Dissecting Allele‐Specific Expression (
ASE
) in Landrace × Meishan Cross Pig Fetal‐Placental Tissues: Distribution, Functional Split, and Mechanisms
Jinbi Zhang, Shiyong Xu, Wangjun Wu, Lifan Zhang, Aiwen Jiang, Ming Shen, Jingli Tao, Honglin Liu, Zengxiang Pan ABSTRACT
Allele‐specific expression (ASE) is a key regulatory mechanism linking genetic variation to phenotypic diversity. This study conducted a genome‐wide ASE analysis in embryonic (brain, kidney, liver) and extraembryonic (chorion) tissues of Landrace × Meishan crossbred pigs. By integrating DNA sequencing of parental and F1 hybrids and RNA‐sequencing of F1 tissues, a high‐resolution ASE landscape was built via strict allele‐specific SNP identification. Genomically, ASE genes (ASEG) were enriched on chromosomes 6, 7, 12, X and sparse on chromosome 11, and can be classified into extreme/moderate types by expression pattern and parental bias. Paternal ASEGs had higher expression levels, while maternal ones had higher abundance. Functionally, tissue‐concordant ASEGs supported embryo/placenta basal development, tissue‐specific ones matched organ core functions; maternal ASEGs were enriched in mitochondrial pathways, paternal ones in cell motility and RNA transcription. Besides, chorion had more allele‐specific methylated regions than embryonic tissues, with opposite ASE directions. We proposed “orthogonal dual regulatory dimensions” for the relationship between ASE and tissue‐specific expression. We also proposed regulatory models of extreme and moderate ASEGs, functional division modes between embryo and extraembryonic tissues, and between paternal and maternal alleles. This study clarifies tissue‐specific ASE patterns and mechanisms, providing a framework for future ASE research.