Chiasma Interference Research Articles

Recombination and sterility in inversion homo- and heterokaryotypes under a general counting model of chiasma interference.

It has long been known that the chiasmata are not independently distributed in most organisms, a phenomenon known as chiasma interference. In this paper, I suggest a model of chiasma interference that generalizes the Poisson model, the counting model, the Poisson-skip model and the two-pathway counting model into a single framework, and use it to derive infinite series expressions for the sterility and recombination pattern probabilities in inversion homo- and heterokaryotypes, and a closed-form expression for the special case of the two-pathway counting model in homokaryotypes. I then use these expressions to perform maximum likelihood parameter estimations for recombination and tetrad data from various species. The results imply that the simpler counting models perform well compared to more complex ones, that interference works in a similar way in homo- and heterokaryotypes, and that the model fits well with data for the latter as well as the former. I also find evidence that the interference signal is broken by the centromere in some species, but not others, suggestions of negative interference in Aspergillus nidulans, and no consistent support for the theory that a second non-interfering chiasma pathway exists only in organisms that require double-strand break for synapsis. I suggest that the latter finding is at least partly due to issues involved in analysing aggregate data from different experiments and individuals.

Unreduced Megagametophyte Production in Lemon Occurs via Three Meiotic Mechanisms, Predominantly Second-Division Restitution.

Unreduced (2n) gametes have played a pivotal role in polyploid plant evolution and are useful for sexual polyploid breeding in various species, particularly for developing new seedless citrus varieties. The underlying mechanisms of 2n gamete formation were recently revealed for Citrus reticulata but remain poorly understood for other citrus species, including lemon (C. limon [L.] Burm. f.). Here, we investigated the frequency and causal meiotic mechanisms of 2n megagametophyte production in lemon. We genotyped 48progeny plants of two lemon genotypes, “Eureka Frost” and “Fino”, using 16 Simple Sequence Repeat (SSR) and 18 Single Nucleotide Polymorphism (SNP) markers to determine the genetic origin of the progenies and the underlying mechanisms for 2n gamete formation. We utilized a maximum-likelihood method based on parental heterozygosity restitution (PHR) of centromeric markers and analysis of PHR patterns along the chromosome. The frequency of 2n gamete production was 4.9% for “Eureka Frost” and 8.3% for “Fino”, with three meiotic mechanisms leading to 2n gamete formation. We performed the maximum-likelihood method at the individual level via centromeric marker analysis, finding that 88% of the hybrids arose from second-division restitution (SDR), 7% from first-division restitution (FDR) or pre-meiotic doubling (PRD), and 5% from post-meiotic genome doubling (PMD). The pattern of PHR along LG1 confirmed that SDR is the main mechanism for 2n gamete production. Recombination analysis between markers in this LG revealed partial chiasma interference on both arms. We discuss the implications of these restitution mechanisms for citrus breeding and lemon genetics.

Linkage Mapping Reveals Strong Chiasma Interference in Sockeye Salmon: Implications for Interpreting Genomic Data.

Meiotic recombination is fundamental for generating new genetic variation and for securing proper disjunction. Further, recombination plays an essential role during the rediploidization process of polyploid-origin genomes because crossovers between pairs of homeologous chromosomes retain duplicated regions. A better understanding of how recombination affects genome evolution is crucial for interpreting genomic data; unfortunately, current knowledge mainly originates from a few model species. Salmonid fishes provide a valuable system for studying the effects of recombination in nonmodel species. Salmonid females generally produce thousands of embryos, providing large families for conducting inheritance studies. Further, salmonid genomes are currently rediploidizing after a whole genome duplication and can serve as models for studying the role of homeologous crossovers on genome evolution. Here, we present a detailed interrogation of recombination patterns in sockeye salmon (Oncorhynchus nerka). First, we use RAD sequencing of haploid and diploid gynogenetic families to construct a dense linkage map that includes paralogous loci and location of centromeres. We find a nonrandom distribution of paralogs that mainly cluster in extended regions distally located on 11 different chromosomes, consistent with ongoing homeologous recombination in these regions. We also estimate the strength of interference across each chromosome; results reveal strong interference and crossovers are mostly limited to one per arm. Interference was further shown to continue across centromeres, but metacentric chromosomes generally had at least one crossover on each arm. We discuss the relevance of these findings for both mapping and population genomic studies.

