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Characterization of SNP markers for the painted bunting (Passerina ciris) and their relevance in population differentiation and genome evolution studies

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Abstract

We developed nuclear single nucleotide polymorphism (SNP) markers for the Painted Bunting (Passerina ciris) using next-generation sequencing genotyping on the Illumina HiSeq4000 platform. Following the best-RAD approach, we sequenced 96 individuals from five breeding populations occurring in the United States. We assessed the discerning power of 105,000 SNPs and confirmed the quality of these markers in population differentiation studies. We detected outlier SNPs within or near protein coding genes, including sequences coding for olfactory receptors which may relate to migratory navigation. Finally, we provide a novel list of 33 primer pairs flanking SNPs to link individuals to regional populations and improve our understanding of the evolution of this migratory songbird.

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Acknowledgements

We thank Ann Harris (OU), Jasmine Rajbhandary (UCLA), and the Supercomputing Center for Education and Research (OSCER) at the University of Oklahoma. We thank OSCER Director Henry Neeman and OSCER System Analyst Jason Speckman for their valuable support. Tyler Michels provided valuable help with sample collection. This research was funded by the National Science Foundation (grants nos. IDBR 1014891 and DEB 0946685) and by the United States Department of Agriculture (grant no. NIFA-AFRI-003536).

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Authors and Affiliations

  1. Oklahoma Biological Survey, University of Oklahoma, 111 East Chesapeake Street, SC Building 134, Norman, OK, 73019, USA

    Andrea Contina, Jeffrey F. Kelly & Eli S. Bridge

  2. Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles 619 Charles E. Young Dr. East, La Kretz Hall, Suite 300, Box 951496, Los Angeles, CA, 90095-1496, USA

    Rachael A. Bay, Vinh Le Underwood, Thomas B. Smith & Kristen C. Ruegg

  3. Department of Ecology and Evolutionary Biology, University of California, Los Angeles 610 Charles E. Young Drive East Terasaki Life Sciences Building, Room 4155, Box 957239, Los Angeles, CA, 90095-7239, USA

    Vinh Le Underwood & Thomas B. Smith

  4. Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA

    Jeffrey F. Kelly

  5. Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95064, USA

    Kristen C. Ruegg

Authors
  1. Andrea Contina
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  2. Rachael A. Bay
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  3. Vinh Le Underwood
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  4. Thomas B. Smith
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  5. Jeffrey F. Kelly
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  6. Eli S. Bridge
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  7. Kristen C. Ruegg
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Corresponding author

Correspondence to Andrea Contina.

Additional information

Data Accessibility The data used in this study are accessible at GenBank (probe accessions Pr032826547 - Pr032826579).

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Contina, A., Bay, R.A., Le Underwood, V. et al. Characterization of SNP markers for the painted bunting (Passerina ciris) and their relevance in population differentiation and genome evolution studies. Conservation Genet Resour 11, 5–10 (2019). https://doi.org/10.1007/s12686-017-0950-7

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  • DOI: https://doi.org/10.1007/s12686-017-0950-7

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