Since its domestication in the inner Niger delta ca. rice, O. glaberrima is significant for its resistance to many pests Generally, African rice has small, pear-shaped grain, reddish bran and green to black hulls, straight, simply-branched panicles, and short, rounded ligules. Genome sequencing and analysis of numerous wild rice (Oryza rufipogon) and Asian cultivated rice (Oryza sativa) accessions have enabled the identification of genome-wide signatures of rice domestication and the unlocking of the origin of Asian cultivated rice. Additional annotations generated by the Gramene and Ensembl Plants traits by finding commonalities and differences with O. sativa. Portères, R. in Origins of African Plant Domestication (ed. eCollection 2020. A previous reference genome was published but newer studies highlighted some missing parts. by many African countries to meet the growing need for rice as a staple Construct DNA fingerprint/BAC-end sequence physical maps from 11 deep coverage BAC libraries that represent the 11 wild genomes of Oryza (830,000 fingerprints; 1,659,000 BAC ends) align the 11 physical maps with the sequenced reference subspecies japonica and indica. & Oliver, R.A.) 43–58 (Cambridge University Press, 1970). Please enable it to take advantage of the complete set of features! Sequence comparisons of OsSh1 and Sh4 . Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Both species have same genome AA (Chang 1976, Morinaga et al. What can I find? Nabholz B, Sarah G, Sabot F, Ruiz M, Adam H, Nidelet S, Ghesquière A, Santoni S, David J, Glémin S. Mol Ecol. project include: Ensembl Plants release 49 - November 2020 International audienceThe African cultivated rice (Oryza glaberrima) was domesticated in West Africa 3000 years ago. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events … Interspecific crosses between African and Asian rice have produced eScholarship, California Digital Library, University of California, Sweeney M, McCouch S. The complex history of the domestication of rice. Get the latest public health information from CDC: https://www.coronavirus.gov. 12 chromosomes and an estimated size of ~358 Mb. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication O. glaberrima contains many important adaptive traits for cultivation in African soils and climates.  |  The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012). USA.gov. provides insight into the genetic basis of domestication and other For complete certainty, a genetic test can be used. The genome was assembled as outlined in Supplementary Figure 1and is composed of 5,309 scaffolds (scaffold N50, 217 kb) assembled into 12 pseudomolecules, result- ing in a total assembly size of 316 Mb (Supplementary Table 2). Niger River Delta from its still extant progenitor, Oryza barthii. The causal genetic factors responsible for the loss of awn in these two rice species remain largely unknown. Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima). Oryza sativa L. and Oryza glaberrima, the domestic rice varieties, are diploid species (2n = 24), with 22 wild relative species, and together, comprise four species complexes: the cultivated rice complex and six primary gene pool relatives; the officinalis complex of nine species with five diploid and four tetraploid: the meyeriana complex with two diploid species; the ridleyi complex with two tetraploid species; and two … 2018 Jul 23;28(14):2274-2282.e6. Identification of candidate regions of…. What can I find? HHS The complex geography of domestication of the African rice Oryza glaberrima. doi: 10.1016/j.cub.2018.05.066. Identification of the domestication center of O. glaberrima . Figure 5. More about the Ensembl Plants microarray annotation strategy. 1957). Li J, Zhou J, Zhang Y, Yang Y, Pu Q, Tao D. Front Plant Sci. 2017), however, some of the 14 non-A genome Oryza species dating from the divergence of Oryza … 2007;100:951–957. They were independently domesticated from divergent progenitor wild species in different geographic locations, South Asia and West Africa, respectively [2] . 