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.

KEYWORDS:

• Eucalyptus
• Corymbia
• Orthologous sequences
• Microsatellites
• Transferability

Acknowledgements

The authors thank Dr. Mohan Varghese and Dr. Rathinam Kamalakannan, Life Science and Technology Centre, ITC Ltd., India, for the support in arranging plant material, Mr. Vishwanath and Neerajakshi for technical assistance in the laboratory and Mr. Suresh Kumar R for helping in bioinformatics analysis.

Disclosure statement

No potential conflict of interest was reported by the authors.

Supplemental material

The supplemental data for this article can be accessed here

Additional information

Funding

This work was supported by the Life Science and Technology Centre, ITC Ltd.

Notes on contributors

Nagabhushana Kotrappa

Nagabhushana Kotrappa is an expert in informed breeding of pulp wood species, particularly working on Eucalyptus and Corymbia improvement.

Prasad Suresh Hendre

Prasad Suresh Hendre is a trained geneticist and plant breeder, applying various molecular genomics tools for enhancing breeding efficiency and developing improved varieties.

Rajkumar Rathinavelu

Rajkumar Rathinavelu is an expertise in Genomics, Bioinformatics, data science and Prediction Biology, aimed at commercial exploitation of plants.