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This will aid our understanding of the precise evolutionary relationships between O. glaberrima and O. barthii. Following the method of [25], both call sets were compared with respect to their patterns of nucleotide diversity (π) and genetic differentiation (FST). Because of the low genomic divergence (<5%), homoplasy was considered unlikely and correction for multiple substitutions was not applied. It is now rarely sold in West African markets, having been replaced by Asian strains. Only biallelic SNPs were retained for analysis. A pair was considered an outlier when the distance separating them fell outside the interquartile range (IQR) by more than 1.5*IQR. 2007-09-12T10:24:36ZMicrosoft® Office Word 20072013-04-16T17:11:49+01:00 In Africa, O. glaberrima has largely been replaced by Asian rice, even though African rice is more resistant to abiotic stresses and is often preferred for its taste and its diversity in maturation time [4]. Since the non-shattering phenotype is a crucial trait in the domestication syndrome, the ancestral state of this substitution in a limited number of OG-II accessions presupposes that another variant—either in the same gene or in a different gene—might be causing the same phenotype. The grey bar labelled ‘OB-V and OG’ indicates the smallest monophyletic clade containing all O. glaberrima and its nearest wild relatives. West Africa Jollof Rice. Remaining haplotypes, consisting of a mix O. barthii and O. glaberrima accessions from a single subpopulation, are expanded with branch colours reflecting their population of origin of the O. glaberrima accessions. For each biallelic SNP, the corresponding position and five flanking bases were extracted from the alignment using a custom perl script. 1 0 obj On average, outliers comprised less than 4% of the data. Positions that did not map to the outgroup, positions with gaps within 5 bp of the SNP, and SNPs that mapped to multiple regions of the O. meridionalis genome were discarded. Since these scans presume that a variant under selection swept through an entire population, the possibility that part of the population escaped the sweep, either due to different selection pressures or due to population substructure, remains unexplored. The available genomic data enable a reinterpretation of previous results and might clarify some of the present ambiguities regarding the origin and diversification of African rice. https://doi.org/10.1371/journal.pone.0203508.t004. Although some candidate genes that were scanned in the CLR test are not necessarily expected to be under universal selection in African rice because of their biological function (such as COLD1), other genes that we expected to be among the outliers (such as Sh4) also lacked a clear signal, casting doubt on the assumptions of the employed method. here. Microsoft® Office Word 2007; modified using iTextSharp 5.1.3 (c) 1T3XT BVBA The debate about African plant domestication has historically revolved around the non-centric model (proposed areas of domestication in dark green) and the centric model, with a single centre of primary domestication (proposed area in dark green) connected by migration (dotted lines) to two additional sites of secondary diversification (proposed areas in medium green). This reduction in diversity is most likely caused by a combination of selection, favouring a small number of preferred alleles, and demographic history, causing a large drop in effective population size (Ne). To reflect the geographic range of the majority of each genetic population, outliers were omitted. In fact, ‘weedy’ rice, which is a genetic mix between the wild and cultivated species, can result from interspecific crosses and has been observed in the case of African rice in both Mali and Cameroon [12]. All trees were annotated in Interactive Tree Of Life (iTOL v3) [61]. 1 . Whether this stems from methodological issues or from the population structure observed in O. glaberrima can only be demonstrated with improved knowledge of the demographic history of O. glaberrima and additional modelling. Using the Trans-Atlantic Slave Trade database, which compiles the documentation for some 37,000 slaving voyages, Deep Roots argues that the West African Rice Coast region, of which coastal Guinea is an important part, was the single region of origin for the majority of captives who disembarked in South Carolina and Georgia during the evolution of the colonies’ commercial rice industries. None of the other genetic studies mentioned in the previous section were able to pinpoint a clear centre of domestication. D. Isolation by distance among the inland populations (OG-IV and OG-V). A re-examination of the other trees subsequently shows that some of the OG-II accessions also cluster with OB-B in other genes (Table 3), although their numbers did not warrant their inclusion as one of the five largest haplotypes. To confirm the clustering of O. glaberrima within O. barthii, a whole genome phylogenetic tree was constructed based on 3,923,601 genome-wide SNPs. Archeologists focusing on East a… The divergence between two genomes X and Y was calculated as: The low levels of nucleotide diversity and the large number of rare variants found in O. glaberrima are consistent with a scenario of population expansion following a sudden drop in effective population size. Filter classes and their thresholds can be found in S8 Fig. This low level of diversity was confirmed by subsequent genomic studies. When population