L'enginyeria genòmica, l'última revolució en la millora genètica de les plantes cultivades

La millora genètica de les plantes cultivades ha permès a les societats humanes obtenir suficient quantitat d'aliments de qualitat al llarg de la història. Aquest procés, que comença al neolític, s'ha anat tecnificant i fent més eficient a mesura que la ciència avançava. La mutagènesi a mitjan segle XX i la transgènia al final dels anys noranta del mateix segle, entre altres tècniques, han permès fer un salt endavant en la millora genètica. Recentment s'han posat a punt tècniques de mutagènesi dirigida amb nucleases específiques que poden revolucionar la millora genètica. En particular, la mutagènesi amb el sistema CRISPR/Cas9 està permetent ja obtenir noves variants al·lèliques amb una eficiència i precisió sense precedents. Malgrat l'interès evident d'aquestes tècniques, el seu èxit dependrà, en gran manera, de la regulació que s'apliqui a les plantes obtingudes, i en particular de si la legislació europea les considera transgèniques o no. En aquest article analitzem l'interès d'aquestes tècniques a la llum de la història de la millora genètica de les plantes i en discutim la possible regulació.La mejora genética de las plantas cultivadas ha permitido a las sociedades humanas obtener suficientes alimentos de calidad a lo largo de la historia. Este proceso, que empieza en el Neolítico, ha ido tecnificándose y haciéndose más eficiente en paralelo al avance científico. La mutagénesis desde mediados del siglo XX y la transgenia desde finales de los años noventa del mismo siglo, entre otras técnicas, permitieron dar un salto cualitativo en la mejora genética. Recientemente se han puesto a punto técnicas de mutagénesis dirigida con nucleasas específicas que pueden revolucionar la mejora genética. En particular, la mutagénesis usando el sistema CRISPR/Cas9 está permitiendo ya obtener nuevas variantes alélicas con una eficiencia y precisión sin precedentes. Aunque el interés en estas técnicas es evidente, su éxito dependerá en gran medida de la regulación que se aplique a los productos obtenidos de estas plantas, y en particular de si la legislación europea las considera transgénicas o no. En este artículo analizamos el interés de estas técnicas a la luz de la historia de la mejora genética de las plantas y discutimos su posible regulación.Plant breeding has allowed human societies to secure the production of food of good quality throughout history. This process, which started in the Neolithic, has become increasingly technologically based and efficient in step with the advance of scientific knowledge. Mutagenesis, since the mid 20th century, and transgenic plants since the late 1990s, among other techniques, allowed a qualitative leap forward in plant breeding. Recently, new site-directed mutagenesis techniques have been developed which may have a large impact on plant breeding. In particular, CRISPR/Cas9 mutagenesis approaches are already allowing new alleles to be obtained with unprecedented efficiency and precision. In spite of the obvious interest of these techniques, their success in plant breeding will greatly depend on the regulation applied to the plants which are obtained and more specifically on whether or not these plants will be considered GMOs. In this article we describe the interest of these new techniques and discuss their possible regulation

Additional ORFs in plant LTR-retrotransposons

Altres ajuts: CERCA Programme/Generalitat de CatalunyaLTR-retrotransposons share a common genomic organization in which the 5' long terminal repeat (LTR) is followed by the gag and pol genes and terminates with the 3' LTR. Although GAG-POL-encoded proteins are considered sufficient to accomplish the LTR-retrotransposon transposition, a number of elements carrying additional open reading frames (aORF) have been described. In some cases, the presence of an aORF can be explained by a phenomenon similar to retrovirus gene transduction, but in these cases the aORFs are present in only one or a few copies. On the contrary, many elements contain aORFs, or derivatives, in all or most of their copies. These aORFs are more frequently located between pol and 3' LTR, and they could be in sense or antisense orientation with respect to gag-pol. Sense aORFs include those encoding for ENV-like proteins, so called because they have some structural and functional similarities with retroviral ENV proteins. Antisense aORFs between pol and 3' LTR are also relatively frequent and, for example, are present in some characterized LTR-retrotransposon families like maize Grande, rice RIRE2, or Silene Retand, although their possible roles have been not yet determined. Here, we discuss the current knowledge about these sense and antisense aORFs in plant LTR-retrotransposons, suggesting their possible origins, evolutionary relevance, and function

Genome engineering and plant breeding : impact on trait discovery and development

Key message: New tools for the precise modification of crops genes are now available for the engineering of new ideotypes. A future challenge in this emerging field of genome engineering is to develop efficient methods for allele mining. Abstract: Genome engineering tools are now available in plants, including major crops, to modify in a predictable manner a given gene. These new techniques have a tremendous potential for a spectacular acceleration of the plant breeding process. Here, we discuss how genetic diversity has always been the raw material for breeders and how they have always taken advantage of the best available science to use, and when possible, increase, this genetic diversity. We will present why the advent of these new techniques gives to the breeders extremely powerful tools for crop breeding, but also why this will require the breeders and researchers to characterize the genes underlying this genetic diversity more precisely. Tackling these challenges should permit the engineering of optimized alleles assortments in an unprecedented and controlled way

An improved melon reference genome with single-molecule sequencing uncovers a recent burst of transposable elements with potential impact on genes

