scholarly journals Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations

2018 ◽  
Author(s):  
Enrique J. Schwarzkopf ◽  
Juan C. Motamayor ◽  
Omar E. Cornejo
Keyword(s):  
Genetic Differentiation ◽  
Recombination Rate ◽  
Plant Domestication ◽  
Population Divergence ◽  
Sequence Motifs ◽  
Recombination Rates ◽  
Genomic Features ◽  
Recombination Hotspots ◽  
Genomic Locations ◽  
Dna Sequence Motifs

AbstractOur study investigates the possible drivers of recombination hotspots in Theobroma cacao using ten genetically differentiated populations. By comparing recombination patterns between multiple populations, we obtain a novel view of recombination at the population-divergence timescale. For each population, a fine-scale recombination map was generated using the coalescent with a standard method based on linkage disequilibrium (LD). These maps revealed higher recombination rates in a domesticated population and a population that has undergone a recent bottleneck. We inferred hotspots of recombination for each population and find that the genomic locations of hotspots correlate with genetic differentiation between populations (FST). We used randomization approaches to generate appropriate null models to understand the association between hotspots of recombination and both DNA sequence motifs and genomic features. We found that hotspot regions contained fewer known retroelement sequences than expected and were overrepresented near transcription start and termination sites. Our findings indicate that recombination hotspots are evolving in a way that is consistent with genetic differentiation but are also preferentially driven to near coding regions. We illustrate that, consistent with predictions in plant domestication, the recombination rate of the domesticated population is orders of magnitude higher than that of other populations. More importantly, we find two fixed mutations in the domesticated population’s FIGL1 protein. FIGL1 has been shown to increase recombination rates in Arabidopsis by several orders of magnitude, suggesting a possible mechanism for the observed increased recombination rate in the domesticated population.

scholarly journals Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2213-2233 ◽  
Author(s):  
Na Li ◽  
Matthew Stephens
Keyword(s):  
Linkage Disequilibrium ◽  
Recombination Rate ◽  
Population Sample ◽  
Simulated Data ◽  
Region Of Interest ◽  
Population Data ◽  
Recombination Rates ◽  
Single Nucleotide ◽  
Recombination Hotspots ◽  
Genomic Regions

AbstractWe introduce a new statistical model for patterns of linkage disequilibrium (LD) among multiple SNPs in a population sample. The model overcomes limitations of existing approaches to understanding, summarizing, and interpreting LD by (i) relating patterns of LD directly to the underlying recombination process; (ii) considering all loci simultaneously, rather than pairwise; (iii) avoiding the assumption that LD necessarily has a “block-like” structure; and (iv) being computationally tractable for huge genomic regions (up to complete chromosomes). We examine in detail one natural application of the model: estimation of underlying recombination rates from population data. Using simulation, we show that in the case where recombination is assumed constant across the region of interest, recombination rate estimates based on our model are competitive with the very best of current available methods. More importantly, we demonstrate, on real and simulated data, the potential of the model to help identify and quantify fine-scale variation in recombination rate from population data. We also outline how the model could be useful in other contexts, such as in the development of more efficient haplotype-based methods for LD mapping.

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 Effect of Heterogeneity in Recombination Rate on Variation in Realised Relationship

2018 ◽  
Author(s):  
Ian M.S. White ◽  
William G. Hill
Keyword(s):  
Recombination Rate ◽  
Genetic Information ◽  
Fine Scale ◽  
Recombination Rates ◽  
Recombination Hotspots ◽  
Identical By Descent ◽  
Small Influence ◽  
Scale Levels ◽  
Pedigree Relationship ◽  
Actual Relationship

ABSTRACTIndividuals of specified pedigree relationship vary in the proportion of the genome they share identical by descent, i.e. in their realised or actual relationship. Basing predictions of the variance in realised relationship solely on the proportion of the map length shared implicitly assumes that both recombination rate and genetic information are uniformly distributed along the genome, ignoring the possible existence of recombination hotspots, and failing to distinguish between coding and non-coding sequences. In this paper we quantify the effects of heterogeneity in recombination rate at broad and fine scale levels on the variation in realised relationship. A chromosome with variable recombination rate usually shows more variance in realised relationship than does one having the same map length with constant recombination rate, especially if recombination rates are higher towards chromosome ends. Reductions in variance can also be found, and the overall pattern of change is quite complex. In general, local (fine-scale) variation in recombination rate, e.g. hotspots, has a small influence on the variance in realised relationship. Differences in rates across longer regions and between chromosome ends can increase or decrease the variance in realised relationship, depending on the genomic architecture.

scholarly journals A glance at recombination hotspots in the domestic cat

2015 ◽  
Author(s):  
Hasan Alhaddad ◽  
Chi Zhang ◽  
Bruce Rannala ◽  
Leslie A Lyons
Keyword(s):  
Recombination Rate ◽  
Gc Content ◽  
Domestic Cat ◽  
Recombination Rates ◽  
Recombination Hotspots ◽  
Regional Population ◽  
Variable Population ◽  
Line Elements ◽  
Population Recombination ◽  
Region Size

