Mechanisms of early- and late-feathering in Qingyuan partridge chickens

Figures & data

Figure 1. Number of differentially expressed lncRNAs identified from each comparison.

Table 1. Overlapped lncRNAs among F1 vs. N1, F1 vs. L2, and L2 vs. N1.

lncRNAs	F1 vs. N1	L2 vs. N1	F1 vs. L2
107054950	Up	Up	Up
107053458	Up	Up	Up
101749149	Up	Up	Up
107053752	Up	Up	Up
107054020	Up	Up	Up
107056782	Down	Down	Down
107052435	Down	Down	Down
XLOC_045182	Down	Down	Down
XLOC_229820	Down	Down	Down
XLOC_229997	Down	Down	Down
XLOC_229891	Down	Down	Down
XLOC_229824	Down	Down	Down
XLOC_229822	Down	Down	Down
XLOC_144890	Up	Up	Up
XLOC_145466	Up	Up	Up
XLOC_043059	Up	Up	Up

Note: XLOC represents novel lncRNA, without XLOC represents known lncRNA.

Figure 2. Validation of lncRNAs expression profiles by qPCR. The expression pattern of five lncRNA were tested between F1 and N1 group (a); between L2 and N1 group (b) and between F1 and L2 group (c).

Table 2. Overlapped lncRNAs that target mRNAs among F1 vs. N1, F1 vs. L2, and N1 vs. L2.

lncRNAs	Target mRNA in F1 vs. N1	Target mRNA in L2 vs. N1	Target mRNA in F1 vs. L2
107054950	COE2	COE2	–
107053458	PAMR1	PAMR1	–
101749149	–	–	–
107053752	COE3	COE3	COE3
107054020	FOXD3	FOXD3	–
107056782	–	–	–
107052435	–	–	–
XLOC_045182	ARHGAP39, FK1L	ARHGAP39, FK1L	FK1L
XLOC_229820	scale keratin-like, feather beta-keratin-like, beta-keratin-related protein	feather beta-keratin-like, Beta-keratin-related protein	–
XLOC_229997	scale keratin-like, beta-keratin-related protein	scale keratin-like, beta-keratin-related protein	–
XLOC_229891	epidermal differentiation protein	epidermal differentiation protein	–
XLOC_229824	scale keratin-like	scale keratin-like	scale keratin-like
XLOC_229822	scale keratin-like	scale keratin-like	scale keratin-like
XLOC_144890	–	–	–
XLOC_145466	–	–	–
XLOC_043059	TMX3, CCDC102B	CCDC102B	CCDC102B

Table 3. Interconnectivity among miRNAs, lncRNAs and mRNAs identified in F1 vs. N1 and L2 vs. N1.

Groups	lncRNA	Expression	miRNA	Expression	Gene	Expression
F1 vs. N1	107052435	Down	gga-miR-31-5p	Down	Inactive phospholipase C-like 2	Up
	107052435	Down	gga-miR-31-5p	Down	CDK15	Down
	107052435	Down	gga-miR-31-5p	Down	ARL14EPL	Up
	107052435	Down	gga-miR-31-5p	Down	LTBP2	Up
	107052435	Down	gga-miR-31-5p	Down	TYRO3	Down
	107054929	Down	gga-miR-200b-5p	Down	SLC22A23	Down
	XLOC_077901	Up	gga-miR-199b	Up	GLPT	Up
L2 vs. N1	107052435	Down	gga-miR-31-5p	Down	TYRO3	Down
	107052435	Down	gga-miR-31-5p	Down	CDK15	Down
	107052435	Down	gga-miR-31-5p	Down	LTBP2	Up

Table 4. Functional enrichment of altered lncRNA highly related to skin and feather development between F1 and N1 group.

Term	Count	P value	LncRNA
GO:0035116∼Embryonic hind-limb morphogenesis	4	0.017	107052525(down);107055065(up);107055066(down); 101751961(down);101751994(down); 107054518(down);107054519(down);XLOC_ 199390(down); 107052611(down)
GO:0008543∼Fibroblast growth factor receptor signalling pathway	4	0.036	107052990(up);107052991(up);107054189(up); XLOC_235660(up); 101748409(up)
GO:0060174∼Limb bud formation	4	0.002	769756(up);101749678(up);417447(up); XLOC_214525(up);107052611(down); XLOC_235660(up)

Table 5. Functional enrichment of altered lncRNA highly related to skin and feather development between L2 and N1 group.

Term	Count	P value	LncRNA
GO:0090090∼Negative regulation of canonical Wnt-signalling pathway	5	0.008	XLOC_214525(up);107051937(up); 107052526(up);107051762 (down); 107052611(down);
GO:0060174∼Limb bud formation	4	0.000	769756(up);XLOC_214525(up); XLOC_235660(up);107052611 (down);
GO:0030855∼Epithelial cell differentiation	3	0.072	XLOC_249634(down);107053920 (down);101752007(down)
GO:0045669∼Positive regulation of osteoblast differentiation	3	0.066	101751961(down);107052611(down); 107053071(down);107053072(down); 107053073(down)
GO:0050680∼Negative regulation of epithelial cell proliferation	3	0.045	XLOC_214525(up);101749492 (up);XLOC_249634(down)
GO:0030326∼Embryonic limb morphogenesis	3	0.037	107052611(down); 107051762(down);101752007(down)
GO:0002076∼Osteoblast development	3	0.007	107052526(up);101751961(down); 107052611(down)
GO:0050673∼Epithelial cell proliferation	2	0.023	XLOC_235660(up);107052611(down)

Figure 3. Network construction of lncRNA-mRNA-miRNA interaction possibly related to skin and feather development identified between groups. Red nodes represent down-regulated genes (F1 or L2 group compared to the N1), and green nodes represent up-regulated genes (F1 or L2 group compared to the N1). Large nodes indicate bigger degrees. The diamond-shaped nodes represent lncRNAs, the round rectangle-shaped nodes represent microRNAs. The Ellipse-shaped nodes represent genes. The number of edges between two nodes represents the number of their enrichment GO terms involved in skin and feather development.

