Meiotic recombination hot spots and human DNA diversity

Jeffreys, Alec J.; Holloway, J. Kim; Kauppi, Liisa; May, Celia A.; Neumann, Rita; Slingsby, M. Timothy; Webb, Adam

doi:10.1098/rstb.2003.1372

Cited by 82 publications

(72 citation statements)

References 38 publications

(67 reference statements)

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“…Fungicide application is a common practice in canola and potato production systems, whereas fungicides are usually not applied in pea and lentil cropping systems. Thus, a combination of ecological, molecular and evolutionary forces such as mutation events, natural selection, genetic drift, population bottleneck and migration in different populations could explain the lack of linear relationship between LD and the distance on a chromosome in all the populations studied (Jeffreys et al, 2004;Hsueh et al, 2006). For example, low levels of polymorphisms at certain loci (because of population bottleneck) could reduce the chance of detecting crossover.…”

Section: Discussionmentioning

confidence: 99%

“…It appears that this DNA region of the chromosome 5 had some level of recombination or high mutation rate, as seven of the eight populations showed linkage equilibrium between markers 19A and 19B (Table 3). Recombination hot spots have been detected in the human genome (Chakravarti et al, 1984;Ardlie et al, 2002;Arnheim et al, 2003;Jeffreys et al, 2004), and also found in many other genomes including Cryptococcus spp. (Hsueh et al, 2006), P. falciparum (Mu et al, 2005) and Schizosaccharomyces pombe (Steiner and Smith, 2005).…”

Section: Discussionmentioning

confidence: 99%

“…Thus, the relationship between LD decay and physical distance cannot be observed in DNA regions of recombination hot spots or in mutation hot spots. In such instances, markers in close proximity may not be in LD (Jeffreys et al, 2004).…”

Section: Discussionmentioning

confidence: 99%

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Inferring outcrossing in the homothallic fungus Sclerotinia sclerotiorum using linkage disequilibrium decay

et al. 2014

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The occurrence and frequency of outcrossing in homothallic fungal species in nature is an unresolved question. Here we report detection of frequent outcrossing in the homothallic fungus Sclerotinia sclerotiorum. In using multilocus linkage disequilibrium (LD) to infer recombination among microsatellite alleles, high mutation rates confound the estimates of recombination. To distinguish high mutation rates from recombination to infer outcrossing, 8 population samples comprising 268 S. sclerotiorum isolates from widely distributed agricultural fields were genotyped for 12 microsatellite markers, resulting in multiple polymorphic markers on three chromosomes. Each isolate was homokaryotic for the 12 loci. Pairwise LD was estimated using three methods: Fisher's exact test, index of association (I A ) and Hedrick's D 0 . For most of the populations, pairwise LD decayed with increasing physical distance between loci in two of the three chromosomes. Therefore, the observed recombination of alleles cannot be simply attributed to mutation alone. Different recombination rates in various DNA regions (recombination hot/ cold spots) and different evolutionary histories of the populations could explain the observed differences in rates of LD decay among the chromosomes and among populations. The majority of the isolates exhibited mycelial incompatibility, minimizing the possibility of heterokaryon formation and mitotic recombination. Thus, the observed high intrachromosomal recombination is due to meiotic recombination, suggesting frequent outcrossing in these populations, supporting the view that homothallism favors universal compatibility of gametes instead of traditionally believed haploid selfing in S. sclerotiorum. Frequent outcrossing facilitates emergence and spread of new traits such as fungicide resistance, increasing difficulties in managing Sclerotinia diseases.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Inferring outcrossing in the homothallic fungus Sclerotinia sclerotiorum using linkage disequilibrium decay

et al. 2014

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“…SSRs, being recombination hot spots aid in genome evolution, sometimes being the basis of diseases [10,11]. Functionally, these sequences are reported to be associated with gene regulation, transcription and protein function [12,13].…”

Section: Introductionmentioning

confidence: 99%

Imex Based Analysis of Repeat Sequences in Flavivirus Genomes, Including Dengue Virus

Alam¹

2016

J Data Mining Genomics Proteomics

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Simple sequence repeats (SSRs), also known as microsatellites, are 1-6 nucleotides repeat motif, present in varying number of iterations, across coding and non-coding regions of prokaryotes, eukaryotes and viruses. Present study focuses on simple sequence repeats (SSRs) in 27 Flavivirus genomes, which includes dengue virus. The comparative viral genomics in the light of SSRs would help us understand the diversity and adaptability to new hosts. A total of 1164 SSRs and 53 cSSRs were uncovered from the 27studied genomes. Mononucleotide A was the most prevalent repeat motif with an average distribution of around 6. This was followed by G (average distribution of 2). Amongst the dinucleotides AG/GA repeat motif was the most prevalent with an average distribution of 14 across studied genomes. The Flavivirus genomes lacked two essential features responsible for genome evolution, dinucleotide repeat motif AT/TA (least represented with average distribution of ~0.5) and cSSR in non-coding regions, suggesting a stable genome or evolution by hitherto unexplained mechanisms. The unveiling of conserved sequences in the isolates of Dengue virus suggests a basis for biomarker development for viral diagnostics.

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“…An alternative technique of sperm typing, which allows for many thousands of meiotic products to be screened from a single individual, produces extremely high-resolution estimates. However, these studies are male-specific, are typically only applied to a few individuals and are currently limited in scale to only small (<1 Mb) regions of the genome (Arnheim et al 2003;Jeffreys et al 2004;Greenawalt et al 2006).…”

mentioning

confidence: 99%

Recombination rate estimation in the presence of hotspots

2007

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Fine-scale estimation of recombination rates remains a challenging problem. Experimental techniques can provide accurate estimates at fine scales but are technically challenging and cannot be applied on a genome-wide scale. An alternative source of information comes from patterns of genetic variation. Several statistical methods have been developed to estimate recombination rates from randomly sampled chromosomes. However, most such methods either make poor assumptions about recombination rate variation, or simply assume that there is no rate variation. Since the discovery of recombination hotspots, it is clear that recombination rates can vary over many orders of magnitude at the fine scale. We present a method for the estimation of recombination rates in the presence of recombination hotspots. We demonstrate that the method is able to detect and accurately quantify recombination rate heterogeneity, and is a substantial improvement over a commonly used method. We then use the method to reanalyze genetic variation data from the HLA and MS32 regions of the human genome and demonstrate that the method is able to provide accurate rate estimates and simultaneously detect hotspots.

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Meiotic recombination hot spots and human DNA diversity

Cited by 82 publications

References 38 publications

Inferring outcrossing in the homothallic fungus Sclerotinia sclerotiorum using linkage disequilibrium decay

Inferring outcrossing in the homothallic fungus Sclerotinia sclerotiorum using linkage disequilibrium decay

Imex Based Analysis of Repeat Sequences in Flavivirus Genomes, Including Dengue Virus

Recombination rate estimation in the presence of hotspots

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