Abstract
Key messageWe applied the phylogenomics to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.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.
Highlights
The last 50 years witnessed an explosion in the human population, which has been supported by a three-fold global expansion in crop production (Tayyib 2013)
The phylogenetic relationships among Oryza species were reconstructed based on their complete chloroplast genomes, as well as the nuclear internal transcribed spacer of ribosomal DNA (ITS), NP78, and R22 genes (Table S2)
The species O. malampuzhaensis and O. minuta of the BC genome type formed a clade with O. punctata, indicating that a species of the B genome type was their maternal parent
Summary
The last 50 years witnessed an explosion in the human population, which has been supported by a three-fold global expansion in crop production (Tayyib 2013). Maize, and wheat, together with some other staple crops, have been key for this expansion. The rapid increase in crop production has been achieved largely through higher yields per unit and crop intensification. Creation of higher-yielding crop varieties requires specific genes from the gene pool of the crop species and/or its close relatives, such as the semidwarfing gene in rice (sd-1) and Rht and Rht in wheat (Gale and Marshall 1973; Jennings 1964). Genetic resources of crops and their close relatives were initially conserved ex situ in seed banks worldwide and later in situ
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