2019 Apr 29;70:639-665. doi: 10.1146/annurev-arplant-050718-100320. However, little is known about the genetic basis of quantitative traits and adaptive variation of … Background African rice, Oryza glaberrima , is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. and diseases and for its tolerance of drought and infertile soils. An evolutionary genomic tale of two rice species. Figure 3. doi: 10.1371/journal.pgen.1007414. Front Plant Sci. Identification of candidate regions of artificial selection during O. glaberrima domestication. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. The Oryza genus contains 11 different genome types across 27 species, both diploid and polyploid, with a 3.6-fold difference in genome sizes (from around 300 Mb in the diploid FF genome of O. brachyantha to 1,283 Mb in the HHJJ polyploid genome of O. ridleyi, with the AA genome of cultivated rice falling in the 400Mb range). The O. glaberrima genome (CG14 v1). glaberrima reference genome and analysed through a combination of population genetic and phylogenetic approaches, details of which can be found in the Materials and methods. Abrouk M, Ahmed HI, Cubry P, Å imoníková D, Cauet S, Pailles Y, Bettgenhaeuser J, Gapa L, Scarcelli N, Couderc M, Zekraoui L, Kathiresan N, Čížková J, Hřibová E, Doležel J, Arribat S, Bergès H, Wieringa JJ, Gueye M, Kane NA, Leclerc C, Causse S, Vancoppenolle S, Billot C, Wicker T, Vigouroux Y, Barnaud A, Krattinger SG. The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes. 2020 Sep 23;11:555572. doi: 10.3389/fpls.2020.555572. cultivars with improved yield and quality traits, that have been adopted ( a ) Orthologous gene relationship of…, NLM Oryza glaberrima genome sequence as a resource for breeding based on genomics. Figure 4. Mussurova S, Al-Bader N, Zuccolo A, Wing RA. Littlefield, D.C. Rice and Slaves: Ethnicity and the Slave Trade in Colonial South Carolina (University of Illinois Press, 1991). Potential of Platinum Standard Reference Genomes to Exploit Natural Variation in the Wild Relatives of Rice. Dong L, Liu S, Kyaing MS, Xu P, Tharreau D, Deng W, Li X, Bi Y, Zeng L, Li J, Zhou J, Tao D, Yang Q. Despite its use, the long life cycle of Nipponbare makes it time-consuming for most genetic analyses. African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. Our analyses showed genetic structure within O. glaberrimathat has a geographical association. Vaughan DA, Lu BR, Tomooka N. The evolving story of rice evolution. This site needs JavaScript to work properly. Mapping to the genome of multiple sequence-based feature sets using. Several studies indicated that it has extremely narrow genetic diversity compared to both its wild progenitor, Oryza barthii and the Asian rice, Oryza sativa which can mainly be attributed to a severe domestication bottleneck. Bot. 1. Variation effect prediction with sequence ontology. Since its domestication in the inner Niger delta ca. Cubry P, Tranchant-Dubreuil C, Thuillet AC, Monat C, Ndjiondjop MN, Labadie K, Cruaud C, Engelen S, Scarcelli N, Rhoné B, Burgarella C, Dupuy C, Larmande P, Wincker P, François O, Sabot F, Vigouroux Y. Curr Biol. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. Most cultivated varieties of Oryza sativa and Oryza glaberrima , however, have lost the ability to form long awns. Similar to Asian rice, African rice is a diploid A-type genome, having 12 chromosomes and an estimated size of ~358 Mb. RepeatMasker with MIPS and AGI repeat libraries, and Dust, TRF. Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Although less cultivated than the Asian rice (O. sativa), O. glaberrima landraces often display interesting adaptation to rustic environment (e.g. 38 39 Keywords 40 African rice, Genome Wide Association Study, flowering … Get the latest research from NIH: https://www.nih.gov/coronavirus. Epub 2007 Jul 6. The cultivation of rice in Africa dates back more than 3,000 years. The genus Oryza probably originated within a relatively short time scale about 15 million years ago (MYA), which includes 23 species categorized into 10 genomic types (AA, BB, BBCC, CC, CCDD, EE, FF, GG, HHJJ, and HHKK) (Aggarwal et al., 1997; Ge et al., 1999; Khush, 2003… O. glaberrima is a west African species of cultivated rice that was domesticated independently of Asian rice (O. sativa ssp. Harlan, J.R.) 409–452 (Mouton Publishers, 1976). Data source Oryza Genome Evolution Project. Figure 4. African rice was independently domesticated ~3000 years ago in the The authors declare no competing financial interests.  |  Concentric circles show structural, functional and evolutionary…, Figure 2. Find NCBI SARS-CoV-2 literature, sequence, and clinical content: https://www.ncbi.nlm.nih.gov/sars-cov-2/. New Insights Into the Nature of Interspecific Hybrid Sterility in Rice. Project funding: National Science Foundation Plant Genome Research Program (#082224) awarded to R. Wing, S. Rounsley and Y. Yu. the japonica genome was expanding relative to indica. This 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. Protein-coding and non-coding genes, splice variants, cDNA and protein sequences, non-coding RNAs. glaberrima originated and is cultivated in West Africa. Ann. Figure 2. 2020 Aug 7;11:1190. doi: 10.3389/fpls.2020.01190. Cubry P, Pidon H, Ta KN, Tranchant-Dubreuil C, Thuillet AC, Holzinger M, Adam H, Kam H, Chrestin H, Ghesquière A, François O, Sabot F, Vigouroux Y, Albar L, Jouannic S. Rice (N Y). sativa (Asian rice). 2014 May;23(9):2210-27. doi: 10.1111/mec.12738. EMBL-EBI, Theobroma cacao Belizian Criollo B97-61/B2. Plant Sci. Abstract. glaberrima, thus we hypothesize that Trinidad rice has a higher proportion of the Oryza glaberrima genome. Figure 1. Figure 5. Oryza glaberrima is one of the two cultivated species of rice, and harbors various interesting agronomic traits, especially in biotic and abiotic resistance, compared with its Asian cousin O. sativa. 2019 Mar 7;15(3):e1007414. The O. glaberrima genome (CG14…. Similar to Asian rice, African rice is a diploid A-type genome, having -. The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) using strain IRGC:96717. 2008;174:394–408. eCollection 2020. its better known cousin Oryza We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes. Portères, R. in Papers in African Prehistory (eds. African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Fage, J.D. Oryza glaberrima (African rice) is a cultivated grain distinct from The complex history of the domestication of rice. Front Plant Sci. Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. ; yellow, gene and repeat density between red and blue); and D paralogous relationships between, Plot of the composite likelihood ratio (CLR) across. In short, we wanted to 1) confirm the genetic bottleneck in African rice as a result of domestication; 2) identify which alleles have been driven to (near) fixation as a result of artificial selection; 3) discover population … [1] Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis.Hiroaki S, Hiroshi I, Tsuyoshi T, Hisataka N, Hiroshi M, Masaki F, Michie S, Kanako K, Ari K, Masao H et al: Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysisThe Plant Journal 2011, 66(5):796-805. Download genes, cDNAs, ncRNA, proteins - FASTA - GFF3. 2020 Sep 8;11(1):4488. doi: 10.1038/s41467-020-18329-4. Annu Rev Plant Biol. © EMBL-EBI There are only two species of cultivated rice in the world: Oryza glaberrima, or African rice, and Oryza sativa, or Asian rice.Native to sub-Saharan Africa, O. glaberrima is thought to have been domesticated from the wild ancestor Oryza barthii (formerly known as Oryza brevilugata) by peoples living in the floodplains at the bend of the Niger River some 2,000–3,000 years ago (1, 2). Clipboard, Search History, and several other advanced features are temporarily unavailable. National Center for Biotechnology Information, Unable to load your collection due to an error, Unable to load your delegates due to an error, Concentric circles show structural, functional and evolutionary aspects of the genome: A, chromosome number; B, heat map view of genes; C, repeat (RNA and DNA TEs without MITEs) density in 200-kb windows (red, average +1 s.d. This organ is thought to aid in seed dispersal and prevent predation by animals. 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