Rice-specific DNA barcodes
Most species in the Oryza genus have an evolutionary history of only a few million years. Very limited genetic variation has accumulated within such a short time and conventional DNA barcodes do not work well at species level, especially for those belonging to the A ,B , and C genome types. The two most variable genes (NP78 and R22) picked out from 142 nuclear genes tested by Zou et al. (2008) served here as rice-specific nuclear DNA barcodes. Despite sequencing difficulties arising from multiple copies in tetraploid species, the combined marker performed sufficiently well. It is unlikely for the two genes to have diverged significantly in different species, thus explaining why they could discriminate between species of the same genome types.
Although species of the A , B or C genome types are very closely related, complete chloroplast genomes have accumulated enough variations to discriminate between them and all rice species are identifiable even with phylogenetic methods. Owing to the single-copy nature of chloroplast genes, mutations in chloroplast genomes become fixed and spread more quickly than those in nuclear genomes. Such mutations may not reflect a true phylogeny but are adequate for species discrimination.
The powerful performance of the complete chloroplast genome for species identification does not imply that it should be used in routine plant material identifications. There are some sensible shortcuts one can take, as a very large proportion of the chloroplast genome does not contribute much to species discrimination. The most variable regions could be an epitome of the whole genome. Here, six hypervariable regions in the chloroplast genome were selected and their combination served as rice-specific DNA barcodes. This epitome worked almost as well as the entire genome in terms of species discrimination using rice seeds from seed banks or field collections.