The relatively low evolution rate of the chloroplast DNA has made it an ideal tool to study evolutionary processes in plants above the species levels. However, recent studies have demonstrated that intraspecific variation in the chloroplast DNA is also common. This variation has provided useful insights into population level evolutionary processes. The polymerase chain reaction and sequencing of a noncoding chloroplast region used to classify onion lines for cytoplasmic type facilitated the identification of one sterile and two normal plastome variants in onion (Allium cepa L.). Sequence comparison revealed that differences between plastome variants included the presence of single-nucleotide polymorphisms associated with cytoplasmic type and variable numbers of tandem repeats, possibly resulting from slipped-strand mispairing. Our observations support the use of chloroplast-specific markers to assist in the selection of specific cytoplasmic types, suggest the potential to facilitate genotype determination, and demonstrate the presence of additional variation within cytoplasm type which gives insight into plastome evolution and may facilitate more accurate genotyping and selection.
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