This would correspond to the accrual of mutations as O. glaberrima dispersed throughout the coastal range. There are rice relatives in other parts of the world, too. This is compatible with the general trend in π ratio (πw/ πc), which is usually well above one (S2 Fig) and takes on particularly high values when Tajima’s D is extremely negative. Genome-wide average statistics were compared using the Kruskal-Wallis test. For each interval, SNP count and Ts:Tv were calculated and plotted in R (v3.3.2) . 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. Average SNP density is almost twice as high in O. barthii (9.04 SNPS per kb) as in O. glaberrima (5.00 SNPs per kb). In addition, we used the no-call rate divided by the number of samples as a measure of missing data. A total of 3,923,601 variants were screened, of which 2,332,467 either did not align to the outgroup species or did not pass the alignment quality filter. approximately 9000 years ago . Relative nucleotide diversity was calculated as the ratio of π in O. glaberrima to π in O. barthii, where π defined as: Serves 4-6. The ω test statistic is calculated as: 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. Jollof Rice is a popular dish eaten in most parts of West Africa, most notably Ghana, Senegal, The Gambia, and Nigeria. So! Variants were annotated using SnpEff (v4.0) . The debate (or if you like, argument) on this topic has always been hot between Nigerians and Ghanaians. C. Isolation by distance among the coastal populations (OG-I, OG-II and OG-III). The geographic component of population structure can prevent instances of position selection from sweeping through the entire population in multiple ways. These statistics were computed in 100 kb regions with VCFtools (v0.1.14). Filter thresholds were determined based on their effect on the Transition:Transversion ratio (Ts:Tv). The collection sites of OG accessions suggest that the observed population structure has a strong geographic component (Fig 3B). The consumption of traditional cereals, mainly sorghum and millet, has fallen by 12 kg per c… Women play a major role in rice cultivation. The excess of rare variants in O. glaberrima is confirmed by the Minor Allele Frequency (MAF) spectrum (S2 Fig), where O. glaberrima has a larger spike in low frequency alleles (MAF < 0.01) than the majority of O. barthii alleles, which are of intermediate frequency (MAF 0.01–0.05).  found evidence for centric domestication, thereby supporting Portères’ hypothesis, whereas Meyer et al. 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. Rice is the world’s most important cereal crop. The divergence between two genomes X and Y was calculated as: Yes Sincere thanks to all members of the lab in New York, specifically Michael and Jae, for many useful discussions. It was first domesticated and grown in West Africa around 3,000 years ago. Two main competing hypotheses have been proposed concerning the domestication of rice in Africa. https://doi.org/10.1371/journal.pone.0203508.g006. This will help to predict the phenotypic consequences of domestication gene haplotypes and in linking phylogenetic patterns to the evolution of functionally significant traits. Without additional modelling, therefore, we cannot be sure that demographic history of African rice did not interfere with the CLR test presented here. Phylogenetic analysis shows that the exact same OG-II accessions form a separate haplotype in this gene as in Sd1 (Table 3). https://doi.org/10.1371/journal.pone.0203508.t002. 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. This West African dish will also be reminiscent of the popular old world paella, as well as a number of other rice … Although it has been shown that cultivated African rice is much less genetically diverse than wild African rice, the ADMIXTURE analysis shows that O. glaberrima is all but homogeneous, even compared to O. barthii. A possible explanation could be the rewilding of ancient O. glaberrima landraces, which have ‘gone feral’ and are now classified as the wild species. This could mean that O. glaberrima still contains a part of the ancestral variation that is observed in O. barthii. These go back to 1800 bc and continue through to 800 bc. Variants were called relative to the O. glaberrima (AGI1.1) reference genome and subsequently filtered to remove false positives. The disproportional skew in favour of high frequency derived alleles in O. glaberrima suggests that large parts of the genome bear signs of recent positive selection. The diversity analyses unequivocally demonstrate that O. glaberrima underwent an extreme bottleneck. Values of ω were log-transformed, prior to creating Manhattan plots in R (v3.3.2) using the ‘qqman’ package . When both species were pooled together (Fig 3C) or O. glaberrima was taken alone (Fig 3D), however, latitude and longitude were found to be significantly correlated with either of the top two principal components. The opposite trend can be seen for average nucleotide diversity, which is smaller in the coastal populations (π < 1.0/kb) than in the inland populations (π > 1.0/kb). Writing – review & editing. The only domesticated populations that do not appear to share ancestry with any of the wild populations, are OG-II and OG-III. Barring a single shared outlier on chromosome 4, there is a remarkable lack of overlap of outliers between the two species, suggesting that the sweeps found in O. glaberrima are unique to the domesticated accessions (S3 Fig). This has been called the ‘rapid transition model’. https://doi.org/10.1371/journal.pone.0203508.g003. The sudden drought meant that the increasing population could no longer rely on traditional