Novel design and deployment of orthologous genic SSR markers in Eucalyptus camaldulensis Dehnh

Background Eucalyptus camaldulensis is a widely planted tree species in India, because of its rapid growth and adaptability to dry regions. Genetic improvement through informed breeding of E. camaldulensis largely depends on availability of molecular markers, linkage maps and genome information. Microsatellite markers, also called as simple sequence repeats (SSRs) have wide application due to their unique advantages over other marker systems. In Eucalyptus, SSR markers have been used in various breeding applications from DNA fingerprinting to QTL mapping [1,4]. Despite of their advantages, the major drawback is the time required for their development [6]. There are less than twenty five E. camaldulensis specific SSR markers available in the public database [5]. Although, there are large number of SSRs available in other Eucalyptus species [2,3], their species transferability in camaldulensis is questionable for practical use. Nevertheless, the existing camaldulensis specific SSRs are insufficient for developing linkage maps, QTL and comparative mapping studies. Besides, EST based markers are handicapped due to exclusion of introns, which sometimes lead to compromise on product sizing. Therefore we have modeled a novel strategy that targets highly conserved domain in the genic region using both publicly available ESTs as well as genome sequences.