RESULTS

After quality control, 95 individuals (76 wild African harlequin quails and 19 domestic Japanese quails) with 499,461 SNPs were retained for further analysis. The wild African harlequin and domestic Japanese quail datasets had 8,024 and 491,441 SNPs, respectively.

Signatures of selection detection using CLR approach

Genome-wide selection signatures were detected using the composite likelihood ratio statistical approach in wild African harlequin and domestic Japanese quails. Potential candidate regions under selection were identified with outliers that fell into the 99th percentile of CLR values distribution in wild African harlequin (CLR > 1.39) and domestic Japanese (CLR > 8.33) quails. Wild African harlequin quail chromosomes 1 and 2 had the highest number of significant CLR values (Figure 1). In contrast, outliers were observed in most Japanese quail chromosomes except chromosomes 10 and 12 (Figure 2). 252 and 424 potential candidate genes were identified across 28 autosomes in wild African harlequin and Japanese quails, respectively.
Figure 1. Manhattan plot showing CLR values distribution across all wild African harlequin quail autosomes. The red line indicates the 99th percentile threshold.
In wild African harlequin quails, functional analysis of the candidate genes showed an association with key biological processes, metabolic pathways, and molecular functions. Wild African harlequin quail candidate genes were implicated in melanogenesis (FZD7, WNT5A, WNT8B, LOC107320948, WNT3, WNT4), Wnt signaling pathway (PPP3R1, FZD7, WNT5A, WNT8B, WNT3, NKD1, WNT4), follicle-stimulating hormone signaling pathway (FSHB, FSHR), ear morphogenesis (SOX2, PTPN11, PROX1), positive regulation of skeletal muscle satellite cell proliferation (HGF, GPC1), among others (see Supporting Information Table S1). Enrichment analysis of the candidate genes revealed cluster groups with enriched terms such as behavior (GO:0007610), brain and sensory organ development (GO:0007420; GO:0007423), inner ear development (GO:0048839), response to growth factor (GO:0070848), regulation of MAPK cascade (GO:0043408), cell morphogenesis (GO:0000902), gliogenesis and glial cell differentiation (GO:0042063, GO:0010001), and tissue morphogenesis (GO:0048729).
Figure 2. Manhattan plot showing CLR values distribution across all domestic Japanese quail autosomes. The red line indicates the 99th percentile threshold.
Some of the top enrichment clusters identified in domestic Japanese quail include cell morphogenesis (GO:0000902), regulation of transmembrane transport (GO:0034762), embryonic morphogenesis (GO:0048598), focal adhesion (GO:0005925), negative regulation of cellular component organization (GO:0051129), platelet activation, signaling and aggregation (GO:0030168), regulation of cell growth (GO:0001558), heart development (GO:0007507), cell-cell adhesion (GO:0098609), mesenchymal cell differentiation (GO:0048762) and brain development (GO:0007420), among others (see Supporting Information Table S2). Key domestic Japanese quail candidate genes identified include VIPR2, RAC1, COL6A3, SLC9A1, MSX2, and PRF1.

Signatures of selection detection using the iHS approach

The standardized iHS values were used to identify genomic regions that showed signatures of selection patterns. Outliers that fell into the 99th percentile in domestic Japanese (|iHS| > 3.2) and wild African harlequin (|iHS| > 3.55) quails were considered to be potential candidate regions under selection. Chromosome 2 had the highest number of outlier SNPs in wild African harlequin quail (Figure 3), whereas, in domestic Japanese quails, outlier SNPs numbers were high in all chromosomes (Figure 4). 150 and 457 potential candidate genes were detected across 28 autosomes in wild African harlequin and domestic Japanese quails, respectively.
Enrichment analysis of the wild African harlequin quail candidate genes showed their association with platelet activation (MAPK14, ITGB3, MAPK13), hematopoietic cell lineage (LOC107324620, ITGB3, LOC107317826), Th1 and Th2 cell differentiation (MAPK14, LOC107317826, MAPK13), Th17 cell differentiation (MAPK14, LOC107317826, MAPK13), adrenergic signaling in cardiomyocytes (CREB1, MAPK14, MAPK13, PPP1CA), among others. Key enrichment terms include focal adhesion (GO:0005925), regulation of secretion (GO:0051046), olfactory transduction (GO:0004984), actin binding, and cytoskeleton organization (GO:0003779; GO:0030036), Osteoclast differentiation (GO:0030316), negative regulation of transcription by competitive promoter binding (GO:0010944), and the regulation of peptidyl-tyrosine phosphorylation (GO:0050730), among others (see Supporting Information Table S3).
Figure 3. Manhattan plot showing standardized iHS values distribution across all wild African harlequin quail autosomes. The red line indicates the 99th percentile threshold.
Some of the top enriched clusters of the domestic Japanese quail candidate genes include the regulation of lipid metabolic process (GO:0019216), cholesterol transport (GO:0030301), spermatogenesis (GO:0007283), cell proliferation (GO:0008283), phagosome (GO:0045335), the intestinal immune network for IgA production (GO:0002387), antigen processing and presentation (GO:0019882), autoimmune thyroid disease (cjo05320), and Th1 and Th2 cell differentiation (GO: 0045063, GO:0045064), among others (see Supporting Information Table S4). Key candidate genes involved in crucial biological processes of the domestic Japanese quail include DYNLL2 and genes from the APOA, ABCA, G12/G13 gene families.
Figure 4. Manhattan plot showing standardized iHS values distribution across all domestic Japanese quail autosomes. The red line indicates the 99th percentile threshold.