The molecular bases of cereal domestication and the history of rice

International audienceIn this review, we discuss the development of molecular genetics and genomics that has allowed one to identify and characterize some of the key genes involved in cereal domestication. The list is far from being complete, but the first conclusion that can be drawn from the published works is that only a few loci have been the target of human selection in the first stages of the domestication process at the late neolithic. Mutations at these few loci have led to dramatic changes in plant morphology and phenology, transforming a wild into a cultivated plant. We also show that in the case of rice, for which the complete genome sequence is available, the development of new molecular markers based on retrotransposon insertion polymorphisms helped to resolve some of the questions regarding the origin of the domestication of the crop in Asia

LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss

Background: LTR retrotransposons are one of the main causes for plant genome size and structure evolution, along with polyploidy. The characterization of their amplification and subsequent elimination of the genomes is therefore a major goal in plant evolutionary genomics. To address the extent and timing of these forces, we performed a detailed analysis of 41 LTR retrotransposon families in rice. Results: Using a new method to estimate the insertion date of both truncated and complete copies, we estimated these two forces more accurately than previous studies based on other methods. We show that LTR retrotransposons have undergone bursts of amplification within the past 5 My. These bursts vary both in date and copy number among families, revealing that each family has a particular amplification history. The number of solo LTR varies among families and seems to correlate with LTR size, suggesting that solo LTR formation is a family-dependent process. The deletion rate estimate leads to the prediction that the half-life of LTR retrotransposon sequences evolving neutrally is about 19 My in rice, suggesting that other processes than the formation of small deletions are prevalent in rice DNA removal. Conclusion: Our work provides insights into the dynamics of LTR retrotransposons in the rice genome. We show that transposable element families have distinct amplification patterns, and that the turn-over of LTR retrotransposons sequences is rapid in the rice genome

Characterization of the complete plastome of Ophrys aveyronensis , a Euro-Mediterranean orchid with an intriguing disjunct geographic distribution

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RetrOryza: a database of the rice LTR-retrotransposons

Long terminal repeat (LTR)-retrotransposons comprise a significant portion of the rice genome. Their complete characterization is thus necessary if the sequenced genome is to be annotated correctly. In addition, because LTR-retrotransposons can influence the expression of neighboring genes, the complete identification of these elements in the rice genome is essential in order to study their putative functional interactions with the plant genes. The aims of the database are to (i) Assemble a comprehensive dataset of LTR-retrotransposons that includes not only abundant elements, but also low copy number elements. (ii) Provide an interface to efficiently access the resources stored in the database. This interface should also allow the community to annotate these elements. (iii) Provide a means for identifying LTR-retrotransposons inserted near genes. Here we present the results, where 242 complete LTR-retrotransposons have been structurally and functionally annotated. A web interface to the database has been made available (), through which the user can annotate a sequence or search for LTR-retrotransposons in the neighborhood of a gene of interest

The impact of transposable elements on the structure, evolution and function of the rice genome

International audienc

Suivi des introgressions dans les croisements interspécifiques chez le riz : utilisation des marqueurs moléculaires

La diversité génétique des espèces sauvages de riz est d'un grand intérêt en amélioration des plantes. Malgré de fortes barrières reproductives, des hybrides interspécifiques peuvent être obtenus grâce à la récupération des embryons par culture #in vitro et être recroisés ensuite pour introduire des caractères utiles dans les riz cultivés. Au fur et à mesure que la carte de liaison génétique RFLP (polymorphisme de longueur de fragment de restriction) devient de plus en plus saturée, les marqueurs moléculaires constituent un nouvel outil puissant pour analyser et comprendre les mécanismes de la recombinaison dans les croisements éloignés. Trois exemples d'application des marqueurs moléculaires au suivi des introgressions sont présentés à partir d'activités développées à l'ORSTOM (Institut Français de Recherche Scientifique pour le Développement en Coopération) de Montpellier ou de collaborations avec l'IRRI (Institut International de Recherche sur le Riz, Philippines) et l'Université Cornell (Etats-Unis). Ils concernent l'analyse de générations précoces ou de lignées isogéniques développées avec des espèces sauvages de riz possédant le même génome que le riz cultivé (#O. longistaminata) ou des génomes cytogénétiquement différents (#O. brachyantha, génome F) et (#O. australiensis, génome E). (Résumé d'auteur