Amplified fragment length polymorphism analysis to assess crossover interference and homozygosity in gynogenetic diploid Pacific abalone (Haliotis discus hannai)

Recombination analysis in gynogenetic diploids is a powerful tool for assessing the degree of inbreeding, investigating crossover events and understanding chiasma interference during meiosis. To estimate the marker-centromere recombination rate, the inheritance pattern of 654 amplified fragment length polymorphism (AFLP) markers was examined in the 72-h veliger larvae of two meiogynogenetic diploid families in the Pacific abalone (Haliotis discus hannai). The second-division segregation frequency (y) of the AFLP loci ranged from 0.00 to 0.96, with 23.9% of loci showing y-values higher than 0.67, evidencing the existence of interference. The average recombination frequency across the 654 AFLP loci was 0.45, allowing estimation of the fixation index of 0.55, indicating that meiotic gynogenesis could provide an effective means of rapid inbreeding in the Pacific abalone. The AFLP loci have a small proportion (4.4%) of y-values greater than 0.90, suggesting that a relatively low or intermediate degree of chiasma interference occurred in the abalone chromosomes. The information obtained in this study will enhance our understanding of the abalone genome and will be useful for genetic studies in the species.

Genetic Positioning of Centromeres through Half-Tetrad Analysis in Gynogenetic Diploid Families of the Zhikong Scallop (Chlamys farreri)

Centromere mapping is a powerful tool for improving linkage maps, investigating crossover events, and understanding chiasma interference during meiosis. Ninety microsatellite markers selected across all linkage groups (LGs) from a previous Chlamys farreri genetic map were studied in three artificially induced meiogynogenetic families for centromere mapping by half-tetrad analysis. Inheritance analyses showed that all 90 microsatellite loci conformed to Mendelian inheritance in the control crosses, while 4.4% of the microsatellite loci showed segregation departures from an expected 1:1 ratio of two homozygote classes in meiogynogenetic progeny. The second division segregation frequency (y) of the microsatellites ranged from 0.033 to 0.778 with a mean of 0.332, confirming the occurrence of partial chiasma interference in this species. Heterogeneity of y is observed in one of 42 cases in which markers were typed in more than one family, suggesting variation in gene-centromere recombination among families. Centromere location was mostly in accordance with the C. farreri karyotype, but differences in marker order between linkage and centromere maps occurred. Overall, this study makes the genetic linkage map a more complete and informative tool for genomic studies and it will also facilitate future research of the structure and function of the scallop centromeres.

Multilocus half-tetrad analysis and centromere mapping in citrus: evidence of SDR mechanism for 2n megagametophyte production and partial chiasma interference in mandarin cv ‘Fortune’

The genetic structure of 2n gametes and, particularly, the parental heterozygosity restitution at each locus depends on the meiotic process by which they originated, with first-division restitution and second-division restitution (SDR) being the two major mechanisms. The origin of 2n gametes in citrus is still controversial, although sexual polyploidisation is widely used for triploid seedless cultivar development. In this study, we report the analysis of 2n gametes of mandarin cv 'Fortune' by genotyping 171 triploid hybrids with 35 simple sequence repeat markers. The microsatellite DNA allele counting-peak ratios method for allele-dosage evaluation proved highly efficient in segregating triploid progenies and allowed half-tetrad analysis (HTA) by inferring the 2n gamete allelic configuration. All 2n gametes arose from the female genitor. The observed maternal heterozygosity restitution varied between 10 and 82%, depending on the locus, thus SDR appears to be the mechanism underlying 2n gamete production in mandarin cv 'Fortune'. A new method to locate the centromere, based on the best fit between observed heterozygosity restitution within a linkage group and theoretical functions under either partial or no chiasmata interference hypotheses was successfully applied to linkage group II. The maximum value of heterozygosity restitution and the pattern of restitution along this linkage group would suggest there is partial chiasma interference. The implications of such a restitution mechanism for citrus breeding are discussed.

