Genome-wide screening and analysis of imprinted genes in rapeseed (Brassica napus L.) endosperm

Species-specific genomic imprinting is an epigenetic phenomenon leading to parent-of-origin specific differential expression of maternally and paternally inherited alleles. To date, no studies of imprinting have been reported in rapeseed, a tetraploid species. Here, we analyzed global patterns of allelic gene expression in developing rapeseed endosperms from reciprocal crosses between inbred lines YN171 and 93275. 14,394 genes were found to harbor diagnostic SNPs between the parental lines. A total of 183 imprinted genes, consisting of 167 maternal expressed genes (MEGs) and 16 paternal expressed genes (PEGs) were identified. Some imprinted genes were validated in different endosperm stages and from other parental combinations by RT-PCR analysis. A clear clustering of imprinted genes throughout the rapeseed genome was identified, which was different from other plants. Unexpectedly, all differentially methylated regions (DMRs) in imprinted genes exhibit low CpG methylation rates no matter in maternal alleles or in paternal alleles and had no big difference between parent alleles, suggesting that cytosine methylation might play a non-essential role to epigenetically differentiate the maternal and paternal alleles in rapeseed imprinted genes. These results extend our understanding of gene imprinting in plants and provide potential avenues for further research in imprinted genes.