Genetic crossovers are predicted accurately by the computed human recombination map

Garcias M, Kratochvíl L, Valenzuela N, Georges A, Waters PD, Ruiz-Herrera A. Meiotic chromosome dynamics and double strand break formation in reptiles

During meiotic prophase I, tightly regulated processes take place, from pairing and synapsis of homologous chromosomes to recombination, which are essential for the generation of genetically variable haploid gametes. These processes have canonical meiotic features conserved across different phylogenetic groups. However, the dynamics of meiotic prophase I in non-mammalian vertebrates are poorly known. Here, we compare four species from Sauropsida to understand the regulation of meiotic prophase I in reptiles: the Australian central bearded dragon (Pogona vitticeps), two geckos (Paroedura picta and Coleonyx variegatus) and the painted turtle (Chrysemys picta). We first performed a histological characterization of the spermatogenesis process in both the bearded dragon and the painted turtle. We then analyzed prophase I dynamics, including chromosome pairing, synapsis and the formation of double strand breaks (DSBs). We show that meiosis progression is highly conserved in reptiles with telomeres clustering forming the bouquet, which we propose promotes homologous pairing and synapsis, along with facilitating the early pairing of micro-chromosomes during prophase I (i.e., early zygotene). Moreover, we detected low levels of meiotic DSB formation in all taxa. Our results provide new insights into reptile meiosis.

Sycp1 Is Not Required for Subtelomeric DNA Double-Strand Breaks but Is Required for Homologous Alignment in Zebrafish Spermatocytes

In meiotic prophase I, homologous chromosomes are bound together by the synaptonemal complex, in which two axial elements are connected by transverse filaments and central element proteins. In human and zebrafish spermatocytes, homologous recombination and assembly of the synaptonemal complex initiate predominantly near telomeres. In mice, synapsis is not required for meiotic double-strand breaks (DSBs) and homolog alignment but is required for DSB repair; however, the interplay of these meiotic events in the context of peritelomeric bias remains unclear. In this study, we identified a premature stop mutation in the zebrafish gene encoding the transverse filament protein Sycp1. In sycp1 mutant zebrafish spermatocytes, axial elements were formed and paired at chromosome ends between homologs during early to mid-zygonema. However, they did not synapse, and their associations were mostly lost in late zygotene- or pachytene-like stages. In sycp1 mutant spermatocytes, γH2AX signals were observed, and Dmc1/Rad51 and RPA signals appeared predominantly near telomeres, resembling wild-type phenotypes. We observed persistent localization of Hormad1 along the axis in sycp1 mutant spermatocytes, while the majority of Iho1 signals appeared and disappeared with kinetics similar to those in wild-type spermatocytes. Notably, persistent Iho1 foci were observed in spo11 mutant spermatocytes, suggesting that Iho1 dissociation from axes occurs in a DSB-dependent manner. Our results demonstrated that Sycp1 is not required for peritelomeric DSB formation but is necessary for complete pairing of homologs in zebrafish meiosis.

Joint Prediction of the Effective Population Size and the Rate of Fixation of Deleterious Mutations

Mutation, genetic drift, and selection are considered the main factors shaping genetic variation in nature. There is a lack, however, of general predictions accounting for the mutual interrelation between these factors. In the context of the background selection model, we provide a set of equations for the joint prediction of the effective population size and the rate of fixation of deleterious mutations, which are applicable both to sexual and asexual species. For a population of N haploid individuals and a model of deleterious mutations with effect s appearing with rate U in a genome L Morgans long, the asymptotic effective population size (Ne) and the average number of generations (T) between consecutive fixations can be approximated by [Formula: see text] and [Formula: see text] The solution is applicable to Muller's ratchet, providing satisfactory approximations to the rate of accumulation of mutations for a wide range of parameters. We also obtain predictions of the effective size accounting for the expected nucleotide diversity. Predictions for sexual populations allow for outlining the general conditions where mutational meltdown occurs. The equations can be extended to any distribution of mutational effects and the consideration of hotspots of recombination, showing that Ne is rather insensitive and not proportional to changes in N for many combinations of parameters. This could contribute to explain the observed small differences in levels of polymorphism between species with very different census sizes.

