Origins and geographic diversification of African rice (Oryza glaberrima)

AbstractRice is a staple food for the majority of our world’s growing population. Whereas Asian rice (Oryza sativaL.) has been extensively studied, the exact origins of African rice (Oryza glaberrimaSteud.) are still contested. Previous studies have supported either a centric or a non-centric origin of African rice domestication. Here we review the evidence for both scenarios through a critical reassessment of 206 whole genome sequences of domesticated and wild African rice. While genetic diversity analyses support a severe bottleneck caused by domestication, signatures of recent and strong positive selection do not unequivocally point to candidate domestication genes, suggesting that domestication proceeded differently than in Asian rice – either by selection on different alleles, or different modes of selection. Population structure analysis revealed five genetic clusters localising to different geographic regions. Isolation by distance was identified in the coastal populations, which could account for parallel adaptation in geographically separated demes. Although genome-wide phylogenetic relationships support an origin in the eastern cultivation range followed by diversification along the Atlantic coast, further analysis of domestication genes shows distinct haplotypes in the southwest - suggesting that at least one of several key domestication traits might have originated there. These findings shed new light on an old controversy concerning plant domestication in Africa by highlighting the divergent roots of African rice cultivation, including a separate centre of domestication activity in the Guinea Highlands. We thus suggest that the commonly accepted centric origin of African rice must be reconsidered in favour of a non-centric or polycentric view.

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Sequence Variants Linked to Key Traits in Interspecific Crosses between African and Asian Rice

Plants ◽

10.3390/plants9121653 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1653

Author(s):

Hayba Badro ◽

Marie-Noelle Ndjiondjop ◽

Agnelo Furtado ◽

Robert Henry

Keyword(s):

Association Analysis ◽

Agronomic Traits ◽

Heading Date ◽

Sucrose Metabolism ◽

Interspecific Crosses ◽

Oryza Glaberrima ◽

Gene Pools ◽

Synonymous Snps ◽

African Rice ◽

Asian Rice

Asian and African rice gene pools vary in many traits that are important in rice breeding. The genetic basis of these differences was evaluated by analysis of important agronomic traits in crosses between African and Asian rice. Trait-associated variants (TAVs) influencing three quantitative agronomic traits, heading date (Hd), tiller number at maturity (T), and 1000 grain weight (TGW), were identified by association analysis of crosses between Asian and African rice. Populations were developed by crossing WAB56-104 (Oryza sativa) and CG14 (Oryza glaberrima). DNA from plants with extremely high or low values for these phenotypes was bulked and sequenced. The reference genome of O. sativa cv Nipponbare was used in general association analysis and candidate gene analysis. A total of 5152 non-synonymous single nucleotide polymorphisms (SNPs) across 3564 genes distinguished the low and the high bulks for Hd, T, and TGW traits; 611 non-synonymous SNPs across 447 genes were found in KEGG pathways. Six non-synonymous SNPs were found in the sequences of LOC107275952, LOC4334529, LOC4326177, LOC107275432, LOC4335790, and LOC107275425 genes associated with Hd, T, and TGW traits. These genes were involved in: abscisic-acid biosynthesis, carotenoid biosynthesis, starch and sucrose metabolism, and cytokinin biosynthesis. Analysis of 24 candidate genes associated with Hd, T, and TGW traits showed seven non-synonymous variations in the sequence of Hd3a and Ehd2 from the Hd genes (not in a KEGG pathway), D10 and D53 from the T genes (strigolactones biosynthetic pathway), and Gn1a and GIF1 from the TGW genes (cytokinin biosynthetic and starch and sucrose metabolism pathways). This study identified significant differences in allele frequencies supported by high sequence depth in analysis of bulks displaying high and low values for these key traits. These trait-associated variants are likely to be useful in rice improvement.

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Comparison of two African rice species through a new pan-genomic approach on massive data

10.1101/245431 ◽

2018 ◽

Cited By ~ 1

Author(s):

Cécile Monat ◽

Christine Tranchant-Dubreuil ◽

Stefan Engelen ◽

Karine Labadie ◽

Emmanuel Paradis ◽

...

