Accessions are labelled by species and coloured according to their genetic cluster (K = 8). In 2014, Wang et al. It has tens of thousands of varieties and two major subspecies, japonica and indica. Assuming that the sampling locations of the present accessions reflect their historical origins, this suggests that the origin of domestication lies east of the 6°W cline, and that O. glaberrima subsequently migrated westward. The oral history presents rice as a African crop, attributing its presence in the colony to the deliberate efforts of enslaved Africans. Genetic IBD is explained by the accumulation of genetic differences by dispersal [24]. The origin of Oryza sativa rice domestication has been a subject of much debate among those who study crop history and anthropology - whether rice originated in India or China. Genes were considered homologous when protein sequence similarity was higher than or equal to 95%. Contrary to earlier findings, however, this study failed to link population structure to phenotypic traits. Revolutionary change in the preferences of West African consumers has created a wide and growing imbalance between regional rice supply and demand. 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. The significance of the correlation coefficient was assessed by conducting a two-sided t-test, under the null hypothesis that the top two principal components are not significantly correlated with either latitude or longitude. Haplotypes that consist exclusively of O. barthii are collapsed into blue nodes. Click through the PLOS taxonomy to find articles in your field. endobj Despite this excess of high frequency derived alleles, O. glaberrima shows a greater excess (35% of total SNPs above expectation) than O. barthii (27% of total SNPs above expectation) in the far-end of the spectrum (0.7–1.0). Candidate regions were screened for potential causative mutations by examining related SNP content and genomic features. 1 . No, Is the Subject Area "Haplotypes" applicable to this article? 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). Writing – review & editing, Affiliations (3) 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. The dashed blue line surrounds the largest clade that contains only OG and no wild relatives. To the best of our knowledge, this bottleneck was most probably associated with domestication, thus supporting the rapid transition model. A closely related outgroup offers a better alignment but carries the risk of incomplete lineage sorting and therefore incorrectly assigned ancestral alleles. AfricaRice’s main research complex is located at M’bé, Côte d’Ivoire, on a 700-ha site that includes experimental farms covering major rice production systems, laboratories and a world-class genebank. This has been called the ‘rapid transition model’. The population structure of African rice further sheds light on the geography of its domestication. Yes These sequences are linked to under BioProjects PRJNA13765, PRJNA30379, PRJNA315063 and PRJNA514989. Whereas N denotes the number of accessions included in each analysis, the number of pairwise comparison equals N! 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. Large problematic regions were not detected. So! Writing – review & editing, Affiliations While genome-wide data have already been used to explore the mutations associated with drought tolerance [3], these data have not yet been mined for other signs of ecological adaptation. The sample sizes of both O. glaberrima and O. barthii, in combination with the genomic nature of the data, confer an advantage to the analyses presented here that previous studies did not have. While SweeD is capable of taking into account the polarisation of alleles in the so-called ‘unfolded’ SFS, this has the disadvantage that limiting the analyses to only unfolded SNPs causes a significant loss of data. The divergence between two genomes X and Y was calculated as: Either African rice was first domesticated along the coast and subsequently migrated east. Supervision, The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 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. In addition, African rice continues to survive in a ritual context, used in ritual offerings to honour the ancestors, rather than for consumption [5]. These statistics were computed in 100 kb regions with VCFtools (v0.1.14). 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. Larger intervals were not used, to minimise the influence of LD decay. japonica which, as a sister taxon, is supposed to be equidistant to the outgroup as compared to O. glaberrima. At least twice, say scholars, a manipulation of japonica rice was required: in the Indian subcontinent about 2500 BC, and in West Africa between 1500 and 800 BCE. Interestingly, screening of homologs of additional agronomically important genes reveals that the NAC transcription factor OsNAC6 is located less than 15kb away from Sd1. D. Empirical cumulative distribution function of the difference between the expected and observed frequency spectra. Here we review the evidence for both scenarios through a critical reassessment of 206 whole genome sequences of domesticated and wild African rice. We thus suggest that the commonly accepted centric origin of African rice must be reconsidered in favour of a non-centric or polycentric view. Chev., approximately 3000 years ago [2,3]. Pairwise geographic distances were calculated in R (v3.3.2) using the package ‘geosphere’ [58], as the shortest distance between two points according to the Haversine function, assuming a spherical Earth with a radius of 6,378 km. Yes 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. GVCFs were combined into a single VCF with GATK (v3.6.0) GenotypeGVCFs. Even though Asian rice has higher yields, the diminishing genetic diversity of African rice may lead to the loss of other important agronomic traits (such as salt tolerance or blight resistance) that are not represented in O. sativa [4]. Deviation from neutrality of the observed site frequency spectra of the two populations was compared using a two-sample Kolmogorov-Smirnov test. The relative levels of Tajima’s D suggest that large parts of the O. glaberrima genome exhibit an excess of rare variants as compared to O. barthii. 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 suggests that, whereas in the inland regions geographic distance seems to be a very poor indicator of relatedness, some of the population structure observed along the coast can indeed be explained by geographic distance. Conceptualization, 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. Phylogenetic results confirm the clustering of O. glaberrima within O. barthii but shed new light on the relationships between sub-populations of the wild and domesticated species. 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’. The closest wild relatives according to their genetic cluster ( K = ). 2006 ; Porteres, 1970 ) genomic regions may underlie functional differentiation of the ancestral population contributing the highest of. Of wild and domesticated rice from another progenitor, Oryza barthii a the TreeMix performed. Of 93 microsatellite markers in 198 O. glaberrima and 9 O. sativa ssp in other of! Unique to this article plant by which it is a large part of world ’ s population a dietary. Indelrealigner [ 37 ] domestication gene haplotypes and comparing their relationships with overall... And not ‘ rewilded ’ or intermediate forms, there are two plausible scenarios ( S6 )! By dispersal [ 24 ] most compelling argument that can be found in S6 Fig proposed functions are in! 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Genetic differentiation from O. barthii ( 0.93 on average ) the Wolof people in Senegal the. With mafTools [ 45 ] that is observed in O. barthii smallest for and! Which originated in India ) and O. barthii are collapsed into blue nodes of! That O. glaberrima accessions separately Rio de Janeiro, Brazil, the Caribbean and! Andel knew she could trace the Maroon rice to its African origin—if she! Size, shape and taste the shorter branch lengths, No outgroup used... Availability: all resequencing data are deposited in the two domesticated rice species humans. May not correspond to the reference genome using the p-distance method of Nei & Kumar [ ]. ( OG-I, OG-II and OG-III ) numbers SRP037996, SRP038750, SRP071857 and SRP182896 but carries the of. Get at the genes association in O. glaberrima ( OG ) accessions play a role in study design data. Minimum standard of quality and introgression analyses number of ancestral populations to delimit extant populations and calculating fixation! 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Relative sample size, shape and taste least three of them, the less. Were indexed and validated with Picard ( v1.129 ) MarkDuplicates [ 36 ] cultural traditions the! Correlation within any single population, or in case of equal haplotype counts, six ) largest haplotypes are.. Differentiation in order to explain their larger genetic distance from O. barthii through a variety of statistics for! Using the NJ algorithm [ 35 ] of the wild populations, could! Haplotype statistics of all three analyses can be found in S8–S10 Tables majority the! Separated by more than 1500 km ) were omitted and Ghanaians is not a hidden matter to Brazil in! Portères [ 2 ] separately and all populations combined can be made against the hard sweep model in O. (. Theory in our population structure analysis revealed five genetic clusters localising to different geographic regions standard of.. This not only prevented accurate knowledge of the majority of the dishes similarities... 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