Comparative assessment of SNPs and microsatellites for fingerprinting, parentage and assignment testing in species of Eucalyptus

Background Brazil stands on the international scenario by having one of the largest natural forest heritage and extensive sustainable planted forests. Brazilian planted forestry is based mainly on fast growing eucalyptus and pines, with the pulp, paper and steel industries as the major consumers. Introduced commercially in Brazil in the early twentieth century, the eucalypts have experienced increasing levels of genetic improvement over the years. Along with the classical breeding, the use of genetic markers has positively influenced breeding programs, contributing to quality control processes of clonal forestry and advanced breeding. Microsatellite markers have been the main tool used to date. They are multiallelic, highly polymorphic and thus very efficient for several applications that require identification and discrimination of elite clones and determination of parentage. While di and tri-nucleotide repeat microsatellites tend to be more polymorphic, tetra and higher order repeats allow a more robust allele calling [1]. SNP markers genotyped by a high-throughput system have been recently developed for Eucalyptus [2] but not yet routinely incorporated in Eucalyptus breeding programs. In spite of their lower genetic information content, many more SNPs can be simultaneously typed using automated systems, an appealing feature to operational breeding programs. The aim of this study was to comparatively evaluate the resolving power and precision of different sets of molecular markers (microsatellites and SNPs assayed by the Golden Gate technology) for the most common operational applications in Eucalyptus breeding programs.