The candidate genes and pathways affecting litter size in sheep
2021
Ghiasi, Heydar | Abdollahi-Arpanahi, Rostam
Litter size is one of the most important traits in the sheep industry. To date, QTL mapping and genome-wide association studies (GWAS) have identified significant SNPs associated with litter size. However, the number of studies exploring the pathways that affect litter size is low. This study aimed to find genes and pathways affecting litter size in sheep using SNP information available in public databases. In the first step, 57 candidate SNPs with known associations with litter size were chosen from the Animal QTL Database. In the second step, 451 SNPs were extracted from the Ensembl database based on their proximity to the candidate SNPs. The annotation of candidate SNPs to the genome was retrieved using the Variant Effect Predictor tool. The pathway analyses were conducted using g:Profiler. In total, 508 SNPs associated with litter size were mapped to 21 genes. The majority of SNPs were mapped to non-coding regions (98 %) and only 2% were mapped to coding regions (classified as missense and synonymous variants). A total of 20 significant pathways related to litter size were identified in this study. The main significant pathway was negative regulation of vascular endothelial cell proliferation, which is enriched by the FLT1 and CCL2 genes. The FLT1 and CCL2 genes were connected to 14 and 9 pathways, respectively. Therefore, FLT1 and CCL2 can be used as candidate genes to improve the litter size in sheep breeding programs.
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