Keyword(s):

Core Genome ◽

Oryza Glaberrima ◽

Large Core ◽

African Rice ◽

Asian Rice ◽

External Reference ◽

Genomic Approach ◽

Cultivated Species ◽

Group Species ◽

High Depth

AbstractPangenome theory implies that individuals from a given group/species share only a given part of their genome (core-genome), the remaining part being the dispensable one. Domestication process implies a small number of founder individuals, and thus a large core-genome compared to dispensable at the first steps of domestication. We sequenced at high depth 120 cultivated African rice Oryza glaberrima and of 74 wild relatives O. barthii, and mapped them on the external reference from Asian rice O. sativa. We then use a novel DepthOfCoverage approach to identif missing genes. After comparing the two species, we shown that the cultivated species has a smaller core-genome than the wild one, as well as an expected smaller dispensable one. This unexpected output however replaces in perspective the inadequacy of cultivated crops to wilderness.

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Genetics and Genomics of African Rice (Oryza glaberrima Steud) Domestication

Rice ◽

10.1186/s12284-020-00449-6 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Peterson W. Wambugu ◽

Marie-Noelle Ndjiondjop ◽

Robert Henry

Keyword(s):

Crop Improvement ◽

Oryza Glaberrima ◽

Crop Species ◽

African Rice ◽

Genome Data ◽

Asian Rice ◽

Species Analysis ◽

History Of ◽

Genetics And Genomics ◽

Made In

AbstractAfrican rice (Oryza glaberrima Steud) is one of the two independently domesticated rice species, the other one being Asian rice (Oryza sativa L.). Despite major progress being made in understanding the evolutionary and domestication history of African rice, key outstanding issues remain controversial. There appears to be an underlying difficulty in identifying the domestication centre and number of times the crop has been domesticated. Advances in genomics have provided unprecedented opportunities for understanding the genetic architecture of domestication related traits. For most of the domestication traits, the underlying genes and mutations have been identified. Comparative analysis of domestication genes between Asian and African rice has revealed that the two species went through an independent but convergent evolution process. The genetic and developmental basis of some of the domestic traits are conserved not only between Asian and African rice but also with other domesticated crop species. Analysis of genome data and its interpretation is emerging as a major challenge facing studies of domestication in African rice as key studies continue giving contradictory findings and conclusions. Insights obtained on the domestication of this species are vital for guiding crop improvement efforts.

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Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

Rice ◽

10.1186/s12284-020-00424-1 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Philippe Cubry ◽

Hélène Pidon ◽

Kim Nhung Ta ◽

Christine Tranchant-Dubreuil ◽

Anne-Céline Thuillet ◽

...

Keyword(s):

Association Study ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Oryza Glaberrima ◽

Rice Yellow Mottle Virus ◽

Adaptive Variation ◽

African Rice ◽

Genome Wide ◽

Genomic Regions

Abstract Background African rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species. Results Using a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we found several association peaks, one of which co-localised with a well described gene in the Asian rice flowering pathway, OsGi, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting genomic regions and candidate genes. Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations. Conclusion Our results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community.

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Endophytes from African Rice (Oryza glaberrima L.) Efficiently Colonize Asian Rice (Oryza sativa L.) Stimulating the Activity of Its Antioxidant Enzymes and Increasing the Content of Nitrogen, Carbon, and Chlorophyll

Microorganisms ◽

10.3390/microorganisms9081714 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1714

Author(s):

Carmen Bianco ◽

Anna Andreozzi ◽

Silvia Romano ◽

Camilla Fagorzi ◽

Lisa Cangioli ◽

...

Keyword(s):

Oryza Sativa ◽

Antioxidant Enzymes ◽

Nitrogenase Activity ◽

Oryza Sativa L ◽

Tropical Region ◽

Oryza Glaberrima ◽

Bacterial Endophytes ◽

African Rice ◽

Asian Rice ◽

Temperate Climates

Bacterial endophytes support the adaptation of host plants to harsh environments. In this study, culturable bacterial endophytes were isolated from the African rice Oryza glaberrima L., which is well-adapted to grow with poor external inputs in the tropical region of Mali. Among these, six N-fixer strains were used to inoculate O. glaberrima RAM133 and the Asian rice O. sativa L. cv. Baldo, selected for growth in temperate climates. The colonization efficiency and the N-fixing activity were evaluated and compared for the two rice varieties. Oryza sativa-inoculated plants showed a fairly good colonization efficiency and nitrogenase activity. The inoculation of Oryza sativa with the strains Klebsiella pasteurii BDA134-6 and Phytobacter diazotrophicus BDA59-3 led to the highest nitrogenase activity. In addition, the inoculation of ‘Baldo’ plants with the strain P. diazotrophicus BDA59-3 led to a significant increase in nitrogen, carbon and chlorophyll content. Finally, ‘Baldo’ plants inoculated with Kl. pasteurii BDA134-6 showed the induction of antioxidant enzymes activity and the maintenance of nitrogen-fixation under salt stress as compared to the unstressed controls. As these endophytes efficiently colonize high-yielding crop varieties grown in cold temperate climates, they become good candidates to promote their growth under unfavorable conditions.

