Microsatellite DNA markers and their usefulness in poplars, and conservation of microsatellite DNA loci in Salicaceae

Abstract

Highly informative genetic markers, such as microsatellites, would facilitate programs in genetics, breeding, biotechnology, and conservation of forest trees. Markers for 12 microsatellite DNA/simple sequence repeat (SSR) loci were developed and characterized in trembling aspen (Populus tremuloides). The compatibility and usefulness of the P. tremuloides SSR primers to resolve microsatellites in 24 other Populus species and three interspecific hybrids belonging to all six sections of the genus Populus and two Salix species were examined. The utility of the microsatellite DNA markers was also evaluated for clone and cultivar identification and for determining somaclonal variation. The (TC/AG)n microsatellites were the most abundant. The primers of one highly polymorphic dinucleotide SSR marker (PTR7) amplified two loci, and alleles could not be assigned to a specific locus. Fifty-four alleles were detected in 36 or 38 P. tremuloides individuals at the 10 polymorphic SSR loci showing single-locus patterns. The number of alleles at thesel0 SSR loci ranged from 2 to 11, with an average of 5.4 alleles per locus, and the observed heterozygosity ranged from 0.05 to 0.82, with a mean of 0.40 per locus. Although the highest polymorphism was observed for a dinucleotide SSR locus, the trinucleotide SSR loci also showed high polymorphism. Microsatellite DNA variants of four SSR loci followed a single-locus and those of PTR7 a two-locus Mendelian inheritance patterns. With a few exceptions, all SSR primer pairs were successful in PCR amplification of genomic DNA and resolving microsatellites of comparable size in all 24 Populus species, three Populus hybrids, and two Salix species. Thus, all SSR loci characterized are conserved in the genus Populus as well as in Salix species. Each clone of six Populus species and each cultivar of P. x canadensis could be uniquely fingerprinted based on their genotypes at one to five SSR loci. Species-specific microsatellite DNA alleles for P. deltoides, P. nigra, and P. balsamifera were detected at one SSR locus. Microsatellite DNA somaclonal variation was detected in micropropagated P. tremuloides plants. The microsatellite DNA markers that we have developed could be used for clonal fingerprinting, tree forensics, species and hybrid identification, certification of controlled crosses, genome mapping, marker-assisted early selection, genetic diversity assessments, and conservation and sustainable forest management programs in poplars and also in willows.