PCR amplification of CMS-specific mitochondrial nucleotide sequences to identify cytoplasmic genotypes of onion (Allium cepa L.)

S-cytoplasm is the most common source of cytoplasmic-genic male sterility (CMS) used to produce hybrid onion seed. CMS determinants are thought to be on the mitochondrial (mt) genome. Although the characterization of polymorphisms in the mtDNA that distinguishes the N- and S-cytoplasms is significantly faster than test crossing, it is still time-consuming to complete RFLP analysis. I identified an unusual transcript pattern for the mitochondrial cob gene in S-cytoplasm, Sequencing of the mitochondrial cob gene revealed an insertion of chloroplast DNA sequence into the upstream region of cob in the S-cytoplasm. This region could be amplified with oligonucleotides flanking the upstream region to cob. PCR-detectable polymorphism based on differences in the sequences of the mtDNA that distinguishes N- and S-cytoplasms allows a quick and confident identification of the cytoplasm of individual plants.