Integrated analysis of ATAC-seq and RNA-seq in endometrial tissues between American and French large white pigs

Abstract Large White pigs are widely used as maternal lines, although reproductive performance varies among populations. The endometrium supports embryo implantation and development, and its molecular state may contribute to reproductive variation. This exploratory extreme-phenotype study compared endometrial tissues from nulliparous estrous gilts from French (FL) and American (AL) Large White source populations with different historical herd-level litter-size records. Uterine horn length was measured in five gilts per line, and the three FL gilts with the longest total uterine horns and the three AL gilts with the shortest were selected for ATAC-seq and RNA-seq. The left and right uterine horns were significantly longer in FL than in AL gilts ATAC-seq identified 11,502 exploratory candidate accessibility regions; these regions were linked to 6,867 unique genes. RNA-seq detected 4,078 differentially expressed genes (DEGs). Integrated analysis identified 1,227 overlapping genes and highlighted oxytocin, calcium, PI3K-Akt, and related signaling pathways as candidate modules. ITPR1 , ITPR2 , PLA2G4A , and CACNA1C , together with several motif- and network-derived candidate transcriptional regulators, were prioritized for further study. These findings describe molecular differences observed in the selected extreme-phenotype gilts and provide hypotheses for validation in larger, unselected populations.