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

Genome-wide analysis of the emigrant family of MITEs: amplification dynamics and evolution of genes in Arabidopsis thaliana

MITEs are structurally similar to defective class II elements but their high copy number and the size and sequence conservation of most MITE families suggest that they can be amplified by a replicative mechanism. Here we present a genome-wide analysis of the Emigrant family of MITEs from Arabidopsis thaliana. In order to be able to detect divergent ancient copies and low copy number subfamilies with a different internal sequence we have developed a computer program (http://www.lsi.upc.es/~alggen) that allows looking for Emigrant elements based solely on its TIR sequence. Our results show that different bursts of amplification of one or very few active, or master, elements have occurred at different times during Arabidopsis evolution, with an insertion dynamics similar to that of some SINEs. The analysis of the insertion sites of the Emigrant elements show that, although Emigrant elements tend to integrate far from ORFs, the elements inserted within or close to genes are preferentially maintained during evolution.Postprint (published version

Genomics of Evolutionary Novelty in Hybrids and Polyploids

It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically recognized as significant in speciation and adaptation, recognition of the importance of interspecific gene flow has dramatically increased during the genomics era, concomitant with an unending flood of empirical examples, with or without genome doubling. Interspecific gene flow is thus increasingly thought to lead to evolutionary innovation and diversification, via adaptive introgression, homoploid hybrid speciation and allopolyploid speciation. Less well understood, however, are the suite of genetic and genomic mechanisms set in motion by the merger of differentiated genomes, and the temporal scale over which recombinational complexity mediated by gene flow might be expressed and exposed to natural selection. We focus on these issues here, considering the types of molecular genetic and genomic processes that might be set in motion by the saltational event of genome merger between two diverged species, either with or without genome doubling, and how these various processes can contribute to novel phenotypes. Genetic mechanisms include the infusion of new alleles and the genesis of novel structural variation including translocations and inversions, homoeologous exchanges, transposable element mobilization and novel insertional effects, presence-absence variation and copy number variation. Polyploidy generates massive transcriptomic and regulatory alteration, presumably set in motion by disrupted stoichiometries of regulatory factors, small RNAs and other genome interactions that cascade from single-gene expression change up through entire networks of transformed regulatory modules. We highlight both these novel combinatorial possibilities and the range of temporal scales over which such complexity might be generated, and thus exposed to natural selection and drift

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