The molecular basis of mitchondrial genome rearrangements in pearl millet and sorghum

The plant mitochondrial genome is retained in a multipartite structure that is highly recombinogenic, and rearrangements often occur spontaneously. Recombinationally active large and small repeated sequences and substoichiometric DNA molecules are responsible for the dynamic nature of the genome. Through comparison of mitochondrial (mt) DNA polymorphisms between the cytoplasmic male sterile (CMS) A1 line of pearl millet (Pennisetum glaucum) and its fertile revertant, it was discovered that fertility reversion results from a two-step recombination event to alter two of the three CoxI -related regions and destroy expression of an abnormal CoxI-3 gene. Copy number of a subgenomic molecule that contains a CoxI-1-2 junction sequence is 10 times higher in revertant lines than in the maintainer B line and CMS A1 line. We propose that increased copy number of this junction sequence triggers a recombination event that leads to fertility reversion in CMS millet. CoxI-3 is prominent in the CMS A1 line, but it is substoichiometric in the maintainer B line. Since RNAi-mediated knockdown of the nuclear gene Msh1 causes substoichiometric shifting and mtDNA rearrangements in dicots, and a diverse collection of naturally occurring CMS lines are available in pearl millet and sorghum (Sorghum bicolor L. Moench), we tested mitochondrial genome response to RNAi-mediated suppression of Msh1 in both millet and sorghum. In derived transgenic millet and sorghum lines, evidence of mitochondrial substoichiometric shifting was observed. Cytoplasmic male sterility and several other plant phenotypes emerged in both monocot species. Some of the emerging mitochondrial DNA patterns resembled those already present in naturally occurring CMS millet and sorghum lines. Phenotypes of leaf variegation and altered stem development, including extremely elongated or stunted internodes, and enhanced tillering were observed in transgenic progeny. These experiments provide evidence that modulation of Msh1 can serve as an approach to induce novel CMS forms in crops or breed for other agronomic variation. This mitochondrial mutation system is also valuable for studying mitochondrialnuclear interactions and their regulation in plant developmental processes