Genome-wide mapping of recombination hotspots in Arabidopsis

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Harnessing natural genetic variation through breeding and genetic recombination is a cornerstone of crop improvement. During domestication crops pass through genetic bottlenecks, meaning that wild progenitor species contain abundant variation that is useful to reintroduce. One limitation to breeding is that recombination rate is highly variable along chromosomes. For example, large regions of wheat, barley and maize chromosomes are non-recombining, despite containing useful genetic variation. We are investigating the mechanistic basis of recombination control, with the aim of rationally manipulating this process to accelerate crop breeding. As the core recombination process is highly conserved between plants, our work focuses on the model species Arabidopsis thaliana, which has extensive genetic and genomic resources. Using a novel experimental technique termed pollen-typing we have recently discovered that A.thaliana chromosomes have narrow hotspot regions with a highly elevated chance of recombination. These hotspots are located in gene promoters, where open chromatin packaging allows access to the DNA, and we hypothesize that this also allows access to the recombination machinery. Hotspots in other species are controlled by a combination of chromatin structure and primary DNA sequence, and we will investigate these relationships in A.thaliana. First we will use population genetics methods to generate a genome-wide hotspot map using patterns of natural genetic polymorphism between A.thaliana populations. As recombination breaks up blocks of linked genetic variation, this effect can be used to measure recombination rate and identify hotspot locations. The A.thaliana genome is well annotated with chromatin maps and this will allow us to determine which aspects of chromosome organisation correlate with hotspot locations. In addition we will test whether hotspots associate with specific DNA sequences, to resolve the extent to which plant hotspots are genetically versus epigenetically determined. Using pollen-typing we will then experimentally validate a subset of the most active hotspots in the A.thaliana genome. To directly test the role of chromatin on hotspot activity we will repeat pollen-typing in mutant backgrounds with altered epigenetic organization. The hotspots we have already observed are located in gene promoters and we will use mutants with altered promoter chromatin to test for effects on recombination. We will also directly target chromatin modifications associated with gene silencing to hotspots and investigate whether this is sufficient to suppress recombination. Knowledge of hotspot control will provide novel insight into manipulating recombination in crop genomes. Our strategic goal is to modulate hotspot activity in crops, for example by boosting, suppressing or relocating them, and thereby facilitating breeding of high-yielding strains.