Cargando…
DNA methylome and transcriptome identified Key genes and pathways involved in Speckled Eggshell formation in aged laying hens
BACKGROUND: The quality of poultry eggshells is closely related to the profitability of egg production. Eggshell speckles reflect an important quality trait that influences egg appearance and customer preference. However, the mechanism of speckle formation remains poorly understood. In this study, w...
Autores principales: | , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9854222/ https://www.ncbi.nlm.nih.gov/pubmed/36658492 http://dx.doi.org/10.1186/s12864-022-09100-8 |
_version_ | 1784873070689779712 |
---|---|
author | Cheng, Xue Li, Xinghua Liu, Yuchen Ma, Ying Zhang, Ruiqi Zhang, Yalan Fan, Cuidie Qu, Lujiang Ning, Zhonghua |
author_facet | Cheng, Xue Li, Xinghua Liu, Yuchen Ma, Ying Zhang, Ruiqi Zhang, Yalan Fan, Cuidie Qu, Lujiang Ning, Zhonghua |
author_sort | Cheng, Xue |
collection | PubMed |
description | BACKGROUND: The quality of poultry eggshells is closely related to the profitability of egg production. Eggshell speckles reflect an important quality trait that influences egg appearance and customer preference. However, the mechanism of speckle formation remains poorly understood. In this study, we systematically compared serum immune and antioxidant indices of hens laying speckled and normal eggs. Transcriptome and methylome analyses were used to elucidate the mechanism of eggshell speckle formation. RESULTS: The results showed that seven differentially expressed genes (DEGs) were identified between the normal and speckle groups. Gene set enrichment analysis (GSEA) revealed that the expressed genes were mainly enriched in the calcium signaling pathway, focal adhesion, and MAPK signaling pathway. Additionally, 282 differentially methylated genes (DMGs) were detected, of which 15 genes were associated with aging, including ARNTL, CAV1, and GCLC. Pathway analysis showed that the DMGs were associated with T cell-mediated immunity, response to oxidative stress, and cellular response to DNA damage stimulus. Integrative analysis of transcriptome and DNA methylation data identified BFSP2 as the only overlapping gene, which was expressed at low levels and hypomethylated in the speckle group. CONCLUSIONS: Overall, these results indicate that aging- and immune-related genes and pathways play a crucial role in the formation of speckled eggshells, providing useful information for improving eggshell quality. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-09100-8. |
format | Online Article Text |
id | pubmed-9854222 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-98542222023-01-21 DNA methylome and transcriptome identified Key genes and pathways involved in Speckled Eggshell formation in aged laying hens Cheng, Xue Li, Xinghua Liu, Yuchen Ma, Ying Zhang, Ruiqi Zhang, Yalan Fan, Cuidie Qu, Lujiang Ning, Zhonghua BMC Genomics Research BACKGROUND: The quality of poultry eggshells is closely related to the profitability of egg production. Eggshell speckles reflect an important quality trait that influences egg appearance and customer preference. However, the mechanism of speckle formation remains poorly understood. In this study, we systematically compared serum immune and antioxidant indices of hens laying speckled and normal eggs. Transcriptome and methylome analyses were used to elucidate the mechanism of eggshell speckle formation. RESULTS: The results showed that seven differentially expressed genes (DEGs) were identified between the normal and speckle groups. Gene set enrichment analysis (GSEA) revealed that the expressed genes were mainly enriched in the calcium signaling pathway, focal adhesion, and MAPK signaling pathway. Additionally, 282 differentially methylated genes (DMGs) were detected, of which 15 genes were associated with aging, including ARNTL, CAV1, and GCLC. Pathway analysis showed that the DMGs were associated with T cell-mediated immunity, response to oxidative stress, and cellular response to DNA damage stimulus. Integrative analysis of transcriptome and DNA methylation data identified BFSP2 as the only overlapping gene, which was expressed at low levels and hypomethylated in the speckle group. CONCLUSIONS: Overall, these results indicate that aging- and immune-related genes and pathways play a crucial role in the formation of speckled eggshells, providing useful information for improving eggshell quality. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-09100-8. BioMed Central 2023-01-19 /pmc/articles/PMC9854222/ /pubmed/36658492 http://dx.doi.org/10.1186/s12864-022-09100-8 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Cheng, Xue Li, Xinghua Liu, Yuchen Ma, Ying Zhang, Ruiqi Zhang, Yalan Fan, Cuidie Qu, Lujiang Ning, Zhonghua DNA methylome and transcriptome identified Key genes and pathways involved in Speckled Eggshell formation in aged laying hens |
title | DNA methylome and transcriptome identified Key genes and pathways involved in Speckled Eggshell formation in aged laying hens |
title_full | DNA methylome and transcriptome identified Key genes and pathways involved in Speckled Eggshell formation in aged laying hens |
title_fullStr | DNA methylome and transcriptome identified Key genes and pathways involved in Speckled Eggshell formation in aged laying hens |
title_full_unstemmed | DNA methylome and transcriptome identified Key genes and pathways involved in Speckled Eggshell formation in aged laying hens |
title_short | DNA methylome and transcriptome identified Key genes and pathways involved in Speckled Eggshell formation in aged laying hens |
title_sort | dna methylome and transcriptome identified key genes and pathways involved in speckled eggshell formation in aged laying hens |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9854222/ https://www.ncbi.nlm.nih.gov/pubmed/36658492 http://dx.doi.org/10.1186/s12864-022-09100-8 |
work_keys_str_mv | AT chengxue dnamethylomeandtranscriptomeidentifiedkeygenesandpathwaysinvolvedinspeckledeggshellformationinagedlayinghens AT lixinghua dnamethylomeandtranscriptomeidentifiedkeygenesandpathwaysinvolvedinspeckledeggshellformationinagedlayinghens AT liuyuchen dnamethylomeandtranscriptomeidentifiedkeygenesandpathwaysinvolvedinspeckledeggshellformationinagedlayinghens AT maying dnamethylomeandtranscriptomeidentifiedkeygenesandpathwaysinvolvedinspeckledeggshellformationinagedlayinghens AT zhangruiqi dnamethylomeandtranscriptomeidentifiedkeygenesandpathwaysinvolvedinspeckledeggshellformationinagedlayinghens AT zhangyalan dnamethylomeandtranscriptomeidentifiedkeygenesandpathwaysinvolvedinspeckledeggshellformationinagedlayinghens AT fancuidie dnamethylomeandtranscriptomeidentifiedkeygenesandpathwaysinvolvedinspeckledeggshellformationinagedlayinghens AT qulujiang dnamethylomeandtranscriptomeidentifiedkeygenesandpathwaysinvolvedinspeckledeggshellformationinagedlayinghens AT ningzhonghua dnamethylomeandtranscriptomeidentifiedkeygenesandpathwaysinvolvedinspeckledeggshellformationinagedlayinghens |