Transcriptome analysis of blastoderms exposed to prolonged egg storage and short periods of incubation during egg storage

Authors: Brady, Kristen; TALBOT, CONOVER - Johns Hopkins University; Long, Julie; WELCH, GLENN - Retired ARS Employee; FRENCH, NICK - Aviagen; DINAH, NICHOLSON - Aviagen; BAKST, MURRAY - Retired ARS Employee

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/5/2022
Publication Date: 4/4/2022
Citation: Brady, K.M., Talbot, C.C., Long, J.A., Welch, G., French, N., Dinah, N., Bakst, M. 2022. Transcriptome analysis of blastoderms exposed to prolonged egg storage and short periods of incubation during egg storage. BMC Genomics. 23:262-286. https://doi.org/10.1186/s12864-022-08463-2.
DOI: https://doi.org/10.1186/s12864-022-08463-2

Interpretive Summary: Egg storage is a common and necessary practice that allows for operational flexibility to meet supply and demand constraints in the broiler industry. Prolonged storage of eggs prior to incubation causes increased mortality and decreased hatchability. Providing short periods of incubation during egg storage (SPIDES) diminishes the negative implications of egg storage, though the rescue mechanisms involved remain unknown. This study utilized a global gene expression approach to understand the mechanisms behind the negative consequences associated with prolonged storage and how these consequences are mitigated through the incorporation of SPIDES treatment. New findings related to embryonic metabolism shifts, cell cycle progression, gene regulation, cell death mechanisms were obtained through this study. The information gathered in this study provides direction for further research aims, with the ultimate goals of optimizing egg storage protocols to better support long term egg storage needs.

Technical Abstract: Background: Cool temperature egg storage prior to incubation is a common practice in the broiler industry; however, prolonged egg storage causes increased embryonic mortality, decreased hatchability, and decreased growth in surviving chicks. Exposing eggs to short periods of incubation during egg storage (SPIDES) reduces the adverse consequences seen with prolonged storage. SPIDES increases blastodermal cell viability by reducing apoptosis, though the counteracting molecular mechanisms are unclear. To further define the impact of prolonged storage and SPIDES, transcriptome analysis was used to compare gene expression from eggs exposed to the following treatments: control (CR, stored at 17 degrees C for 4 days), prolonged storage (NSR, stored at 17 degrees C for 21 days), SPIDES (SR, stored at 17 degrees C for 21 days with SPIDES), and incubated control (C2, stored at 17 degrees C for 4 days followed by incubation to HH stage 2) (n=3/group). Data analysis was performed using the CLC Genomics Workbench. Functional annotation was performed using DAVID and Ingenuity Pathway Analysis. Results: In total, 4726 DEGs were identified across all experimental group comparisons (q<0.05, FPKM>20, |fold change|>1.5). DEGs common across all experimental comparisons were involved in cellular homeostasis, nitric oxide production, and cytoskeletal protein binding. The NSR group exhibited activation of ubiquitination, apoptotic, cell senescence processes. The SR group showed activation of cell viability, division, and metabolism processes. Through comparison analysis, oxidative phosphorylation, tRNA charging, cell cycle control, the TCA cycle, and HMBG1 signaling pathways were significantly impacted by treatment and potential regulatory roles for ribosomal protein L23a (RPL23A) and MYC proto-oncogene, BHLH transcription factor (MYC) were identified. Conclusions: Prolonged egg storage resulted in enrichment of pathways associated with cell stress and death; while SPIDES resulted in enrichment of pathways associated with basic cell and anti-apoptotic functions. New insights into DNA repair mechanisms, RNA processing, shifts in metabolism, and chromatin dynamics in relation to prolonged storage and SPIDES treatment were obtained through this study. Although egg storage protocols have been examined through targeted gene expression approaches, this study provided a global view of the extensive molecular networks affected in blastodermal cells and helped to identify potential upstream regulators for future experiments.