Use Of a Capture Platform For Target Enrichment and Massively Parallel Sequencing To Assess Variation In The Turkey MHC

Locus remodeling (gene rearrangement) and copy number variation (CNV) within the Major Histocompatibility Complex (MHC) are increasingly identified as having significant impact on disease susceptibility/resistance.  Although our knowledge of the MHC of the turkey (Meleagris gallopavo) has increased dramatically, we have not addressed these potentially important components of MHC variation.  The directionality of locus remodeling and the significance of CNV can only be determined by the comparison of sequences within species in the context of between-species variation. This study investigates locus remodeling and CNV within the turkey MHC using a high-throughput sequencing  approach.  An MHC-specific SureSelect capture array (Agilent) was developed for comparative sequencing of turkeys from diverse genetic backgrounds.  Libraries were created for 14 turkeys (domestic, heritage and wild birds), an Ocellated turkey, and a chicken (RJF-256).  Libraries were hybridized to over 12K baits (120 bp) and the resulting pools were sequenced on the Illumina MiSeq platform (151 PE) producing an average of 439K paired reads per library.  Results of the sequence analysis and variant discovery are presented.