Adaptation analysis
Results from the population structure and fixation index (FST ) analyses show that all three chicken breeds exhibit genetic differentiation between the in situ and ex situ conserved populations. Since climate and living conditions differ between the populations maintained in in situ and ex situprograms, we hypothesized that genetic adaptation has occurred in response to these changes. Livestock populations that have adapted to different environmental niches (known as ecotypes) cannot always be distinguished easily by phenotype. In order to detect the signals of genetic differentiation, we determinedFST , Pi, and XP-EHH in 100 kb windows across the genome in the three chicken breeds (Figure 8). Candidates were defined as regions with signals that ranked in the uppermost 5% of values. In order to decrease the number of false positives, only regions identified by all three methods were retained in the final list of positive selection candidates. 186, 212, and 161 candidate regions were obtained for the three chicken breeds, Beijing You chicken, Langshan chicken, and Baier Yellow chicken, respectively (Table S7). Genes that may have experienced selection and adaptation were identified in the regions by comparison with annotated sequences. Protein-coding genes with highFST values (3719 genes), XP-EHH values (4435 genes), and θπ ratios (2504 genes) were identified in Beijing You chickens. Of these genes, 857 were identified by all three methods (Figure S5(a)). Figures S5b and S5c shows the corresponding results for Baier Yellow chickens and Langshan chickens, respectively. Clusterprofiler (Yu et al., 2012) was used to conduct Gene Ontology (GO) and KEGG pathway analyses to investigate potential functions associated with the candidate genes. Significantly enriched GO terms and KEGG pathways are shown in Figure S6.