Investigating the effects of genetic variation on heterochromatic crossover events in Arabidopsis thaliana

Crossover events result in the reciprocal exchange of genetic material between homologous chromosomes during meiosis. Numerous genetic and environmental factors have been shown to influence the meiotic recombination landscape in many different species. My thesis uses the model plant *Arabidopsis thaliana* to explore control of heterochromatic meiotic crossover frequency by natural genetic variation. Genome-wide effects on crossover frequency were evaluated using natural variation and biotic stress. Significant crossover frequency variation was recorded throughout the genome in Col- 0/relict F1 hybrids. A diverse panel of Arabidopsis accessions further investigated the influence of *cis* effects on heterochromatic crossover events. Significant changes to heterochromatic crossover frequency and segregation distortion within hybrid populations was identified. Heterochromatic crossover variation was likely due to both *cis*- and *trans*-acting factors. The effect of disease on genome-wide crossover frequency was explored and results from these experiments did not show a positive correlation between pathogen challenge and altered crossover frequency. Col-0/Tanz-1 hybrid populations showed a significant increase in crossover frequency across *CEN3*. Quantitative trait loci (QTL) mapping identified a strong recombination QTL (rQTL) on the lower arm of chromosome 1. The strongest candidate gene for the rQTL is At1g53250 which acts in a semi-dominant behaviour. The effects of the rQTL are independent of *CEN3* genotype and influences heterochromatic crossover frequency on other chromosomes. Assays using diverse genetic backgrounds and altered epigenetic states characterised the *trans* effect of the rQTL on heterochromatic crossover frequency. Non-Mendelian segregation of heterochromatic chromosome intervals was investigated in Col-0 inbred and Col-0/relict hybrid populations revealing evidence for centromere drive. Preliminary observations suggest that segregation distortion may be significantly associated with aberrant heterochromatic crossover rate in predominantly homozygous populations. These experiments highlight the substantial influence genetic variation can have on crossover frequency. Factors governing heterochromatic crossover frequency and segregation distortion are complex, with *cis* and *trans* modifiers exerting significant effects on these phenotypes. Understanding the mechanisms behind the factors influencing heterochromatic crossover frequency will provide insight to how heterochromatic crossovers can be manipulated in crop species.

Name dc:type.qualificationname

Doctor of Philosophy (PhD)

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

University of Cambridge

Year dc:date.issued

2024

Author dc:creator

• Gorringe, Nicola

Advisor dc:contributor.advisor

• Henderson, Ian

• Arabidopsis thaliana
• Centromere biology
• Centromeres
• Cloning
• Crossover events
• Genome biology
• Genotyping
• Meiosis
• Meiotic recombination
• Natural variation
• Non-Mendelian meiotic events
• Oxford Nanopore Sequencing
• Pathogen
• Plant disease
• Plant science
• Quantitative Trait Loci (QTL)

Licence

• https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/cfcf4f20-9504-465a-ac34-21e41f85b602/download
• https://www.rioxx.net/licenses/all-rights-reserved/

Language dc:language

eng

DOI dc:identifier.doi

https://doi.org/10.17863/CAM.111387

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/372517