Recombining without Hotspots: A Comprehensive Evolutionary Portrait of Recombination in Two Closely Related Species of Drosophila

Meiotic recombination rate varies across the genome within and between individuals, populations, and species in virtually all taxa studied. In almost every species, this variation takes the form of discrete recombination hotspots, determined in some mammals by a protein called PRDM9. Hotspots and their determinants have a profound effect on the genomic landscape, and share certain features that extend across the tree of life. Drosophila, in contrast, are anomalous in their absence of hotspots, PRDM9, and other species-specific differences in the determination of recombination. To better understand the evolution of meiosis and general patterns of recombination across diverse taxa, we present a truly comprehensive portrait of recombination across time, combining recently published cross-based contemporary recombination estimates from each of two sister species with newly obtained linkage-disequilibrium-based historic estimates of recombination from both of these species. Using Drosophila pseudoobscura and Drosophila miranda as a model system, we compare recombination rate between species at multiple scales, and we suggest that Drosophila replicate the pattern seen in human-chimpanzee in which recombination rate is conserved at broad scales. We also find evidence of a species-wide recombination modifier(s), resulting in both a present and historic genome-wide elevation of recombination rates in D. miranda, and identify broad scale effects on recombination from the presence of an inversion. Finally, we reveal an unprecedented view of the distribution of recombination in D. pseudoobscura, illustrating patterns of linked selection and where recombination is taking place. Overall, by combining these estimation approaches, we highlight key similarities and differences in recombination between Drosophila and other organisms.

Meiotic recombination hotspots - a comparative view

During meiosis homologous chromosomes pair and undergo reciprocal genetic exchange, termed crossover. Meiotic recombination has a profound effect on patterns of genetic variation and is an important tool during crop breeding. Crossovers initiate from programmed DNA double-stranded breaks that are processed to form single-stranded DNA, which can invade a homologous chromosome. Strand invasion events mature into double Holliday junctions that can be resolved as crossovers. Extensive variation in the frequency of meiotic recombination occurs along chromosomes and is typically focused in narrow hotspots, observed both at the level of DNA breaks and final crossovers. We review methodologies to profile hotspots at different steps of the meiotic recombination pathway that have been used in different eukaryote species. We then discuss what these studies have revealed concerning specification of hotspot locations and activity and the contributions of both genetic and epigenetic factors. Understanding hotspots is important for interpreting patterns of genetic variation in populations and how eukaryotic genomes evolve. In addition, manipulation of hotspots will allow us to accelerate crop breeding, where meiotic recombination distributions can be limiting.

DNA recombination. Recombination initiation maps of individual human genomes

DNA double-strand breaks (DSBs) are introduced in meiosis to initiate recombination and generate crossovers, the reciprocal exchanges of genetic material between parental chromosomes. Here, we present high-resolution maps of meiotic DSBs in individual human genomes. Comparing DSB maps between individuals shows that along with DNA binding by PRDM9, additional factors may dictate the efficiency of DSB formation. We find evidence for both GC-biased gene conversion and mutagenesis around meiotic DSB hotspots, while frequent colocalization of DSB hotspots with chromosome rearrangement breakpoints implicates the aberrant repair of meiotic DSBs in genomic disorders. Furthermore, our data indicate that DSB frequency is a major determinant of crossover rate. These maps provide new insights into the regulation of meiotic recombination and the impact of meiotic recombination on genome function.

Pairomics, the omics way to mate choice

The core aspects of the biology and evolution of sexual reproduction are reviewed with a focus on the diploid, sexually reproducing, outbreeding, polymorphic, unspecialized, altricial and cultural human species. Human mate choice and pair bonding are viewed as central to individuals' lives and to the evolution of the species, and genetic assistance in reproduction is viewed as a universal human right. Pairomics is defined as an emerging branch of the omics science devoted to the study of mate choice at the genomic level and its consequences for present and future generations. In pairomics, comprehensive genetic information of individual genomes is stored in a database. Computational tools are employed to analyze the mating schemes and rules that govern mating among the members of the database. Mating models and algorithms simulate the outcomes of mating any given genome with each of a number of genomes represented in the database. The analyses and simulations may help to understand mating schemes and their outcomes, and also contribute a new cue to the multicued schemes of mate choice. The scientific, medical, evolutionary, ethical, legal and social implications of pairomics are far reaching. The use of genetic information as a search tool in mate choice may influence our health, lifestyle, behavior and culture. As knowledge on genomics, population genetics and gene-environment interactions, as well as the size of genomic databases expand, so does the ability of pairomics to investigate and predict the consequences of mate choice for the present and future generations.