size is constant and there is no selection on the genome (so-called neutral conditions), the two estimators should equal each other and Tajima’s D equals 0. In addition, site depth, call rate and mean heterozygosity per individual were calculated for all accessions using VCFtools (v0.1.14). Observed and expected marginal derived allele frequency spectrum of O. glaberrima. Haplotypes that consist exclusively of O. barthii are collapsed into blue nodes. The resulting ancestry fractions were plotted as stacked bar charts in R (v3.3.2). Furthermore, the use of widely divergent types and quantities of data, including RNA transcripts, microsatellites, gene markers and genome-wide SNPs, precludes a systematic comparison of the results of these studies. Jollof Rice is a popular dish eaten in most parts of West Africa, most notably Ghana, Senegal, The Gambia, and Nigeria. Despite this evidence, the identification of exact regions in the genome that have been under positive selection is notoriously difficult due to the confounding effects of demographic history, which are known to produce local reductions in genetic diversity that can look remarkably like selective sweeps [28]. The fifth objective was met by phasing gene haplotypes and comparing their relationships with the overall phylogeny based on genomic distances. The protracted transition model with multiple domestication centres, or alternatively a polycentric view, might offer a valuable alternative perspective on the observed geographic distribution of genetic variation found in African rice. This would explain the shorter branch lengths of some of these closely related O. barthii accessions. (1) Variants were annotated using SnpEff (v4.0) [46]. indica (which originated in India) and O. sativa ssp. This has recently been confirmed by functional characterisation of another gene, called Sh3, that is on its own responsible for a non-shattering phenotype in African rice [26]. Genes were considered homologous when protein sequence similarity was higher than or equal to 95%. The first principal component is correlated significantly with longitude and the second principal component is correlated significantly with latitude. For each interval, SNP count and Ts:Tv were calculated and plotted in R (v3.3.2) [39]. Relative nucleotide diversity between the two species was significantly lower in the cultivated species (πc = 0.0007) than in the wild species (πw = 0.0013) at p < 1.0E-05. Whereas Asian rice can be milled mechanically, facilitating large-scale production, African rice grains break easily and have to be milled manually with a mortar and pestle. Observed and expected marginal derived allele frequency spectra of O. barthii. Hence, it can be concluded that the centric, rapid transition model of domestication does not tell the whole story of the evolution of O. glaberrima. Alternatively, the geographic separation of the inland populations and their wild relatives can be explained by domestication in the eastern cultivation range and a subsequent range shift of the wild progenitor from the east to the west. L and R represent the left and right set of polymorphic sites, respectively, and r2ij is r2, a common measure of LD [51], between the ith and the jth site. Only one species in Asia and one in Africa were domesticated, however. Asian rice, Oryza sativa, is one of oldest crop species. In addition, food demand is rising in many African countries as a result of the growing population, a trend which is reflected in annual rice consumption [7]. In 2015, while at a conference in Western Cape, South Africa, van Andel met up with New York University postdoc Rachel Meyer and hatched a collaboration to sequence rice genomes of Maroon and African traditional varieties in search of a match. FST between O. glaberrima and O. barthii was included as a baseline. The O. meridionalis x O. glaberrima multiple alignment was retrieved from Ensembl Genomes (release 33) and parsed with mafTools [45]. These characteristics have favoured the cultivation of Asian rice over African rice in large parts of the world. An overview of these statistics and the number and types of SNPs in the two sets can be found in S6 Table. https://doi.org/10.1371/journal.pone.0203508.g002. Variant discovery was performed following the Genome Analysis Tool Kit (GATK) Best Practices [34]. As a matter of fact, Jollof rice probably traveled to America too, as jambalaya and especially Lowcountry red rice share a lot of similarities with Jollof rice. A. NJ tree with all O. barthii (OB) and O. glaberrima (OG) accessions. is a cereal crop species closely related to Asian rice (Oryza sativa L.) but was independently domesticated in West Africa ∼3,000 years ago. This pattern breaks down when considering phylogenies at the level of individual genes; there we see that some landraces are far removed from the majority of O. glaberrima and cluster with a different O. barthii sub-population instead. Several studies have tried to illuminate the question of how and where African rice originated, either implicitly or explicitly addressing the domestication hypotheses described above. The previous statistics show a deviation from neutrality that could be caused both by changes in the effective population size as well as selection. [22] found evidence for centric domestication, thereby supporting Portères’ hypothesis, whereas Meyer et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The consumption of traditional cereals, mainly sorghum and millet, has fallen by 12 kg per c… These go back to 1800 bc and continue through to 800 bc. The fact that O. glaberrima shows a larger excess of high frequency derived alleles than O. barthii, as evidenced by their empirical cumulative distribution functions, is an indication that it at least underwent stronger positive selection than its wild relative. The result is that different Oryza species are strung out over the tropical regions of the globe, including South America and Australia. Relative nucleotide diversity was calculated as the ratio of π in O. glaberrima to π in O. barthii, where π defined as: A U-shaped derived allele frequency spectrum is therefore used as evidence of positive selection, but has not been demonstrated in African rice to date. Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates, Roles A recent study of the AfricaRice gene bank collection also revealed exactly five genetic clusters based on a study of 27,560 SNPs across 2,179 accessions. To test whether the observed population structure could be the result of geography, isolation by distance (IBD) was assessed among all West African accessions. Putative effects of segregating SNPs were predicted using SnpEff (v4.0). A closer inspection of the neighbouring O. barthii accessions reveals that their closest relatives all belong to the OB-B subpopulation, rather than the expected OB-C and OB-D populations (Fig 6). https://doi.org/10.1371/journal.pone.0203508.t001. Considering the extensive LD in O. glaberrima and the fact that strong candidates for high impact substitutions could not be identified, it cannot be excluded that associated functional mutations lie outside the intervals included in our phylogenetic analyses and that the gene haplotypes identified here may have hitchhiked on the selection of a different genomic feature altogether. Tree and haplotype statistics of all genes are summarised in S3 Table. These genetic analyses will have to be balanced with suitable morphological evidence. Jollof Rice. Contrary to expectation, moderate isolation by distance was observed in three out of five genetic sub-populations. In addition, focus should be given to more even sampling across the geographic range of both species, especially in the eastern range for O. glaberrima and in the western range for O. barthii, where collections of these species are presently scarce. Oryza punctata was rejected because of its high genomic divergence (>5%) and associated data loss. The complementation of computational studies with experimental data will be indispensable in the future—not just for understanding the broad patterns of evolution and domestication of African rice, but also to provide insights into the emergence of local adaptive traits connected with the diversification of this crop in its different geographic contexts. This is either because they did not play a role in the domestication of African rice, because the chosen selection scan has problems separating the effects of demography from those of selection, or because the model of a single, hard sweep fails to explain the history of these genes. For these SNPs, the derived allele frequency spectra and cumulative densities were plotted using the R (v3.3.2). Lastly, more functional analyses are needed to improve the annotation of the African rice genome, which is still lacking in many ways in comparison to the Asian rice genome. We labelled the five most common haplotypes per gene and then annotated the trees based on population structure, to see which of the O. glaberrima subpopulations segregate into different haplotypes and whether they cluster with the expected OB-C and OB-D accessions. Two main competing hypotheses have been proposed concerning the domestication of rice in Africa. The effect of filtering on Ts:Tv ratio was quantified with VCFTools (v0.1.14) [40]. Output was converted to FASTA format with a custom perl script. (2) endstream Future research into the origins of African rice should investigate the possibility that the closest wild relatives of O. glaberrima are in fact hybrids or rewilded ancient landraces. Yes Isolation by distance was identified in the coastal populations, which could account for parallel adaptation in geographically separated demes. Serves 4-6. application/pdfOverseas Development InstituteThe history of rice in West Africa - Cultivated rice (as opposed to wild rice), all originates, according to genetic research, from a single crop in China somewhere around 10,000 years ago.From that one batch, the two species of rice (one generally referred to as Asian rice, the other as African rice… Rice is a staple food for the majority of the world’s population. A new reference book, “Realizing Africa’s Rice Promise,” which provides a comprehensive overview of Africa’s rice sector, was released. japonica which, as a sister taxon, is supposed to be equidistant to the outgroup as compared to O. glaberrima. Rice cultivation began in at least three of them, the middle and lower Yangtze, the Ganges plains and west Africa. To see what phenotypes might be associated with the segregating haplotypes in these genes, we evaluated the impact of the responsible substitutions using variant prediction software. Oryza longistaminata was rejected because of its low genomic divergence from O. glaberrima (~2%). Here πij is the number of differences per site between sequences i and j, xi is the frequency of sequence i, xj is the frequency of sequence j and n is the total number of sequences in the data set. 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