DNA barcoding of Oryza: conventional, specific, and super barcodes


作  者:Zhang W, Sun YZ, Liu J, Xu C, Zou XH, Chen X, Liu YL, Wu P, Yang XY*, Zhou SL*
刊物名称:Plant Molecular Biology
卷:  期:  页码:DOI: 10.1007/s11103-020-01054-3
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.



版权所有 © 系统与进化植物学国家重点实验室[中国科学院植物研究所]
ICP备16067583号-12 网站管理 技术支持:青云软件


  • 地址:北京市海淀区 香山南辛村20号
  • 邮编:100093
  • 电话:010-6283 6086
  • 传真:010-6283 6095
  • 电邮:lseb@ibcas.ac.cn