Population-specific recombination sites within the human MHC region

Genetic rearrangement by recombination is one of the major driving forces for genome evolution, and recombination is known to occur in non-random, discreet recombination sites within the genome. Mapping of recombination sites has proved to be difficult, particularly, in the human MHC region that is complicated by both population variation and highly polymorphic HLA genes. To overcome these problems, HLA-typed individuals from three representative populations: Asian, European and African were used to generate phased HLA haplotypes. Extended haplotype homozygosity (EHH) plots constructed from the phased haplotype data revealed discreet EHH drops corresponding to recombination events and these signatures were observed to be different for each population. Surprisingly, the majority of recombination sites detected are unique to each population, rather than being common. Unique recombination sites account for 56.8% (21/37 of total sites) in the Asian cohort, 50.0% (15/30 sites) in Europeans and 63.2% (24/38 sites) in Africans. Validation carried out at a known sperm typing recombination site of 45 kb (HLA-F-telomeric) showed that EHH was an efficient method to narrow the recombination region to 826 bp, and this was further refined to 660 bp by resequencing. This approach significantly enhanced mapping of the genomic architecture within the human MHC, and will be useful in studies to identify disease risk genes.

Fine-scale mapping of meiotic recombination in Asians

Background

Meiotic recombination causes a shuffling of homologous chromosomes as they are passed from parents to children. Finding the genomic locations where these crossovers occur is important for genetic association studies, understanding population genetic variation, and predicting disease-causing structural rearrangements. There have been several reports that recombination hotspot usage differs between human populations. But while fine-scale genetic maps exist for European and African populations, none have been constructed for Asians.

Results

Here we present the first Asian genetic map with resolution high enough to reveal hotspot usage. We constructed this map by applying a hidden Markov model to genotype data for over 500,000 single nucleotide polymorphism markers from Korean and Mongolian pedigrees which include 980 meioses. We identified 32,922 crossovers with a precision rate of 99%, 97% sensitivity, and a median resolution of 105,949 bp. For direct comparison of genetic maps between ethnic groups, we also constructed a map for CEPH families using identical methods. We found high levels of concordance with known hotspots, with approximately 72% of recombination occurring in these regions. We investigated the hypothesized contribution of recombination problems to age-related aneuploidy. Our large sample size allowed us to detect a weak but significant negative effect of maternal age on recombination rate.

Conclusions

We have constructed the first fine-scale Asian genetic map. This fills an important gap in the understanding of recombination pattern variation and will be a valuable resource for future research in population genetics. Our map will improve the accuracy of linkage studies and inform the design of genome-wide association studies in the Asian population.

Meiotic recombinations within major histocompatibility complex of human embryos

We studied the rate and pattern of recombinations within the extended major histocompatibility complex (MHC) locus of the human embryos obtained during preimplantation genetic diagnosis (PGD) for HLA compatibility. Recombinant allele frequency was on average 5.33 %, and recombination rate was 0.44 cM/Mb in the 12.2 Mb of the extended MHC locus. Recombination rate varied up to 14-fold (0.19-2.73 cM/Mb) between cases, and maternal recombination rate was on average 3.8 times higher than paternal alleles. More than 69 % of the recombination hot spots were clustered within the extended class II region where the recombination rate was 5.4 times more than that in extended class I region. These findings indicate the potential of PGD to study the mechanisms of linkage disequilibrium within MHC locus of human embryos, demonstrate the recombination characteristics within extended MHC loci of human embryos in comparison to sperm and family studies, and point to the significance of design and interpretation of PGD for HLA compatibility to avoid misdiagnosis because of meiotic recombinations.

Population demographic history can cause the appearance of recombination hotspots

Although the prevailing view among geneticists suggests that recombination hotspots exist ubiquitously across the human genome, there is only limited experimental evidence from a few genomic regions to support the generality of this claim. A small number of true recombination hotspots are well supported experimentally, but the vast majority of hotspots have been identified on the basis of population genetic inferences from the patterns of linkage disequilibrium (LD) seen in the human population. These inferences are made assuming a particular model of human history, and one of the assumptions of that model is that the effective population size of humans has remained constant throughout our history. Our results show that relaxation of the constant population size assumption can create LD and variation patterns that are qualitatively and quantitatively similar to human populations without any need to invoke localized hotspots of recombination. In other words, apparent recombination hotspots could be an artifact of variable population size over time. Several lines of evidence suggest that the vast majority of hotspots identified on the basis of LD information are unlikely to have elevated recombination rates.

Recombination rate variation in closely related species

Despite their importance to successful meiosis and various evolutionary processes, meiotic recombination rates sometimes vary within species or between closely related species. For example, humans and chimpanzees share virtually no recombination hotspot locations in the surveyed portion of the genomes. However, conservation of recombination rates between closely related species has also been documented, raising an apparent contradiction. Here, we evaluate how and why conflicting patterns of recombination rate conservation and divergence may be observed, with particular emphasis on features that affect recombination, and the scale and method with which recombination is surveyed. Additionally, we review recent studies identifying features influencing fine-scale and broad-scale recombination patterns and informing how quickly recombination rates evolve, how changes in recombination impact selection and evolution in natural populations, and more broadly, which forces influence genome evolution.