forest products. We did not filter for heterozygous sites, because both species are primarily inbreeding and therefore exhibit low levels of heterozygosity. The first call set contained a full set of SNPs considered to adhere to a minimum standard of quality. Asian and African rice have distinct phenotypic characteristics: their grains differ in colour, size, shape and taste. In addition, while the sampling locations of the analysed O. glaberrima accessions are quite precise, for most O. barthii only the country was known and detailed coordinates were not available. The relation between kinship and geographic distance was quantified by fitting a linear model to the data points. Removal of low coverage individuals (< 4X) in both species revealed a higher heterozygosity in O. barthii (9.29%) than in O. glaberrima (5.33%), consistent with a higher level of inbreeding. These characteristics have favoured the cultivation of Asian rice over African rice in large parts of the world. Rice cultivation began in at least three of them, the middle and lower Yangtze, the Ganges plains and west Africa. According to this hypothesis, rice was domesticated in multiple areas of domestication in West Africa, without a defined moment and centre of origin . Despite these limitations, the marked population structure observed in O. glaberrima points to geographic differentiation during or following domestication. SNPs with a higher Ts:Tv are thus likely to be enriched for true SNPs, while SNPs with a lower Ts:Tv will contain more false positives. https://doi.org/10.1371/journal.pone.0203508.t003. predate the Portuguese-derived words associated with Asian rice (Blench, 2006; Porteres, 1970). Thus, while many questions concerning the domestication and migration of African rice are still outstanding, the complete genome sequences of more than a hundred O. glaberrima accessions—and an almost equal number of O. barthii accessions—provide a wealth of genetic data that can be used to reconstruct the evolutionary history of African rice, and to compare the genetic diversity of O. glaberrima in its different localities. The third objective was met by estimating the number of ancestral populations to delimit extant populations and calculating the fixation index between them. Candidate regions were screened for potential causative mutations by examining related SNP content and genomic features. A joint ADMIXTURE analysis was performed to infer which ancestor fractions are shared between the species and which are unique. Outliers (separated by more than 3500 km) were omitted. Jollof rice is one of the most common dishes in West Africa.There are several regional variations in name and ingredients, for example, in Mali it is called zaamè in Bamanankan.The dish's most common name of Jollof derives from the name of the Wolof people, though in Senegal and Gambia the dish is referred to in Wolof as ceebu jën or benachin. Funding: This study was funded by the National Science Foundation (nsf.gov) Grant No. Geographically separated populations may also undergo local adaptation due to geographically localised selection. Distribution of the pairwise geographic distances between individuals in kilometres, grouped per population. The results were deemed sufficiently comparable to proceed with both call sets (S9 Fig). Evolutionary distances were calculated using the p-distance method of Nei & Kumar . Writing – original draft, Current address: Natural History Museum, University of Oslo, Oslo, Norway, Affiliation This is called Cereal grain and is consumed as staple food in a large part of world’s human population. Observed and expected marginal derived allele frequency spectrum of O. glaberrima. The resulting BAM files were indexed and validated with Picard (v1.129). 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 . 2007-09-12T10:24:36ZMicrosoft® Office Word 20072013-04-16T17:11:49+01:00 The top 20 principal components were calculated for both species together and for both species separately using PLINK (v1.9). The fact that O. glaberrima does not form a monophyletic clade, however, calls into question the assumption that it speciated through a discrete domestication event. Microsoft® Office Word 2007; modified using iTextSharp 5.1.3 (c) 1T3XT BVBA Genomic features containing putative moderate to high impact mutations within close proximity (< 25 kb) of candidate regions were extracted for closer inspection using a custom R script. Joint variant calling and quality filtering resulted in a total of 3,923,601 SNPs. Output was converted to FASTA format with a custom perl script. We thus observe that, even though the total number of polymorphic sites in larger in OG-I through OG-III, the average number of pairwise differences between these individuals is lower. We therefore see strong evidence of Portères’ domestication theory in our population structure analysis. Positions within the top 0.5% values were considered candidate regions. In addition, ongoing hybridisation with O. barthii and later cultivation alongside O. sativa may have caused interspecific gene flow, which further complicates inferences about domestication origin . All these accessions have in common that they cluster with O. barthii accessions of similar ancestry and share a single haplotype with other O. glaberrima individuals for the genes that are marked with an ‘x’. The resulting ancestry fractions were plotted as stacked bar charts in R (v3.3.2). , and with the domestication hypothesis proposed by Portères . In contrast, the competing scenario of diversification in this region makes no claims as to the original centre of domestication, and even provide evidence for the protracted model . We evaluated genetic IBD as the correlation between pairwise relatedness, measured by the kinship coefficient (φ), and pairwise geographic distance, measured by the shortest distance between the collection sites of two accessions in kilometres. Several CLR tests that are widely used for detecting ‘hard’ sweeps are available as open source software, including OmegaPlus , SweeD  and SweepFinder . 