Populations
Individuals from three Chinese indigenous breeds were selected fromin situ and ex situ conserved populations (361 total, consisting of 120 Beijing You chickens, 120 Baier Yellow chickens, and 121 Langshan chickens). Of these, 270 chickens (representing three successive conserved generations from an ex situ conserved population) had been used in our previous study (Zhang et al., 2018). The three breeds originate from three different regions within China (see sampling information in Table 1 and Figure 1). The mating systems used in the two conservation systems differ (R:R for in situ and R:F for ex situ (Zhang et al., 2018)). In addition, the in situ conserved chickens have been subjected to conservation for a longer time, and have a larger population size relative to the ex situ chickens.
Blood samples were collected from the wing vein and stored at −20°C. We used the Qiagen DNeasy Tissue kit (Qiagen, Germany) to extract genomic DNA from blood, and verified the integrity and purity of DNA by agarose gel electrophoresis and optical density (A260/A280 ratio). 3 μg of high-quality DNA was used to construct sequencing libraries for each sample.