Skip to main content
SpringerLink
Log in

Development of eighteen novel microsatellite loci for Masked Bobwhite, Colinus virginianus ridgwayi

  • Short Communication
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

Background

Masked Bobwhite (Colinus virginianus ridgwayi) is a critically-endangered New World quail species endemic to Sonoran Desert grasslands of North America. It suffered severe population declines during the nineteenth and twentieth centuries, with its persistence now reliant upon a captive breeding program that requires careful genetic management to maintain extant genetic diversity. Although nuclear microsatellite DNA markers existed for the closely related Northern Bobwhite (C. virginianus), none were available for Masked Bobwhite to inform necessary management decisions.

Methods and results

Paired-end Illumina© sequencing was conducted to screen the Masked Bobwhite genome for microsatellite loci. We identified 18 loci exhibiting high polymorphism and limited deviations from genetic equilibrium expectations. These loci were amplified in 78 individuals. Familial relationships were reconstructed via sibship methods and compared to manually-curated pedigree data. Thirteen of fifteen full-sibling groups in the pedigree were exactly reconstructed (86.6%). Three other full-sibling groups partially matched pedigree relationships with high statistical confidence, and likely represented pedigree inaccuracies. Four additional full-sibling pairs were identified with low statistical confidence and likely resulted from analytical artifacts.

Conclusions

The novel microsatellite loci accurately reconstructed parent–offspring and sibling relationships. These loci will be useful for guiding genetic management decisions and identifying pedigree inaccuracies in the captive breeding program.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

© data. Repeat motif lengths are measured in base pairs (bp). Counts for specific microsatellite motifs in (B) are provided only for motifs observed ≥ 100 times. All other motifs (N = 179) are counted in the ‘Others’ category

Data availability

The datasets generated and/or analyzed during the current study are available in the Open Science Framework repository, https://doi.org/https://doi.org/10.17605/OSF.IO/8NFE7.

References

  1. Lacy RC, Ballou JD, Pollak JP (2012) PMx: software package for demographic and genetic analysis and management of pedigreed populations. Methods Ecol Evol 3:433–437. https://doi.org/10.1111/j.2041-210X.2011.00148.x

    Article  Google Scholar 

  2. Moran BM, Thomas SM, Judson JM, et al (2021) Correcting parentage relationships in the endangered California condor: improving mean kinship estimates for conservation management. Ornithol Appl 123:duab17 https://doi.org/10.1093/ornithapp/duab017

  3. Bergner LM, Jamieson IG, Robertson BC (2014) Combining genetic data to identify relatedness among founders in a genetically depauperate parrot, the kakapo (Strigops habroptilus). Conserv Genet 15:1013–1020. https://doi.org/10.1007/s10592-014-0595-y

    Article  Google Scholar 

  4. Brown DE, Clark KB (2017) The saga of the masked bobwhite: lessons learned and unlearned. Natl Quail Symp Proc 8:404–415. https://doi.org/10.7290/nqsp08z7kl

    Article  Google Scholar 

  5. Hernández F, Kuvlesky WP Jr, DeYoung RW et al (2006) Recovery of rare species: case study of the Masked Bobwhite. J Wildl Manag 70:617–631

    Article  Google Scholar 

  6. Kuvlesky WP Jr, Gall SA, Dobrott SJ et al (2000) The status of masked bobwhite recovery in the United States and Mexico. Natl Quail Symp Proc 4:42–57. https://doi.org/10.7290/nqsp04jvm6

    Article  Google Scholar 

  7. Westemeier RL, Brawn JD, Simpson SA et al (1998) Tracking the long-term decline and recovery of an isolated population. Science 282:1695–1698. https://doi.org/10.1126/science.282.5394.1695

    Article  CAS  PubMed  Google Scholar 

  8. Meek MH, Larson WA (2019) The future is now: amplicon sequencing and sequence capture usher in the conservation genomics era. Mol Ecol Resour 19:795–803. https://doi.org/10.1111/1755-0998.12998

    Article  PubMed  Google Scholar 

  9. Puckett EE (2017) Variability in total project and per sample genotyping costs under varying study designs including with microsatellites or SNPs to answer conservation genetic questions. Conserv Genet Resour 9:289–304. https://doi.org/10.1007/s12686-016-0643-7

    Article  Google Scholar 

  10. Campbell NR, Harmon SA, Narum SR (2015) Genotyping-in-thousands by sequencing (GT-seq): a cost effective SNP genotyping method based on custom amplicon sequencing. Mol Ecol Resour 15:855–867. https://doi.org/10.1111/1755-0998.12357

    Article  CAS  PubMed  Google Scholar 

  11. Faircloth BC, Terhune TM, Schable NA et al (2009) Ten microsatellite loci from northern bobwhite (Colinus virginianus). Conserv Genet 10:535–538. https://doi.org/10.1007/s10592-008-9559-4

