 2004b) Number of loci amplified with primers in family 13. Only one locus was mapped to the rust-resistance regions for each primer set.…”