Abstract
Meiotic recombination breaks down linkage disequilibrium (LD) and forms new haplotypes, meaning that it is an important driver of diversity in eukaryotic genomes. Understanding the causes of variation in recombination rate is important in interpreting and predicting evolutionary phenomena and in understanding the potential of a population to respond to selection. However, despite attention in model systems, there remains little data on how recombination rate varies at the individual level in natural populations. Here we used extensive pedigree and high-density SNP information in a wild population of Soay sheep (Ovis aries) to investigate the genetic architecture of individual autosomal recombination rates. Individual rates were high relative to other mammal systems and were higher in males than in females (autosomal map lengths of 3748 and 2860 cM, respectively). The heritability of autosomal recombination rate was low but significant in both sexes (h2 = 0.16 and 0.12 in females and males, respectively). In females, 46.7% of the heritable variation was explained by a subtelomeric region on chromosome 6; a genome-wide association study showed the strongest associations at locus RNF212, with further associations observed at a nearby ∼374-kb region of complete LD containing three additional candidate loci, CPLX1, GAK, and PCGF3. A second region on chromosome 7 containing REC8 and RNF212B explained 26.2% of the heritable variation in recombination rate in both sexes. Comparative analyses with 40 other sheep breeds showed that haplotypes associated with recombination rates are both old and globally distributed. Both regions have been implicated in rate variation in mice, cattle, and humans, suggesting a common genetic architecture of recombination rate variation in mammals.
Highlights
MEIOTIC recombination is a fundamental feature of sexual reproduction in most multicellular organisms
Additional loci that were significantly associated with autosomal crossover count (ACC) and in strong linkage disequilibrium (LD) with these hits are not shown; full genome-wide association studies (GWASs) results are provided in Table S5 and Table S6
Females had significantly higher additive genetic and residual variance in the trait in comparison with males, and GWAS and regional heritability analyses showed that the ring finger protein 212 (RNF212)/complexin 1 (CPLX1) region was associated with female recombination rate only
Summary
MEIOTIC recombination is a fundamental feature of sexual reproduction in most multicellular organisms. The locus PRDM9 is associated with the positioning and proportion of crossovers that occur in mammalian recombination hotspots (i.e., regions of the genome with high recombination rates) (Baudat et al 2010; Ma et al 2015), this locus is not functional in some mammal species, such as canids (Auton et al 2013) These studies suggest that recombination rate has a relatively oligogenic architecture and has the potential to respond rapidly to selection over relatively short evolutionary timescales. Our objectives were as follows: (1) to determine the relative importance of common environment and other individual effects to recombination rates (e.g., age, sex, and inbreeding coefficients), (2) to determine whether individual recombination rates were heritable, (3) to identify specific genetic variants associated with recombination rate variation, and (4) to determine whether the genetic architecture of recombination rate variation is similar to that observed in other mammal species
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