Recombination has essential roles in increasing genetic variability within a population and in ensuring successful meiotic events. The objective of this study is to (i) infer the population scaled recombination rate (ρ), and (ii) identify and characterize localities of increased recombination rate for the domestic cat, Felis silvestris catus. SNPs (n = 701) were genotyped in twenty-two cats of Eastern random bred origin. The SNPs covered ten different chromosomal regions (A1, A2, B3, C2, D1, D2, D4, E2, F2, X) with an average region size of 850 Kb and an average SNP density of 70 SNPs/region. The Bayesian method in the program inferRho was used to infer regional population recombination rates and hotspots localities. The regions exhibited variable population recombination rates and four decisive recombination hotspots were identified on cat chromosome A2, D1, and E2 regions. No correlation was detected between the GC content and the locality of recombination spots. The hotspots enclosed L2 LINE elements and MIR and tRNA-Lys SINE elements in agreement with hotspots found in other mammals.

scholarly journals PRDM9 directs recombination hotspots to prevent competition with meiotic transcription

2021 ◽  
Author(s):  
Enrique Jimenez Schwarzkopf ◽  
Omar E Cornejo
Keyword(s):  
Dna Sequence ◽  
Genomic Data ◽  
Whole Genome ◽  
Sequence Motifs ◽  
Potential Competition ◽  
Recombination Hotspots ◽  
Dna Sequence Motifs ◽  
Mouse Genomic ◽  
Functional Orthologs

PRDM9 drives recombination hotspots in some mammals, including mice and apes. Non-functional orthologs of PRDM9 are present in a wide variety of vertebrates, but why it is functionally maintained in some lineages is not clear. One possible explanation is that PRDM9 plays a role in ensuring that meiosis is successful. During meiosis, available DNA may be a limiting resource given the tight packaging of chromosomes and could lead to competition between two key processes: meiotic transcription and recombination. Here we explore this potential competition and the role that PRDM9 might play in their interaction. Leveraging existing mouse genomic data, we use resampling schemes that simulate shuffled features along the genome and models that account for the rarity of features in the genome, to test if PRDM9 influences interactions between recombination hotspots and meiotic transcription in a whole genome framework. We also explored possible DNA sequence motifs associated to clusters of hotspots not tied to transcription or PRDM9. We find evidence of competition between meiotic transcription and recombination, with PRDM9 appearing to relocate recombination to avoid said conflict. We also find that retrotransposons may be playing a role in directing hotspots in the absence of other factors.

scholarly journals Constructing a high-density linkage map to infer the genomic landscape of recombination rate variation in European Aspen (Populus tremula)

2019 ◽  
Author(s):  
Rami-Petteri Apuli ◽  
Carolina Bernhardsson ◽  
Bastian Schiffthaler ◽  
Kathryn M. Robinson ◽  
Stefan Jansson ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Linkage Map ◽  
Recombination Rate ◽  
Nucleotide Diversity ◽  
Populus Tremula ◽  
Rate Variation ◽  
Recombination Rates ◽  
Genomic Features ◽  
European Aspen ◽  
Recombination Rate Variation

AbstractThe rate of meiotic recombination is one of the central factors determining levels of linkage disequilibrium and the efficiency of natural selection, and many organisms show a positive correlation between local rates of recombination and levels of nucleotide diversity indicating that linked selection is an important factor determining genome-wide levels of nucleotide diversity. Several methods for estimating recombination rates from segregating polymorphisms in natural populations have recently been developed. These methods have been extensively used in part because they are relatively simple to implement even in many non-model organisms, but also because they potentially offer higher resolution than traditional map-based methods. However, thorough comparisons of LD and map-based estimates of recombination are not readily available in plants. Here we present a new, high-resolution linkage map for Populus tremula and use this to estimate variation in recombination rates across the P. tremula genome. We compare these results to recombination rates estimated based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with 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 identify a number of genomic regions with very high recombination rates that the map-based method fail 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.

scholarly journals A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Nicolas Altemose ◽  
Nudrat Noor ◽  
Emmanuelle Bitoun ◽  
Afidalina Tumian ◽  
Michael Imbeault ◽  
...  
Keyword(s):  
Histone Modifications ◽  
Meiotic Recombination ◽  
Binding Sites ◽  
Human Cell Line ◽  
Sequence Motifs ◽  
Recombination Rates ◽  
Recombination Suppression ◽  
Specific Sequence ◽  
Recombination Hotspots ◽  
Almost All

PRDM9 binding localizes almost all meiotic recombination sites in humans and mice. However, most PRDM9-bound loci do not become recombination hotspots. To explore factors that affect binding and subsequent recombination outcomes, we mapped human PRDM9 binding sites in a transfected human cell line and measured PRDM9-induced histone modifications. These data reveal varied DNA-binding modalities of PRDM9. We also find that human PRDM9 frequently binds promoters, despite their low recombination rates, and it can activate expression of a small number of genes including CTCFL and VCX. Furthermore, we identify specific sequence motifs that predict consistent, localized meiotic recombination suppression around a subset of PRDM9 binding sites. These motifs strongly associate with KRAB-ZNF protein binding, TRIM28 recruitment, and specific histone modifications. Finally, we demonstrate that, in addition to binding DNA, PRDM9's zinc fingers also mediate its multimerization, and we show that a pair of highly diverged alleles preferentially form homo-multimers.

