Heterozygous Inversion Breakpoints Suppress Meiotic Crossovers by Altering Recombination Repair Outcomes

Abstract

Heterozygous chromosome inversions suppress meiotic crossover (CO) formation within an inversion, potentially because they lead to gross chromosome rearrangements that produce inviable gametes. Interestingly, COs are also severely reduced in regions nearby but outside of inversion breakpoints even though COs in these regions do not result in rearrangements. Our mechanistic understanding of why COs are suppressed outside of inversion breakpoints is limited by a lack of data on the frequency of noncrossover gene conversions (NCOGCs) in these regions. To address this critical gap, we mapped the location and frequency of rare CO and NCOGC events that occurred outside of the dl-49 chrX inversion in D. melanogaster. We created full-sibling wildtype and inversion stocks and recovered COs and NCOGCs in the syntenic regions of both stocks, allowing us to directly compare rates and distributions of recombination events. We show that COs are completely suppressed within 500 kb of inversion breakpoints, are severely reduced within 2 Mb of an inversion breakpoint, and increase above wildtype levels 2-4 Mb from the breakpoint. We find that NCOGCs occur evenly throughout the chromosome and, importantly, occur at wildtype levels near inversion breakpoints. We propose a model in which COs are suppressed by inversion breakpoints in a distance-dependent manner through mechanisms that influence DNA double-strand break repair outcome but not double-strand break location or frequency. We suggest that subtle changes in the synaptonemal complex and chromosome pairing might lead to unstable interhomolog interactions during recombination that permits NCOGC formation but not CO formation.

The effects of inversion polymorphisms on patterns of neutral genetic diversity

“…This raises the question of whether recombinational exchange in heterokaryotypes occurs at a sufficient rate that the condition T Sw = 1 is likely to hold. At least for simple inversions (with only a single pair of breakpoints) there is ample experimental evidence for recombination between In and St at sites within and adjacent to the inversion in species of Drosophila , much of which appears to be caused by gene conversion rather than double crossovers(Chovnick 1973; Korunes and Noor 2019; Li et al 2022; Koury 2023), with r = 10 -5 per basepair per generation being a commonly accepted typical rate (Chovnick 1973; Korunes and Noor 2019). Complex inversions, with three or more breakpoints, might be expected to have much lower rates of exchange than simple inversions, but heterozygotes for multiply inverted chromosomes in D. melanogaster have been found to experience non-crossover associated gene conversion events at rates that are even higher than in the absence of inversions (Crown et al 2018), so that this expectation may not be well founded.…”

“…A major mechanism by which crossing over is suppressed or reduced in frequency during Drosophila female meiosis in heterozygotes for a paracentric inversion and the standard arrangement was elucidated by Sturtevant and Beadle (1936), whose genetic data suggested that single crossovers produce dicentric and acentric chromosomes that fail to be included in the egg nucleus. While several factors contribute to crossover suppression in inversion heterozygotes, with the conversion of double strand breaks into non-crossover associated gene conversion events playing an important role (Gong et al 2005; Crown et al 2018; Li et al 2022), there is no doubt that crossover suppression in inversion heterozygotes must cause different arrangements to become substantially genetically isolated from each other. Recent studies of heterozygous Drosophila inversions suggest a total suppression of crossing over within the regions covered by the inversion and for a substantial distance outside it (Li et al 2022; Koury 2023).…”

“…While several factors contribute to crossover suppression in inversion heterozygotes, with the conversion of double strand breaks into non-crossover associated gene conversion events playing an important role (Gong et al 2005; Crown et al 2018; Li et al 2022), there is no doubt that crossover suppression in inversion heterozygotes must cause different arrangements to become substantially genetically isolated from each other. Recent studies of heterozygous Drosophila inversions suggest a total suppression of crossing over within the regions covered by the inversion and for a substantial distance outside it (Li et al 2022; Koury 2023).…”

“…It is evident that the genetic isolation of different gene arrangements must play a major role in the evolutionary processes that lead to the evolution of inversion polymorphisms, although the nature of these processes is still an open research question, which may well have more than one answer (Krimbas and Powell 1992b; Wellenreuther and Bernatchez 2018; Kapun and Flatt 2019; Villoutreix et al 2021). It is also clear that recombination suppression between arrangements is often incomplete, with gene conversion and/or double crossing over causing exchanges of alleles between arrangements in heterokaryotypes (Sturtevant and Beadle 1936; Chovnick 1973; Krimbas and Powell 1992b; Navarro et al 1997; Crown et al 2018; Korunes and Noor 2019; Li et al 2022).…”

“…These patterns are all reflections of the same process of divergence by drift and mutation among the partially isolated populations represented by the alleles at the target of selection, with a strong analogy with the outcome of mutation and drift in a geographically structured population (Hudson 1990; Charlesworth et al 2003). Inversions are only special because of the strong suppression of recombination within the inversion, and in regions outside it but close to the inversion breakpoints (Navarro et al 1997; Crown et al 2018; Korunes and Noor 2019; Li et al 2022; Koury 2023), so that these patterns are much more likely to be observed with inversions than with single locus polymorphisms, due to the much larger region of the genome covered by inversions.…”