RESULTS
A total of 1,122,858 InDels were obtained from the genome of127 goats.
Most of these InDels were found in intergenic (63.8430%) and intron
(29.7546%), and some were located in UTR3 (0.4220%), exon region
(0.1584%) and UTR5 (0.0636%) (Figure 1). The InDels located in the
exon region include 1,065 (59.6973%) deletion mutations, which are
composed of 673 (37.72%) frameshift mutations and 392 (21.9730%)
non-frameshift mutations, and 614 (34.417%) insertion mutations, which
are composed of 446 (25%) frameshift mutations and 168 (9.4170%)
non-frameshift mutations. A total of 105 (5.886%) InDel variants were
located in the initiation/ termination code.
The FST value of 1,122,858 InDels between case and
control group was obtained (Figure 2). A total of 11,229 InDels with
high signal were collected according to the top 1% threshold of
FST statistical parameters
(FST≥0.623043, S Table 2).
Then 3,488 of that 11,229 InDels which distributed in the exon, intron,
3’UTRn and 5’UTR region were extracted for candidate gene annotation.
Finally, 1,239 candidate genes were annotated. In addition, 1,193
candidate genes were enriched to 4,726 GO terms (S Table 3), and the top
20 significantly enriched GO terms are shown in Figure 3. The protein
binding GO terms (ZCCHC10 , NCBP1 , WLS , etc.) with
the largest number of genes were selected, and 791 candidate genes was
enriched.
94 candidate genes were enriched in 88 GO terms related to muscle
development. In particular, 36 GO terms were related to skeletal muscle
development, skeletal muscle cell differentiation (MEF2C ,ZNF689 ), and skeletal muscle tissue development (MAPK14 );
39 GO terms were related to myocardial development and cardiac muscle
cell proliferation (TGFBR3 , TGFB2 , and TENM4 ); and
19 GO terms were related to smooth muscle development, such as in the
positive regulation of vascular associated smooth muscle cell
proliferation (GNAI3 ). Enrichment was also observed in a large
number of GO terms related to immune cells, such as B cell proliferation
(MEF2C , HSPD1 , LEF1 , BCL2 ), T cell
differentiation (VAV1 , RUNX2 , PTPN22 ,ZAP70 ), and positive regulation of immune response (TGFB2 ,RSAD2 ). Sixty-two reproductive function-relative GO terms were
also enriched, such as spermatogenesis (LRGUK ), which is related
to germ cell development and differentiation, and estrogen receptor
activity (LEF1 , ESR1 ), which is related to reproductive
hormones. A large number of GO terms related to metabolism were also
enriched, such as the protein catabolic process (LNPEP ,P2RX7 , RNF165 ), amino acid metabolism (UCHL3 ),
glycerolipid metabolism (DGKH ), and fatty acid metabolism
(LCP1) .
KEGG results showed that 476 candidate genes were enriched to 299 KEGG
signaling pathways, 98 of which were significantly enriched (corrected P
<0.05, S Table 4). Information on the top 20 significant KEGG
enrichment pathways is shown in Figure 4. The 29 candidate genes were
significantly enriched in two signaling pathways related to muscle
regulation, namely, vascular smooth muscle contraction (ACTA2 ,MYH11 , PRKCB , etc.) and cardiac muscle contraction
(RYR2 , SLC9A, CASQ2 etc.). In addition, 45 candidate genes
were enriched in 7 signaling pathways related to reproduction, such as
GnRH signaling pathway (PLCB1 , PRKCB , and PLCB4 ).
Multiple signaling pathways related to growth and development were also
enriched, such as cGMP-PKG signaling pathway (NFATC1 ,PLCB3 , and PLCB4 ). A large number of immune-related
signaling pathways were also enriched, such as NF-kappa B signaling
pathway (TRAF6 , IL1R1 , and ERC1 ). Many metabolism
relative pathways were also enriched, such as insulin signaling pathways
(RPTOR , PPP1CC , and PRKAG2 ), ether lipid metabolism
(PLA2G4A , PLA2G4, and PLA2G4E ), and beta-alanine
metabolism (EHHADH , HIBCH , CNDP1 , and DPY ).