Maize plants defective for the AGO104 protein show defects in chromatin condensation during meiosis, and subsequent failure to segregate chromosomes. AGO104 is a member of the ARGONAUTE family of proteins. AGO104 accumulates specifically in somatic cells surrounding the female meiocyte, suggesting a mobile signal rather than cell-autonomous control. AGO104 is necessary for non-CG methylation of centromeric and knob repeat DNA. Digital Gene Expression Tag Profiling experiments using high-throughput sequencing show that AGO104 influences the transcription of many targets in the ovaries, with a strong effect on centromeric repeats. AGO104 is related to Arabidopsis AGO9, but while AGO9 acts to repress germ cell fate in somatic tissues, AGO104 acts to repress somatic fate in germ cells. Thus, female germ cell development in maize is dependent upon conserved small RNA pathways acting non-cell autonomously in the ovule. Interfering with this repression leads to apomixis-like phenotypes in maize. Overall design: Profiling of gene expression in mutant versus wilt type ovaries.