scholarly journals A genomic region containing RNF212 and CPLX1 is associated with sexually-dimorphic recombination rate variation in Soay sheep (Ovis aries)

2015 ◽  
Author(s):  
Susan E. Johnston ◽  
Camillo Bérénos ◽  
Jon Slate ◽  
Josephine M. Pemberton
Keyword(s):  
Recombination Rate ◽  
Genetic Architecture ◽  
Wild Population ◽  
Genomic Region ◽  
Ovis Aries ◽  
Rate Variation ◽  
Recombination Rates ◽  
Heritable Variation ◽  
Soay Sheep ◽  
Recombination Rate Variation

ABSTRACTMeiotic recombination breaks down linkage disequilibrium and forms new haplotypes, meaning thatit 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 forunderstanding the potential of a population to respond to selection. However, despite attention inmodel 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 rate. Individual rates were high relative to other mammal systems, and were higher in males than in females (autosomal map lengths of 3748 cM and 2860 cM, respectively). The heritability of autosomal recombination rate was low but significant in both sexes(h2 = 0.16 & 0.12 in females and males, respectively). In females, 46.7% of the heritable variation was explained by a sub-telomeric region on chromosome 6; a genome-wide association study showed the strongest associations at the locus RNF212, with further associations observed at a nearby ~374kb region of complete linkage disequilibrium 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.AUTHOR SUMMARYRecombination offers an escape from genetic linkage by forming new combinations of alleles, increasing the potential for populations to respond to selection. Understanding the causes and consequences of individual recombination rates are important in studies of evolution and genetic improvement, yet little is known on how rates vary in natural systems. Using data from a wild population of Soay sheep, we show that individual recombination rate is heritable and differs between the sexes, with the majority of genetic variation in females explained by a genomic region containing thegenes RNF212 and CPLX1.

scholarly journals A genomic region containing REC8 and RNF212B is associated with individual recombination rate variation in a wild population of red deer (Cervus elaphus)

2018 ◽  
Author(s):  
Susan E. Johnston ◽  
Jisca Huisman ◽  
Josephine M. Pemberton
Keyword(s):  
Linkage Group ◽  
Cervus Elaphus ◽  
Recombination Rate ◽  
Genetic Architecture ◽  
Red Deer ◽  
Wild Population ◽  
Genomic Region ◽  
Rate Variation ◽  
Phenotypic Variance ◽  
Recombination Rate Variation

AbstractRecombination is a fundamental feature of sexual reproduction, ensuring proper disjunction, preventing mutation accumulation and generating new allelic combinations upon which selection can act. However it is also mutagenic, and breaks up favourable allelic combinations previously built up by selection. Identifying the genetic drivers of recombination rate variation is a key step in understanding the causes and consequences of this variation, how lociassociated with recombination are evolving and how they affect the potential of a population to respond to selection. However, to date, few studies have examined the genetic architecture of recombination rate variation in natural populations. Here, we use pedigree data from ‐2,600 individuals genotyped at ‐38,000 SNPs to investigate the genetic architecture of individual autosomal recombination rate in a wild population of red deer (Cervus elaphus). Female red deer exhibited a higher mean and phenotypic variance in autosomal crossover counts (ACC). Animal models fitting genomic relatedness matrices showed that ACC was heritable in females (h2 = 0.12) but not in males. A regional heritability mapping approach showed that almost all heritable variation in female ACC was explained by a genomic region on deer linkage group 12 containing the candidate loci REC8 and RNF212B, with an additional region on linkage group 32 containing TOP2B approaching genome-wide significance. The REC8/RNF212B region and its paralogue RNF212 have been associated with recombination in cattle, mice, humans and sheep. Our findings suggest that mammalian recombination rates have a relatively conserved genetic architecture in both domesticated and wild systems, and provide a foundation for understanding the association between recombination lociand individual fitness within this population.

scholarly journals Variants at RNF212 and RNF212B are associated with recombination rate variation in Soay sheep (Ovis aries)

2020 ◽  
Author(s):  
Susan E. Johnston ◽  
Martin A. Stoffel ◽  
Josephine M. Pemberton
Keyword(s):  
Recombination Rate ◽  
Association Studies ◽  
Ovis Aries ◽  
Genome Wide Association ◽  
Rate Variation ◽  
Genome Wide Association Studies ◽  
Mammal Species ◽  
Soay Sheep ◽  
Genome Wide ◽  
Recombination Rate Variation

