Chromatin accessibility of the jejunum in two high-yielding laying hen strains under divergent mineral phosphorus supply during the transition to egg laying

Optimizing dietary phosphorus (P) levels is crucial for sustainable egg production, hen welfare, productivity, and reducing excessive P excretion. Dietary P influences systemic physiological responses, including gene expression dynamics and epigenetic regulation, particularly in the gut. Epigenetic modifications, including chromatin accessibility, play a crucial role in gene regulation by integrating genetic and environmental signals. It is hypothesized that age, strain, and mineral P levels together influence the epigenetic and transcriptional landscape in the jejunum during the transition to egg-laying. Using the domestic chicken ( Gallus gallus domesticus ), two commercial laying-hen strains, Lohmann Brown (LB) and Lohmann Selected Leghorn (LSL) were studied. The experiment followed a 2 × 2 × 2 factorial design including two strains (LB vs. LSL), two production periods (transition before the onset of egg laying vs. onset of laying), and two dietary P levels (without supplemental mineral P [P−] or with 1 g/kg supplemental P from monocalcium phosphate [P+]). A total of 80 hens were used, 10 per strain × period × diet combination, in a randomised complete block design. In each period, hens were housed individually in metabolic units for 4 weeks, beginning either before the onset of egg-laying (transition; placed at 15 weeks of age, sampled at week 19) or after the onset of egg-laying (onset of laying; placed at 20 weeks of age, sampled at week 24). At placement, mean initial body weight was 1228 ± 134 g (LB) and 1036 ± 70 g (LSL) in the transition period, and 1552 ± 93 g (LB) and 1244 ± 64 g (LSL) in the onset-of-laying period. Chromatin accessibility was assessed using an assay for transposase-accessible chromatin with sequencing (ATAC-Seq). The analysis revealed distinct strain-specific chromatin accessibility profiles, identifying 6610 differentially accessible regions (DAR) (adjusted P < 0.01). The LSL strain genome exhibited more regions with reduced accessibility (3603 DAR) compared to the LB strain (adjusted P < 0.01). Extensive chromatin remodelling was observed during the transition to laying onset (7884 DARs), with greater loss of accessibility at 24 weeks (4193 DARs). Dietary P had subtler effects (1671 DARs; P < 0.01), including increased accessibility at loci such as CALB1 under the P- diet. Enrichment analysis of transcripts nearest these DARs revealed pathways related to lipid transport, fatty acid metabolism, Wnt signalling, transforming growth factor-β (TGF-β) signalling, and calcium signalling. Additionally, ANalysis Algorithm for Networks Specified by Enhancers (ANANSE) integrates predicted transcription factor (TF) binding in accessible chromatin with RNA-Seq expression to weight gene regulatory networks (GRN) edges and rank TF influence (P+ vs. P-), highlighting regulators linked to bone/cartilage remodelling ( RUNX2, STAT3, and CLOCK ) and stress signalling ( ATF3 and JUND ). This study elucidated the complex interplay between sexual maturation period, genetic background, and nutritional mineral status in shaping the regulatory architecture of the jejunum, a key site for P absorption.