Academic literature on the topic 'Arabidopsis suecica'

Genomic in situ hybridization (GISH) is a useful tool to analyse natural polyploids, hybrid plants, and their backcross progenies as to their origin, genomic composition, and intergenomic rearrangements. However, in angiosperms with very small genomes (<0.6 pg/1 C), often only heterochromatic regions were found to be labeled. We have modified the GISH technique to label entire mitotic and meiotic chromosomes of Arabidopsis thaliana (2n = 10) and closely related species with very small genomes by using high concentrations of DNA (7.5–15 µg per probe per slide) or 5 µg of probe and long hybridization times (>60 h). According to our GISH data, Cardaminopsis carpatica (2n = 16) is most likely the diploid ancestor of the autotetraploid Arabidopsis arenosa (2n = 32). Furthermore, within the allotetraploid species Arabidopsis suecica (2n = 26), it was possible to elucidate the origin of chromosomes contributed by the parental species A. thaliana and A. arenosa for a specimen with 2n = 26 or a deviating chromosome number.Key words: genomic in situ hybridization (GISH), Arabidopsis, Brassicaceae, allopolyploids, synthetic hybrids.

L'allopolyploïdie, un processus où des espèces hybrides possèdent des ensembles complets de chromosomes issues de différentes espèces, joue un rôle crucial dans l'évolution et la spéciation des plantes. Cependant, les allopolyploïdes nouvellement formés doivent surmonter des défis complexes liés à l'instabilité génétique, épigénétique et méiotique, principalement en raison de la recombinaison méiotique entre chromosomes homéologues (similaires mais non identiques). Cette situation peut entraîner des erreurs de ségrégation, de l'aneuploïdie et une fertilité réduite. En revanche, les allopolyploïdes évolués sont hautement fertiles et se comportent comme de vrais diploïdes pendant la méiose, favorisant la formation de crossing-overs entre chromosomes homologues tout en inhibant ceux entre chromosomes homéologues. Ainsi, les allopolyploïdes de première génération subissent une forte pression sélective pour limiter ou éviter les crossing-overs entre chromosomes homéologues.Pour explorer les mécanismes sous-jacents à la stabilisation de la méiose après l'allopolyploïdisation, nous avons étudié l'adaptation méiotique chez Arabidopsis suecica, une plante issue de l'hybridation entre A. thaliana et A. arenosa. Dans cette étude, nous avons examiné la fertilité et le comportement méiotique de plantes néosynthétiques d'A. suecica issues d'un unique croisement sur les quatre premières générations après l'hybridation. Les résultats ont révélé des altérations significatives au début de la méiose, avec des interactions anormales entre centromères homéologues pendant le stade zygotène et une recombinaison homéologue fréquente associée à une réduction de la recombinaison homologue, suggérant fortement que la fidélité du choix du partenaire de recombinaison est perturbée pendant la première méiose des plantes néoallopolyploïdes d'A. suecica. De plus, cette étude a montré une considérable variabilité de la fertilité, du comportement méiotique et du niveau de recombinaison homéologue entre des plantes néosynthétiques sœurs de première génération. Après 4 générations, nous avons identifié quatre voies distinctes d'évolution de la stabilité méiotique chez ces plantes néoallopolyploïdes.Ces travaux ont également mis en évidence le rôle des protéines MSH, en particulier MSH7, qui semble être impliquée dans la régulation de la recombinaison homéologue. La mutation du gène MSH7 chez A. suecica entraîne une légère diminution du nombre de crossing-overs et une augmentation des cellules méiotiques au stade métaphase I avec des univalents et des multivalents, suggérant que MSH7 pourrait aider à discriminer les chromosomes homologues des homéologues, stabilisant ainsi la méiose allopolyploïde.Une analyse transcriptomique de méiocytes mâles de plantes néosynthétiques et évoluées a révélé une sous-expression de gènes clés, tels qu'ASY4 et SCEP2, qui sont essentiels pour la formation du complexe synaptonémal, une structure nécessaire à l'appariement correct des chromosomes pendant la méiose. Les anomalies dans l'expression de ces gènes, combinées à la sous-expression des protéines ZMM impliquées dans la formation des crossing-overs de classe I telles que MSH5 et HEI10, pourraient être à l'origine de l'instabilité méiotique observée dans les plantes néosynthétiques d'A. suecica.En conclusion, mes travaux de thèse soulignent l'importance des mécanismes moléculaires dans la stabilisation méiotique des plantes allopolyploïdes, et révèlent le rôle potentiel des protéines MSH7, ASY4, SCEP2, MSH5 et HEI10 dans la régulation de la recombinaison méiotique. Ces découvertes ouvrent la voie à de nouvelles recherches pour approfondir notre compréhension de l'adaptation et de la stabilité méiotique des plantes allopolyploïdes
Allopolyploidy, a process in which hybrid species possess complete sets of chromosomes from different species, plays a crucial role in plant evolution and speciation. However, newly formed allopolyploids must overcome complex challenges related to genetic, epigenetic, and meiotic instability, primarily due to meiotic recombination between homeologous chromosomes (similar but not identical). This situation can lead to segregation errors, aneuploidy, and reduced fertility. In contrast, evolved allopolyploids are highly fertile and behave as true diploids during meiosis, promoting crossing-over between homologous chromosomes while inhibiting those between homeologous chromosomes. Consequently, first generation allopolyploids undergo stong selection pressure to limit or avoid crossovers between homeologous chromosomes.To explore the mechanisms underlying meiotic stabilization following allopolyploidy, we investigated meiotic adaptation in Arabidopsis suecica, a plant derived from the hybridization of A. thaliana and A. arenosa. This study examined fertility and meiotic behavior of neo-synthetic A. suecica plants from a single cross over the first four generations post-hybridization. The results revealed significant alterations early in meiosis, including abnormal interactions between homeologous centromeres during the zygotene stage and frequent homeologous recombination associated with reduced homologous recombination. These findings strongly suggest that the fidelity of recombination partner choice is disrupted during the first meiosis of neo-allopolyploid A. suecica plants. Furthermore, this study demonstrated considerable variability in fertility, meiotic behavior, and levels of homeologous recombination among first-generation neo-synthetic sibling plants. After four generations, we identified four distinct pathways of meiotic stability evolution in these neo-allopolyploid plants.This study also highlighted the role of MSH proteins, particularly MSH7, which appears to be involved in the regulation of homeologous recombination. Mutation of the MSH7 gene in A. suecica leads to a slight decrease in the number of crossing-overs and an increase in meiotic cells at metaphase I with univalents and multivalents, suggesting that MSH7 may help discriminate between homologous and homeologous chromosomes, thereby stabilizing allopolyploid meiosis.Transcriptomic analysis of male meiocytes of both neo-synthetic and evolved plants revealed downregulation of key genes, such as ASY4 and SCEP2, which are essential for the formation of the synaptonemal complex, a structure necessary for correct chromosome pairing during meiosis. The anomalies in the expression of these genes, combined with the downregulation of ZMM proteins involved in the formation of class I crossing-overs, such as MSH5 and HEI10, may contribute to the meiotic instability observed in neo-synthetic A. suecica plants.In conclusion, my thesis emphasizes the importance of molecular mechanisms in the meiotic stabilization of allopolyploid plants and highlights the potential roles of MSH7, ASY4, SCEP2, MSH5, and HEI10 proteins in regulating meiotic recombination. These findings pave the way for further research to deepen our understanding of adaptation and meiotic stability in allopolyploid plants

