DNA methylation dynamics in the small intestine of egg-selected laying hens along egg production stages

Decades of artificial selection have markedly enhanced egg production efficiency, yet the epigenetic underpinnings, notably DNA methylation dynamics in the gut, remain largely unexplored. Here, we investigate how breeds and developmental stages influence DNA methylation profiles in laying hens, and their potential relationship to laying performance and gut health. We compared two highly selected laying hen strains, Lohmann Brown-Classic (LB) and Lohmann Selected Leghorn-Classic (LSL), which exhibited similar egg production but divergent physiological, metabolic, and immunological characteristics. Our sampling encompassed key developmental stages: the pullet stage (10 and 16 wk old), peak production (24 and 30 wk old), and later stage (60 wk old) (n = 99; 10 per group), allowing us to elucidate the temporal dynamics of epigenetic regulation. Our findings highlight a crucial window of epigenetic modulation during the prelaying period, characterized by stage-specific methylation alterations and the involvement of predicted transcription factor motifs within methylated regions. This observation was consistent with the expression patterns of DNA methyltransferases (DNMTs), including DNMT1, DNMT3A, and DNMT3B. In addition, a higher methylation level was observed in specific loci or regions in the LSL compared with the LB strain. Notably, we uncover strain-specific differences in methylation levels, particularly pronounced in genomic regions associated with intestinal integrity, inflammation, and energy homeostasis. Our research contributes to the multidisciplinary framework of epigenetics and egg-laying performance, offering valuable implications for poultry production and welfare.NEW & NOTEWORTHY Our study reveals key methylation changes in the jejunum mucosa of laying hens across developmental stages and between strains, with implications for gut health, immune function, and egg production. These findings highlight a crucial role of epigenetic regulation in optimizing performance.