It was thought that cytoplasmic male sterility (CMS), exhibiting maternal inheritance, was associated with cytoplasmic genomes, especially mitochondrial genome because of mitochondrion as the center for energy metabolism in eukaryotic cells. Up to now, most of the results demonstrate that pollen abortion in CMS lines is accompanied by expression of novel open reading frames (ORFs) encoding in mitochondrial DNA (mtDNA), which result in the dysfunction of the cells. However, why the cell dysfunction is not taken place in oogamete or somatic cells? Furthermore, because many process, such as the gene transcription, transcript processing, translation and post-translation, and protein importing, folding and assembly, in mtDNA are controlled by nuclear genome, what role does the nuclear genome play in CMS line? Some evidence, e.g. HSP70 and cms-9E, indicate the differences in nuclear genes between CMS line and its maintainer although they are thought to be isonuclear lines. This paper presents an assumption that the sperm nucleus can be modified by ovum cytoplasm in the fertilized egg cell of CMS line during or after fertilization. The modifications include methylation pattern, 5mCpG, and sequences of nuclear DNA, e.g. insertion, deletion, transition and transversion of bases, and control the gene expression, processing and protein folding etc during subsequent events in ontogenesis. The modifications involve in identification of special site in the nuclear genome that is different between CMS line and restorer line, so the latter is not modified. Or the nuclear DNA of restorer is also modified same as CMS line, but other differences in DNA sequence could alter the development during microsporogenesis because the methylation pattern is altered during development. Fig 2, Ref
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