40 research outputs found
Molecular basis of African yam domestication: Analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes
Background: After cereals, root and tuber crops are the main source of starch in the human diet. Starch biosynthesis was certainly a significant target for selection during the domestication of these crops. But domestication of these root and tubers crops is also associated with gigantism of storage organs and changes of habitat. Results: We studied here, the molecular basis of domestication in African yam, Dioscorea rotundata. The genomic diversity in the cultivated species is roughly 30% less important than its wild relatives. Two percent of all the genes studied showed evidences of selection. Two genes associated with the earliest stages of starch biosynthesis and storage, the sucrose synthase 4 and the sucrose-phosphate synthase 1 showed evidence of selection. An adventitious root development gene, a SCARECROW-LIKE gene was also selected during yam domestication. Significant selection for genes associated with photosynthesis and phototropism were associated with wild to cultivated change of habitat. If the wild species grow as vines in the shade of their tree tutors, cultivated yam grows in full light in open fields. Conclusions: Major rewiring of aerial development and adaptation for efficient photosynthesis in full light characterized yam domestication. (Résumé d'auteur
Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments
Pearl millet [Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) Morrone], is a staple food for over 90 million poor farmers in arid and semi-arid regions of sub-Saharan Africa and South Asia. We report the ~1.79 Gb genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. Resequencing analysis of 994 (963 inbreds of the highly cross-pollinated cultigen, and 31 wild accessions) provides insights into population structure, genetic diversity, evolution and domestication history. In addition we demonstrated the use of re-sequence data for establishing marker trait associations, genomic selection and prediction of hybrid performance and defining heterotic pools. The genome wide variations and abiotic stress proteome data are useful resources for pearl millet improvement through deploying modern breeding tools for accelerating genetic gains in pearl millet.publishersversionPeer reviewe
Etude de mécanismes génétiques impliqués dans l'adaptation climatique de populations expérimentales de blé tendre
Local adaptation resulting from selection pressure acts on heritable characters and is a major force shaping the phenotypic diversity of natural populations. Currently, numerous questions exist surrounding the impact of selection on the evolution of genes involved in the structure of adaptive traits, which are often complex characters involving many interacting genes. The objective of this thesis is to identify certain genetic mechanisms which are activated during the adaptation of experimental wheat populations to different climactic contexts. The adaptive trait studied was flowering time, which permits the plant to synchronize reproduction with favorable seasonal conditions. The experimental populations considered had a common genetic origin and have evolved independently since 1984 in different sites in France, without conscious human selection or migration, but subject to the influence of natural selection and genetic drift. Using a base of knowledge on genes implicated in flowering in Arabidopsis thaliana and rice, and recent publications on wheat, the evolution of nucleotide polymorphisms in candidate genes was followed during 12 generations (2, 7 and 12) in three experimental populations (Vervins in the north of France, Le Moulon in the Parisian region and Tolouse in the South). These populations were also characterized for precocity of flowering time measured under different day length and vernalization regimes (duration of exposure to low temperatures) and for diversity of microsatellite loci sampled from throughout the genome. The comparison of levels of genetic differentiation among populations for these three measures of genetic diversity showed that precocity was subject to divergent selection from the first generations. However, it appears that this selection was not directly for flowering time, but instead achieved through indirect selection on correlated traits in the different environments, such as plant height or grain weight. Selection for precocity can be related to climactic characteristics of the experimental locations, with the northern populations flowering later than the southern population. This rapid evolution of the trait accompanied significant changes in allele frequencies for major genes involved in flowering time, and the development of specific multi-locus allelic combinations in the different climatic contexts considered. This evolution did not diminish the existing within-population genetic diversity because multiple combinations were favored in the different populations. The work presented in this thesis is an important contribution to our understanding of the maintenance of evolutionary potential in cultivated species.L'adaptation locale rĂ©sultant de pressions de sĂ©lection agissant sur des caractĂšres hĂ©ritables est une force majeure façonnant la diversitĂ© phĂ©notypique des populations dans la