Dissecting Allele-Specific Expression (ASE) in Landrace × Meishan Cross Pig Fetal-Placental Tissues: Distribution, Functional Split, and Mechanisms.

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.