Journal Article

DNA methylome and transcriptome identified Key genes and pathways involved in Speckled Eggshell formation in aged laying hens

Liu, Yuchen, Cheng, Xue, Zhang, Yalan, Ning, Zhonghua, Li, Xinghua, Zhang, Ruiqi, Fan, Cuidie, Qu, Lujiang, Ma, Ying

2023

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Aging / Analysis / Animal Genetics and Genomics / Animals / Antioxidants / Biomedical and Life Sciences / Calcium channels (voltage-gated) / Calcium signalling / Cell-mediated immunity / Chickens - genetics / Deoxyribonucleic acid / DNA / DNA damage / DNA methylation / Economics / Egg production / Egg Shell - metabolism / Egg shells / Eggs / Eggshells / Epigenome / Female / Gene expression / Gene set enrichment analysis / Genes / Genetic aspects / Genomes / Genomics / Immunity / Immunoglobulins / Laying hens / Life Sciences / Lymphocytes / Lymphocytes T / MAP kinase / Messenger RNA / Methylation / Microarrays / Microbial Genetics and Genomics / Ontology / Oxidative stress / Physiological aspects / Physiology / Plant Genetics and Genomics / Poultry / Profitability / Proteomics / Quality control / Signal transduction / Signaling / Speckled eggs / Transcriptome / Transcriptomes