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. Though many of the dishes share similarities, there are variations in nomenclature and differences in the kind of ingredients used. African rice (Oryza glaberrima Steud.) This difference was found to be significant in a two-sample Kolmogorov-Smirnov test (p < 0.5E-04). This is corroborated by the effect of geographic distance on genetic relatedness and by experimental evidence confirming the phenotypic consequences of spatially restricted genetic variation [3,26,33]. To minimise the effect of missing data, an equal number of individuals (n = 15) that were sequenced at high coverage were selected from the O. barthii population. Both processes have accelerated the shift in cultivation from local African varieties to the more productive Asian varieties. In contrast, the vast majority of polymorphic sites in O. glaberrima are shared with O. barthii, suggesting very little species-specific variation among the domesticated accessions. 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 structure and differentiation within and between the two species; 4) assess the influence of geography on the distribution of genetic variation; 5) explore discordances between the evolutionary histories of candidate domestication genes and the genome-wide species tree; and 6) predict the functional relevance of gene regions with divergent histories. It is also the source of heated discussion online among Nigerians, Ghanaians and Senegalese as to who owns the bragging rights to the dish. A pair was considered an outlier when the distance separating them fell outside the interquartile range (IQR) by more than 1.5*IQR. Synonymous and non-coding SNPs were extracted using SnpSift (v4.0) . (S7 Table). All these accessions have in common that they cluster with OB-B rather than OB-C and OB-D and share a single haplotype with other O. glaberrima individuals for the genes that are marked with an ‘x’. For these SNPs, the derived allele frequency spectra and cumulative densities were plotted using the R (v3.3.2). https://doi.org/10.1371/journal.pone.0203508.t004. (Note: LD is defined by Hill and Robertson  as r2 = D/p1p2q1q2, where p1 and p2 are the allele frequencies of SNP1, q1 and q2 are the allele frequencies of SNP2, and D measures the absolute difference between the observed and the expected haplotype frequencies p1q1, p2q1, p1q2 and p2q2 respectively). This article begins with information about the past and present status of African rice and then moves to a detailed example of when, how, and why it was cultivated by the Jola, a population of ancient rice growing peoples living in the swampy coastal areas of Casamance, in southern Senegal. In addition, site depth, call rate and mean heterozygosity per individual were calculated for all accessions using VCFtools (v0.1.14). According to a particular theory supporting the latter hypothesis, domestication was triggered at an acute time point when climate change started transforming forests into savannah around 4000 years ago . Hence, it is not unlikely that population substructure further complicates the detection of sites that are universally under positive selection throughout the entire species. Firstly, isolation by distance delays the migration of a beneficial allele, thus diminishing the effect of genetic hitchhiking that is observed in a hard sweep . The combined evidence of the previous sections suggests that the increase in genetic differentiation from the inland to the coastal populations may be linked to geographic range expansion. Whole genome resequencing of 94 O. barthii and 20 O. glaberrima accessions revealed that domesticated rice consistently clustered with one of five sub-populations of wild rice, suggesting a single origin in the area of Senegal, Gambia, Guinea and Sierra Leone . Finally, the sixth objective was met by identifying high impact mutations based on computational analyses and previously published experimental results. D. Isolation by distance among the inland populations (OG-IV and OG-V). These statistics were computed using VCFtools (v0.1.14) for both call sets. A total of 2,580,362 and 1,419,601 SNPs were used to calculate SNP density, π, and Tajima’s D in O. barthii and O. glaberrima, respectively, where Tajima’s D is defined according to  and measures the difference between two estimators of ϴ (the scaled mutation rate), namely the average number of differences between two sequences (π) as per Eq (1) and the expected number of segregating sites between two sequences under neutral theory according to Watterson’s estimator ϴω (), where S is the total number of segregating sites in the population, , and i is the ith sequence in a total of n sequences. Interestingly, OB-C and OB-D represent the individuals that were previously found to form a clade with O. glaberrima . 