Whole-genome sequencing revealed genetic diversity, structure and selection of Guizhou indigenous chickens

The eight phenotypically distinguishable indigenous chicken breeds in Guizhou are great resources for high-quality development of the poultry industry in China, however, most of their value and potential are yet to be discovered. To illustrate the genetic diversity, the relationship and population structure, and the genetic variation patterns shaped by selection in Guizhou indigenous chickens, we performed genome-wide analysis of 240 chickens from 8 phenotypically and geographically representative Guizhou chicken breeds and 60 chickens from 2 commercial breeds (one broiler and one layer), together with 10 red jungle fowls (RJF) genomes available from previous studies. As a result, Guizhou populations harbored higher genetic diversity than the commercial ones, but unequal polymorphisms were present among themselves. Population structure analysis remarkably mirrored the breeding history and geographical distribution of Guizhou indigenous chickens, nevertheless, some breeds with complex genetic structure did not group well into one cluster. Additionally, the mutual introgression within Guizhou chicken breeds and from commercial breeds were also confirmed. Selective sweep analysis revealed the selected candidate genes which were underlying specific and common phenotypic characteristics evolved rapidly after domestication in Guizhou local chicken breeds and economic traits (typically related to egg production performance, growth performance, and body size). This work will provide useful genetic information for further breeding strategy establishment, genetic basis detection (economically important traits), and effective conservation programs of domestic chicken resources formulation.