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Previous studies have supported either a centric or a non-centric geographic origin of African rice domestication. These sequences are linked to under BioProjects PRJNA13765, PRJNA30379, PRJNA315063 and PRJNA514989. The ancestral variant was found to be represented exclusively in the OG-II haplotype. This could mean that O. glaberrima still contains a part of the ancestral variation that is observed in O. barthii. Suriname’s Maroons, whose freedom-seeking forebears escaped enslavement in the seventeenth and eighteenth centuries, and for whom rice remains an indispensable dietary staple, commemorate rice as food from Africa. However, the nature of hunter-gatherer and pastoral societies in West Africa calls into question whether a definite centre of origin is likely ever to be found [11]. endobj Without additional modelling, therefore, we cannot be sure that demographic history of African rice did not interfere with the CLR test presented here. If we assume that these relatives are genuinely O. barthii and not ‘rewilded’ or intermediate forms, there are two plausible scenarios. These results were subsequently used to weigh the evidence for local versus global adaptation, discuss the taxonomic implications for species delimitation, argue for a single or multiple domestication events, and ultimately to reconsider the dominant domestication hypotheses. The dashed blue line surrounds the largest clade that contains only OG and no wild relatives. The fact that OG-IV and OG-V appear to be the most genetically diverse and least genetically differentiated from O. barthii, while the reverse can be seen in the coastal populations, seems to suggest that the population bottleneck occurred in an east to west direction, followed by differentiation between the north and south in the coastal region. This recurrent pattern stands in stark contrast with the genome-wide phylogeny, where the OB-B population is genetically most distant from O. glaberrima (Fig 5). Serves 4-6. %���� Genomic features were retrieved from the general feature format (GFF) file of the O. glaberrima reference genome on Ensembl (release 33). This analysis was repeated for O. glaberrima and O. barthii separately. 6 0 obj No, Is the Subject Area "Genomics" applicable to this article? This may be due to the low number of geo-referenced individuals, a lack of geographic structure or both. D. PCA of all geo-referenced O. glaberrima accessions separately. 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. One proposes that plant domestication in Africa occurred in a non-centric (geographically diffuse) manner, over a protracted period of time [9], and has been called the ‘protracted transition model’. Origin of Rice 2. C. Isolation by distance among the coastal populations (OG-I, OG-II and OG-III). 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. 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. Yes The rice of Africa (O. glaberrima) has a long and noteworthy history” . The first principal component is correlated significantly with longitude and the second principal component is correlated significantly with latitude. 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 [42] 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. For this reason, gene trees may not correspond to the overall genomic tree. None of the other genetic studies mentioned in the previous section were able to pinpoint a clear centre of domestication. Population structure analysis revealed five genetic clusters localising to different geographic regions. Archeologists focusing on East a… As a staple food for more than half of the world’s seven billion people, it is of crucial importance in providing food security for an exponentially growing population. Filter thresholds were determined based on their effect on the Transition:Transversion ratio (Ts:Tv). 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. To assess whether certain domestication traits of O. glaberrima could have had multiple origins, NJ trees were constructed for several domestication genes known from recent rice genetics literature [22,25], a list of which can be found in S2 Table. 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. The effect of filtering on Ts:Tv ratio was quantified with VCFTools (v0.1.14) [40]. While O. glaberrima and O. barthii are differentiated greatly (FST > 0.181), the western and eastern groups were differentiated moderately (FST = 0.10) and the northern and southern groups were differentiated only a by a small degree (FST < 0.042). Two of the eight ancestral populations were predominantly found in O. barthii alone, and three others almost exclusively occur in O. glaberrima (Fig 3A). Genetic differentiation from O. barthii is the smallest for OG-IV and the largest for OG-II (Table 2). A study of 14 unlinked nuclear genes in 40 individuals found O. glaberrima to have 70% lower genetic diversity and hardly any population structure compared to its wild relative, supporting a single origin around the Inner Niger Delta [19]. Evolutionary distances were calculated using the p-distance method of Nei & Kumar [71]. Most notably, accessions from the OG-IV subpopulation do not only cluster separately in qSh1 and OsLG1, but are also part of smaller haplotypes in Phr1, MOC1, Rc and Ipa1 (Table 4). Both O. barthii and O. glaberrima are predominantly selfing plants, which is reflected in their low levels of heterozygosity, averaging around 5%. Like other cereals, rice has been domesticated by humans multiple times independently. The presence of separate OG-II haplotypes in multiple domestication genes might mean that the segregating landraces acquired domestication traits independently of the majority of O. glaberrima and would support a polycentric scenario as illustrated in Fig 1C. 