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Detailed characterization of repeat motifs of nine canid microsatellite loci in African painted dogs (Lycaon pictus)

  • Cassandra Miller-ButterworthEmail author
  • Karen Vacco
  • Kenneth Kaemmerer
  • Joseph Gaspard
Short Communication
  • 15 Downloads

Abstract

Microsatellite loci identified in domestic species are frequently amplified and genotyped in wildlife species for which limited genomic information is available. However, even when the loci amplify successfully, genotyping them accurately in novel species can be complicated when the repeat motif is unknown or when the expected product size in the new target species differs from that reported for the domestic species from which the locus was identified. In this study, we amplified nine microsatellite loci that were identified previously in the domestic dog and genotyped them in 114 endangered African painted dog (Lycaon pictus) individuals. Although primer sequences for these loci were published, minimal details about the repeat motifs were available in the literature, and some of our product sizes differed substantially from those reported for the domestic dog, which complicated initial multiplexing and genotyping efforts. We therefore cloned and sequenced these loci to characterize the repeat structures and amplicon size for each locus, specific to L. pictus. Seven of the nine loci contained imperfect, compound repeats that often were a combination of di- and tetranucleotide repeats or which contained strings of single nucleotides. The resulting amplicons were also considerably smaller or larger than expected based on the homologous domestic dog loci. This information may assist other researchers who are conducting molecular studies on this endangered species or on other closely related canids.

Keywords

African wild dog Short tandem repeats Canidae Genotyping Endangered species 

Notes

Acknowledgments

Lycaon pictus samples were provided by the Pittsburgh Zoo & PPG Aquarium and by 32 other zoological organizations in the USA.

Funding information

Funding for this project was provided by the Pittsburgh Zoo & PPG Aquarium and by Penn State Beaver.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical statement

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed. All procedures performed were in accordance with the ethical standards of the Pennsylvania State University (IACUC No. 46117) and of the Pittsburgh Zoo & PPG Aquarium.

References

  1. Adams JR, Waits LP (2007) An efficient method for screening faecal DNA genotypes and detecting new individuals and hybrids in the red wolf (Canis rufus) experimental population area. Conserv Genet 8:123–131CrossRefGoogle Scholar
  2. Bohling JH, Waits LP (2011) Assessing the prevalence of hybridization between sympatric Canis species surrounding the red wolf (Canis rufus) recovery area in North Carolina. Mol Ecol 20:2142–2156CrossRefGoogle Scholar
  3. Breen M, Jouquand S, Renier C et al (2001) Chromosome-specific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/linkage map of the domestic dog genome to all chromosomes. Genome Res 11:1784–1795CrossRefGoogle Scholar
  4. Casas-Marce M, Soriano L, Opez-Bao JVL (2013) Genetics at the verge of extinction: insights from the Iberian lynx. Mol Ecol 22:5503–5515CrossRefGoogle Scholar
  5. Croteau EK, Heist EJ, Nielsen CK, Hutchinson JR, Hellgren EC (2012) Microsatellites and mitochondrial DNA reveal regional population structure in bobcats (Lynx rufus) of North America. Conserv Genet 13:1637–1651CrossRefGoogle Scholar
  6. Culver M, Johnson WE, Pecon-Slattery J, O’Brien SJ (2000) Genomic ancestry of the American Puma (Puma concolor). J Hered 91(3):186–197CrossRefGoogle Scholar
  7. Diefenbach D, Hansen L, Bohling J, Miller-Butterworth C (2015) Population and genetic outcomes 20 years after reintroducing bobcats (Lynx rufus) to Cumberland Island, Georgia USA. Ecol Evol 5(21):4885–4895CrossRefGoogle Scholar
  8. Eichmann C, Berger B, Parson W (2006) Relevant aspects for forensic STR analysis of canine DNA: repeat-based nomenclature and sensitive PCR multiplexes. Int Congr Ser 1288:813–815CrossRefGoogle Scholar
  9. Engel SR, Linn RA, Taylor JF, Davis SK (1996) Conservation of microsatellite loci across species of artiodactyls: implications for population studies. J Mammal 77:504–518CrossRefGoogle Scholar
  10. Fernández ME, Goszczynski DE, Lirón JP, Villegas-Castagnasso EE, Carino MH, Ripoli MV, Rogberg-Muñoz A, Posik DM, Peral-García P, Giovambattista G (2013) Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd. Genet Mol Biol 36:185–191CrossRefGoogle Scholar
  11. Francisco LV, Langston AA, Mellersh CS, Neal CL, Ostrander EA (1996) A class of highly polymorphic tetranucleotide repeats for canine genetic mapping. Mamm Genome 7:359–362CrossRefGoogle Scholar
  12. Guichoux E, Lagache L, Wagner S et al (2011) Current trends in microsatellite genotyping. Mol Ecol Resour 11:591–611CrossRefGoogle Scholar
  13. Guyon R, Lorentzen TD, Hitte C, Kim L, Cadieu E, Parker HG, Quignon P, Lowe JK, Renier C, Gelfenbeyn B, Vignaux F, DeFrance HB, Gloux S, Mahairas GG, Andre C, Galibert F, Ostrander EA (2003) A 1-Mb resolution radiation hybrid map of the canine genome. P Natl Acad Sci 100:5296–5301CrossRefGoogle Scholar
  14. Haynes GD, Latch EK (2012) Identification of novel single nucleotide polymorphisms (SNPs) in deer (Odocoileus spp.) using the BovineSNP50 BeadChip. PLoS One 7:e36536CrossRefGoogle Scholar
  15. Marsden CD, Woodroffe R, Mills MGL et al (2012) Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus). Mol Ecol 21(6):1379–1393CrossRefGoogle Scholar
  16. Marsden CD, Verberkmoes H, Thomas R, Wayne EK, Mable BK (2013) Pedigrees, MHC and microsatellites: an integrated approach for genetic management of captive African wild dogs (Lycaon pictus). Conserv Genet 14(1):171–183CrossRefGoogle Scholar
  17. Neff MW, Broman KW, Mellersh CS, Ray K, Acland GM, Aguirre GD, Ziegle JS, Ostrander EA, Rine J (1999) A second-generation genetic linkage map of the domestic dog, Canis familiaris. Genetics 151:803–820Google Scholar
  18. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539CrossRefGoogle Scholar
  19. Tensen L, Groom RJ, van Belkom J, Davies-Mostert HT, Marnewick K, Jansen van Vuuren B (2016) Genetic diversity and spatial genetic structure of African wild dogs (Lycaon pictus) in the Greater Limpopo Transfrontier conservation area. Conserv Genet 17:785–794CrossRefGoogle Scholar

Copyright information

© Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland 2019

Authors and Affiliations

  1. 1.Penn State BeaverMonacaUSA
  2. 2.Pittsburgh Zoo & PPG Aquarium, One Wild PlacePittsburghUSA

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