Similarity in recombination rate estimates highly correlates with genetic differentiation in humans

Recombination varies greatly among species, as illustrated by the poor conservation of the recombination landscape between humans and chimpanzees. Thus, shorter evolutionary time frames are needed to understand the evolution of recombination. Here, we analyze its recent evolution in humans. We calculated the recombination rates between adjacent pairs of 636,933 common single-nucleotide polymorphism loci in 28 worldwide human populations and analyzed them in relation to genetic distances between populations. We found a strong and highly significant correlation between similarity in the recombination rates corrected for effective population size and genetic differentiation between populations. This correlation is observed at the genome-wide level, but also for each chromosome and when genetic distances and recombination similarities are calculated independently from different parts of the genome. Moreover, and more relevant, this relationship is robustly maintained when considering presence/absence of recombination hotspots. Simulations show that this correlation cannot be explained by biases in the inference of recombination rates caused by haplotype sharing among similar populations. This result indicates a rapid pace of evolution of recombination, within the time span of differentiation of modern humans.

Isolation of meiotic recombinants from mouse sperm

Homologous recombination during meiosis is critical for the formation of gametes. Recombination is initiated by programmed DNA double-strand breaks which preferentially occur at hotspots dispersed throughout the genome. These double-strand breaks are repaired from the homolog, resulting in either a crossover or noncrossover product. Multiple noncrossover events are required for homolog pairing, and at least one crossover is critical for proper chromosome segregation at the first meiotic division. Consequently, homologous recombination in meiosis occurs at high frequencies. This chapter describes how to characterize crossovers and noncrossovers at a hotspot in mice using allele-specific PCR. Amplification of recombinant products directly from sperm DNA is a powerful approach to determine recombination frequencies and map recombination breakpoints, providing insight into homologous recombination mechanisms.

Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome

Background

Meiotic recombination events tend to cluster into narrow spans of a few kilobases long, called recombination hotspots. Such hotspots are not conserved between human and chimpanzee and vary between different human ethnic groups. At the same time, recombination hotspots are heritable. Previous studies showed instances where differences in recombination rate could be associated with sequence polymorphisms.

Results

In this work we developed a novel computational approach, LDsplit, to perform a large-scale association study of recombination hotspots with genetic polymorphisms. LDsplit was able to correctly predict the association between the FG11 SNP and the DNA2 hotspot observed by sperm typing. Extensive simulation demonstrated the accuracy of LDsplit under various conditions. Applying LDsplit to human chromosome 6, we found that for a significant fraction of hotspots, there is an association between variations in intensity of historical recombination and sequence polymorphisms. From flanking regions of the SNPs output by LDsplit we identified a conserved 11-mer motif GGNGGNAGGGG, whose complement partially matches 13-mer CCNCCNTNNCCNC, a critical motif for the regulation of recombination hotspots.

Conclusions

Our result suggests that computational approaches based on historical recombination events are likely to be more powerful than previously anticipated. The putative associations we identified may be a promising step toward uncovering the mechanisms of recombination hotspots.

Genetic and evolutionary correlates of fine-scale recombination rate variation in Drosophila persimilis

Recombination is fundamental to meiosis in many species and generates variation on which natural selection can act, yet fine-scale linkage maps are cumbersome to construct. We generated a fine-scale map of recombination rates across two major chromosomes in Drosophila persimilis using 181 SNP markers spanning two of five major chromosome arms. Using this map, we report significant fine-scale heterogeneity of local recombination rates. However, we also observed "recombinational neighborhoods," where adjacent intervals had similar recombination rates after excluding regions near the centromere and telomere. We further found significant positive associations of fine-scale recombination rate with repetitive element abundance and a 13-bp sequence motif known to associate with human recombination rates. We noted strong crossover interference extending 5-7 Mb from the initial crossover event. Further, we observed that fine-scale recombination rates in D. persimilis are strongly correlated with those obtained from a comparable study of its sister species, D. pseudoobscura. We documented a significant relationship between recombination rates and intron nucleotide sequence diversity within species, but no relationship between recombination rate and intron divergence between species. These results are consistent with selection models (hitchhiking and background selection) rather than mutagenic recombination models for explaining the relationship of recombination with nucleotide diversity within species. Finally, we found significant correlations between recombination rate and GC content, supporting both GC-biased gene conversion (BGC) models and selection-driven codon bias models. Overall, this genome-enabled map of fine-scale recombination rates allowed us to confirm findings of broader-scale studies and identify multiple novel features that merit further investigation.