Evolution of plant phenotypes, from genomes to traits

Connecting genotype to phenotype is a grand challenge of biology. Over the past 50 years, there have been numerous and powerful advances to meet this challenge, including next-generation sequencing approaches (Jackson et al. 2011), molecular genetic mapping techniques, computational modeling, and the integration of evolutionary theory and tools. In plants, the long history of domestication and breeding has provided multiple insights into the genotype–phenotype equation (Meyer and Purugganan 2013; Olsen and Wendel 2013). Domestication and breeding provide unique systems with which to study the evolution of traits and adaptation to new environments. At present, agriculture faces unprecedented challenges, with the need to continue to increase food quality and food production for a population that will likely exceed 9 billion by 2050, combined with the urgent need to make agriculture more sustainable in an environment that will be altered by climate change (Diouf 2009). Crop wild relatives, however, have evolved under ecological settings that often are more extreme than those under cultivation and thus represent a reservoir of useful adaptive traits. This genetic diversity has mostly been untapped because of a lack of appropriate tools, both at the genetic level and in describing plant phenotypes and adaptation (Mace et al. 2013). In this context, crop improvement needs to undergo a qualitative leap forward by exploiting the knowledge from the interface of the fields of molecular evolution, bioinformatics, plant physiology, and genetics. With the objective of reviewing the most recent advances and identifying unanswered questions at this interface, a group of scientists met in Barcelona in March 2015 for a workshop organized by B-Debate (www.bdebate.org) and the Center for Research in Agricultural Genomics (CRAG, www.cragenomica.es), with the support of the US National Science Foundation. The meeting was divided into three scientific sessions. The first concentrated on the mechanisms that generate genomic diversity in plants, with a particular emphasis on transposable elements and polyploidy, while the second and third sessions were devoted to the evolution of plant phenotypes in wild and domesticated species, and to domestication and plant improvement processes, respectively

Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae

<p>Abstract</p> <p>Background</p> <p>Horizontal transfers (HTs) refer to the transmission of genetic material between phylogenetically distant species. Although most of the cases of HTs described so far concern genes, there is increasing evidence that some involve transposable elements (TEs) in Eukaryotes. The availability of the full genome sequence of two cereal species, (<it>i.e</it>. rice and <it>Sorghum</it>), as well as the partial genome sequence of maize, provides the opportunity to carry out genome-wide searches for TE-HTs in <it>Poaceae</it>.</p> <p>Results</p> <p>We have identified an LTR-retrotransposon, that we named <it>Route66</it>, with more than 95% sequence identity between rice and <it>Sorghum</it>. Using a combination of <it>in silico </it>and molecular approaches, we are able to present a substantial phylogenetic evidence that <it>Route66 </it>has been transferred horizontally between Panicoideae and several species of the genus <it>Oryza</it>. In addition, we show that it has remained active after these transfers.</p> <p>Conclusion</p> <p>This study constitutes a new case of HTs for an LTR-retrotransposon and we strongly believe that this mechanism could play a major role in the life cycle of transposable elements. We therefore propose to integrate classe I elements into the previous model of transposable element evolution through horizontal transfers.</p

Amplification dynamics of miniature inverted-repeat transposable elements and their impact on rice trait variability

Ministerio de Ciencia y Innovación (PID2019-106374RB-I00) - DOI 10.13039/501100011033Transposable elements (TEs) are a rich source of genetic variability. Among TEs, miniature inverted-repeat TEs (MITEs) are of particular interest as they are present in high copy numbers in plant genomes and are closely associated with genes. MITEs are deletion derivatives of class II transposons, and can be mobilized by the transposases encoded by the latter through a typical cut-and-paste mechanism. However, MITEs are typically present at much higher copy numbers than class II transposons. We present here an analysis of 103 109 transposon insertion polymorphisms (TIPs) in 738 Oryza sativa genomes representing the main rice population groups. We show that an important fraction of MITE insertions has been fixed in rice concomitantly with its domestication. However, another fraction of MITE insertions is present at low frequencies. We performed MITE TIP-genome-wide association studies (TIP-GWAS) to study the impact of these elements on agronomically important traits and found that these elements uncover more trait associations than single nucleotide polymorphisms (SNPs) on important phenotypes such as grain width. Finally, using SNP-GWAS and TIP-GWAS we provide evidence of the replicative amplification of MITEs