Chicken Little Can Blame It On Her Epigenetics!
While most of us will be hopping on the scale and hoping for a relatively low weight this holiday season, poultry farmers will be weighing their birds hoping for just the opposite. Chickens are the most commonly eaten poultry in the world and those bred for consumption are categorized as fryers, broilers, or roasters. They are named after their most appropriate cooking method, which is determined by the surface area to volume ratio. While rapid chicken growth is a desired trait in poultry production, scientists are still trying to pinpoint the factors that determine the rate of growth. Genetics, nutrition, and the environment are known factors that affect chicken growth, but the specifics of the genetic component still remain largely unknown. Quantitative trait loci and polymorphisms do not fully account for growth rates, leading Hu and colleagues to turn to epigenetics for potential answers. The group took a Methylated DNA immunoprecipitation (MeDIP) approach to analyze DNA methylation levels among four sample groups and was able to identify a panel of 75 genes which were differentially methylated – some of which encode well-known growth factors.
The two breeds of broilers used in this study – Recessive White Rock (WRR) and Xinhua (XH) – were chosen due to the significant difference in their growth rates at 7 weeks of age. Each breed was divided into two subgroups, “low” and “high”, depending on body weight, to establish four subgroups: WRRL, WRRH, XHL, and XHH. DNA was extracted from breast tissue of each broiler and samples were then subjected to MeDIP-Seq. Analysis of the MeDIP-Seq data showed that most of the methylation-enriched regions among all four subgroups were found to be within introns. Of the genes that were differentially methylated between WRRH and WRRL, more gene regions within the WRRH subgroup showed a higher degree of methylation than the same regions in WRRL. Similar results were seen between WRRH and XHH, with WRRH displaying more methylation-enriched peaks. However, contrary to the pattern between WRRH and WRRL, more peaks were found in XHL when compared separately to both XHH and WRRL. While there was no obvious pattern among the different comparisons with respect to which subgroups had higher degrees of methylation, further analysis of four pairings of the subgroups (WRRH vs. WRRL, XHH vs. XHL, WRRH vs. XHH, WRRL vs. XHL) resulted in the identification of 75 shared, differentially methylated genes. Functional annotation analysis revealed that growth factors such as IGF1R, FGF12, FGF14, FGF18, FGFR2, and FGFR3 were among the 75 shared, differentially methylated genes, suggesting that epigenetic factors may contribute to growth rates among broilers at 7 weeks of age.
Identifying the key epigenetic modifications that are involved in fast broiler growth and determining the nutritional and environmental components that affect these modifications can not only help improve the pace of poultry production, but also give us a better understanding of growth and development in general. So when you’re giving thanks to family, friends, and the plump turkey on your dinner table this weekend, whisper a quick thanks to epigenetics!
Hu Y, Xu H, Li Z, Zheng X, Jia X, Nie Q, & Zhang X (2013). Comparison of the genome-wide DNA methylation profiles between fast-growing and slow-growing broilers. PloS one, 8 (2) PMID: 23441189