{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T13:08:07Z","timestamp":1776517687853,"version":"3.51.2"},"reference-count":88,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2025,4,22]],"date-time":"2025-04-22T00:00:00Z","timestamp":1745280000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Scientific Research Projects Coordination Unit of Erciyes University","award":["FOA-2023-12802"],"award-info":[{"award-number":["FOA-2023-12802"]}]},{"name":"Scientific Research Projects Coordination Unit of Erciyes University","award":["6040-32000-085"],"award-info":[{"award-number":["6040-32000-085"]}]},{"name":"Scientific Research Projects Coordination Unit of Erciyes University","award":["6040-32000-079"],"award-info":[{"award-number":["6040-32000-079"]}]},{"name":"USDA-ARS","award":["FOA-2023-12802"],"award-info":[{"award-number":["FOA-2023-12802"]}]},{"name":"USDA-ARS","award":["6040-32000-085"],"award-info":[{"award-number":["6040-32000-085"]}]},{"name":"USDA-ARS","award":["6040-32000-079"],"award-info":[{"award-number":["6040-32000-079"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: Hatchery fumigation is recognized as a crucial step to control microbial bloom in the environment, and formaldehyde is one of the most widely used disinfectants to ensure successful hatchability and healthy production. While many of the benefits are thought to be derived from disinfectant properties, it is possible that additional host gene and genetic pathway modulation could contribute to these outcomes. The current study aimed to capture the in ovo transcriptional response of liver tissue to formaldehyde treatment. Methods: Chick embryos were subjected to formaldehyde fumigation treatment for 25 min at 24\u201325 \u00b0C and 75% relative humidity, keeping a control group as untreated. On the 18th day of incubation at 37.8 \u00b0C and 58\u201363% humidity, eggs were broken, and liver tissue was obtained for RNA isolation, cDNA library preparation, and RNA sequencing. Results: Bioinformatics analysis revealed 908 significant differentially expressed genes (DEGs), among which 814 were known genes and 94 were novel genes. A total of 672 DEGs were upregulated, whereas 236 genes were downregulated in response to FA treatment. Of the 94 novel genes, 80 were upregulated. Key DEGs, associated QTLs, and transcription factors were involved in immuno-inflammatory responses, oxidative stress, epigenetic modification, and cellular adaptation-related activities. Further research should focus on biological validation of key DEGs to clarify their roles, pathways, and relationships to FA treatment. Conclusions: Overall, these findings (1) provide critical molecular detail as a first step towards genetic selection to improve formaldehyde treatment response and effectiveness, and (2) provide DEG signatures for FA treatment as a reference against which to compare other interventions to achieve hatchability and production benefits.<\/jats:p>","DOI":"10.3390\/genes16050471","type":"journal-article","created":{"date-parts":[[2025,4,22]],"date-time":"2025-04-22T03:50:57Z","timestamp":1745293857000},"page":"471","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["RNA-Seq of Chicken Embryo Liver Reveals Transcriptional Pathways Influenced by Egg Formaldehyde Treatment"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6160-2484","authenticated-orcid":false,"given":"Mustafa","family":"\u00d6zdemir","sequence":"first","affiliation":[{"name":"Department of Animal Science, Faculty of Agriculture, Erciyes University, 38280 Kayseri, T\u00fcrkiye"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4445-9457","authenticated-orcid":false,"given":"Ghulam Asghar","family":"Sajid","sequence":"additional","affiliation":[{"name":"Department of Animal Science, Faculty of Agriculture, Erciyes University, 38280 Kayseri, T\u00fcrkiye"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4622-0645","authenticated-orcid":false,"given":"Selma","family":"B\u00fcy\u00fckk\u0131l\u0131\u00e7 Beyzi","sequence":"additional","affiliation":[{"name":"Department of Animal Science, Faculty of Agriculture, Erciyes University, 38280 Kayseri, T\u00fcrkiye"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mehmet","family":"K\u0131z\u0131laslan","sequence":"additional","affiliation":[{"name":"Department of Animal and Dairy Sciences, University of Wisconsin\u2013Madison, Madison, WI 53706, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3068-8155","authenticated-orcid":false,"given":"Yunus","family":"Arz\u0131k","sequence":"additional","affiliation":[{"name":"Department of Animal Science, Faculty of Veterinary Medicine, Aksaray University, 68100 Aksaray, T\u00fcrkiye"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Servet","family":"Yal\u00e7\u0131n","sequence":"additional","affiliation":[{"name":"Department of Animal Science, Faculty of Agriculture, Ege University, 35100 \u0130zmir, T\u00fcrkiye"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9255-6054","authenticated-orcid":false,"given":"Stephen N.","family":"White","sequence":"additional","affiliation":[{"name":"Poultry Microbiological Safety & Processing Research, United States National Poultry Research Center, United States Department of Agriculture-Agricultural Research Service, Athens, GA 30605, USA"},{"name":"Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5894-5072","authenticated-orcid":false,"given":"Mehmet Ulas","family":"Cinar","sequence":"additional","affiliation":[{"name":"Department of Animal Science, Faculty of Agriculture, Erciyes University, 38280 Kayseri, T\u00fcrkiye"},{"name":"Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,4,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/j.molcel.2015.08.020","article-title":"Endogenous formaldehyde is a hematopoietic stem cell genotoxin and metabolic carcinogen","volume":"60","author":"Pontel","year":"2015","journal-title":"Mol. 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