Genome Wide Association Study Based on Pathway Analysis Relate to Total Number of Lambs Born and First Lambing Age in Prolificacy Sheep

Genetic architecture of sheep reproduction is increasingly gaining scientific interest due to the major impact on sheep production systems. The present study aimed to conduct for identifying the loci associated with total number of progeny born and first lambing age in highly prolific Chios sheep using the 50K arrays.

In this research, phenotypic and genotypic data related to total number of lambs born and first lambing age in lifetime and first lambing age were obtained from 538 highly prolific sheep. The gene set analysis consists basically in three different steps: the assignment of SNPs to genes, the assignment of genes to functional categories and finally the association analysis between each functional category and the phenotype of interest. Genome wide association study was performed with reproductive traits using GEMMA software. Using the biomaRt2 R package the SNP were assigned to genes if they were within the genomic sequence of the gene or within a flanking region of 15 kb up- and downstream of the gene. Finally, a gene enrichment analysis was performed with the KOBAS platform from online bioinformatics databases for the assignment of the genes to functional categories, the GO, KEGG, DAVID and PANTHER databases were used.

In this research, 11 SNP markers on chromosomes 1, 2, 5, 7, 8, 10, 13, 15, 17, 22 and 23 were identified. Also, we identified different sets of candidate genes related to reproductive traits: QULP1, AURKA, TEX12, DLG1T, ACVR1, LCP2 and PPFIA2 in Chios sheep. Some of these genes identified in this research were consistent with previous studies. In the enrichment analysis of gene sets, 19 biological pathways related to reproduction traits were identified. Some of these pathways have important role in fertilization, ovulation rate, estrogen biosynthesis, conception rate, skeletal muscle development, early development of the fetus and puberty.

The results of this research can further reveal the role of genetic mechanisms affecting reproductive traits. Considering the conformation of previous genomic region and the new genomic regions identified in this study, the findings of this research can be used more confidently in breeding programs for important economic traits in sheep.