Dokument: The recombination rate variation and genomic distribution in plants using barley as a model: assessment, associated genomic features, and manipulation.
| Titel: | The recombination rate variation and genomic distribution in plants using barley as a model: assessment, associated genomic features, and manipulation. | |||||||
| URL für Lesezeichen: | https://docserv.uni-duesseldorf.de/servlets/DocumentServlet?id=68025 | |||||||
| URN (NBN): | urn:nbn:de:hbz:061-20250107-125306-5 | |||||||
| Kollektion: | Dissertationen | |||||||
| Sprache: | Englisch | |||||||
| Dokumententyp: | Wissenschaftliche Abschlussarbeiten » Dissertation | |||||||
| Medientyp: | Text | |||||||
| Autor: | Casale, Federico Agustin [Autor] | |||||||
| Dateien: |
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| Beitragende: | Stich, Benjamin [Gutachter] Prof. Dr. Schneeberger, Korbinian [Gutachter] | |||||||
| Dewey Dezimal-Klassifikation: | 500 Naturwissenschaften und Mathematik » 570 Biowissenschaften; Biologie | |||||||
| Beschreibung: | Meiotic recombination is a fundamental mechanism for the adaptation of sexually reproducing eukaryotes. Furthermore, it is also crucial for accumulating favorable alleles in plant breeding populations. However, the effective manipulation of the recombination rate still requires a better understanding of the mechanisms regulating the rate and distribution of recombination events in plant genomes. The present paper accumulation thesis aims to pave the road in such direction using barley (Hordeum vulgare L.) as a model species. The core plant material throughout the work is a set of 45 segregating populations derived from crosses that followed a double round-robin design (DRR populations) among 23 inbreds with origins worldwide. Firstly, the recombination rate variation among the DRR populations has been assessed using genetic maps, revealing extensive variation genome-wide and locally in the genome among populations. A mixed-model approach (Best linear unbiased prediction, BLUP) has been used to quantify the importance of the general recombination effects (GRE) of individual parental inbreds from the specific recombination effects (SRE) caused by the combinations of parental inbreds. The variance of the genome-wide GRE was found to be several times the variance of the SRE, indicating that parental inbreds differ in the efficiency of their recombination machinery. Genomic selection (GS) using BLUP was shown to provide a high ability to predict the recombination rate of an inbred line. This demonstrated the possibility to screen large genetic materials for their recombining effect in their progeny and to manipulate the recombination rate using natural variation. Secondly, the genomic features that better explain the recombination variation among the DRR populations were identified at a resolution of 1 Mbp. The genetic effects (GREs not assigned to methylation) were found to be the most important factor explaining differences in recombination rates among populations along with the methylation and the parental sequence divergence. The parental sequence divergence had a sigmoidal correlation with recombination, indicating an upper limit of mismatch among homologous chromosomes for crossover (CO) formation. In addition, the occurrence of hotspots and coldspots for recombination was detected at 10 kb genomic windows, and how methylation and structural variants (SVs) determine such regions was investigated. The inheritance of a highly methylated genomic fragment from one parent only was enough to generate a coldspot but both parents must be equally low methylated at a genomic segment to allow a hotspot. Our findings suggest that recombination in barley is highly predictable, occurring mostly in multiple short sections located in proximity to genes and being modulated by local levels of methylation and SV load. Lastly, the reliability of a new approach that uses the allele frequency differences and physical distance of neighboring polymorphisms to estimate the recombination rate from pool sequencing was demonstrated with computer simulations and experimentally on the DRR populations. This approach implies a reduction in the cost compared to recombination rate estimations based on genotyping single individuals. | |||||||
| Lizenz: |  Dieses Werk ist lizenziert unter einer Creative Commons Namensnennung 4.0 International Lizenz | |||||||
| Fachbereich / Einrichtung: | Mathematisch- Naturwissenschaftliche Fakultät | |||||||
| Dokument erstellt am: | 07.01.2025 | |||||||
| Dateien geändert am: | 07.01.2025 | |||||||
| Promotionsantrag am: | 09.08.2024 | |||||||
| Datum der Promotion: | 18.12.2024 |
