Genomic imprinting, methylation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean.

W Xu,F Li,M Dai,A Liu

doi:10.1093/nar/gku375

Abstract

Genomic imprinting often results in parent-of-origin specific differential expression of maternally and paternally inherited alleles. In plants, the triploid endosperm is where gene imprinting occurs most often, but aside from studies on Arabidopsis, little is known about gene imprinting in dicotyledons. In this study, we inspected genomic imprinting in castor bean (Ricinus communis) endosperm, which persists throughout seed development. After mapping out the polymorphic SNP loci between accessions ZB306 and ZB107, we generated deep sequencing RNA profiles of F1 hybrid seeds derived from reciprocal crosses. Using polymorphic SNP sites to quantify allele-specific expression levels, we identified 209 genes in reciprocal endosperms with potential parent-of-origin specific expression, including 200 maternally expressed genes and 9 paternally expressed genes. In total, 57 of the imprinted genes were validated via reverse transcriptase-polymerase chain reaction sequencing, and analysis of the genomic DNA methylation distribution between embryo and endosperm tissues showed significant hypomethylation in the endosperm and an enrichment of differentially methylated regions around the identified genes. Curiously, the expression of the imprinted genes was not tightly linked to DNA methylation. These results largely extended gene imprinting information existing in plants, providing potential directions for further research in gene imprinting.

Highlights

Genomic imprinting is a typical epigenetic phenomenon that mainly manifests itself in the placenta of mammals and the endosperm of flowering plants [1,2]
To discriminate the parental origin of allelic expression in hybrids, we conducted a deep high-throughput RNA sequencing for seed libraries of two castor bean varieties ZB107 and ZB306 to discover single nucleotide polymorphisms (SNPs) between the two varieties, yielding some 50 million reads
Clean reads were aligned to the ZB107 and ZB306 windows to allow for calling SNP coverage reads and characterizing the allelic expression of a given hybrid endosperm

Summary

Introduction

Genomic imprinting is a typical epigenetic phenomenon that mainly manifests itself in the placenta of mammals and the endosperm of flowering plants [1,2]. There is other evidence showing that imprinted genes affect the demand and supply of nutrients in both the mammalian placenta and during plant endosperm development [4,9]. If correct, this last possibility may imply that gene imprinting could be an essential element of successful reproduction that manifests itself in both flowering plants and mammals [9,10,11]

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