Transcriptome analysis of blastoderms exposed to prolonged egg storage and short periods of incubation during egg storage
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 and decreased hatchability and growth in surviving chicks. Exposing eggs to short periods of incubation during egg st...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-04-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-022-08463-2 |
| _version_ | 1811272520327757824 |
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| author | K. Brady C. C. Talbot J. A. Long G. Welch N. French D. Nicholson M. R. Bakst |
| author_facet | K. Brady C. C. Talbot J. A. Long G. Welch N. French D. Nicholson M. R. Bakst |
| author_sort | K. Brady |
| collection | DOAJ |
| description | 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 and decreased hatchability and growth in surviving chicks. Exposing eggs to short periods of incubation during egg storage (SPIDES) reduces the adverse consequences of prolonged storage. SPIDES increases blastodermal cell viability by reducing apoptosis, though the counteracting mechanisms are unclear. To define the impact of prolonged storage and SPIDES, transcriptome analysis compared gene expression from blastoderms isolated from eggs exposed to the following treatments: control (CR, stored at 17 °C for 4 days), prolonged storage (NSR, stored at 17 °C for 21 days), SPIDES (SR, stored at 17 °C for 21 days with SPIDES), and incubated control (C2, stored at 17 °C for 4 days followed by incubation to HH (Hamburger–Hamilton) stage 2, used as the ideal standard development) (n = 3/group). Data analysis was performed using the CLC Genomics Workbench platform. Functional annotation was performed using DAVID and QIAGEN Ingenuity Pathway Analysis. Results In total, 4726 DEGs (differentially expressed genes) were identified across all experimental group comparisons (q < 0.05, FPKM> 20, |fold change| > 1.5). DEGs common across experimental comparisons were involved in cellular homeostasis and cytoskeletal protein binding. The NSR group exhibited activation of ubiquitination, apoptotic, and cell senescence processes. The SR group showed activation of cell viability, division, and metabolic processes. Through comparison analysis, cellular respiration, tRNA charging, cell cycle control, 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 (NSR) resulted in enriched cell stress and death pathways; while SPIDES (SR) resulted in enriched basic cell and anti-apoptotic pathways. New insights into DNA repair mechanisms, RNA processing, shifts in metabolism, and chromatin dynamics in relation to egg storage 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 by prolonged storage and SPIDES and helped to identify potential upstream regulators for future experiments to optimize egg storage parameters. |
| first_indexed | 2024-04-12T22:41:49Z |
| format | Article |
| id | doaj.art-aecf71dfb2994270b7e70763a78be825 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-12T22:41:49Z |
| publishDate | 2022-04-01 |
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| series | BMC Genomics |
| spelling | doaj.art-aecf71dfb2994270b7e70763a78be8252022-12-22T03:13:43ZengBMCBMC Genomics1471-21642022-04-0123112410.1186/s12864-022-08463-2Transcriptome analysis of blastoderms exposed to prolonged egg storage and short periods of incubation during egg storageK. Brady0C. C. Talbot1J. A. Long2G. Welch3N. French4D. Nicholson5M. R. Bakst6Animal Biosciences and Biotechnology Laboratory, BARC, ARS, USDAInstitute for Basic Biomedical Sciences, Johns Hopkins University School of MedicineAnimal Biosciences and Biotechnology Laboratory, BARC, ARS, USDAAnimal Biosciences and Biotechnology Laboratory, BARC, ARS, USDAAviagen Ltd., NewbridgeAviagen Ltd., NewbridgeAnimal Biosciences and Biotechnology Laboratory, BARC, ARS, USDAAbstract Background Cool temperature egg storage prior to incubation is a common practice in the broiler industry; however, prolonged egg storage causes increased embryonic mortality and decreased hatchability and growth in surviving chicks. Exposing eggs to short periods of incubation during egg storage (SPIDES) reduces the adverse consequences of prolonged storage. SPIDES increases blastodermal cell viability by reducing apoptosis, though the counteracting mechanisms are unclear. To define the impact of prolonged storage and SPIDES, transcriptome analysis compared gene expression from blastoderms isolated from eggs exposed to the following treatments: control (CR, stored at 17 °C for 4 days), prolonged storage (NSR, stored at 17 °C for 21 days), SPIDES (SR, stored at 17 °C for 21 days with SPIDES), and incubated control (C2, stored at 17 °C for 4 days followed by incubation to HH (Hamburger–Hamilton) stage 2, used as the ideal standard development) (n = 3/group). Data analysis was performed using the CLC Genomics Workbench platform. Functional annotation was performed using DAVID and QIAGEN Ingenuity Pathway Analysis. Results In total, 4726 DEGs (differentially expressed genes) were identified across all experimental group comparisons (q < 0.05, FPKM> 20, |fold change| > 1.5). DEGs common across experimental comparisons were involved in cellular homeostasis and cytoskeletal protein binding. The NSR group exhibited activation of ubiquitination, apoptotic, and cell senescence processes. The SR group showed activation of cell viability, division, and metabolic processes. Through comparison analysis, cellular respiration, tRNA charging, cell cycle control, 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 (NSR) resulted in enriched cell stress and death pathways; while SPIDES (SR) resulted in enriched basic cell and anti-apoptotic pathways. New insights into DNA repair mechanisms, RNA processing, shifts in metabolism, and chromatin dynamics in relation to egg storage 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 by prolonged storage and SPIDES and helped to identify potential upstream regulators for future experiments to optimize egg storage parameters.https://doi.org/10.1186/s12864-022-08463-2SPIDESEgg storageProlonged storageChickenTranscriptomeBlastoderm |
| spellingShingle | K. Brady C. C. Talbot J. A. Long G. Welch N. French D. Nicholson M. R. Bakst Transcriptome analysis of blastoderms exposed to prolonged egg storage and short periods of incubation during egg storage BMC Genomics SPIDES Egg storage Prolonged storage Chicken Transcriptome Blastoderm |
| title | Transcriptome analysis of blastoderms exposed to prolonged egg storage and short periods of incubation during egg storage |
| title_full | Transcriptome analysis of blastoderms exposed to prolonged egg storage and short periods of incubation during egg storage |
| title_fullStr | Transcriptome analysis of blastoderms exposed to prolonged egg storage and short periods of incubation during egg storage |
| title_full_unstemmed | Transcriptome analysis of blastoderms exposed to prolonged egg storage and short periods of incubation during egg storage |
| title_short | Transcriptome analysis of blastoderms exposed to prolonged egg storage and short periods of incubation during egg storage |
| title_sort | transcriptome analysis of blastoderms exposed to prolonged egg storage and short periods of incubation during egg storage |
| topic | SPIDES Egg storage Prolonged storage Chicken Transcriptome Blastoderm |
| url | https://doi.org/10.1186/s12864-022-08463-2 |
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