Gastrocnemius transcriptome analysis reveals domestication induced gene expression changes between wild and domestic chickens

Artificial selection of chicken for human-preferred traits has manifested great phenotypic differences between wild and domestic chickens. Study on the formation of these phenotypic variations will contribute to comprehensive understanding of the molecular mechanism of animal domestication. We used three kinds of chicken breeds for transcriptome analysis, including the red jungle fowl which was the wild ancestor of chickens, and two other domestic breeds, the chahua chicken and the avian broiler. More than 12,000 genes' expression levels were compared between different chicken breeds, and hundreds of genes displayed differential expression levels compared with wild chicken. Gene ontology analysis showed that differentially expressed genes in domestic chickens tended to be enriched in extracellular matrix, DNA binding and immune system development, etc. Some genes with important biological functions were differentially expressed in the domestic chickens, including titin, myostatin ubiquitin related genes, and transforming growth factor-beta receptor III, indicating possible selection pressures on these genes.