A comprehensive genome-wide scan for parent-of-origin expressed genes in the pig clarifies the conservation landscape of genomic imprinting.

backgroundGenomic imprinting, a mechanism resulting in parent-of-origin expression of genes through epigenetic regulation, intersects with a broad range of biological fields, including evolution, molecular genetics and epigenetics, and determinism of complex traits. Although next generation sequencing technologies nowadays enable imprinted genes to be detected in a genome-wide manner, a wide spectrum of this phenomena is evaluated only in humans and rodents.

resultsHere, we propose to map genes showing a parental expression imbalance in hypothalamus, muscle and placenta in piglets around birth using an extensive strategy that minimized biases and relied on reciprocal crosses, reconstruction of parental phases after imputation, and statistical analyses discriminating parent-of-origin from allele-specific expression. We detected 141 genes with strong to exclusive parental expression imbalance (ratio > 25:75). A large proportion (80%) of these genes have never been shown to exhibit parent-of-origin expression and a small proportion (15%) are shared by at least two tissues, suggesting an overall weak conservation landscape of genomic imprinting. Interestingly, we identified novel parent-of-origin expressed genes involved in neurodevelopmental (PREPL, Prolyl Endopeptidase Like) and fetal growth (FAM20B, Glycosaminoglycan Xylosylkinase, and POU6F2, POU Class 6 Homeobox 2) functions. In-depth analyses of specific loci highlighted specific imprinted isoforms of COPG2 (COPI Coat Complex Subunit Gamma 2) and confirmed livestock-specific imprinted genes such as the Zinc Finger Protein 300-like gene.

conclusionsAltogether, our results provide an atlas of parent-of-origin expressed genes in the pig, making it the most documented species for genomic imprinting after humans and rodents. Our findings indicate weak conservation of this mechanism across species and tissues, suggesting a small number of core imprinted genes shared across eutherians and another imprinted genes that seem specific to species or tissues. These latter parent-of-origin expressed genes may have been subjected to evolutionary forces that have determine their imprinting status in either a livestock-specific or a tissue-specific manner.