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Click through the PLOS taxonomy to find articles in your field. Naturalis Biodiversity Center, Leiden, The Netherlands, Roles https://doi.org/10.1371/journal.pone.0203508.g003. OsNAC6 has been identified as a key regulator of rice stress responses and has been shown to enhance drought and salinity tolerance [27]. 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]. (3) 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. More surprising, however, is the fact that out of 20 candidate domestication genes identified from the O. sativa literature (S2 Table), not a single one shows clear-cut evidence of a recent, strong selective sweep (S4 Fig). No, PLOS is a nonprofit 501(c)(3) corporation, #C2354500, based in San Francisco, California, US, https://doi.org/10.1371/journal.pone.0203508, http://irri.org/rice-today/trends-in-global-rice-consumption. B. 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. Hence, we chose O. meridionalis as an outgroup. The results were deemed sufficiently comparable to proceed with both call sets (S9 Fig). These characteristics have favoured the cultivation of Asian rice over African rice in large parts of the world. Conceptualization, For more information about PLOS Subject Areas, click Only biallelic SNPs were retained for analysis. 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]. In addition, this study supports a period of low-intensity cultivation that may have started as early as 10,000 years before the effective population size reached a low point around 3000 years ago, when African rice was reputedly domesticated. Oryza punctata was rejected because of its high genomic divergence (>5%) and associated data loss. This study has aimed to resolve some of the confusion introduced in this debate. The most common haplotypes, containing accessions from multiple sub-populations O. glaberrima, are collapsed into orange nodes. <>stream 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. 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. [3] do the opposite; they propose that domestication was protracted, but not necessarily non-centric. 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. Supervision, Copyright: © 2019 Veltman et al. Although the first genome study of African rice supported a single origin of domestication [22], the suggested place of origin is not located along the Inner Niger Delta as suggested by Portères [2], but rather in what Portères proposes to be the secondary diversification centre(s) on the Atlantic coast. 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. Large problematic regions were not detected. 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. Although this is well outside the zone of cultivation today, African rice was probably common in the Sahara in wetter periods (Chevalier, 1932:86). Although the functional relevance of these genetic differences has been demonstrated for one gene (Sh4), both in silico and in vitro, the phenotypic consequences of haplotype variation in the other genes remain to be determined. C. PCA of all geo-referenced accessions of O. glaberrima (dots, filled) and O. barthii (triangles, open) together. 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. Contrary to earlier findings, however, this study failed to link population structure to phenotypic traits. 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. V an Andel knew she could trace the Maroon rice to its African origin—if only she could get at the genes. To avoid distortion of branch lengths, no outgroup was used. As a result, many traditional landraces of O. glaberrima are disappearing, or have already disappeared [4]. 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. 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. Although these accessions are exclusively surrounded by O. barthii accessions sharing the same ancestry, the fact that they frequently form a distant clade provides further support for the separate roots of domestication in the coastal and inland regions of West Africa. Writing – review & editing. The expected site frequency spectrum under a neutral model of evolution was calculated using the estimation of the population scaled mutation rate [42]. Individual genotypes were called using GATK (v3.6.0) HaplotypeCaller on reads with a minimum mapping quality score of 30. This has been observed in the case of drought tolerance in the coastal populations of O. glaberrima [3]. FST between O. glaberrima and O. barthii was included as a baseline. Available evidences drawn from biosystematics, evolutionary biology, biogeography, archaeology, history, anthropology, paleo-geology and paleo-meteorology are pooled to reconstruct the series of events that led to the cosmopolitan cultivation of the Asian cultivated rice (O. sativa) and the regionalized planting of the African cultigen (O. glaberrima) in West Africa. Nabholz et al. Asian rice, Oryza sativa, is one of oldest crop species. Genetic differentiation from O. barthii for all five O. glaberrima populations was found to be large (FST > 0.15), but relatively larger for the three coastal populations (FST > 0.25) than for the two inland populations (FST 0.15–0.25). We were unable to detect any such association in O. barthii alone. Observed and expected marginal derived allele frequency spectrum of O. glaberrima. 