Intra and intergeneric transferable gene-derived orthologous microsatellite markers in Eucalyptus and Corymbia species

Abstract

This study describes the development and application of a novel strategy that targets repeat domains in the orthologous genic region of two Eucalyptus species to derive Expressed Sequence Tags (EST)-based functional orthologous microsatellite markers and their characterization in four Eucalyptus and two Corymbia species. About 13,468 ESTs of Eucalyptus globulus were assembled into unigenes, screened for repeat motifs and then mapped on the Eucalyptus grandis genome. The simple sequence repeat (SSR)-positive orthologous sequences of E. grandis, along with 13,380 genomic sequences of Eucalyptus camaldulensis, 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 E. grandis transcript database. Of 230 SSRs, 179 were validated in E. camaldulensis and a subset of 20 SSRs was used for characterization and cross species/genera transferability using 130 individuals from both Eucalyptus and Corymbia. 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 E. camaldulensis. High marker transferability within the genus Eucalyptus (up to 98%) and Corymbia (up to 80%) was observed. © 2017 The Japanese Forest Society