Comparative Analysis of Three-Dimensional Chromatin Architecture in the Shell Gland Between Blue- and White-Shelled Laying Ducks

Chromosomal three-dimensional (3D) structural variations can mediate phenotypic differentiation in animals and plants by altering chromatin interaction patterns and regulating gene transcription. Eggshell color is an important economic trait of laying ducks, and the uterus (shell gland) of the oviduct is the core functional site for eggshell formation and pigment deposition. To reveal the 3D genomic regulatory mechanism underlying eggshell color differentiation in blue-shelled laying ducks, this study employed high-throughput chromosome conformation capture (Hi-C) technology to systematically compare chromosomal spatial conformation differences in the shell glands between blue-shelled and white-shelled laying ducks and to dissect the regulatory characteristics of chromatin architecture at different hierarchical levels. The results showed that both phenotypic groups possessed typical and conserved chromatin interaction patterns; however, their spatial folding characteristics differed significantly. Blue-shelled laying ducks (Q1) exhibited predominantly short-range loose chromatin interactions, whereas white-shelled laying ducks (B1) tended to have medium- and long-range large-scale DNA looping interactions. A/B compartment analysis revealed that chromosomal compartmentalization differed little between the two groups, with dynamic transitions occurring in both A and B compartments. Differentially compartmentalized genes were mainly enriched in pathways such as immune response, basal metabolism, reproductive development, calcium signaling, and estrogen signaling. TAD topological structure analysis revealed obvious TAD boundary remodeling on chromosome 4 in blue-shelled laying ducks and significant differences in TAD number, length, and boundary signal strength between the two groups. Changes in specific TAD boundaries also led to altered gene functions. Differentially expressed genes were mainly enriched in processes such as cell–cell adhesion, metabolism, and cell cycle, as well as regulatory pathways closely related to pigment deposition, including porphyrin and chlorophyll metabolism, melanin biosynthesis, riboflavin metabolism, and bile secretion. In summary, based on chromatin spatial conformation analysis, this study found that the eggshell color trait of laying ducks did not appear to depend primarily on macroscopic A/B compartment structural regulation; however, it was primarily associated with local specific TAD topological remodeling. This remodeling may be linked to gene expression in pigment deposition-related pathways by altering local chromatin interaction patterns. Given the limited sample size, these findings are preliminary and suggest a potential association between 3D chromatin architecture and eggshell color, which warrants further functional validation.