A genome-wide study of recombination rate variation in Bartonella henselae

AbstractBackgroundIn this paper, we estimated recombination rate variation within the genome and between individuals in the pig using multiocus iterative peeling for 150,000 pigs across nine genotyped pedigrees. We used this to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig.ResultsOur results confirmed known features of the pig recombination landscape, including differences in chromosome length, and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, the lines also showed differences in average genome-wide recombination rate. The heritability of genome-wide recombination was low but non-zero (on average 0.07 for females and 0.05 for males). We found three genomic regions associated with recombination rate, one of them harbouring the RNF212 gene, previously associated with recombination rate in several other species.ConclusionOur results from the pig agree with the picture of recombination rate variation in vertebrates, with low but nonzero heritability, and a major locus that is homologous to one detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes.

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Genome-wide recombination rate variation in a recombination map of cotton

PLoS ONE ◽

10.1371/journal.pone.0188682 ◽

2017 ◽

Vol 12 (11) ◽

pp. e0188682 ◽

Cited By ~ 8

Author(s):

Chao Shen ◽

Ximei Li ◽

Ruiting Zhang ◽

Zhongxu Lin

Keyword(s):

Recombination Rate ◽

Rate Variation ◽

Genome Wide ◽

Recombination Rate Variation

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

10.1101/2020.05.27.118877 ◽

2020 ◽

Cited By ~ 3

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.

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

10.1101/2020.07.26.217802 ◽

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.

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Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster

PLoS Genetics ◽

10.1371/journal.pgen.1003090 ◽

2012 ◽

Vol 8 (12) ◽

pp. e1003090 ◽

Cited By ~ 146

Author(s):

Andrew H. Chan ◽

Paul A. Jenkins ◽

Yun S. Song

Keyword(s):

Drosophila Melanogaster ◽

Recombination Rate ◽

Rate Variation ◽

Fine Scale ◽

Genome Wide ◽

Recombination Rate Variation

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Variation in recombination rate affects detection of outliers in genome scans under neutrality

10.1101/2020.02.06.937813 ◽

2020 ◽

Cited By ~ 3

Author(s):

Tom R. Booker ◽

Sam Yeaman ◽

Michael C. Whitlock

Keyword(s):

Recombination Rate ◽

Wide Distribution ◽

Rate Variation ◽

Summary Statistic ◽

Genome Scans ◽

Coalescent Process ◽

Genome Wide ◽

Genomic Landscape ◽

Recombination Rate Variation ◽

Linked Selection

AbstractGenome scans can potentially identify genetic loci involved in evolutionary processes such as local adaptation and gene flow. Here, we show that recombination rate variation across a neutrally evolving genome gives rise to mixed sampling distributions of mean FST, a common population genetic summary statistic. In particular, we show that in regions of low recombination the distribution of estimates have more variance and a longer tail than in more highly recombining regions. Determining outliers from the genome-wide distribution without taking local recombination rate into consideration may therefore increase the frequency of false positives in low recombination regions and be overly conservative in more highly recombining ones. We perform genome-scans on simulated and empirical Drosophila melanogaster datasets and, in both cases, find patterns consistent with this neutral model. Similar patterns are observed for other summary statistics used to capture variation in the coalescent process. Linked selection, particularly background selection, is often invoked to explain heterogeneity in across the genome, but here we point out that even under neutrality, statistical artefacts can arise due to variation in recombination rate. Our results highlight a flaw in the design of genome scan studies and suggest that without estimates of local recombination rate, interpreting the genomic landscape of any summary statistic that captures variation in the coalescent process will be very difficult.

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