Microsatellite-centromere mapping in walking catfish Clarias macrocephalus (Günther, 1864) using gynogenetic diploids

Thirty new microsatellite loci were isolated from a microsatellite-enriched genomic library of walking catfish Clarias macrocephalus. The CA motif was the most abundant, although several other motifs were also isolated. Two gynogenetic diploid families, each consisting of a female and 50 offspring, were genotyped at 56 microsatellite loci, including 30 loci developed in the present study and 26 loci reported in the previous study. Overall, 33 anonymous microsatellites derived from genomic library and 11 EST-linked microsatellites were mapped to their centromeres. High levels of chiasma interference were apparent in the walking catfish genome as indicated by an average frequency of second-division segregation (y) of 0.643 ± 0.248. Twenty-six loci (59%) showed a high microsatellite–centromere recombination, with a frequency >0.67, and three loci had recombination frequencies >0.9. This study demonstrated that gene–centromere mapping provided a rapid method for the expansion of the initial linkage map of walking catfish.

CHIASMA FORMATION AND CHIASMA INTERFERENCE IN THE ODONATA

HereditasVolume 38, Issue 4 p. 449-480 Open Access CHIASMA FORMATION AND CHIASMA INTERFERENCE IN THE ODONATA TARVO OKSALA, TARVO OKSALA INSTITUTE OF GENETICS, UNIVERSITY OF HELSINKI, FINLANDSearch for more papers by this author TARVO OKSALA, TARVO OKSALA INSTITUTE OF GENETICS, UNIVERSITY OF HELSINKI, FINLANDSearch for more papers by this author First published: September 1952 https://doi.org/10.1111/j.1601-5223.1952.tb02937.xCitations: 3AboutPDF ToolsExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume38, Issue4September 1952Pages 449-480 ReferencesRelatedInformation

The occurrence of B chromosomes and their effect on meiosis in Najas marina

Two races of Najas marina, designated A and B, can be distinguished on the basis of chromosome morphology. No B chromosomes have been found in plants from three localities of race A. However, in race B, plants with B chromosomes occurred in three out of the nine populations. Since the B chromosomes in these isolated populations were morphologically indistinguishable it was concluded that they are old and of common origin. A B chromosome causes a shift in bivalent types towards lower numbers of chiasmata. B chromosomes have a twofold effect on meiosis: a reduction in chiasma interference in euchromatic regions, and a decrease in chiasma frequency as well as a change in terminalization of chiasmata in the heterochromatic regions.

Centromere-linkage in the turbot (Scophthalmus maximus) through half-tetrad analysis in diploid meiogynogenetics

Seventy nine microsatellite markers selected across all linkage groups (LG) from a previous turbot genetic map were studied in a diploid meiogynogenetic family for centromere mapping using half-tetrad analysis. Significant deviations from Mendelian segregation were observed at 25% loci analyzed. The clustering of distorted loci at specific LGs, suggested the existence of genes of different deleterious effects. The lack of Mendelian segregation distortion at 1 day and 10 days post-hatching larvae at these loci precluded an explanation based on aberrant meiotic segregation. Heterozygote frequency distribution in gynogenetic offspring showed close to 50% values above 0.667, which suggested high chiasma interference in turbot. Complete interference appeared as the best fitting function when estimating centromere position. However, Kosambi and Haldane functions performed better at specific LGs as a consequence of the variable crossover pattern of centromere-distant markers among LG. Great concordance between half-tetrad data and the positions previously reported in the turbot map was observed. Most centromeres were localized with an error around or below 5 cM and closely linked markers exist now in 8 LGs. Centromere location was mostly in accordance with previous karyotypic information.

Sex-specific crossover patterns in Zebrafish (Danio rerio)

Some species display intersex variation in their rate of meiotic recombination, where recombination is usually suppressed in the heterogametic sex. Although no heteromorphic sex chromosomes have been detected in zebrafish (Danio rerio), genetic analysis has indicated a lower frequency of recombination in males relative to females. Our study of the meiotic recombination pattern in female zebrafish indicates that adult females have only a few meiotic oocytes that are found in groups in the ventral zone of the ovarian surface. We used antibody staining of human mutL homolog 1 (MLH1) protein to mark the sites of putative chiasmata to seek a physical basis for the pattern of recombination and its relative frequency in both sexes. We report that MLH1 foci are found mostly in distal regions of the synaptonemal complexes (SCs) in males, but tend to be more evenly distributed in females. Our cytological analysis yields a ratio of MLH1 foci per chromosome in males versus females of 1:1.55. This lower level of recombination in males is in general agreement with previously published results from linkage map analysis. However, the similar ratio of MLH1 foci per unit length of SCs in both sexes demonstrates a correlation between SC length and the frequency of recombination rather than a mechanism that suppresses recombination in males. Thus, chiasma interference seems to provide similar expression in males and females in agreement with the situation in humans, where oocytes with longer SCs display a higher level of recombination that is not a consequence of more closely spaced crossovers along the SCs.

