Intra and intergeneric transferable gene-derived orthologous microsatellite markers in <i>Eucalyptus</i> and <i>Corymbia</i> species

This study describes the development and application of a novel strategy that targets repeat domains in the orthologous genic region of two <i>Eucalyptus</i> species to derive Expressed Sequence Tags (EST)-based functional orthologous microsatellite markers and their characterization in four <i>Eucalyptus</i> and two <i>Corymbia</i> species. About 13,468 ESTs of <i>Eucalyptus</i> <i>globulus</i> were assembled into unigenes, screened for repeat motifs and then mapped on the <i>Eucalyptus</i> <i>grandis</i> genome. The simple sequence repeat (SSR)-positive orthologous sequences of <i>E. grandis</i>, along with 13,380 genomic sequences of <i>Eucalyptus</i> <i>camaldulensis</i>, were then screened for di- and tri-nucleotide repeat motifs and 230 primer pairs were designed. Functional annotation was carried out through homology search and gene ontology using <i>E. grandis</i> transcript database. Of 230 SSRs, 179 were validated in <i>E. camaldulensis</i> and a subset of 20 SSRs was used for characterization and cross species/genera transferability using 130 individuals from both <i>Eucalyptus</i> and <i>Corymbia</i>. The average values of number of alleles, polymorphic information content, observed and expected heterozygosity were 10.57, 0.59, 0.43 and 0.62, respectively, in <i>E. camaldulensis</i>. High marker transferability within the genus <i>Eucalyptus</i> (up to 98%) and <i>Corymbia</i> (up to 80%) was observed.