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DNA barcoding of Oryza: conventional, specific, and super barcodes
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  • Wen Zhang,
  • Yuzhe Sun,
  • Jia Liu,
  • Chao Xu,
  • Xinhui Zou,
  • Xun Chen,
  • Yanlei Liu,
  • Ping Wu,
  • Xueying Yang,
  • Shi-Liang Zhou
Wen Zhang
Institute of Botany Chinese Academy of Sciences
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Yuzhe Sun
Institute of Botany Chinese Academy of Sciences
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Jia Liu
Institute of Botany Chinese Academy of Sciences
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Chao Xu
Institute of Botany Chinese Academy of Sciences
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Xinhui Zou
Institute of Botany Chinese Academy of Sciences
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Xun Chen
Northeast Forestry University
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Yanlei Liu
Institute of Botany Chinese Academy of Sciences
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Ping Wu
Institute of Botany Chinese Academy of Sciences
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Xueying Yang
Institute of Forensic Science, Ministry of Public Security
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Shi-Liang Zhou
Institute of Botany Chinese Academy of Sciences
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Abstract

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.