The misuse of the three-point cross for estimating chiasma interference

The building of genetic maps in diploid organisms by crosses between different genotypes and estimation of recombination frequencies from the obtained segregation data has been successfully used since a very young step in the birth of genetics. The three-point cross methodology has facilitated this task and has demonstrated at the same time that genetic distances are not additive, as some recombinant products are not recognised in the progeny. Three-point cross also allows to examine if chiasma interference exists and its evaluation. Here I show that the classical method of this estimation is erroneous and inevitably determines the apparition of a spurious, positive interference, which has been claimed to be an almost general phenomenon. Interference can only be estimated from a precise knowledge of the number of crossing over events occurring in meiocytes.

Construction of a 10,000-Marker Ultradense Genetic Recombination Map of Potato: Providing a Framework for Accelerated Gene Isolation and a Genomewide Physical Map

An ultradense genetic linkage map with >10,000 AFLP loci was constructed from a heterozygous diploid potato population. To our knowledge, this is the densest meiotic recombination map ever constructed. A fast marker-ordering algorithm was used, based on the minimization of the total number of recombination events within a given marker order in combination with genotyping error-detection software. This resulted in "skeleton bin maps," which can be viewed as the most parsimonious marker order. The unit of distance is not expressed in centimorgans but in "bins." A bin is a position on the genetic map with a unique segregation pattern that is separated from adjacent bins by a single recombination event. Putative centromeres were identified by a strong clustering of markers, probably due to cold spots for recombination. Conversely, recombination hot spots resulted in large intervals of up to 15 cM without markers. The current level of marker saturation suggests that marker density is proportional to physical distance and independent of recombination frequency. Most chromatids (92%) recombined once or never, suggesting strong chiasma interference. Absolute chiasma interference within a chromosome arm could not be demonstrated. Two examples of contig construction and map-based cloning have demonstrated that the marker spacing was in accordance with the expected physical distance: approximately one marker per BAC length. Currently, the markers are used for genetic anchoring of a physical map of potato to deliver a sequence-ready minimal tiling path of BAC contigs of specific chromosomal regions for the potato genome sequencing consortium (http://www.potatogenome.net).

Microsatellite–centromere mapping in the Japanese eel (Anguilla japonica) by half-tetrad analysis using induced triploid families

Genetic improvement of the Japanese eel (Anguilla japonica) can be achieved by artificially controlling its life cycle using recent advances in reproductive biology. In this study, we developed 43 microsatellite loci to confirm Mendelian inheritance at 10 of them as well at 16 previously reported in two full-sib families produced by artificial insemination. In order to establish a base for aquaculture genetics of this species in the near future, these microsatellite loci were mapped in relation to the centromere by half-tetrad analysis using four artificially induced triploid families. The second division segregation frequency (y) of the microsatellite loci ranged from 0.008 to 0.968 (mean±SD=0.645±0.298). These results suggest the presence of strong chiasma interference in the eel. Significant differences were observed for the map distances of microsatellite loci between the two isolation procedures. Microsatellites isolated using the enrichment procedure were mapped to various sites starting from the centromere to the telomere, whereas those from the conventional size-selected library showed a tendency to be distributed in the telomeric region.

Zebrafish: chiasmata and interference

With immunofluorescence microscopy, the positions of centromeres and MLH1 (MutL homolog) foci representing the sites of presumptive chiasmata are shown for zebrafish (Danio rerio Hamilton 1822) synaptonemal complexes (SCs) in spermatocyte nuclei at meiotic prophase. Most SCs have a single focus and a few (7 of 140) have 2 chiasmata. MLH1 foci tend to be in the distal regions of SCs, with progressively fewer occurring towards the middle of the SCs. This non-random distribution suggests chiasma interference. Synaptic initiation, as well as replication protein A (RPA) foci at the chromosome ends, correlates with the distal localization of MLH1 foci. These observations may provide the physical basis for the reported limited genetic recombination in the centromeric region of androgenetic offspring of a male.

