Comprehensive analysis of imprinted genes in maize reveals limited conservation with other species and allelic variation for imprinting

TL;DR

This study provides a comprehensive analysis of maize imprinting, revealing limited conservation with rice and significant allelic variation, indicating that imprinting affects a small subset of genes with potential functional importance.

Contribution

It offers the first extensive genome-wide characterization of imprinting in maize, highlighting its limited conservation with other species and allelic variability.

Findings

Over 500 genes show parent-of-origin effects in maize endosperm.

Only 13% of syntenic orthologs are conserved in imprinting between maize and rice.

Imprinted genes with conserved imprinting have higher dN/dS ratios, indicating rapid evolution.

Abstract

In plants, a subset of genes exhibit imprinting in endosperm tissue such that expression is primarily from the maternal or paternal allele. Imprinting may arise as a consequence of mechanisms for silencing of transposons during reproduction, and in some cases imprinted expression of particular genes may provide a selective advantage such that it is conserved across species. Separate mechanisms for the origin of imprinted expression patterns and maintenance of these patterns may result in substantial variation in the targets of imprinting in different species. Here we present deep sequencing of RNAs isolated from reciprocal crosses of four diverse maize genotypes, providing a comprehensive analysis of imprinting in maize that allows evaluation of imprinting at more than 95% of endosperm-expressed genes. We find that over 500 genes exhibit statistically significant parent-of-origin effects in maize endosperm tissue, but focused our analyses on a subset of these genes that had >90% expression from the maternal allele (69 genes) or from the paternal allele (108 genes) in at least one reciprocal cross. Over 10% of imprinted genes show evidence of allelic variation for imprinting. A comparison of imprinting in maize and rice reveals that only 13% of genes with syntenic orthologs in both species exhibit conserved imprinting. Genes that exhibit conserved imprinting in maize relative to rice have elevated dN/dS ratios compared to other imprinted genes, suggesting a history of more rapid evolution. Together, these data suggest that imprinting only has functional relevance at a subset of loci that currently exhibit imprinting in maize.