VIMa and paternal-specifically expressed VIMb are involved in regulating DNA methylation and endosperm development in...

Kernel development is a pivotal determinant of grain yield in maize (Zea mays), a cereal crop that is fundamentally important for global food security. Here, we elucidated the essential role of VIM family genes in maize endosperm development by characterizing a miniature seed9 (mn9) mutant, in which the kernel size is reduced. Through map-based cloning, we demonstrated that the mn9 phenotype is caused by the concurrent disruption of 2 homologous genes, VIMa and VIMb. Notably, VIMa is broadly expressed and follows Mendelian segregation, whereas VIMb is an endosperm-specific imprinted gene with near-exclusive paternal expression. In maize, there exists another broadly expressed nonimprinted VIM family gene, VIMc, which is closest to VIMa in terms of expression pattern and sequence similarity, and we were unable to obtain vima;vimc double mutants. Single mutants of VIMa, VIMb, or VIMc exhibited no visible phenotypes or alterations in DNA methylation levels, whereas simultaneous loss of VIMa and VIMb function induced a reduction in genome-wide CG methylation specifically in the endosperm. In addition, we found that endoreduplication is impaired in vima;vimb mutant endosperm, leading to reduced endosperm cell ploidy, decreased cell size, and consequently diminished kernel weight. In summary, our results reveal that loss of VIMa and VIMb causes endosperm-specific CG hypomethylation, defective endoreduplication, and reduced kernel size and provide a systematic characterization of VIM family functions in maize endosperm development.