nature. A l'heure actuelle, de nombreuses questions subsistent quant Ă l'impact de la sĂ©lection sur l'Ă©volution des gĂšnes impliquĂ©s dans l'architecture des caractĂšres adaptatifs qui sont souvent des caractĂšres complexes impliquant de nombreux gĂšnes en interaction. L'objectif de cette thĂšse est d'identifier certains mĂ©canismes gĂ©nĂ©tiques mis en jeu lors de l'adaptation de populations expĂ©rimentales de blĂ© tendre Ă diffĂ©rents contextes climatiques. Le caractĂšre Ă©tudiĂ© est la prĂ©cocitĂ© de floraison, caractĂšre adaptatif majeur chez les plantes annuelles. Les populations expĂ©rimentales considĂ©rĂ©es dans cette Ă©tude ont une origine gĂ©nĂ©tique commune et Ă©voluent de façon indĂ©pendante depuis 1984 dans diffĂ©rents sites en France sans sĂ©lection humaine consciente ni migration, mais sous l'influence de la sĂ©lection naturelle et de la dĂ©rive. En se basant sur les connaissances des gĂšnes impliquĂ©s dans la floraison chez le blĂ©, l'Ă©volution de polymorphismes nuclĂ©otidiques de diffĂ©rents gĂšnes candidats a Ă©tĂ© suivie durant 12 gĂ©nĂ©rations (2, 7 et 12) dans 3 populations expĂ©rimentales (Vervins au Nord de la France, Le Moulon en rĂ©gion parisienne et Toulouse au Sud). Ces populations ont Ă©galement Ă©tĂ© caractĂ©risĂ©es pour la prĂ©cocitĂ© et pour la diversitĂ© de locus microsatellites rĂ©partis sur l'ensemble du gĂ©nome. La comparaison des niveaux de diffĂ©renciation gĂ©nĂ©tique inter population obtenue pour les trois types de diversitĂ© montre que la prĂ©cocitĂ© est sĂ©lectionnĂ©e de façon divergente dĂšs les premiĂšres gĂ©nĂ©rations. Cependant cette sĂ©lection ne se fait pas de façon directe et semble ĂȘtre le fait de la sĂ©lection agissant sur des caractĂšres corrĂ©lĂ©s dans les diffĂ©rents environnements, tels que la hauteur ou le poids de grains. La sĂ©lection pour la prĂ©cocitĂ© peut ĂȘtre mise en relation avec les caractĂ©ristiques climatiques des sites de culture, les populations du Nord fleurissant plus tardivement que la population du Sud. Cette Ă©volution rapide du caractĂšre s'accompagne de changements importants de frĂ©quences allĂ©liques pour des gĂšnes majeurs de prĂ©cocitĂ©, et la mise en place de combinaisons allĂ©liques multi-locus spĂ©cifiques des diffĂ©rents contextes climatiques considĂ©rĂ©s. Cette Ă©volution ne remet pas en cause la diversitĂ© existant Ă l'intĂ©rieure de chaque population puisque plusieurs combinaisons diffĂ©rentes sont favorisĂ©es dans les diffĂ©rentes populations. Ce travail de thĂšse ouvre des perspectives intĂ©ressantes quant au problĂšme du maintien du potentiel adaptatif des espĂšces cultivĂ©es
Evolution of flowering time in experimental wheat populations: a comprehensive approach to detect genetic signatures of natural selection.
International audienceIn annual plant species, flowering time is a major adaptive trait that synchronizes the initiation of reproduction with favorable environmental conditions. Here, we aimed at studying the evolution of flowering time in three experimental populations of bread wheat, grown in contrasting environments (Northern to Southern France) for 12 generations. By comparing the distribution of phenotypic and presumably neutral variation, we first showed that flowering time responded to selection during the 12 generations of the experiment. To get insight into the genetic architecture of that trait, we then tested whether the distribution of genetic polymorphisms at six candidate genes, presumably involved in the trait expression, departed from neutral expectation. To that end, we focused on the temporal variation during the course of the experiment, and on the spatial differentiation at the end of the experiment, using previously published methods adapted to our experimental design. Only those genes that were strongly associated with flowering time variation were detected as responding to selection. For genes that had low-to-moderate phenotypic effects, or when there was interaction across different genes, we did not find evidence of selection using methods based on the distribution of temporal or spatial variation. In such cases, it might be more informative to consider multilocus and multiallelic combinations across genes, which could be the targets of selection
Flowering time trait, gene and microsatellite differentiation among experimental populations of wheat
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Flowering time trait, gene and microsatellite differentiation among experimental populations of wheat
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Dynamic management of crop diversity: From an experimental approach to on-farm conservation