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The complex geography of domestication of the African riceOryza glaberrima

10.1101/321851 ◽

2018 ◽

Author(s):

Jae Young Choi ◽

Katherine Dorph ◽

Michael D. Purugganan

Keyword(s):

West Africa ◽

Oryza Glaberrima ◽

Sequencing Data ◽

African Rice ◽

Asian Rice ◽

Genetic Groups ◽

Multiple Regions ◽

History Of ◽

Domestication Process ◽

Wild Progenitors

AbstractWhile the domestication history of Asian rice has been extensively studied, details of the evolution of African rice remains elusive. The inner Niger delta has been suggested as the center of origin but molecular data for its support are lacking. Here, we present the most comprehensive analysis to date on the evolutionary and domestication history of African rice. By analyzing whole genome re-sequencing data from 282 individuals in domesticated African riceOryza glaberrimaand its progenitorO. barthii, we hypothesize a non-centric domestication origin for African rice. Our analyses show geographically based population structure inO. glaberrima, as well as significant evidence of admixture between genetic groups. Furthermore, we have evidence that the previously hypothesizedO. barthiiprogenitor populations in West Africa have evolutionary signatures similar to domesticated rice and carried causal domestication mutations, suggesting those progenitors may actually represent feral wild-domesticated hybrid rice. Demography modeling suggested the inlandO. glaberrimahad a protracted period of bottlenecking that preceded the coastal population by 800–1,800 years. Phylogeographic analysis of genes involved in the core domestication process suggests that the origins of causal domestication mutations could be traced to wild progenitors in multiple different locations in West and Central Africa. Based on our evidence, we hypothesizeO. glaberrimawas not domesticated from a single centric location but was rather a diffuse process where multiple regions contributed key alleles for different domestication traits.Author SummaryFor many crops it is not clear how they got domesticated from their wild progenitors. Transition from a wild to domesticated state required a series of genetic changes, and studying the evolutionary origin of these domestication-causing mutations are key to understanding the domestication origins of a crop. Moreover, population relationships within a crop holds insight into the evolutionary history of domestication and whether there was gene flow between different genetic groups. In this study, we investigate the domestication history ofOryza glaberrima, a rice species that was domesticated in West Africa independently from the Asian rice speciesO. sativa. Using genome-wide data from a large sample of domesticated and wild African rice samples we did not find evidence that supported the established domestication model forO. glaberrima—a single domestication origin. Rather, our evidence suggests the domestication process for African rice was initiated in multiple regions of West Africa, caused potentially by the local environmental and cultivation preference of people. Admixture between different genetic groups had facilitated the exchange and spread of core domestication mutations. Hence domestication of African rice was a multi-regional process.

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The Genomics ofOryzaSpecies Provides Insights into Rice Domestication and Heterosis

Annual Review of Plant Biology ◽

10.1146/annurev-arplant-050718-100320 ◽

2019 ◽

Vol 70 (1) ◽

pp. 639-665 ◽

Cited By ~ 12

Author(s):

Erwang Chen ◽

Xuehui Huang ◽

Zhixi Tian ◽

Rod A. Wing ◽

Bin Han

Keyword(s):

Complex Traits ◽

Oryza Rufipogon ◽

Oryza Species ◽

Oryza Glaberrima ◽

Cultivated Rice ◽

African Rice ◽

Genome Wide ◽

Genome Variations ◽

Genomic Studies ◽

Rice Domestication

Here, we review recent progress in genetic and genomic studies of the diversity of Oryza species. In recent years, unlocking the genetic diversity of Oryza species has provided insights into the genomics of rice domestication, heterosis, and complex traits. 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. Moreover, similar studies on genome variations of African rice ( Oryza glaberrima) cultivars and their closely related wild progenitor Oryza barthii accessions have provided strong evidence to support a theory of independent domestication in African rice. Integrated genomic approaches have efficiently investigated many heterotic loci in hybrid rice underlying yield heterosis advantages and revealed the genomic architecture of rice heterosis. We conclude that in-depth unlocking of genetic variations among Oryza species will further enhance rice breeding.

