Characterization of 29 polymorphic microsatellite markers developed by genomic screening of Sumatran rhinoceros (Dicerorhinus sumatrensis)

Jessica R. Brandt, Sinta H. Saidah, Kai Zhao, Yasuko Ishida, Isabella Apriyana, Oliver A. Ryder, Widodo Ramono, Herawati Sudoyo, Helena Suryadi, Peter J. Van Coeverden de Groot, Alfred L. Roca

Research output: Contribution to journalArticlepeer-review


Objective: The Sumatran rhinoceros is critically endangered, with fewer than 100 individuals surviving across its current range. Accurate census estimates of the remaining populations are essential for development and implementation of conservation plans. In order to enable molecular censusing, we here develop microsatellite markers with amplicon sizes of short length, appropriate for non-invasive fecal sampling. Results: Due to limited sample quantity and potential lack of genome-wide diversity, Illumina sequence reads were generated from two Sumatran rhinoceros samples. Genomic screening identified reads with short tandem repeats and loci that were polymorphic within the dataset. Twenty-nine novel polymorphic microsatellite markers were characterized (A = 2.4; HO = 0.30). These were sufficient to distinguish among individuals (PID < 0.0001), and to distinguish among siblings (PID(sib) < 0.0001). Among rhinos in Indonesia, almost all markers were established as polymorphic and effective for genotyping DNA from fecal samples. Notably, the markers amplified and displayed microsatellite polymorphisms using DNA extracted from 11 fecal samples collected non-invasively from wild Sumatran rhinoceros. These microsatellite markers provide an important resource for a census and genetic studies of wild Sumatran rhinos.

Original languageEnglish (US)
Article number119
JournalBMC Research Notes
Issue number1
StatePublished - Dec 2021


  • Dicerorhinus sumatrensis
  • Non-invasive sampling
  • Short tandem repeats

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)


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