All Paired Up with No Place to Go: Pairing, Synapsis, and DSB Formation in a Balancer Heterozygote

The multiply inverted X chromosome balancer FM7 strongly suppresses, or eliminates, the occurrence of crossing over when heterozygous with a normal sequence homolog. We have utilized the LacI-GFP: lacO system to visualize the effects of FM7 on meiotic pairing, synapsis, and double-strand break formation in Drosophila oocytes. Surprisingly, the analysis of meiotic pairing and synapsis for three lacO reporter couplets in FM7/X heterozygotes revealed they are paired and synapsed during zygotene/pachytene in 70%–80% of oocytes. Moreover, the regions defined by these lacO couplets undergo double-strand break formation at normal frequency. Thus, even complex aberration heterozygotes usually allow high frequencies of meiotic pairing, synapsis, and double-strand break formation in Drosophila oocytes. However, the frequencies of failed pairing and synapsis were still 1.5- to 2-fold higher than were observed for corresponding regions in oocytes with two normal sequence X chromosomes, and this effect was greatest near a breakpoint. We propose that heterozygosity for breakpoints creates a local alteration in synaptonemal complex structure that is propagated across long regions of the bivalent in a fashion analogous to chiasma interference, which also acts to suppress crossing over.

Sex, Not Genotype, Determines Recombination Levels in Mice

Recombination, the precise physical breakage and rejoining of DNA between homologous chromosomes, plays a central role in mediating the orderly segregation of meiotic chromosomes in most eukaryotes. Despite its importance, the factors that control the number and placement of recombination events within a cell remain poorly defined. The rate of recombination exhibits remarkable species specificity, and, within a species, recombination is affected by the physical size of the chromosome, chromosomal location, proximity to other recombination events (i.e., chiasma interference), and, intriguingly, the sex of the transmitting parent. To distinguish between simple genetic and nongenetic explanations of sex-specific recombination differences in mammals, we compared recombination in meiocytes from XY sex-reversed and XO females with that in meiocytes from XX female and XY male mice. The rate and pattern of recombination in XY and XO oocytes were virtually identical to those in normal XX females, indicating that sex, not genotype, is the primary determinant of meiotic recombination patterns in mammals.

Meiosis When even two is a crowd

In this review (Curr Biol 2003 13 R831-R833), we proposed that chiasma interference might act to suppress the occurrence of two-strand double exchange events involving nearby exchanges because such double exchanges might lack the ability to ensure segregation. Since publication of this article, we have learned that a very similar model was published previously by Nilsson and Sall (1995) [1Nilsson N.O. Sall T. A model of chiasma reduction of closely formed crossovers.J. Theor. Biol. 1995; 173: 93-98Crossref PubMed Scopus (10) Google Scholar]. We regret the omission of this citation.

The effect of a deficiency and a deletion on recombination in chromosome 1BL in wheat.

To test two models of chiasma allocation and the distribution of crossing-over in chromosomes, genetic mapping was performed in normal, deletion and deficiency chromosome arms 1BL of wheat, Triticum aestivum L. Shortening of the chromosome arm, either by a deletion of the proximal half of the arm or by a deficiency of the terminal quarter of the arm's length, significantly reduced the frequency of multiple crossovers but did not affect the distribution of the distal, presumably the first, crossover in the arm. In the deficiency chromosome, the recombination rate in the terminal segment was much higher than that in the same segment of the complete arm. This suggests that recombination frequency is not an inherent characteristic of a segment but depends on the segment's position on the centromere-telomere axis. These observations support the classical model of chiasma distribution along the chromosome based on the point of pairing initiation, chromosome length and the positive chiasma interference. The study also demonstrates that the distribution and frequency of recombination in a chromosome segment can be manipulated. Therefore, even the segments with very low recombination frequencies could be saturated with large numbers of crossover events to produce high-density genetic maps.

Cost–Benefit Analysis of Recombination and its Application for Understanding of Chiasma Interference

A cost–benefit analysis of recombination was undertaken. The beneficial effects of crossing-over are proportional to the frequency of recombinant offspring, while its harmful effects (errors of crossing-over leading to mutations) are proportional to the number of crossover exchanges. An equilibrium point should exist where the beneficial effects of crossing-over are balanced by its harmful effects. It is suggested that natural selection sustains a number of crossover exchanges per meiosis at the level that provides highest benefit–cost difference. Chiasma interference prevents the arising of closely located exchanges which are less effective in the production of recombinants than exchanges separated by some “interference distance”. Computer simulation shows that chiasma interference increases the recombination effectiveness of the multiple crossover exchanges as compared to the case without interference.