Table 6. lncRNA-mRNA pairs possibly related to skin and feather development identified between F1 and N1 groups.

Gene	Log2FC	lncRNA	log2FC	Biological process
CTNNB1	−1.3	107052525	−1.5	Embryonic hind-limb morphogenesis
ZBTB16	1.8	107055065	2.0
ZBTB16	1.8	107055066	2.1
MSX-2	−2.5	101751961	−2.5
MSX-2	−2.5	101751994	−2.4
MSX-2	−2.5	107054518	−2.0
MSX-2	−2.5	107054519	−1.7
MSX-2	−2.5	XLOC_199390	−3.8
SHH	−2.8	107052611	−3.4
CTGF	1.8	107052990	2.5	Fibroblast growth factor receptor signalling pathway
CTGF	1.8	107052991	2.6
FGF7	2.5	107054189	1.7
FGF10	2.8	XLOC_235660	3.0
FGF18	1.8	101748409	1.8
HAND2	1.7	769756	1.3	Limb bud formation
HAND2	1.7	101749678	2.1
SOX9	1.4	417447	1.5
SOX9	−1.4	XLOC_214525	−1.1
SHH	2.8	107052611	3.4
FGF10	−2.8	XLOC_235660	−3.0

Table 7. lncRNA-mRNA pairs possibly related to skin and feather development identified between L2 and N1 groups.

Gene	Log2FC	lncRNA	log2FC	Biological process
SOX-9	1.2	XLOC_214525	1.2	Negative regulation of canonical Wnt-signalling pathway
SHH	−2.8	107052611	−2.9
LIMD1	1.4	107052526	1.0
LEF1	−2.0	107051762	−1.6
ISL-1	2.3	107051937	2.4
HAND2	1.2	769756	1.3	Limb bud formation
SOX9	1.2	XLOC_214525	1.2
SHH	−2.5	107052611	−2.9
FGF10	1.8	XLOC_235660	2.5
KRT6A	−1.3	XLOC_249634	−1.8	Epithelial cell differentiation
NR5A2	1.1	107053920	−1.5
DLX6	−2.4	101752007	−2.5
MSX-2	−2.4	101751961	−2.4	Positive regulation of osteoblast differentiation
SHH	−2.5	107052611	−2.9
GJA1	−3.6	107053071	−3.2
GJA1	−3.6	107053072	−2.7
GJA1	−3.6	107053073	−2.3
SOX-9	1.2	XLOC_214525	1.2	Negative regulation of epithelial cell proliferation
AR	1.7	101749492	1.6
KRT6A	−1.3	XLOC_249634	−1.4
SHH	−2.5	107052611	−2.9	Embryonic limb morphogenesis
LEF1	−1.7	107051762	−1.6
DLX6	−2.4	101752007	−2.5
MSX-2	−2.4	101751961	−2.5	Osteoblast development
SHH	−2.5	107052611	−2.9
LIMD1	1.1	107052526	1.0
COL8A1	−1.8	107054903	−1.1	Epithelial cell proliferation
FOXN1	−1.9	107054799	−3.3

Table 8. miRNA-mRNA pairs correlated to lncRNA possibly related to skin and feather development identified between F1 and N1 groups.

Gene	Log2FC	miRNA	log2FC	Biological process
CTNNB1	−1.3	novel_mir_50	−4.9	Embryonic hind-limb morphogenesis
CTNNB1	−1.3	novel_mir_72	−3.8
CTNNB1	−1.3	novel_mir_123	−1.8
FGF18	1.8	novel_mir_176	−3.9	Fibroblast growth factor receptor signalling pathway
FGF18	1.8	novel_mir_72	−3.8
FGF18	1.8	gga-miR-211	−3.0
FGF18	1.8	gga-miR-204	−3.0
HAND2	1.7	novel_mir_50	−4.9	Limb bud formation
HAND2	1.7	novel_mir_176	−3.9
SOX9	1.4	novel_mir_184	−2.9
SOX9	1.4	gga-miR-449a	−2.0

Table 9. miRNA-mRNA pairs correlated to lncRNA possibly related to skin and feather development identified between L2 and N1 groups.

Gene	Log2FC	miRNA	log2FC	Biological process
LIMD1	1.4	gga-miR-365-2-5p	−2.0	Negative regulation of canonical Wnt-signalling pathway
DLX6	−2.4	gga-miR-1552-5p	−1.0	Epithelial cell differentiation
DLX6	−2.4	novel_mir_321	−4.4
MSX-2	−2.4	novel_mir_121	−3.2	Positive regulation of osteoblast differentiation
DLX6	−2.4	gga-miR-1552-5p	−1.0	Embryonic limb morphogenesis
DLX6	−2.4	novel_mir_321	−4.4
LIMD1	1.1	gga-miR-365-2-5p	−2.0	Osteoblast development
MSX-2	−2.4	novel_mir_121	−3.2
AR	1.7	novel_mir_321	−4.4	Negative regulation of epithelial cell proliferation

Availability of data and materials

The raw sequencing data in this study is deposited into the Sequence Read Archive Repository (https://www.ncbi.nlm.nih.gov/bioproject/) with accession number PRJNA376472. The N1 group included N11, N12 and N13 individuals; the L1 group included L21, L22 and L23 individuals; and the F1 group included F11, F12 and F13 individuals.