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

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.

Genetic Diversity of MHC B-F/B-L Region in 21 Chicken Populations

“…In this study, we conducted target enrichment sequencing to evaluate the polymorphism in the BF/BL region of 21 diverse chicken populations. Our capture efficiency was 99%, which was higher than a previous study in turkey (capture efficiency 53%) using a custom MHC SureSelect capture array (Reed et al, 2016). The average depth of our data in the target region reached about 200×, and the coverage of target region with more than 30× were 55 kb on average.…”

Profiling the immunome of little brown myotis provides a yardstick for measuring the genetic response to white‐nose syndrome

“…GBS assays involve enriching for genomic subsets of DNA via restriction enzyme‐, amplicon‐, or hybridization‐based methods (Jones & Good, ), conducting high‐throughput sequencing and identifying single nucleotide polymorphisms (SNPs). Targeted approaches, including amplicon‐ and hybridization‐based GBS, have been used in wildlife studies to identify SNPs in specific coding and regulatory regions of immune genes, collectively called the “immunome.” Targeted GBS can identify population‐level immunogenetic shifts in response to pathogens, and has been applied to a range of species, including the Tasmanian devil ( Sarcophilus harrisii ; Morris, Wright, Grueber, Hogg, & Belov, ), turkey ( Meleagris gallopavo ; Reed, Mendoza, & Settlage, ), gray wolf ( Canis lupus ; Schweizer et al., ), thinhorn sheep ( Ovis dalli ; Roffler et al., ), and red fox ( Vulpes vulpes ; Donaldson et al., unpublished). GBS is an attractive option for understanding the impacts of WNS on immunogenetic diversity in bat populations, because it allows accurate characterization of diversity at duplicated loci, and cost‐effective targeting of multiple, relevant genes.…”