Spontaneous and RNAi-Induced Epimutants of a Kinesin Gene Family in Maize

Maize abnormal chromosome 10 (Ab10) converts heterochromatic regions called knobs into motile neocentromeres that are preferentially transmitted to progeny. We have recently identified a novel gene family called the Kinesin driver (Kindr) complex that is responsible for this phenotype. At least nine Kindr genes are clustered in a ~1 Mb region of the Ab10 chromosome that is absent in the reference genome. RNA-seq shows that at least five of the nine Kindr genes are expressed. Screens for mutants of meiotic drive and neocentromere activity identified two mutants that show little or no expression of Kindr. Small RNA analysis and whole genome bisulfite sequencing revealed that both mutants are in fact epimutants, with shifts in small RNA targeting and dramatic increases in DNA methylation affecting all copies of the Kindr gene family. We also transformed plants with a hairpin construct designed to knock down Kindr expression by RNAi. In some lines RNAi abolished Kindr expression and caused a complete loss of meiotic drive. The RNAi-induced mutant phenotype was stable even in the absence of the RNAi inducer. Spontaneous and induced epimutants of this type have not been previously described in maize. The data suggest that genes may be targeted for RNA-dependent DNA methylation at a reasonably high frequency, particularly if they are multi-copy and dispensable to the plant.