Genomic Regions associated with Necrotic Enteritis Resistance in Fayoumi and White Leghorn Chickens

In this study, we used two breeds of chicken to identify genomic regions corresponding to necrotic enteritis (NE) resistance. We scanned the genomes of a resistant and susceptible line of Fayoumi and White Leghorn chickens (20 birds/line) using a chicken 60 K Illumina SNP panel. A total of 235 loci with divergently fixed alleles were identified across the genome in both breeds; particularly, several clusters of multiple loci with fixed alleles were found in five narrow regions. Moreover, consensus 15-SNP haplotypes that were shared by the resistant lines of both breeds were identified on chromosomes 3, 7 and 9. Genes responsible for NE resistance were identified in chicken lines selected for resistance and susceptibility. Annotation of the regions spanning clustered divergently fixed regions revealed a set of interesting candidate genes such as phosphoinositide-3-kinase, regulatory subunit 5, p101 (PIK3R5) and inositol 1,4,5-trisphosphate receptor 1 (ITPR1), which participate in immune response. Consensus haplotypes were found in regions containing possibly relevant genes, such as myostatin and myosin, which play important roles in muscle development. Thus, genome scans of divergent selection in multiple chicken lines and breeds can be used to identify genomic regions associated with NE resistance.