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In plants, a subset of genes exhibit imprinting in endosperm tissue such thatexpression is primarily from the maternal or paternal allele. Imprinting mayarise as a consequence of mechanisms for silencing of transposons duringreproduction, and in some cases imprinted expression of particular genes mayprovide a selective advantage such that it is conserved across species.Separate mechanisms for the origin of imprinted expression patterns andmaintenance of these patterns may result in substantial variation in thetargets of imprinting in different species. Here we present deep sequencing ofRNAs isolated from reciprocal crosses of four diverse maize genotypes,providing a comprehensive analysis of imprinting in maize that allowsevaluation of imprinting at more than 95% of endosperm-expressed genes. We findthat over 500 genes exhibit statistically significant parent-of-origin effectsin maize endosperm tissue, but focused our analyses on a subset of these genesthat had >90% expression from the maternal allele (69 genes) or from thepaternal allele (108 genes) in at least one reciprocal cross. Over 10% ofimprinted genes show evidence of allelic variation for imprinting. A comparisonof imprinting in maize and rice reveals that only 13% of genes with syntenicorthologs in both species exhibit conserved imprinting. Genes that exhibitconserved imprinting in maize relative to rice have elevated dN/dS ratioscompared to other imprinted genes, suggesting a history of more rapidevolution. Together, these data suggest that imprinting only has functionalrelevance at a subset of loci that currently exhibit imprinting in maize.

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