Genetic Variation and Signatures of Selection in the Genomes of Kenyan Indigenous Chicken and Commercial Layers

Breeding of indigenous chicken in developing countries is mainly done by the resource-poor rural households that raise birds in a scavenging system characterized by low inputs, adverse climatic conditions and high disease pressure. As a result, indigenous chicken may have developed specific genetic adaptations for such challenging environments. In this study, genomic variation of indigenous chicken kept under low input production systems was assessed using autosomal microsatellite markers and whole genome re-sequence data. Indigenous chickens were further compared to high input commercial layers to identify selection signatures and candidate mutations that may explain the phenotypic divergence between these populations. Commercial layers had much lower nucleotide diversity (0.31 - 0.36) than indigenous chicken (0.58 - 0.62). We also identified up to 59 genomic regions with high Fst values (0.44 - 0.85) between indigenous and commercial chickens, overlapping 16 genes. Five genes (SLC26A8, BRPF3, MAPK13, PDIA4 and MRPL32) out of the 16 are associated with the missense variants that could explain partially the phenotypic divergence between these populations. Differently to commercial chickens, indigenous chickens preserved a high genomic variability that may be important, for addressing present and future challenges associated with adaptability to the environment and to cope with farmers breeding goals.