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Genome wide association study pinpoints key agronomic QTLs in African rice Oryza glaberrima

10.1101/2020.01.07.897298 ◽

2020 ◽

Cited By ~ 1

Author(s):

Philippe Cubry ◽

Hélène Pidon ◽

Kim Nhung Ta ◽

Christine Tranchant-Dubreuil ◽

Anne-Céline Thuillet ◽

...

Keyword(s):

Association Study ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Oryza Glaberrima ◽

Adaptive Variation ◽

African Rice ◽

Genome Wide ◽

Genomic Regions ◽

Panicle Architecture

AbstractBackgroundAfrican rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species.ResultsUsing a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we demonstrated that we could successfully retrieve known genes from the rice flowering pathway, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting QTLs and candidate genes (including Rymv1 for resistance and SP1, Ghd7.1, APO1 and OsMADS1 for panicle architecture). Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations.ConclusionOur results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community.

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Rice Cultivation in the History of Slavery

Oxford Research Encyclopedia of African History ◽

10.1093/acrefore/9780190277734.013.713 ◽

2020 ◽

Author(s):

Judith Carney

Keyword(s):

20Th Century ◽

New World ◽

Coastal Region ◽

Rice Cultivation ◽

Oryza Glaberrima ◽

African Rice ◽

Asian Rice ◽

Wild Rice Species ◽

Slave Ships ◽

History Of

There are many wild rice species, but only two are domesticated. The most widely known is Asian rice, Oryza sativa. Domesticated in China approximately 10,000 years ago, it has been a primary staple in Asia for millennia, becoming by the 20th century one of the world’s most consumed cereals. Less known is Oryza glaberrima, or African rice, which was not recognized as a unique species until the mid-20th century. Glaberrima’s history begins not in Asia, but in the inland delta of West Africa’s Niger River, where it was domesticated some 3,500 years ago. Africans adapted glaberrima to a variety of landscapes and developed specialized farming practices that advanced its diffusion elsewhere in the continent, notably to wetland swamps and the tropical coastal region between Senegal and Cameroon. Cultivated there for millennia, African rice became (and still is) a principal dietary staple of West Africa. Women play a major role in rice cultivation. They plant, harvested, mill, and cook this important food crop. Since the so-called Age of Discovery, Oryza glaberrima has been entwined with the history of transatlantic slavery, which lasted from the mid-15th century to the last quarter of the 19th century. Over 400 years, nearly 13 million Africans were kidnapped and imprisoned on European slave ships bound for the Americas. Once landed, the survivors were sold as chattel labor to work colonial mines and plantations. Many had experience growing rice. African rice often accompanied slave voyages. As slave ships plied the West African coast, their captains purchased it in bulk to feed their captives during the weeks-long Middle Passage. Eventually, unmilled seed rice found its way from ships’ larders into the hands of New World Africans, who planted it in their provision gardens or maroon hideaways. By the end of the 17th century, plantation owners in Carolina (and later Brazil) were beginning to cultivate rice in response to rising demand from Europe. They very likely grew glaberrima at first—acquired as leftover slave ship provisions—and were almost certainly tutored by slaves already proficient at growing it. The development of rice as a lucrative export crop, cultivated on a massive scale in the tropical and semi-tropical swamps and tidewater estuaries of the Americas, is also a story of African agency and know-how. Nearly all the technologies employed on New World rice plantations bear African antecedents, from the irrigation systems that made fields productive, to the milling and winnowing of grain by African female labor wielding traditional African tools. The recovery of African rice history dispels long-held beliefs that Africans contributed little to the global table and added nothing more than muscle to the agricultural history of the Americas. It upends the myth that they only provided labor, existing as less-than-human “hands” that uncomprehendingly carried out slaveholder directives. Rice history has directed scholars to new geographical spaces, such as the provision gardens of the enslaved, while integrating contributions from archaeology, botany, geography, linguistics, and genomics. Not least, it gives to slavery’s victims a voice rarely heard in traditional sources.

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