Fig. 1: Integrated experimental design and analytical strategies for comprehensive characterization of allelic expression in reciprocal cross pigs.

a Duroc pigs and lulai pigs underwent reciprocal crosses at various developmental stages. b Overview of tissue sample size and sequencing contents across developmental stages. c Genome assignment of sequencing data in hybrid offspring. The sequencing reads were mapped to individualized genomes, and the origin of reads is determined based on mismatches with informative variants in the personalized genome. If a read matches with an A base, it is attributed to duroc pigs; if it matches with a G base, it is attributed to lulai pigs. If there are no informative variants at the matching position, the origin of the read remains unclear. d Quantification of allele expression. e Allelic expression comparison and ASE evaluation across tissues and developmental stages. If the expression level of the maternal allele is higher, regardless of whether the maternal parent is duroc or lulai pig, the gene is classified as a POE gene. If the expression level of the duroc allele is higher, regardless of whether duroc is used as the maternal or paternal parent, the gene is classified as an AGE gene.