Short amplicon microsatellite markers for low quality elephant DNA

Many elephant genetic studies have relied on non-invasively collected samples. To improve the success rate for microsatellite genotyping of degraded DNA, we redesigned primers to generate shorter PCR amplicon sizes. Twelve novel primer pairs successfully amplified DNA extracted from dung of African forest and savanna elephants. The novel microsatellite primers were significantly more effective at amplifying dung DNA than the original primers, especially in cases where the original amplicon size was more than 200 bp. The improvement was especially evident when the DNA was of poor quality. Most of the novel primers generated allele sizes that were reduced by a consistent length relative to allele sizes amplified by the original primers. These novel microsatellite primers may improve genotyping success for degraded DNA from dung, museum specimens or ivory, contributing to African elephant conservation.