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). Cross-validation error estimates shows that model fit was optimised for both species at K = 8 and at K = 5 when either O. glaberrima or O. barthii were considered by themselves (S5 Fig). These subspecies of rice have separate origins, although later domestication stages saw extensive gene flow between the two, which has been associated with the transfer of domestication alleles [15]. The diversity measures reported in this study are consistent with previous reports [3,22] and provide strong evidence for a large reduction in diversity in the genome of O. glaberrima as a result of domestication. Yes The three other groups were specific to O. glaberrima and associated with different phenotypic traits, corresponding to the floating, non-floating and upland ecotypes, respectively [20]. These genes were identified according to criteria published in Meyer & Purugganan [62]. These characteristics have favoured the cultivation of Asian rice over African rice in large parts of the world. A distantly related outgroup circumvents this problem but is more difficult to align, and hence will cause larger loss of data. For these reasons, OmegaPlus was chosen as the preferred method. The O. meridionalis x O. glaberrima multiple alignment was retrieved from Ensembl Genomes (release 33) and parsed with mafTools [45]. This will aid our understanding of the precise evolutionary relationships between O. glaberrima and O. barthii. It was first domesticated and grown in West Africa around 3,000 years ago. 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. Gene structures of these genes were retrieved from Ensembl Plants (release 37). Indeed, it is a widely observed phenomenon that incomplete lineage causes mixed phylogenetic signals [32]. Rice accompanied African slaves across the Middle Passage throughout the New World to Brazil, the Caribbean, and the southern United States. (Note: LD is defined by Hill and Robertson [51] 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 has been called the ‘rapid transition model’. The SNPs within the selected genomic coordinates were phased with PHASE (v2.1.1) [66,67], using the general model for recombination rate variation as found in Li & Stephens [68]. This suggests that a smaller number of individuals carries a larger fraction of the polymorphic sites, which is consistent with a population expansion scenario, as explained before. 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. Windows containing domestication genes with previous evidence for positive selection were highlighted. Tajima’s D was significantly different between the two species at p < 1.0E-05, being predominantly negative in O. glaberrima (-0.6761) and positive in O. barthii (0.5172). O. glaberrima indeed shares characteristics with a subset of O. barthii individuals; however, the majority of the coastal accessions form a monophyletic clade that does not contain any wild relatives. Domestication and Cultivation. In addition, African rice continues to survive in a ritual context, used in ritual offerings to honour the ancestors, rather than for consumption [5]. Funding: This study was funded by the National Science Foundation (nsf.gov) Grant No. FST between O. glaberrima and O. barthii was included as a baseline. 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. Geographic populations of O. glaberrima have been proposed before by Meyer et al. https://doi.org/10.1371/journal.pone.0203508.g001. [3] found evidence for the protracted transition model advocated by Harlan. An optimal number of ancestral populations was selected by choosing the level of K with the lowest cross-validation error. Mean depth of coverage, fraction of missing data and mean variant quality per SNP were calculated in 100 kb sliding windows along the entire genome in order to assess the distribution and quality of SNPs. For this reason, homoplasy was considered unlikely and correction for multiple substitutions was not applied. Outliers (separated by more than 1500 km) were omitted. [3], four geographic sub-populations were identified, separating the arid and tropical populations by the 11° N cline and coastal and inland populations by the 6° W cline, respectively. 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. Joint variant calling and quality filtering resulted in a total of 3,923,601 SNPs. 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. Supervision, Linear models and correlation coefficients were estimated in R (v3.3.2). Population structure was determined with ADMIXTURE (v1.3.0) [53]. 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 [10].
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