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. One proposes that plant domestication in Africa occurred in a non-centric (geographically diffuse) manner, over a protracted period of time , and has been called the ‘protracted transition model’. https://doi.org/10.1371/journal.pone.0203508.g005. If the latter is the case, this calls into question the ‘single origin’ hypothesis and the domestication of O. glaberrima might have resulted from more complex processes than simple selection scans are able to detect. Deviation from neutrality of the observed site frequency spectra of the two populations was compared using a two-sample Kolmogorov-Smirnov test. These results are in congruence with previous findings [3,21,22] and indicate that a strong reduction in diversity in O. glaberrima occurred as a result of domestication. For this reason, gene trees may not correspond to the overall genomic tree. In 2014, Wang et al. Here aibi is the genotype at position i in X, and cidi is the genotype at position i in Y. Oryza longistaminata was rejected because of its low genomic divergence from O. glaberrima (~2%). Whereas Asian rice (Oryza sativa) has been extensively studied, the exact origins of African rice (Oryza glaberrima) are still contested. Rice is a staple food for the majority of the world’s population. Isolation by distance was identified in the coastal populations, which could account for parallel adaptation in geographically separated demes. Larger intervals were not used, to minimise the influence of LD decay. in History from the Federal University of Rio de Janeiro, Brazil, in 2004 and earned his M.A. Filter classes and their thresholds can be found in S8 Fig. Polarisation of this SNP against O. meridionalis as an outgroup demonstrated that the variant responsible for truncation of the protein is derived, and the variant encoding the intact protein is ancestral. Oryza glaberrima, commonly known as African rice, is one of the two domesticated rice species. Evolutionary histories were inferred using the NJ algorithm  as implemented in MEGA7 . The subdivision of the species in coastal and inland populations is suggestive of geographic structure, as is the differentiation along a north-south gradient on the coast. (2) Uncertainty in species delimitation could be further examined through phylogenetic networks and introgression analyses. Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands, Roles Kinship coefficients were estimated based on 1,419,601 SNPs, using the KING robust relationship inference method  as implemented in PLINK (v2.0) . A list of all used accessions and their metadata can be found in S1 Table. Over the whole spectrum, the discrepancy between observed and expected frequencies as observed in an empirical cumulative distribution plot, is greater in O. glaberrima than in O. barthii (Fig 2). 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 . 2 0 obj Filtering criteria with different levels of strictness were applied (S5 Table). This gives further credibility to the idea that the segregating haplotypes in these genomic regions may underlie functional differentiation of the coastal OG-II accessions. Both the negative values of Tajima’s D and the skewed MAF distribution in favour of rare alleles support the notion that O. glaberrima underwent population expansion following a severe bottleneck. Regardless of whether this happened at the onset of domestication or during a secondary wave, the phylogenetic clustering of these haplotypes with different O. barthii accessions provides evidence for a separate genetic origin that may have been caused by introgression or domestication from this otherwise seemingly unrelated wild population. 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. Rice accompanied African slaves across the Middle Passage throughout the New World to Brazil, the Caribbean, and the southern United States. Accessions were assigned to a cluster according to their genetic background, with the colour of each sample representing the ancestral population (K = 5) that accounted for the majority (>50%) of pruned SNPs in that accession. Current scholarly estimates are that plants were domesticated in perhaps 20 different areas around the world. No, Is the Subject Area "Population genetics" applicable to this article? An overview of these statistics and the number and types of SNPs in the two sets can be found in S6 Table. India and Indonesia For quite some time, scholars have been divided about the presence of rice in India and Indonesia, where it came from and when it got there. However, evidence of persisting ancestral variation and multiple gene haplotypes among different sub-populations of O. glaberrima suggests that important functional traits may have arisen out of parallel evolution or local adaption, rather than single selective sweeps. Dr Adama Traoré was named Interim Director General of AfricaRice (2013-2015) with the departure of the Director General Dr Papa Abdoulaye Seck, who was nominated by the President of Senegal as Minister of Agriculture and Rural Equipment. This makes sense in light of the observation that these individuals contain ancestor fractions that are also found in O. glaberrima, in contrast to the individuals from populations OB-A and OB-B. This study used publicly available whole genome data of 111 O. glaberrima and 94 O. barthii accessions. Previous studies have supported either a centric or a non-centric geographic origin of African rice domestication. In order to elucidate the origin and diversification of O. glaberrima in West Africa, we performed a critical reassessment of the publicly available whole genome resequencing data of O. glaberrima and O. barthii accessions from across the species range (S1 Table and S1 Fig). We did not explore alternative models of selection in this study, because the existence of several haplotypes due to multiple novel mutations or standing variation renders the detection of soft sweeps exceedingly complex. 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. Supervision, Trees were pruned and annotated in Interactive Tree Of Life (iTOL v3) .