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.