Targeted capture enrichment and sequencing identifies extensive nucleotide variation in the turkey MHC-B

Kent M. Reed, Kristelle M. Mendoza, Robert E. Settlage

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

Variation in the major histocompatibility complex (MHC) is increasingly associated with disease susceptibility and resistance in avian species of agricultural importance. This variation includes sequence polymorphisms but also structural differences (gene rearrangement) and copy number variation (CNV). The MHC has now been described for multiple galliform species including the best defined assemblies of the chicken (Gallus gallus) and domestic turkey (Meleagris gallopavo). Using this sequence resource, this study applied high-throughput sequencing to investigate MHC variation in turkeys of North America (NA turkeys). An MHC-specific SureSelect (Agilent) capture array was developed, and libraries were created for 14 turkeys representing domestic (commercial bred), heritage breed, and wild turkeys. In addition, a representative of the Ocellated turkey (M. ocellata) and chicken (G. gallus) was included to test cross-species applicability of the capture array allowing for identification of new species-specific polymorphisms. Libraries were hybridized to ∼12 K cRNA baits and the resulting pools were sequenced. On average, 98 % of processed reads mapped to the turkey whole genome sequence and 53 % to the MHC target. In addition to the MHC, capture hybridization recovered sequences corresponding to other MHC regions. Sequence alignment and de novo assembly indicated the presence of several additional BG genes in the turkey with evidence for CNV. Variant detection identified an average of 2245 polymorphisms per individual for the NA turkeys, 3012 for the Ocellated turkey, and 462 variants in the chicken (RJF-256). This study provides an extensive sequence resource for examining MHC variation and its relation to health of this agriculturally important group of birds.

Original languageEnglish (US)
Pages (from-to)219-229
Number of pages11
JournalImmunogenetics
Volume68
Issue number3
DOIs
StatePublished - Mar 1 2016

Bibliographical note

Funding Information:
The authors thank Kevin Willis, Minnesota Zoo and Chris Brown, Dallas Zoo for assistance in obtaining blood samples of Ocellated turkey; Ed Smith (VT) and Karen Mock (USU) for supplying Heritage and wild turkey DNA; and Jerry Dodgson (MSU) for supplying chicken DNA (RJF-256). This study was funded in part by the University of Minnesota Agricultural Experiment Station. The authors acknowledge the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing resources that contributed to the research results reported within this paper.

Publisher Copyright:
© 2016, Springer-Verlag Berlin Heidelberg.

Keywords

  • BG
  • CNV
  • Capture array
  • MHC
  • Turkey

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