AbstractMeiotic recombination is a ubiquitous feature of sexual reproduction, ensuring proper disjunction of homologous chromosomes, and creating new combinations of alleles upon which selection can act. By identifying the genetic drivers of recombination rate variation, we can begin to understand its evolution. Here, we revisit an analysis investigating the genetic architecture of gamete autosomal crossover counts (ACC) in a wild population of Soay sheep (Ovis aries) using a much larger dataset (increasing from 3,300 to 7,235 gametes and from ∼39,000 to ∼415,000 SNPs for genome-wide association analysis). Animal models fitting genomic relatedness confirmed that ACC was heritable in both females (h2 = 0.18) and males (h2 = 0.12). Genome-wide association studies identified two regions associated with ACC variation. A region on chromosome 6 containing RNF212 explained 46% of heritable variation in female ACC, but was not associated with male ACC, confirming the previous finding. A region on chromosome 7 containing RNF212B explained 20-25% of variation in ACC in both males and females. Both RNF212 and RNF212B have been repeatedly associated with recombination rate in other mammal species. These findings confirm that moderate to large effect loci can underpin ACC variation in wild mammals, and provide a foundation for further studies on the evolution of recombination rates.

scholarly journals The genetic architecture of helminth-specific immune responses in a wild population of Soay sheep (Ovis aries)

PLoS Genetics ◽  
2019 ◽  
Vol 15 (11) ◽  
pp. e1008461 ◽  
Author(s):  
Alexandra M. Sparks ◽  
Kathryn Watt ◽  
Rona Sinclair ◽  
Jill G. Pilkington ◽  
Josephine M. Pemberton ◽  
...  
Keyword(s):  
Immune Responses ◽  
Genetic Architecture ◽  
Wild Population ◽  
Ovis Aries ◽  
Soay Sheep

scholarly journals Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen (Populus tremula)

2019 ◽  
Vol 10 (1) ◽  
pp. 299-309 ◽  
Author(s):  
Rami-Petteri Apuli ◽  
Carolina Bernhardsson ◽  
Bastian Schiffthaler ◽  
Kathryn M. Robinson ◽  
Stefan Jansson ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Linkage Map ◽  
Recombination Rate ◽  
Gene Density ◽  
Populus Tremula ◽  
Rate Variation ◽  
Recombination Rates ◽  
Genomic Features ◽  
European Aspen ◽  
Recombination Rate Variation

The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.

scholarly journals What drives the evolution of condition-dependent recombination in diploids? Some insights from simulation modelling

2017 ◽  
Vol 372 (1736) ◽  
pp. 20160460 ◽  
Author(s):  
Sviatoslav R. Rybnikov ◽  
Zeev M. Frenkel ◽  
Abraham B. Korol
Keyword(s):  
Recombination Rate ◽  
External Environment ◽  
Theoretical Models ◽  
Simulation Modelling ◽  
Condition Dependence ◽  
Rate Variation ◽  
Theoretical Studies ◽  
Recombination Rates ◽  
Modifier Locus ◽  
Recombination Rate Variation

While the evolutionary advantages of non-zero recombination rates have prompted diverse theoretical explanations, the evolution of essential recombination features remains underexplored. We focused on one such feature, the condition dependence of recombination, viewed as the variation in within-generation sensitivity of recombination to external (environment) and/or internal (genotype) conditions. Limited empirical evidence for its existence comes mainly from diploids, whereas theoretical models show that it only easily evolves in haploids. The evolution of condition-dependent recombination can be explained by its advantage for the selected system (indirect effect), or by benefits to modifier alleles, ensuring this strategy regardless of effects on the selected system (direct effect). We considered infinite panmictic populations of diploids exposed to a cyclical two-state environment. Each organism had three selected loci. Examining allele dynamics at a fourth, selectively neutral recombination modifier locus, we frequently observed that a modifier allele conferring condition-dependent recombination between the selected loci displaced the allele conferring the optimal constant recombination rate. Our simulations also confirm the results of theoretical studies showing that condition-dependent recombination cannot evolve in diploids on the basis of direct fitness-dependent effects alone. Therefore, the evolution of condition-dependent recombination in diploids can be driven by indirect effects alone, i.e. by modifier effects on the selected system. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.

scholarly journals Genetic architecture and lifetime dynamics of inbreeding depression in a wild mammal

2020 ◽  
Author(s):  
M.A. Stoffel ◽  
S.E. Johnston ◽  
J.G. Pilkington ◽  
J.M Pemberton
Keyword(s):  
Life History ◽  
Inbreeding Depression ◽  
Genetic Architecture ◽  
Rate Variation ◽  
Wild Mammal ◽  
Annual Survival ◽  
Soay Sheep ◽  
Genome Wide ◽  
A Genome ◽  
Recombination Rate Variation

