Gene-set enrichment analysis to identify genes and biological pathways associated with egg weight in the whole laying period

Identifying genes with large effects on economically important traits, has been one of the important goals in chicken breeding. The present study aimed to conduct a genome wide association studies (GWAS) based on Gene-set enrichment analysis for identifying the loci associated with egg weight in Rhode Island Red chicken using the high-density SNPs.

Phenotypes records and genotypic data were obtained from the Figshare online public repository. 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 for 1,078 hens was performed with egg weight including first egg weight, eggs weight at 28, 36, 56, 66, 72, and 80 weeks of age using GenABEL 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 20 kb up- and downstream of the gene. Subsequently, gene enrichment analysis was performed with the goseq R package and bioinformatics analysis was implemented to identify the biological pathways performed in GO, KEEG, DAVID and PANTHER databases.

In this research, 9 SNP markers on chromosomes 3, 4, 6, 7, 8, 9, 19, 20 and 22 located in MC3R, LEPR, ECT2, SH3GL2, KCNMA1, SPP1, PCK1, MMP9, PPP1CB, ACOX1, and IGFBP2 genes were identified. Some of the genes that were found are consistent with some previous studies related to egg weights. According to pathway analysis, 28 pathways from gene ontology and biological pathways were associated with the egg weight (P˂0.01). Among these pathways, the regulation of feeding behavior, positive regulation of the apoptotic process, positive regulation of protein phosphorylation, osteoblast differentiation, positive regulation of gluconeogenesis, cell-cell junction, and focal adhesion have important functions in creating the egg weight and process production through the development and ovulation of the oocytes, the formation of albumen, and the formation of eggshell.

 In total, this study supported previous results from GWAS of egg weights, also revealed additional regions in the chicken genome associated with these economically important traits, using these findings could potentially be useful for genetic selection in the breeding programs.