Rice (genus Oryza) is one of the most important crops in the world,
supporting half of the world’s population. Breeding of high-yielding and
quality cultivars relies on genetic resources from both cultivated and
wild species, which are collected and maintained in seed banks.
Unfortunately, numerous seeds are mislabeled due to taxonomic issues or
misidentifications. Here, we applied the phylogenomics of 58 complete
chloroplast genomes and two hypervariable nuclear genes to determine
species identity in rice seeds. Twenty-one Oryza species were
identified. Conspecific relationships were determined between O.
glaberrima and O. barthii, O. glumipatula and O. longistaminata, O.
grandiglumis and O. alta, O. meyeriana and O. granulata, O. minuta and
O. malampuzhaensis, O. nivara and O. sativa subsp. indica, and O. sativa
subsp. japonica and O. rufipogon. D and L genome types were not found
and the H genome type was extinct. Importantly, we evaluated the
performance of four conventional plant DNA barcodes (matK, rbcL,
psbA-trnH, and ITS), six rice-specific chloroplast DNA barcodes
(psaJ-rpl33, rpoB-trnC, rps16-trnQ, rps19-rpl22, trnK-matK, and
trnV-ndhC), two rice-specific nuclear DNA barcodes (NP78 and R22), and a
chloroplast genome super DNA barcode. The latter was the most reliable
marker. The six rice-specific chloroplast barcodes revealed that 17% of
the 53 seed accessions from rice seed banks or field collections were
mislabeled. These results are expected to clarify the concept of rice
species, aid in the identification and use of rice germplasms, and
support rice biodiversity.