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Analyzing sequence variants of two divergent and highly inbred Fayoumi and Leghorn chicken lines allows for examination of the genomic factors underlying phenotypic dissimilarity between breeds. Pooled resequence data using sixteen birds per breed were analyzed to characterize the genetic differences inherent in the two breeds. Downstream analysis by FST to discern population differences and subsequent GSEA elucidated major genetic differences between the two lines. Gene ontology annotations for over-enriched terms for Fayoumi and Leghorn related to breed-characteristic traits of pathogen resistance and reproductive ability when examined for between and within line variants, respectively. Ontology terms having the highest level of differentiation between the lines appear to group into metabolic processes, with GO terms over-enriched for immune system process, sexual reproduction, and growth. Variant analysis of the lines elucidated GO functions indicative of breed-predominant phenotypes.

SNP Discovery and Genomic Architecture of Highly Inbred Leghorn and Fayoumi Chicken Breeds Using Whole Genome Resequencing