AbstractInbreeding depression is a phenomenon of long-standing importance, but we know surprisingly little about its genetic architecture, precise effects and life-history dynamics in wild populations. Here, we combined 417K imputed SNP genotypes for 5952 wild Soay sheep with detailed long-term life-history data to explore inbreeding depression on a key fitness component, annual survival. Inbreeding manifests in long runs of homozygosity (ROH) and these are abundant in Soay sheep, covering on average 24% of the autosomal genome and up to 50% in the most inbred individuals. The ROH landscape is shaped by recombination rate variation and differs widely across the genome, including islands where up to 87% of the population have an ROH and deserts where the ROH prevalence is as low as 4%. We next quantified individual inbreeding as the proportion of the autosomal genome in ROH (FROH) and estimated its effect on annual survival. The consequences of inbreeding are severe; a 10% increase in FROH was associated with a 68% [95% CI 55-78%] decrease in the odds of survival. However, the strength of inbreeding depression is dynamic across the lifespan. We estimate depression to peak in young adults, to decrease into older ages and to be weaker in lambs, where inbreeding effects are possibly buffered by maternal care. Finally, using a genome-wide association scan on ROH, we show that inbreeding causes depression predominantly through many loci with small effects, but we also find three regions in the genome with putatively strongly deleterious mutations. Our study reveals population and genome-wide patterns of homozygosity caused by inbreeding and sheds light on the strength, dynamics and genetic architecture of inbreeding depression in a wild mammal population.

scholarly journals Genomics of recombination rate variation in temperature-evolved Drosophila melanogaster populations

2020 ◽  
Author(s):  
Ari Winbush ◽  
Nadia D Singh
Keyword(s):  
Drosophila Melanogaster ◽  
Temperature Regime ◽  
Recombination Rate ◽  
Evolutionary Biology ◽  
Genetic Basis ◽  
Rate Variation ◽  
Potential Candidate ◽  
Nucleotide Polymorphisms ◽  
Recombination Rates ◽  
Recombination Rate Variation

Abstract Meiotic recombination is a critical process that ensures proper segregation of chromosome homologues through DNA double strand break repair mechanisms. Rates of recombination are highly variable among various taxa, within species, and within genomes with far-reaching evolutionary and genomic consequences. The genetic basis of recombination rate variation is therefore crucial in the study of evolutionary biology but remains poorly understood. In this study we took advantage of a set of experimental temperature-evolved populations of Drosophila melanogaster with heritable differences in recombination rates depending on the temperature regime in which they evolved. We performed whole genome sequencing and identified several chromosomal regions that appear to be divergent depending on temperature regime. In addition, we identify a set of single nucleotide polymorphisms and associated genes with significant differences in allele frequency when the different temperature populations are compared. Further refinement of these gene candidates emphasizing those expressed in the ovary and associated with DNA binding reveals numerous potential candidate genes such as Hr38, EcR, and mamo responsible for observed differences in recombination rates in these experimental evolution lines thus providing insight into the genetic basis of recombination rate variation.

scholarly journals Variation in recombination frequency and distribution across eukaryotes: patterns and processes

2017 ◽  
Vol 372 (1736) ◽  
pp. 20160455 ◽  
Author(s):  
Jessica Stapley ◽  
Philine G. D. Feulner ◽  
Susan E. Johnston ◽  
Anna W. Santure ◽  
Carole M. Smadja
Keyword(s):  
Recombination Rate ◽  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Essential Feature ◽  
Rate Variation ◽  
Evolutionary Processes ◽  
Recombination Rates ◽  
Great Opportunity ◽  
Patterns And Processes ◽  
Recombination Rate Variation

Recombination, the exchange of DNA between maternal and paternal chromosomes during meiosis, is an essential feature of sexual reproduction in nearly all multicellular organisms. While the role of recombination in the evolution of sex has received theoretical and empirical attention, less is known about how recombination rate itself evolves and what influence this has on evolutionary processes within sexually reproducing organisms. Here, we explore the patterns of, and processes governing recombination in eukaryotes. We summarize patterns of variation, integrating current knowledge with an analysis of linkage map data in 353 organisms. We then discuss proximate and ultimate processes governing recombination rate variation and consider how these influence evolutionary processes. Genome-wide recombination rates (cM/Mb) can vary more than tenfold across eukaryotes, and there is large variation in the distribution of recombination events across closely related taxa, populations and individuals. We discuss how variation in rate and distribution relates to genome architecture, genetic and epigenetic mechanisms, sex, environmental perturbations and variable selective pressures. There has been great progress in determining the molecular mechanisms governing recombination, and with the continued development of new modelling and empirical approaches, there is now also great opportunity to further our understanding of how and why recombination rate varies. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.

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