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

  • Andrea Contina
  • Rachael A. Bay
  • Vinh Le Underwood
  • Thomas B. Smith
  • Jeffrey F. Kelly
  • Eli S. Bridge
  • Kristen C. Ruegg
Technical Note

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.

Keywords

SNPs development Painted Bunting Illumina HiSeq4000 Protein coding regions Olfactory receptors Songbird migration 

Notes

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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Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2017

Authors and Affiliations

  1. 1.Oklahoma Biological SurveyUniversity of OklahomaNormanUSA
  2. 2.Center for Tropical Research, Institute of the Environment and SustainabilityUniversity of CaliforniaLos AngelesUSA
  3. 3.Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesUSA
  4. 4.Department of BiologyUniversity of OklahomaNormanUSA
  5. 5.Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzUSA

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