Comparative transcriptional profiling and differential expression analysis of pectoralis major muscle in modern and legacy Gallus broiler lines

Schmidt, Carl J.Agriculture provides excellent model systems for understanding how selective pressure, as applied by humans, can affect the genomes of plants and animals. One such system is found in modern poultry breeding in which intensive genetic selection has been applied for meat production in the domesticated chicken. As a result, modern meat-type chickens (broilers) exhibit enhanced growth, especially of the skeletal muscle, relative to their legacy counterparts. Comparative studies of modern and legacy broiler chickens provide an opportunity to identify genes and pathways affected by this human-directed evolution. This study used messenger RNA-sequencing and microRNA-sequencing to compare the transcriptional profiles of a modern and a legacy broiler line to identify differentially enriched genes in the pectoralis major at days 6 and 21 post-hatch, which bracket a previously observed inflection in allometric growth that occurs around day 14 post-hatch. ☐ All 15,945 genes transcripts and 1,071 microRNAs that were present on the available genome build were analyzed. At day 6 post-hatch 189 gene transcripts and 20 microRNAs were significantly differentially regulated between the two lines. These differentially enriched factors included several regulators of myogenic growth and development. The transcriptional profiles between lines at day 21 post-hatch identify 193 gene transcripts differentially enriched but only 7 differentially enriched microRNAs. Despite less overall differential enrichment, at the D21 timepoint, many of the differentially regulated transcripts were also related to muscle growth and development. ☐ This study identified differentially enriched genes that regulate myogenic growth and differentiation between the modern and legacy broiler lines. Specifically, differences in the ratios of several positive (IGF1, IGF1R, WFIKKN2) and negative (MSTN, ACE) myogenic growth regulators are likely to explain, at least in part, the differences underlying the enhanced growth characteristics of the modern broilers. In addition, the microRNA-sequencing results revealed differential expression of microRNAs that target, or are predicted to target, important myogenic and metabolic regulators. Several of the microRNAs potentially directly interact with key elements of the pro-growth IGF pathway and/or the growth-inhibitory myostatin signaling pathway. ☐ In addition to factors affecting myogenic growth and development, numerous gene transcripts and several microRNAs indicate a marked difference in the oxidative metabolic profile of the pectoralis major muscle between the modern and legacy lines. Intriguingly, the results suggest that activated p53 could play a central role in regulating this metabolic shift via several p53-inducible microRNAs. Many of the differentially enriched microRNAs are inducible by p53. Most important among these differentially regulated microRNAs is likely miR-34, which forms a positive feedback loop by targeting an inhibitor of p53 activation, thus relieving the inhibition. ☐ The recent improvements in sequencing technologies have allowed for access to previously unimaginable quantities of information. Utilizing next-generation sequencing technologies with a comparative model, such as with the broilers, has provided incredible insight into an array of biological disciplines; from helping to elucidate the underlying factors of myogenic growth and development; to providing insight on cellular energy production and resource utilization; to identifying potential positive and negative target genes for future breeding; or adding to our understanding of the process of selection and evolution, particularly in the sphere of domestication and human-directed evolution. ☐ However these improvements have unearthed at least as many new questions as they have helped to answer and it is clear that our understanding of these topics has not yet come close to being complete. A primary goal of this project was that the messenger RNA and microRNA transcriptional profiles, which have already helped to further clarify the transcriptional profiles of these two broiler lines and formulate hypotheses about the factors that underlie the remarkable differences that have arisen over the last 70 years, would provide a strong foundation for experimental extensions and future inquiry.University of Delaware, Department of Biological SciencesPh.D