Characterization of Imprinted Genes in Rice Reveals Conservation of Regulation and Imprinting with Other Plant Species

Abstract

Genomic imprinting is an epigenetic phenomenon by which certain genes display differential expression in a parent-of-origin-dependent manner. Hundreds of imprinted genes have been identified from several plant species. Here, we identified, with a high level of confidence, 208 imprinted gene candidates from rice (). Imprinted genes of rice showed limited association with the transposable elements, which contrasts with findings from Arabidopsis (). Generally, imprinting in rice is conserved within a species, but intraspecific variation also was detected. The imprinted rice genes do not show signatures of selection, which suggests that domestication has had a limited evolutionary consequence on genomic imprinting. Although conservation of imprinting in plants is limited, we show that some loci are imprinted in several different species. Moreover, our results suggest that different types of epigenetic regulation can be established either before or after fertilization. Imprinted 24-nucleotide small RNAs and their neighboring genes tend to express alleles from different parents. This association was not observed between 21-nucleotide small RNAs and their neighboring genes. Together, our findings suggest that the regulation of imprinting can be diverse, and genomic imprinting has evolutionary and biological significance.

Accurate Determination of Genotypic Variance of Cell Wall Characteristics of a Populus trichocarpa Pedigree Using High-Throughput Pyrolysis-Molecular Beam Mass Spectrometry

“…Also, parent-of-origin effects have been implicated in interspecific reproductive barriers (51, 52) with a high rate of diversifying evolution among plant species through genomic imprinting (53). However, imprinted expression is conserved in other genes across plant lineages, suggesting stabilizing selection for these loci (53,54).…”

MADS78 and MADS79 Are Essential Regulators of Early Seed Development in Rice

“…and rice(Folsom et al, 2014;Chen et al, 2018;Wang et al, 2018) are imprinted. Therefore, we examined the DNA methylation status of MADS78 and MADS79.…”

The hybrid protein interactome contributes to rice heterosis as epistatic effects

“…The results indicate that the number of co‐localized PPIs and the GO similarities of F 1 ‐specific PPIs are higher than those of any random network (empirical P < 0.001). Further, we examined the co‐expression of japonica and indica alleles from the genes involved in F 1 ‐specific PPIs by using the RNA‐seq data in accession of GS113769 (Chen et al , ) in NCBI GEO (Experimental Procedures). In http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE113769, the RNA‐seq samples were collected from the endosperm tissues of F 1 hybrids generated from two distinct, reciprocal crosses of japonica and indica rice.…”

“…Further, the number of co‐localized PPIs and the GO similarities between F 1 ‐specific PPIs and randomly generated PPIs were compared. We downloaded previously published RNA‐seq dataset of japonica × indica F 1 hybrids profiled in endosperm from NCBI GEO http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE113769 (Chen et al , ). Based on http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE113769, the co‐expression of japonica and indica alleles from the genes involved in F 1 ‐specific PPIs can be verified by using the SNPs between japonica and indica , which can be used to differentiate allelic expression.…”