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.