    Article  CAS  Google Scholar 

  12. Schable NA, Faircloth BC, Palmer WE et al (2004) Tetranucleotide and dinucleotide microsatellite loci from the northern bobwhite (Colinus virginianus). Mol Ecol Notes 4:415–419. https://doi.org/10.1111/j.1471-8286.2004.00670.x

    Article  CAS  Google Scholar 

  13. Castoe TA, Poole AW, de Koning APJ et al (2012) Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake. PLoS ONE 7:e30953. https://doi.org/10.1371/journal.pone.0030953

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3. Bioinformatics 23:1289–1291. https://doi.org/10.1093/bioinformatics/btm091

    Article  CAS  PubMed  Google Scholar 

  15. Untergasser A, Cutcutache I, Koressaar T et al (2012) Primer3—new capabilities and interfaces. Nucleic Acids Res 40:e115. https://doi.org/10.1093/nar/gks596

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Rousset F (2008) genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8:103–106. https://doi.org/10.1111/j.1471-8286.2007.01931.x

    Article  PubMed  Google Scholar 

  17. Wang J (2018) Effects of sampling close relatives on some elementary population genetics analyses. Mol Ecol Resour 18:41–54. https://doi.org/10.1111/1755-0998.12708

    Article  PubMed  Google Scholar 

  18. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538. https://doi.org/10.1111/j.1471-8286.2004.00684.x

    Article  CAS  Google Scholar 

  19. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539. https://doi.org/10.1093/bioinformatics/bts460

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Jones OR, Wang J (2010) COLONY: a program for parentage and sibship inference from multilocus genotype data. Mol Ecol Resour 10:551–555. https://doi.org/10.1111/j.1755-0998.2009.02787.x

    Article  PubMed  Google Scholar 

  21. Harrison HB, Saenz-Agudelo P, Planes S et al (2013) Relative accuracy of three common methods of parentage analysis in natural populations. Mol Ecol 22:1158–1170. https://doi.org/10.1111/mec.12138

    Article  PubMed  Google Scholar 

  22. Rodríguez-Ramilo ST, Wang J (2012) The effect of close relatives on unsupervised Bayesian clustering algorithms in population genetic structure analysis. Mol Ecol Resour 12:873–884. https://doi.org/10.1111/j.1755-0998.2012.03156.x

    Article  PubMed  Google Scholar 

  23. Mussmann SM, Douglas MR, Anthonysamy WJB et al (2017) Genetic rescue, the greater prairie chicken and the problem of conservation reliance in the Anthropocene. Roy Soc Open Sci. https://doi.org/10.1098/rsos.160736

    Article  Google Scholar 

  24. Douglas MR, Anthonysamy WJB, Mussmann SM et al (2020) Multi-targeted management of upland game birds at the agroecosystem interface in midwestern North America. PLoS ONE 15:e0230735. https://doi.org/10.1371/journal.pone.0230735

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Kayang BB, Inoue-Murayama M, Hoshi T et al (2002) Microsatellite loci in Japanese quail and cross-species amplification in chicken and guinea fowl. Genet Sel Evol 34:233. https://doi.org/10.1186/1297-9686-34-2-233

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank Buenos Aires National Wildlife Refuge staff, including R. Chester, P. O’Briant, and B. Radke for providing support. Southwestern ARRC staff provided laboratory and logistical support, especially N. Bertrand, T. Diver, M. Ulibarri, and G. York. Library preparation and sequencing was performed by S. Lance at the Savannah River Ecology Laboratory, University of Georgia. We also thank two anonymous reviewers for providing suggestions that improved the quality of our manuscript. The findings and conclusions in this article are those of the author(s) and do not necessarily represent the views of the U.S. Fish and Wildlife Service. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Funding

This work was supported by within-agency funding from the U.S. Fish and Wildlife Service.

Author information

Author notes

  1. Steven M. Mussmann

    Present address: Abernathy Fish Technology Center, U.S. Fish and Wildlife Service, 1440 Abernathy Creek Rd., Longview, WA, 98632, USA

Authors and Affiliations

  1. Southwestern Native Aquatic Resources and Recovery Center, U.S. Fish and Wildlife Service, 7116 Hatchery Rd., Dexter, NM, 88230, USA

    Steven M. Mussmann & Wade D. Wilson

Authors
  1. Steven M. Mussmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wade D. Wilson
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

All authors contributed to the study conception and design. Material preparation, data collection, and analysis were performed by Steven Mussmann. The first draft of the manuscript was written by Steven Mussmann and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Steven M. Mussmann.

Ethics declarations

Competing interests

The authors have no relevant financial or non-financial interests to disclose.

Ethical approval

Animal care and tissue sampling was carried out according to U.S. Fish and Wildlife Service policies. All work was carried out under U.S. Fish and Wildlife permit TE676811-0.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Mussmann, S.M., Wilson, W.D. Development of eighteen novel microsatellite loci for Masked Bobwhite, Colinus virginianus ridgwayi. Mol Biol Rep 51, 210 (2024). https://doi.org/10.1007/s11033-023-09094-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11033-023-09094-w

Keywords

Search

Navigation