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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The African Rice Oryza glaberrima Steud: Knowledge Distribution and Prospects

International Journal of Biology ◽

10.5539/ijb.v4n3p158 ◽

2012 ◽

Vol 4 (3) ◽

Cited By ~ 9

Author(s):

Yves Agnoun ◽

Samadori S. H. Biaou ◽

M. Sié ◽

R. S. Vodouhè ◽

A. Ahanchédé

Keyword(s):

Oryza Glaberrima ◽

African Rice

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High-throughput phenotyping reveals a link between transpiration efficiency and transpiration restriction under high evaporative demand and new loci controlling water use-related traits in African rice, Oryza glaberrima Steud.

10.1101/2021.11.28.470237 ◽

2021 ◽

Author(s):

Pablo Affortit ◽

Branly Effa Effa ◽

Mame Sokhatil Ndoye ◽

Daniel Moukouanga ◽

Nathalie Luchaire ◽

...

Keyword(s):

Water Use Efficiency ◽

Water Use ◽

Association Studies ◽

Crop Improvement ◽

Oryza Glaberrima ◽

Genome Wide Association Studies ◽

Transpiration Efficiency ◽

Evaporative Demand ◽

African Rice ◽

Use Efficiency

Because water availability is the most important environmental factor limiting crop production, improving water use efficiency, the amount of carbon fixed per water used, is a major target for crop improvement. In rice, the genetic bases of transpiration efficiency, the derivation of water use efficiency at the whole-plant scale, and its putative component trait transpiration restriction under high evaporative demand, remain unknown. These traits were measured in a panel of 147 African rice Oryza glaberrima genotypes, known as potential sources of tolerance genes to biotic and abiotic stresses. Our results reveal that higher transpiration efficiency is associated with transpiration restriction in African rice. Detailed measurements in a subset of highly differentiated genotypes confirmed these associations and suggested that the root to shoot ratio played an important role in transpiration restriction. Genome wide association studies identified marker-trait associations for transpiration response to evaporative demand, transpiration efficiency and its residuals, that links to genes involved in water transport and cell wall patterning. Our data suggest that root shoot partitioning is an important component of transpiration restriction that has a positive effect on transpiration efficiency in African rice. Both traits are heritable and define targets for breeding rice with improved water use strategies.

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The complex geography of domestication of the African rice Oryza glaberrima

PLoS Genetics ◽

10.1371/journal.pgen.1007414 ◽

2019 ◽

Vol 15 (3) ◽

pp. e1007414 ◽

Cited By ~ 11

Author(s):

Jae Young Choi ◽

Maricris Zaidem ◽

Rafal Gutaker ◽

Katherine Dorph ◽

Rakesh Kumar Singh ◽

...

Keyword(s):

Oryza Glaberrima ◽

African Rice

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Screening of African rice, oryza glaberrima steud, for resistance to the African rice gall midge orseolia oryzivora Harris and Gagne

Journal of Food Technology in Africa ◽

10.4314/jfta.v4i3.48072 ◽

2009 ◽

Vol 4 (3) ◽

Author(s):

MN Ukwungwe ◽

CT Williams ◽

O Okhidlevble

Keyword(s):

Gall Midge ◽

Oryza Glaberrima ◽

Orseolia Oryzivora ◽

African Rice ◽

Rice Gall Midge

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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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