Factors affecting genotyping success in giant panda fecal samples
Fecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH), EtOH −20 °C,...
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PeerJ Inc.
2017-05-01
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| author | Ying Zhu Hong-Yi Liu Hai-Qiong Yang Yu-Dong Li He-Min Zhang |
| author_facet | Ying Zhu Hong-Yi Liu Hai-Qiong Yang Yu-Dong Li He-Min Zhang |
| author_sort | Ying Zhu |
| collection | DOAJ |
| description | Fecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH), EtOH −20 °C, 2-step storage medium, DMSO/EDTA/Tris/salt buffer (DETs) and frozen at −20 °C), storage time (one, three and six months), fragment length, and repeat motif of microsatellite loci) on the success rate of microsatellite amplification, allelic dropout (ADO) and false allele (FA) rates from giant panda fecal samples. Amplification success and ADO rates differed between the storage types. Freezing was inferior to the other four storage methods based on the lowest average amplification success and the highest ADO rates (P < 0.05). The highest microsatellite amplification success was obtained from either EtOH or the 2-step storage medium at three storage time points. Storage time had a negative effect on the average amplification of microsatellites and samples stored in EtOH and the 2-step storage medium were more stable than the other three storage types. We only detected the effect of repeat motif on ADO and FA rates. The lower ADO and FA rates were obtained from tri- and tetra-nucleotide loci. We suggest that freezing should not be used for giant panda fecal preservation in microsatellite studies, and EtOH and the 2-step storage medium should be chosen on priority for long-term storage. We recommend candidate microsatellite loci with longer repeat motif to ensure greater genotyping success for giant panda fecal studies. |
| first_indexed | 2024-03-09T06:26:59Z |
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| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:26:59Z |
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| spelling | doaj.art-8574692410634047814b51c4e3e3e09a2023-12-03T11:19:23ZengPeerJ Inc.PeerJ2167-83592017-05-015e335810.7717/peerj.3358Factors affecting genotyping success in giant panda fecal samplesYing Zhu0Hong-Yi Liu1Hai-Qiong Yang2Yu-Dong Li3He-Min Zhang4Sichuan Nature Resources Science Academy, Chengdu, Sichuan, ChinaCo-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, ChinaSichuan Nature Resources Science Academy, Chengdu, Sichuan, ChinaSichuan Nature Resources Science Academy, Chengdu, Sichuan, ChinaSichuan Province Laboratory for Natural Resources Protection and Sustainable Utilization, Chengdu, Sichuan, ChinaFecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH), EtOH −20 °C, 2-step storage medium, DMSO/EDTA/Tris/salt buffer (DETs) and frozen at −20 °C), storage time (one, three and six months), fragment length, and repeat motif of microsatellite loci) on the success rate of microsatellite amplification, allelic dropout (ADO) and false allele (FA) rates from giant panda fecal samples. Amplification success and ADO rates differed between the storage types. Freezing was inferior to the other four storage methods based on the lowest average amplification success and the highest ADO rates (P < 0.05). The highest microsatellite amplification success was obtained from either EtOH or the 2-step storage medium at three storage time points. Storage time had a negative effect on the average amplification of microsatellites and samples stored in EtOH and the 2-step storage medium were more stable than the other three storage types. We only detected the effect of repeat motif on ADO and FA rates. The lower ADO and FA rates were obtained from tri- and tetra-nucleotide loci. We suggest that freezing should not be used for giant panda fecal preservation in microsatellite studies, and EtOH and the 2-step storage medium should be chosen on priority for long-term storage. We recommend candidate microsatellite loci with longer repeat motif to ensure greater genotyping success for giant panda fecal studies.https://peerj.com/articles/3358.pdfGiant pandaMicrosatellite fragment lengthLong-term fecal DNA storageMicrosatellite base pair repeat unitStorage timeStorage type |
| spellingShingle | Ying Zhu Hong-Yi Liu Hai-Qiong Yang Yu-Dong Li He-Min Zhang Factors affecting genotyping success in giant panda fecal samples PeerJ Giant panda Microsatellite fragment length Long-term fecal DNA storage Microsatellite base pair repeat unit Storage time Storage type |
| title | Factors affecting genotyping success in giant panda fecal samples |
| title_full | Factors affecting genotyping success in giant panda fecal samples |
| title_fullStr | Factors affecting genotyping success in giant panda fecal samples |
| title_full_unstemmed | Factors affecting genotyping success in giant panda fecal samples |
| title_short | Factors affecting genotyping success in giant panda fecal samples |
| title_sort | factors affecting genotyping success in giant panda fecal samples |
| topic | Giant panda Microsatellite fragment length Long-term fecal DNA storage Microsatellite base pair repeat unit Storage time Storage type |
| url | https://peerj.com/articles/3358.pdf |
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