Transcription itself, including maternal deposition of RNAs, transport of RNAs from other tissues, and transcript degradation. The most stringent test of imprinting is to show that transcription itself is differential between alleles, which our method cannot address. Our initial analysis of gene imprinting based on DNA methylation profiling discovered a subset of imprinted genes associated with TE-derived differentially methylated regions. Our present survey shows that about a third of imprinted genes, often encoding regulatory proteins, are associated with differential DNA methylation within 2 kb of the coding sequence. However, a number of MEGs, many of which encode enzymes like pectinmethylesterases, pectinesterase inhibitors and glycosyl hydrolases, all involved in cell wall modification, are not associated with DMRs. The mechanism of parentally AbMole Gambogic-acid biased expression at these loci likely does not directly involve DNA methylation. Striking features of our data are that most genes exhibit partial imprintingratherthanstrictmonoallelicexpressionandthatMEGsare more numerous than PEGs. The kinship theory of imprinting predicts that monoallelic expression is the evolutionary stable strategy for genes in which the maternally and paternally derived alleles favor different optimal levels of expression. If not due to conflict, why do so many Arabidopsis thaliana genes exhibit parent-of-origin specific biased expression patterns? One possibility is that partial imprinting is an evolutionary echo of complete imprinting that existed at these genes when A. thaliana possessed a different mating system. A. thaliana is primarily selffertilizing, with low but variable rates of outcrossing observed in the wild. Because maternal and paternal genomes are usually identical, conflict is expected to be very low in A. thaliana seeds. However, A. thaliana is estimated to have been self-fertilizing for a short amount of evolutionary time – perhaps only 400,000 years. Furthermore, despite the loss of genetic conflict, as a mating system shifts from outcrossing to selfing, loss of imprinting is not predicted to be rapid. Genes that are partially imprinted could reflect an adjustment of maternal and paternal allele expression to a new level of optimal total gene expression that relies on the mechanisms of gene expression regulation already in place from when the gene was expressed monoallelically. Interestingly, the kinship theory does predict that the expressionofPEGswillbereducedasplantsbecomeself-fertilizing and we find that partial imprinting appears to be more common for PEGs than MEGs. The preponderance of MEGs over PEGs, regardless of partial vs. complete imprinting, also fits predictions of the maternal-offspring AbMole (-)-Tetramisole coadaptation theory of imprinting. An alternative, non mutually exclusive, possibility is that the partially imprinted genes do not reflect a record of past conflict but are instead imprinted as a form of gene dosage regulation.