Identification of Candidate Genes Under Selection and Gene Annotation
Candidate genes under selection were determined using an outlier approach where SNPs above the cutoff value were highly considered (Wang et al., 2018). The 99th percentile of the observed genome-wide distribution of all standardized iHS values and CLR values was used as the threshold to identify outliers. SNPs that met the threshold and were located within a 250 kb window were highly considered and used to determine candidate genes under positive selection.
The annotation of the candidate regions was based on the Japanese quail genome assembly (Accession number GCF_001577835.1) from NCBI. Gene Ontology (GO) terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways identification was performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) version 6.8 browser tool (Huang et al., 2009) and Metascape v3.5.20230101 (Zhou et al., 2019). The biological significance of the enriched terms and pathways was considered if P < 0.05 .