Identification of cytoplasms using the polymerase chain reaction to aid in the extraction of maintainer lines from open-pollinated populations of onion.

S-cytoplasm is the most common source of cytoplasmic-genic male sterility (CMS) used to produce hybrid-onion seed. Identification of the cytoplasm of a single plant takes from 4 to 8 years and is complicated by the segregation of a nuclear gene that restores fertility. Although CMS in onion may be due to an incompatibility between the mitochondrial and nuclear genomes, Southern analyses of DNA from individual plants from crosses of S- and N-cytoplasmic plants supported maternal inheritance of the chloroplast and mitochondrial DNA and, therefore, polymorphisms in the chloroplast DNA may be used to classify cytoplasms. Amplification by the polymerase chain reaction of a fragment that carries an autapomorphic 100-bp insertion in the chloroplast DNA of N-cytoplasm offers a significantly quicker and cheaper alternative to crossing or Southern analysis. Molecular characterization of N- and S-cytoplasms and frequencies of the nuclear non-restoring allele allow onion breeders to determine the proportion of plants in open-pollinated populations that maintain CMS and can significantly reduce the investment required to identify individual maintainer plants.