Abstract Despite recent progresses, the driving force of evolution and domestication of chickens remains poorly understood. To fill this gap, we recently sequenced and assembled genomes of four distinct indigenous chickens from Yunnan, China. Unexpectedly, we found large numbers of pseudogenes which have lost their functions and are fixed in their corresponding populations, and we also found highly variable proteomes in the genomes of the four indigenous chickens as well as the sequenced wild red jungle fowl (RJF) (GRCg6a). Although the four indigenous chicken breeds are closely related to the G. g. spadiceous subspecies, for the first time, we found that the RJF (GRCg6a) is of the G. g. bankiva origin. Thus, the five chicken share the most recent common ancestor (MRCA) before subspeciation. Our results support a scenario that the MRCA of the four indigenous chickens and the RJF possessed at least 21,972 genes, of which 7,993 are dispensable. Each chicken has lost functions of thousands of the dispensable genes during their evolution and domestication via complete gene loss and pseudogenization. The occurring pattens of completely lost genes and pseudogenes segregate the chickens as their phylogenetic tree does. Therefore, loss-of-function mutations might play important roles in chicken evolution and domestication.

Large scale loss-of-function mutations during chicken evolution and domestication