Development of orthologous microsatellite markers in Eucalyptus camaldulensis L

Development of orthologous microsatellite markers in Eucalyptus camaldulensis L

Nagabhushana K Hendre P, Ashok VK and R Rajkumar ITC R&D Center, Hyderabad

Being a commercially important tree species, the tree improvement of E. camaldulensis,

E. camaldulensis has been lacking for simple sequence repeat (SSR) based markers due to non availability of genome sequences. Expressed Sequence Tags (EST) based SSR markers do not completely exploit the polymorphism at intronic and intergenic regions. Therefore we modeled a pipeline that targets highly conserved domains using publicly available ESTs and genome sequences of Eucalyptus and developed SSR markers for cross amplification across species. We collected 13468 E globulus ESTs and 13380 E. camaldulensis genomic sequences. The ESTs were assembled as unigene and mapped on E. grandis whole genome scaffolds. A total of 173 unique scaffolds were further selected based on the EST mapping and were further mined for repeats. A total of 124 scaffolds were identified SSR containing regions and were found to be orthologous to E. globulus, E. grandis and E. camaldulensis. Further oligos were designed, flanking repeat motifs and validated on E. camaldulensis. The detailed pipeline of both in-silco and wet-validation will be presented.