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.