Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
Department of Biology, Marian University, Fond du Lac, WI, 54935, USA.
BMC Res Notes. 2021 Mar 26;14(1):119. doi: 10.1186/s13104-021-05522-x.
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.
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; H = 0.30). These were sufficient to distinguish among individuals (P < 0.0001), and to distinguish among siblings (P < 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.
苏门答腊犀牛处于极度濒危状态，其现存数量不足 100 头。准确的种群普查估计对于制定和实施保护计划至关重要。为了实现分子普查，我们在此开发了扩增子长度较短的微卫星标记，适用于非侵入性粪便采样。
由于样本数量有限且可能缺乏全基因组多样性，我们从两个苏门答腊犀牛样本中生成了 Illumina 测序reads。基因组筛选确定了具有短串联重复和在数据集内具有多态性的reads 。表征了 29 个新的多态性微卫星标记（A = 2.4；H = 0.30）。这些标记足以区分个体（P < 0.0001），并区分兄弟姐妹（P < 0.0001）。在印度尼西亚的犀牛中，几乎所有的标记都被确定为多态性，并可有效地对来自粪便样本的 DNA 进行基因分型。值得注意的是，这些标记使用从野生苏门答腊犀牛非侵入性收集的 11 个粪便样本中提取的 DNA 进行扩增和显示微卫星多态性。这些微卫星标记为野生苏门答腊犀牛的普查和遗传研究提供了重要资源。
