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

Brandt J.R., Saidah S.H., Zhao K., Ishida Y., Apriyana I., Ryder O.A., Ramono W., Sudoyo H., Suryadi H., Van Coeverden de Groot P.J., Roca A.L.

Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States; Department of Biology, Marian University, Fond du Lac, WI 54935, United States; Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jl. Diponegoro No. 69, Jakarta, 10430, Indonesia; Institute of Conservation Research, San Diego Zoo Global, Escondido, CA 92027, United States; Rhino Foundation of Indonesia, Jl. Bima IV/10, Bogor, 16153, Indonesia; Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States


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. © 2021, The Author(s).

Dicerorhinus sumatrensis; Non-invasive sampling; Short tandem repeats


BMC Research Notes

Publisher: BioMed Central Ltd

Volume 14, Issue 1, Art No 119, Page – , Page Count

Journal Link:

doi: 10.1186/s13104-021-05522-x

Issn: 17560500

Type: All Open Access, Gold


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