The published melon (Cucumis melo L.) reference genome assembly (v3.6.1) has still 41.6 Mb (Megabases) of sequences unassigned to pseudo-chromosomes and about 57 Mb of gaps. Although different approaches have been undertaken to improve the melon genome assembly in recent years, the high percentage of repeats (~40%) and limitations due to read length have made it difficult to resolve gaps and scaffold's misassignments to pseudomolecules, especially in the heterochromatic regions. Taking advantage of the PacBio single- molecule real-time (SMRT) sequencing technology, an improvement of the melon genome was achieved. About 90% of the gaps were filled and the unassigned sequences were drastically reduced. A lift-over of the latest annotation v4.0 allowed to re-collocate protein-coding genes belonging to the unassigned sequences to the pseudomolecules. A direct proof of the improvement reached in the new melon assembly was highlighted looking at the improved annotation of the transposable element fraction. By screening the new assembly, we discovered many young (inserted less than 2Mya), polymorphic LTR-retrotransposons that were not captured in the previous reference genome. These elements sit mostly in the pericentromeric regions, but some of them are inserted in the upstream region of genes suggesting that they can have regulatory potential. This improved reference genome will provide an invaluable tool for identifying new gene or transposon variants associated with important phenotypes.info:eu-repo/semantics/publishedVersio

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

Impact of transposable elements on polyploid plant genomes

Background: the growing wealth of knowledge on whole-plant genome sequences is highlighting the key role of transposable elements (TEs) in plant evolution, as a driver of drastic changes in genome size and as a source of an important number of new coding and regulatory sequences. Together with polyploidization events, TEs should thus be considered the major players in evolution of plants. -- Scope: this review outlines the major mechanisms by which TEs impact plant genome evolution and how polyploidy events can affect these impacts, and vice versa. These include direct effects on genes, by providing them with new coding or regulatory sequences, an effect on the epigenetic status of the chromatin close to genes, and more subtle effects by imposing diverse evolutionary constraints to different chromosomal regions. These effects are particularly relevant after polyploidization events. Polyploidization often induces bursts of transposition probably due to a relaxation in their epigenetic control, and, in the short term, this can increase the rate of gene mutations and changes in gene regulation due to the insertion of TEs next to or into genes. Over longer times, TE bursts may induce global changes in genome structure due to inter-element recombination including losses of large genome regions and chromosomal rearrangements that reduce the genome size and the chromosome number as part of a process called diploidization. - Conclusions: TEs play an essential role in genome and gene evolution, in particular after polyploidization events. Polyploidization can induce TE activity that may explain part of the new phenotypes observed. TEs may also play a role in the diploidization that follows polyploidization events. However, the extent to which TEs contribute to diploidization and fractionation bias remains unclear. Investigating the multiple factors controlling TE dynamics and the nature of ancient and recent polyploid genomes may shed light on these processes

Transposable element polymorphisms improve prediction of complex agronomic traits in rice

Acord transformatiu CRUE-CSICKey message: Transposon insertion polymorphisms can improve prediction of complex agronomic traits in rice compared to using SNPs only, especially when accessions to be predicted are less related to the training set. Abstract: Transposon insertion polymorphisms (TIPs) are significant sources of genetic variation. Previous work has shown that TIPs can improve detection of causative loci on agronomic traits in rice. Here, we quantify the fraction of variance explained by single nucleotide polymorphisms (SNPs) compared to TIPs, and we explore whether TIPs can improve prediction of traits when compared to using only SNPs. We used eleven traits of agronomic relevance from by five different rice population groups (Aus, Indica, Aromatic, Japonica, and Admixed), 738 accessions in total. We assess prediction by applying data split validation in two scenarios. In the within-population scenario, we predicted performance of improved Indica varieties using the rest of Indica accessions. In the across population scenario, we predicted all Aromatic and Admixed accessions using the rest of populations. In each scenario, Bayes C and a Bayesian reproducible kernel Hilbert space regression were compared. We find that TIPs can explain an important fraction of total genetic variance and that they also improve genomic prediction. In the across population prediction scenario, TIPs outperformed SNPs in nine out of the eleven traits analyzed. In some traits like leaf senescence or grain width, using TIPs increased predictive correlation by 30-50%. Our results evidence, for the first time, that TIPs genotyping can improve prediction on complex agronomic traits in rice, especially when accessions to be predicted are less related to training accessions

The proteins encoded by the pogo-like Lemi1 element bind the TIRs and subterminal repeated motifs of the Arabidopsis Emigrant MITE: consequences for the transposition mechanism of MITEs

MITEs (miniature inverted-repeated transposable elements) are a particular class of defective DNA transposons usually present within genomes as high copy number populations of highly homogeneous elements. Although an active MITE, the mPing element, has recently been characterized in rice, the transposition mechanism of MITEs remains unknown. It has been proposed that transposases of related transposons could mobilize MITEs in trans. Moreover, it has also been proposed that the presence of conserved terminal inverted-repeated (TIR) sequences could be the only requirement of MITEs for mobilization, allowing divergent or unrelated elements to be mobilized by a particular transposase. We present here evidence for a recent mobility of the Arabidopsis Emigrant MITE and we report on the capacity of the proteins encoded by the related Lemi1 transposon, a pogo-related element, to specifically bind Emigrant elements. This suggests that Lemi1 could mobilize Emigrant elements and makes the Lemi1/Emigrant couple an ideal system to study the transposition mechanism of MITEs. Our results show that Lemi1 proteins bind Emigrant TIRs but also bind cooperatively to subterminal repeated motifs. The requirement of internal sequences for the formation of proper DNA/protein structure could affect the capacity of divergent MITEs to be mobilized by distantly related transposases