A new method for DNA extraction from feces and hair shafts of the South China tiger (Panthera tigris amoyensis)

Abstract

It is commonly known that tigers (Panthera tigris) groom themselves by licking their coats, which leads to an abundance of hairs in their feces. These hairs are designated specially as "fecal hairs". In our study, in order to explore fecal hairs potential as a DNA source for genetic analysis, 55 fecal hair samples were collected from 23 captive South China tigers (P. t. amoyensis). According to the amplification of mitochondrial primers loop F and loop R, DNA quality of noninvasive samples were grouped into three grades: grade I-the highest-quality DNA, grade II--high-quality DNA, and grade III--poor-quality DNA. No failed amplifications on microsatellite primers and only 0.27% genotyping errors occurred with grade I fecal hair DNA, as compared with 9.4% failed amplifications on microsatellite primers and 9.5% genotyping errors with grade II fecal hair DNA. It was found that 25.45% of fecal hair DNA was grade I and 65.45 and 10.00% of fecal hair DNA were grades II and III, respectively, as compared with 4.35% grade I fecal DNA and 34.78 and 60.87% grades II and III fecal DNA, respectively. Thus, higher-quality DNA can be extracted from fecal hairs than feces. In addition, DNA could be extracted from hair shafts of tigers and a minimum of 2000 hair shafts were required for visible DNA bands on a 1% agarose gel. These findings demonstrate that fecal hairs may serve as a convenient and reliable genomic DNA source for genotype analysis.

Sequence Analysis of Mitochondrial DNAs of 12S rRNA, 16S rRNA, and Cytochrome Oxidase Subunit 1(COI) Regions in Slow Lorises (Genus Nycticebus) May Contribute to Improved Identification of Confiscated Specimens

“…Amplification and determination of the mitochondrial DNA from the hair root was not difficult in our study. In recent years, it has become possible to use hair shafts or feces for the extraction of DNA [23]. In the present study, skin, buccal mucosa, or hair root were used to avoid DNA contamination from animals living in the same cage or previously hosted individuals.…”

Determination of Baylisascaris schroederi Infection in Wild Giant Pandas by an Accurate and Sensitive PCR/CE-SSCP Method

“…It is well-known that the use of fecal material as noninvasive sources of genetic material has a number of problems, such as co-purifying contaminants and low amounts of DNA [23]. In order to overcome these problems, we ran the samples at different input DNA volumes.…”

Non-invasive DNA extraction for molecular identification of royal Bengal tiger Panthera tigris tigris

“…Fecal samples (scat) has been used in many studies for DNA extraction, and its utility in genetic studies has been well reported (5)(6)(7)(8) . Fecal hairs are also used as a source of genetic material (9) . To extract better quality DNA from feces, special care is required to avoid DNA degradation, the presence of PCR inhibitors, and DNA contamination.…”