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. Oryza longistaminata was rejected because of its low genomic divergence from O. glaberrima (~2%). Specifically, the ancestral character of a functionally important SNP in Sh4 has been confirmed independently and proposed to “support the deep and separate roots of domestication practices in the west versus the eastern cultivation range” [33]. West Africa Jollof Rice. Roles 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… C. Isolation by distance among the coastal populations (OG-I, OG-II and OG-III). Origin of Rice: Rice is the seed of monocot plants Oryza sativa (African rice) or Oryza glaberrima (African rice). broad scope, and wide readership – a perfect fit for your research every time. The fixation index (FST) between O. glaberrima and O. barthii is based on the implementation of [41] and calculated as: , where p is the allele frequency in the total population,σ2T is the variance in allele frequency in the total population, and σ2S is the variance in allele frequency between the two sub-populations. 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). A list of all used accessions and their metadata can be found in S1 Table. Rice Growing Environment 3. It has tens of thousands of varieties and two major subspecies, japonica and indica. Filter classes and their thresholds can be found in S8 Fig. https://doi.org/10.1371/journal.pone.0203508.s001, https://doi.org/10.1371/journal.pone.0203508.s002, https://doi.org/10.1371/journal.pone.0203508.s003, https://doi.org/10.1371/journal.pone.0203508.s004, https://doi.org/10.1371/journal.pone.0203508.s005, https://doi.org/10.1371/journal.pone.0203508.s006, https://doi.org/10.1371/journal.pone.0203508.s007, https://doi.org/10.1371/journal.pone.0203508.s008, https://doi.org/10.1371/journal.pone.0203508.s009, https://doi.org/10.1371/journal.pone.0203508.s010, https://doi.org/10.1371/journal.pone.0203508.s011, https://doi.org/10.1371/journal.pone.0203508.s012, https://doi.org/10.1371/journal.pone.0203508.s013, https://doi.org/10.1371/journal.pone.0203508.s014, https://doi.org/10.1371/journal.pone.0203508.s015, https://doi.org/10.1371/journal.pone.0203508.s016, https://doi.org/10.1371/journal.pone.0203508.s017, https://doi.org/10.1371/journal.pone.0203508.s018, https://doi.org/10.1371/journal.pone.0203508.s019. The third objective was met by estimating the number of ancestral populations to delimit extant populations and calculating the fixation index between them. The authors found no isolation by distance and therefore argued that the maintenance of sub-populations was mainly caused by artificial selection and human-mediated gene flow. These genes were identified according to criteria published in Meyer & Purugganan [62]. For this reason, gene trees may not correspond to the overall genomic tree. <>stream While the combined results do not support either a fully centric or fully non-centric origin, evidence for multiple origins of domestication traits hints at the complex domestication history of African rice and suggests that the commonly accepted narrative of a single geographic origin of domestication should be reconsidered in favour of a polycentric or non-centric view. 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. Previous studies have supported either a centric or a non-centric geographic origin of African rice domestication. 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]. These statistics were computed in 100 kb regions with VCFtools (v0.1.14). 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. We therefore see strong evidence of Portères’ domestication theory in our population structure analysis. This West African dish will also be reminiscent of the popular old world paella, as well as a number of other rice … Proposed centric origin of African rice, after Portères in [17]. In order to make an informed decision as to which version of call set to use and whether or not to adjust the filtering parameters, we calculated additional statistics. 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. These genetic analyses will have to be balanced with suitable morphological evidence. Both O. barthii and O. glaberrima are predominantly selfing plants, which is reflected in their low levels of heterozygosity, averaging around 5%. The clustering of inland samples with O. barthii implies that they share a common pool of genetic variation from which O. glaberrima was domesticated, and that the coastal lineages branched off at a later point in time. 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. Although this theory has not been proposed in the context of African rice, a hypothetical scenario of two origins of O. glaberrima is visualised for illustration purposes, alongside the two other hypotheses in Fig 1. https://doi.org/10.1371/journal.pone.0203508.t002. Rice is a staple food for the majority of the world’s population. This could have led to the observed genetic differences in various parts of the genome. 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. Without additional modelling, therefore, we cannot be sure that demographic history of African rice did not interfere with the CLR test presented here. This will help to predict the phenotypic consequences of domestication gene haplotypes and in linking phylogenetic patterns to the evolution of functionally significant traits.

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