Conservation Genetics Resources

, Volume 7, Issue 3, pp 635–638 | Cite as

A novel multiplex PCR assay for individual identification in the vulnerable Chinese Egret (Egretta eulophotes) using molted feathers

Technical Note
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Abstract

Noninvasive DNA may be used in individual identification for counting or tracking animals. Here a multiplex PCR assay, in which 16 highly polymorphic microsatellite markers were chosen and allocated into four multiplex PCR panels, was described for the individual identification of the Chinese Egret (Egretta eulophotes) using molted feathers. In this study, the combined exclusion probability for unrelated individuals (PID) and for individuals with sibling relationship (PID(sib)) were 7.02 × 10−19 and 2.9 × 10−7, respectively. Molted feathers (n = 59) of E. eulophotes amplified by more than 7 loci were unambiguously identified as 43 different individuals (32 females and 11 males). The results indicated that our newly developed assay could be used for noninvasive individual identification in the vulnerable Chinese Egret and other Ardeids.

Keywords

Multiplex PCR Microsatellite genotyping Individual identification Noninvasive DNA Egret 

Notes

Acknowledgments

We thank Wei Lei, Site Luo, Leiguan Li and Changfu Mao who helped collect some samples for this study. This research was supported by the National Natural Science Foundation of China (Grant Nos. 41476113, 31000963 and 31272333) and by the Fujian Natural Science Foundation of China (2010Y2007 and 2012J01149).

Supplementary material

12686_2015_464_MOESM1_ESM.doc (2.9 mb)
Supplementary material 1 (DOC 2987 kb)

References

  1. Dai Y, Zhou X, Fang W, Lin Q, Chen X (2013) Development and cross-species transferability of 23 microsatellite markers from the vulnerable Chinese Egret (Egretta eulophotes) using 454 sequencing. Conserv Genet Resour 5:1035–1038. doi: 10.1007/s12686-013-9962-0 CrossRefGoogle Scholar
  2. Hill A, Green MC (2011) Characterization of 12 polymorphic microsatellites for the Reddish Egret, Egretta rufescens. Conserv Genet Resour 3:13–15. doi: 10.1007/s12686-010-9267-5 CrossRefGoogle Scholar
  3. Horvâth MB, Martìnez CB, Negro JJ, Kalmâr L, Godoy JA (2005) An overlooked DNA source for non-invasive genetic analysis in birds. J Avian Biol 36:84–88. doi: 10.1111/j.0908-8857.2005.03370.x CrossRefGoogle Scholar
  4. Huang X, Zhou X, Chen M, Fang W, Chen X (2010) Isolation and characterization of microsatellite loci in vulnerable Chinese Egret (Egretta eulophotes: Aves). Conserv Genet 11:1211–1214. doi: 10.1007/s10592-009-9921-1 CrossRefGoogle Scholar
  5. Huang X, Zhou X, Lin Q, Peng Z, Fang W, Chen X (2012) A novel multiplex PCR assay for species identification in the Chinese Egret (Egretta eulophotes) and Little Egret (E. garzetta). Conserv Genet Resour 4:31–33. doi: 10.1007/s12686-011-9466-8 CrossRefGoogle Scholar
  6. Isabel Miño C, Nassif Del Lama S (2009) Molted feathers as a source of DNA for genetic studies in waterbird populations. Waterbirds 32:322–329. doi: 10.1675/063.032.0212 CrossRefGoogle Scholar
  7. IUCN (2014) IUCN red list of threatened species. http://www.iucnredlist.org/. Accessed 7 October 2014
  8. Johansson MP, Mcmahon BJ, Höglund J, Segelbacher G (2012) Amplification success of multilocus genotypes from feathers found in the field compared with feathers obtained from shot birds. Ibis 154:15–20. doi: 10.1111/j.1474-919X.2011.01194.x CrossRefGoogle Scholar
  9. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106. doi: 10.1111/j.1365-294X.2007.03089.x CrossRefPubMedGoogle Scholar
  10. Oosterhout VC, Hutchinson WF, Wills DP, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538. doi: 10.1111/j.1471-8286.2004.00684.x CrossRefGoogle Scholar
  11. Rousset F (2008) GENEPOP’ 007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8:103–106. doi: 10.1111/j.1471-8286.2007.01931.x CrossRefPubMedGoogle Scholar
  12. Rudnick JA, Katzner TE, Bragin EA, Rhodes OE, Dewoody JA (2005) Using naturally shed feathers for individual identification, genetic parentage analyses, and population monitoring in an endangered Eastern imperial eagle (Aquila heliaca) population from Kazakhstan. Mol Ecol 14:2959–2967. doi: 10.1111/j.1365-294X.2005.02641.x CrossRefPubMedGoogle Scholar
  13. Segelbacher G (2002) Noninvasive genetic analysis in birds: testing reliability of feather samples. Mol Ecol Notes 2:367–369. doi: 10.1046/j.1471-8286.2002.00180.x Google Scholar
  14. Shen Z, Qu W, Wang W, Lu Y, Wu Y, Li Z, Zhang C (2010) MPprimer: a program for reliable multiplex PCR primer design. BMC Bioinform 11:143. doi: 10.1186/1471-2105-11-143 CrossRefGoogle Scholar
  15. Wang Z, Zhou X, Lin Q, Fang W, Chen X (2011) New primers for sex identification in the Chinese Egret and other Ardeid species. Mol Ecol Resour 11:176–179. doi: 10.1111/j.1755-0998.2010.02879.x CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  1. 1.Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems,School of Life SciencesXiamen UniversityXiamenPeople’s Republic of China
  2. 2.Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and EcologyXiamen UniversityXiamenPeople’s Republic of China

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