Dna Barcoding Oforyza: Conventional, Specific, And Super Barcodes

Key message We applied the phylogenomics to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity. Rice (genusOryza) 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-oneOryzaspecies were identified. Conspecific relationships were determined betweenO. glaberrimaandO. barthii,O. glumipatulaandO. longistaminata,O. grandiglumisandO. alta,O. meyerianaandO. granulata,O. minutaandO. malampuzhaensis,O. nivaraandO. sativasubsp.indica, andO. sativasubsp.japonicaandO. rufipogon.DandLgenome types were not found and theHgenome 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,trnC-rpoB,rps16-trnQ,rpl22-rps19,trnK-matK, andndhC-trnV), 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.