Genome-Wide Association Analysis of Growth and Development Traits in Qira Black Sheep Using a 50K SNP Chip Array in Xinjiang, China
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Growth and development traits in sheep are complex quantitative traits regulated by multiple genes with small effects. In this study, 186 Qira Black sheep were genotyped using the Illumina Ovine SNP50K BeadChip, and genome-wide association studies were performed for 11 growth-related traits using a mixed linear model. After quality control and association analysis, significant SNPs were identified and annotated to 104 candidate genes based on the Oar_v4.0 reference genome. Gene Ontology enrichment analysis indicated that these genes were mainly involved in skeletal system development, regulation of growth, cell proliferation, and developmental processes. KEGG pathway analysis revealed significant enrichment in growth hormone synthesis, secretion and action, insulin secretion, cGMP–PKG signaling pathway, and apelin signaling pathway. These pathways are closely associated with endocrine regulation and growth-related signaling mechanisms. The identified candidate genes provide valuable molecular resources for marker-assisted selection and genetic improvement of Qira Black sheep.
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Figure 5. KEGG pathway enrichment analysis of candidate genes associated with growth and development traits in Xinjiang Qira Black Sheep. The top significantly enriched pathways are presented. Bubble size represents the number of genes involved in each pathway, and color intensity indicates the level of significance expressed as −log10(P-value).
Table 3. Gene Ontology (GO) biological process enrichment analysis of GWAS-associated genes
Candidate overlap (k/104)
regulation of GTPase activity
protein phosphorylation
regulation of transcription by RNA polymerase II
activation of GTPase activity
Table 3. The enrichment analysis was performed using 2,551 genes identified from the 11 sheep traits. "Gene Count" indicates the number of genes from this set that mapped to the specific GO term. "Candidate overlap (k/104)" represents the number of prioritized candidate genes (n = 104) found within each enriched GO term. "Cluster Enrichment" represents the fold enrichment score. FDR, false discovery rate.
Table 4. KEGG pathway enrichment analysis of GWAS-associated genes.
Candidate overlap (k/104)
Growth hormone synthesis, secretion and action
Insulin secretion
Apelin signaling pathway
Vascular smooth muscle contraction
cGMP-PKG signaling pathway
GnRH secretion
Cortisol synthesis and secretion
Aldosterone synthesis and secretion
Oxytocin signaling pathway
Table 4. Enrichment analysis was performed using the 2,551 GWAS-associated genes. “Gene count” indicates the number of genes from this set mapped to each KEGG pathway. “Candidate overlap (k/104)” indicates the number of prioritized candidate genes (n=104) included in each enriched pathway. P-values were corrected for multiple testing using FDR.