DNA barcoding of Oryza : conventional, specific, and super barcodes
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DNA barcoding of Oryza: conventional, specific, and super barcodes Wen Zhang1,2 · Yuzhe Sun1,2 · Jia Liu1,4 · Chao Xu1 · Xinhui Zou1 · Xun Chen1,3 · Yanlei Liu1,2 · Ping Wu1,2 · Xueying Yang5 · Shiliang Zhou1 Received: 19 April 2020 / Accepted: 13 August 2020 © The Author(s) 2020
Abstract 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. 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, trnC-rpoB, rps16-trnQ, rpl22-rps19, trnK-matK, and ndhC-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. Keywords Chloroplast genome · DNA barcode · Oryza · Phylogenomics · Seed identification Wen Zhang and Yuzhe Sun contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11103-020-01054-3) contains supplementary material, which is available to authorized users. * Xueying Yang [email protected] * Shiliang Zhou [email protected] 1
State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
2
College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
3
College of Landscape Architecture, Northeast Forestry University, Haerbin 150040, China
4
College of Life Science, Sichuan Agricultural University, Yaan 625014, Sichuan, China
5
Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, China, Beijing 100038, China
Introduction The last 50 years witnessed
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