BACKGROUND:Allotetraploids carry pairs of diverged homoeologs for most genes. With the genome doubled in size, the number of putative interactions is enormous. This poses challenges on how to coordinate the two disparate genomes, and creates opportunities by enhancing the phenotypic variation. New combinations of alleles co-adapt and respond to new environmental pressures. Three stages of the allopolyploidization process - parental species divergence, hybridization, and genome duplication - have been well analyzed. The last stage of evolutionary adjustments remains mysterious.RESULTS:Homoeolog-specific retention and use were analyzed in Arabidopsis suecica (As), a species derived from A. thaliana (At) and A. arenosa (Aa) in a single event 12,000 to 300,000 years ago. We used 405,466 diagnostic features on tiling microarrays to recognize At and Aa contributions to the As genome and transcriptome: 324 genes lacked Aa contributions and 614 genes lacked At contributions within As. In leaf tissues, 3,458 genes preferentially expressed At homoeologs while 4,150 favored Aa homoeologs. These patterns were validated with resequencing. Genes with preferential use of Aa homoeologs were enriched for expression functions, consistent with the dominance of Aa transcription. Heterologous networks - mixed from At and Aa transcripts - were underrepresented.CONCLUSIONS:Thousands of deleted and silenced homoeologs in the genome of As were identified. Since heterologous networks may be compromised by interspecies incompatibilities, these networks evolve co-biases, expressing either only Aa or only At homoeologs. This progressive change towards predominantly pure parental networks might contribute to phenotypic variability and plasticity, and enable the species to exploit a larger range of environments.

Doutoramento em Biologia - Instituto Superior de Agronomia
The discovery of small RNAs has added a new level to our understanding of gene regulation mechanisms. Small interfering RNAs (siRNAs) are involved in the establishment of repressive epigenetic marks in a variety of organisms by guiding RNA induced silencing complexes to homologous DNA sequences. Could the endogenous siRNA heterochromatic pathway be linked to the establishment of nucleolar dominance? The latter is a large scale manifestation of directed epigenetic gene silencing, resulting in the transcriptional inactivation of the entire rRNA gene cluster from one parent in a hybrid species. Inactivation of rRNA genes is linked to the establishment of heterochromatic marks, both at the DNA and histone levels, in the promoter region. We were able to identify 24nt siRNAs homologous to the rRNA gene promoter in Arabidopsis sp., whose biogenesis is dependent on nuclear RNA polymerase IV and other known proteins of the endogenous siRNA pathway in Arabidopsis. RNAi mediated knockdown of genes in this pathway in the natural allopolyploid hybrid A. suecica (A. thaliana x A. arenosa) disrupted nucleolar dominance, causing the production of rRNA transcripts from the underdominant A. thaliana rDNA genes. This observation implicates nuclear siRNAs in the establishment of nucleolar dominance in A. suecica.