Gene set enrichment analysis to identify genes and biological pathways associated with body weight in chicken

The aim of the present study was to conduct a genome wide association studies (GWAS) based on gene set enrichment analysis for identifying the loci associated with body weight in four chicken breeds including Chahua, Silkie, Langshan, and Beard using the high throughput single nucleotide polymorphisms (SNPs). Phenotypic and genotypic data were obtained from the Frontiersin online public repository. In this study, the 402 cocks and hens were used with body weight from 1 to 15 weeks using GenABEL software. The gene enrichment analysis was performed with the goseq R package. In the next step, a bioinformatics analysis was implemented to identify the biological pathways performed in GO, KEEG, DAVID and PANTHER databases. Ten SNP markers on  chromosomes 1, 2, 5, 7, 10, 14, 18, 19, 20 and 27 located in ABCG1, MYOD1, MYH10, MYH11, MYO1B, MYO1C, MYO1E, MYL1, MYL2, MYL3, SLC2A8, ACACA, ACOX1, ACOX2, and PNPLA2 genes were identified. Some of the genes were found are consistent with some previous studies and to be involved in biological pathways related to body weight. According to pathway analysis, 17 pathways from gene ontology and KEGG pathway were associated with the body weight (P˂0.01). Among those pathways, the cytoskeletal protein binding, anatomical structure development and tricarboxylic acid cycle had significant association with skeletal muscle fiber and metabolism lipid traits. In total, this study supported previous results from GWAS of body weight; also revealed additional regions in the chicken genome associated with these economically important traits. The use of these findings can accelerate the genetic progress in the breeding programs.