scholarly journals The genetic architecture of genome‐wide recombination rate variation in allopolyploid wheat revealed by nested association mapping

2018 ◽  
Vol 95 (6) ◽  
pp. 1039-1054 ◽  
Author(s):  
Katherine W. Jordan ◽  
Shichen Wang ◽  
Fei He ◽  
Shiaoman Chao ◽  
Yanni Lun ◽  
...  
Keyword(s):  
Association Mapping ◽  
Recombination Rate ◽  
Genetic Architecture ◽  
Rate Variation ◽  
Nested Association Mapping ◽  
Genome Wide ◽  
Recombination Rate Variation

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

PLoS ONE ◽  
2017 ◽  
Vol 12 (11) ◽  
pp. e0188682 ◽  
Author(s):  
Chao Shen ◽  
Ximei Li ◽  
Ruiting Zhang ◽  
Zhongxu Lin
Keyword(s):  
Recombination Rate ◽  
Rate Variation ◽  
Genome Wide ◽  
Recombination Rate Variation

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 Genetics of recombination rate variation in the pig

2020 ◽  
Author(s):  
Martin Johnsson ◽  
Andrew Whalen ◽  
Roger Ros-Freixedes ◽  
Gregor Gorjanc ◽  
Ching-Yi Chen ◽  
...  
Keyword(s):  
Recombination Rate ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Chromosome Length ◽  
Rate Variation ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions ◽  
Iterative Peeling ◽  
Recombination Rate Variation

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.

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

2012 ◽  
Vol 12 (1) ◽  
pp. 65 ◽  
Author(s):  
Lionel Guy ◽  
Björn Nystedt ◽  
Yu Sun ◽  
Kristina Näslund ◽  
Eva C Berglund ◽  
...  
Keyword(s):  
Recombination Rate ◽  
Bartonella Henselae ◽  
Rate Variation ◽  
Genome Wide ◽  
A Genome ◽  
Recombination Rate Variation ◽  
Genome Wide Study

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

2020 ◽  
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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