scholarly journals Big data reveals fewer recombination hotspots than expected in human genome

2019 ◽  
Author(s):  
Ziqian Hao ◽  
Haipeng Li
Keyword(s):  
Artificial Intelligence ◽  
Sample Size ◽  
Recombination Rate ◽  
Genetic Maps ◽  
Recombination Activity ◽  
Recombination Rates ◽  
Accurate Identification ◽  
Data Set ◽  
Recombination Hotspots ◽  
Precise Estimation

AbstractRecombination is a major force that shapes genetic diversity. The inference accuracy of recombination rate is important and can be improved by increasing sample size. However, it has never been investigated whether sample size affects the distribution of inferred recombination activity along the genome, and the inference of recombination hotspots. In this study, we applied an artificial intelligence approach to estimate recombination rates in the UK10K human genomic data set with 7,562 genomes and in the OMNI CEU data set with 170 genomes. We found that the fluctuation of local recombination rate along the UK10K genomes is much smaller than that along the CEU genomes, and recombination activity in the UK10K genomes is also much less concentrated. The same phenomena were also observed when comparing UK10K with its two subsets with 200 and 400 genomes. In all cases, analyses of a larger number of genomes result in a more precise estimation of recombination rate and a less concentrated recombination activity with fewer recombination hotpots identified. Generally, UK10K recombination hotspots are about 2.93-14.25 times fewer than that identified in previous studies. By comparing the recombination hotspots of UK10K and its subsets, we found that the false inference of population-specific recombination hotspots could be as high as 75.86% if the number of sampled genomes is not super large. The results suggest that the uncertainty of estimated recombination rate is substantial when sample size is not super large, and more attention should be paid to accurate identification of recombination hotspots, especially population-specific recombination hotspots.Author summaryWe applied FastEPRR, an artificial intelligence method to estimate recombination rates in the UK10K data set with 7,562 genomes and established the most accurate human genetic map. By comparing with other human genetic maps, we found that analyses of a larger number of genomes result in a more precise estimation of recombination rate and a less concentrated recombination activity with fewer recombination hotpots identified. The false inference of population-specific recombination hotspots could be substantial if the number of sampled genomes is not super large.

scholarly journals Diverse DNA Sequence Motifs Activate Meiotic Recombination Hotspots Through a Common Chromatin Remodeling Pathway

Genetics ◽  
2019 ◽  
Vol 213 (3) ◽  
pp. 789-803 ◽  
Author(s):  
Tresor O. Mukiza ◽  
Reine U. Protacio ◽  
Mari K. Davidson ◽  
Walter W. Steiner ◽  
Wayne P. Wahls
Keyword(s):  
Dna Sequence ◽  
Chromatin Remodeling ◽  
Meiotic Recombination ◽  
Sequence Motifs ◽  
Recombination Hotspots ◽  
Dna Sequence Motifs ◽  
Meiotic Recombination Hotspots

scholarly journals DNA motifs are not general predictors of recombination in two Drosophila sister species

2018 ◽  
Author(s):  
James M. Howie ◽  
Rupert Mazzucco ◽  
Thomas Taus ◽  
Viola Nolte ◽  
Christian Schlötterer
Keyword(s):  
Recombination Rate ◽  
Large Scale ◽  
Strong Association ◽  
Natural Populations ◽  
Sister Species ◽  
Rate Variation ◽  
Sequence Motifs ◽  
Recombination Rates ◽  
The Difference ◽  
Recombination Rate Variation

ABSTRACTMeiotic recombination is crucial for chromosomal segregation, and facilitates the spread of beneficial and removal of deleterious mutations. Recombination rates frequently vary along chromosomes and Drosophila melanogaster exhibits a remarkable pattern. Recombination rates gradually decrease towards centromeres and telomeres, with dramatic impact on levels of variation in natural populations. Two close sister species, D. simulans and D. mauritiana do not only have higher recombination rates, but also exhibit a much more homogeneous recombination rate that only drops sharply close to centromeres and telomeres. Because certain sequence motifs are associated with recombination rate variation in D. melanogaster, we tested whether the difference in recombination landscape between D. melanogaster and D. simulans can be explained by the genomic distribution of recombination-rate associated sequence motifs. We constructed the first high resolution recombination map for D. simulans, and searched for motifs linked with high recombination in both sister species. We identified five consensus motifs, present in either species. While the association between motif density and recombination is strong and positive in D. melanogaster, the results are equivocal in D. simulans. Despite the strong association in D. melanogaster, we do not find a decreasing density of these repeat motifs towards centromeres and telomeres. We conclude that the density of recombination-associated repeat motifs cannot explain the large-scale recombination landscape in D. melanogaster, nor the differences to D. simulans. The strong association seen for the sequence motifs in D. melanogaster likely reflects their impact influencing local differences in recombination rates along the genome.

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