Integrative 3D Genomics with Multi-Omics Analysis and Functional Validation of Genetic Regulatory Mechanisms of Abdominal Fat Deposition in Chickens (ATAC-seq).

Chickens are the most abundant agricultural animals globally, with controlling abdominal fat deposition (AFD) being a key objective in poultry breeding. While GWAS can identify genetic variants associated with AFD traits, the precise roles and mechanisms of these variants remain largely unclear. This study used two distinct chicken lines, selectively bred for differing AFD, as experimental models. Through the integration of genomic, epigenomic, 3D genomic, and transcriptomic data, a comprehensive chromatin 3D regulatory network map was developed to reveal the genetic regulatory mechanisms that influence AFD traits. Abdominal fat tissue from six randomly selected NEAUHLF individuals (three from each line) from the initial pool of 330 chickens underwent ATAC-seq sequencing by Frasergen, (Wuhan, China).