International audienceIn agricultural systems, biodiversity includes diversity within species and among species and provides many benefits for production, resilience and conservation. This article addresses the effects of a strategy of in situ conservation called dynamic management (DM) on population evolution, adaptation and diversity. Two French DM initiatives are considered, the first one corresponding to an experimental context, the second to an on-farm management. Results from a study over 26 years of experimental DM of bread wheat (Triticum aestivum L.) are first presented, including the evolution of agronomic traits and genetic diversity at neutral and fitness related loci. While this experiment greatly increased scientific knowledge of the effects of natural selection on cultivated populations, it also showed that population conservation cannot rely only on a network of experimental stations. In collaboration with a farmersâ network in France, researchers have begun studying the effects of on-farm DM (conservation and selection) on diversity and adaptation. Results from these studies show that on-farm DM is a key element for the long-term conservation and use of agricultural biodiversity. This method of in situ conservation deserves more attention in industrialised countries.Lâimportance de lâagrobiodiversitĂ©, câest-Ă -dire la biodiversitĂ© prĂ©sente dans les espaces agricoles, fait lâobjet dâune reconnaissance toute rĂ©cente. Cette biodiversitĂ©, qui englobe Ă la fois la diversitĂ© observĂ©e Ă lâintĂ©rieur des espĂšces et la richesse en espĂšces, est Ă lâorigine de nombreux bĂ©nĂ©fices pour les fonctions de production, rĂ©silience et conservation des espaces agricoles. Dans cet article, nous nous intĂ©ressons aux principaux effets dâune stratĂ©gie de conservation in situ de lâagrobiodiversitĂ©, la gestion dynamique (GD), sur lâĂ©volution de la diversitĂ© et lâadaptation des populations. Notre analyse est construite sur la base de deux initiatives françaises de GD, lâune dans un contexte expĂ©rimental, et la seconde se dĂ©roulant Ă la ferme. Une premiĂšre approche expĂ©rimentale de GD est menĂ©e depuis 26 annĂ©es sur le blĂ© tendre (Triticum aestivum L.), et a fait lâobjet de nombreuses Ă©tudes, portant sur lâĂ©volution des caractĂšres agronomiques et de la diversitĂ© gĂ©nĂ©tique de locus neutres ou sĂ©lectionnĂ©s. Cette expĂ©rience a contribuĂ© Ă la meilleure connaissance des effets de la sĂ©lection naturelle sur les populations cultivĂ©es, mais elle a Ă©galement montrĂ© quâun rĂ©seau de stations expĂ©rimentales ne pouvait constituer lâunique dispositif de conservation de populations cultivĂ©es. En collaboration avec un rĂ©seau dâagriculteurs français, les scientifiques ont initiĂ© lâĂ©tude de lâeffet de la conservation Ă la ferme et de la sĂ©lection participative sur la diversitĂ© et lâadaptation des populations. Les rĂ©sultats des premiĂšres Ă©tudes montrent que la conservation in situ Ă la ferme et la sĂ©lection participative sont des Ă©lĂ©ments essentiels pour la conservation Ă long terme et lâutilisation de la biodiversitĂ© agricole, un rĂŽle encore peu reconnu dans les pays industrialisĂ©s
No excess of cis-regulatory variation associated with intra-specific selection in wild pearl millet (Cenchrus americanus)
International audienceSeveral studies suggestthat cis-regulatory mutations are the favorite target of evolutionary changes, one reason being that cis-regulatory mutations might have fewer deleterious pleiotropic effects than protein-coding mutations. A review of the process also suggests that this bias towards adaptive cis-regulatory variation might be less pronounced at the intraspecific level compared with the interspecific level. In this study, we assessed the contribution of cis-regulatory variation to adaptation at the intraspecific level using populations of wild pearl millet (Cenchrus americanus ssp. monodii) sampled along an environmental gradient in Niger. From RNA sequencing of hybrids to assess allele-specific expression, we identified genes with cis-regulatory divergence between two parental accessions collected in contrasted environmental conditions. This revealed that similar to 15% of transcribed genes showed cis-regulatory variation. Intersecting the gene set exhibiting cis-regulatory variation with the gene set identified as targets of selection revealed no excess of cis-acting mutations among the selected genes. We additionally found no excess of cis-regulatory variation among genes associated with adaptive traits. As our approach relied on methods identifying mainly genes submitted to strong selection pressure or with high phenotypic effect, the contribution of cis-regulatory changes to soft selection or polygenic adaptive traits remains to be tested. However our results favor the hypothesis that enrichment of adaptive cis-regulatory divergence builds up over time. For short evolutionary time-scales, cis-acting mutations are not predominantly involved in adaptive evolution associated with strong selective signal
A Quantitative Theory for Genomic Offset Statistics
International audienceGenomic offset statistics predict the maladaptation of populations to rapid habitat alteration based on association of genotypes with environmental variation. Despite substantial evidence for empirical validity, genomic offset statistics have well-identified limitations, and lack a theory that would facilitate interpretations of predicted values. Here, we clarified the theoretical relationships between genomic offset statistics and unobserved fitness traits controlled by environmentally selected loci and proposed a geometric measure to predict fitness after rapid change in local environment. The predictions of our theory were verified in computer simulations and in empirical data on African pearl millet (Cenchrus americanus) obtained from a common garden experiment. Our results proposed a unified perspective on genomic offset statistics and provided a theoretical foundation necessary when considering their potential application in conservation management in the face of environmental change