Dynamics of rye chromosome 1R regions with high or low crossover frequency in homology search and synapsis development

In many organisms, homologous pairing and synapsis depend on the meiotic recombination machinery that repairs double-strand DNA breaks (DSBs) produced at the onset of meiosis. The culmination of recombination via crossover gives rise to chiasmata, which locate distally in many plant species such as rye, Secale cereale. Although, synapsis initiates close to the chromosome ends, a direct effect of regions with high crossover frequency on partner identification and synapsis initiation has not been demonstrated. Here, we analyze the dynamics of distal and proximal regions of a rye chromosome introgressed into wheat to define their role on meiotic homology search and synapsis. We have used lines with a pair of two-armed chromosome 1R of rye, or a pair of telocentrics of its long arm (1RL), which were homozygous for the standard 1RL structure, homozygous for an inversion of 1RL that changes chiasma location from distal to proximal, or heterozygous for the inversion. Physical mapping of recombination produced in the ditelocentric heterozygote (1RL/1RL(inv)) showed that 70% of crossovers in the arm were confined to a terminal segment representing 10% of the 1RL length. The dynamics of the arms 1RL and 1RL(inv) during zygotene demonstrates that crossover-rich regions are more active in recognizing the homologous partner and developing synapsis than crossover-poor regions. When the crossover-rich regions are positioned in the vicinity of chromosome ends, their association is facilitated by telomere clustering; when they are positioned centrally in one of the two-armed chromosomes and distally in the homolog, their association is probably derived from chromosome elongation. On the other hand, chromosome movements that disassemble the bouquet may facilitate chromosome pairing correction by dissolution of improper chromosome associations. Taken together, these data support that repair of DSBs via crossover is essential in both the search of the homologous partner and consolidation of homologous synapsis.     

Inversions of chromosome arms 4AL and 2BS in wheat invert the patterns of chiasma distribution

In many species, including wheat, crossing over is distal, and the proximal regions of chromosome arms contribute little to genetic maps. This was thought to be a consequence of terminal initiation of synapsis favoring distal crossing over. However, in an inverted rye chromosome arm, the pattern of metaphase I chiasmata was also inverted, suggesting that crossover frequencies were specific to chromosome segments. Here, wheat chromosome arms 2BS and 4AL, with essentially entire arms inverted in reverse tandem duplications (rtd), were studied in the MI of meiosis. Inversion–duplication placed the recombining segments in the middle of the arms. While the overall pairing frequencies of the inverted–duplicated arms were considerably reduced relative to normal arms, chiasmata, if present, were always located in the same regions as in structurally normal arms, and relative chiasma frequencies remained the same. The frequencies of fragment or fragment + bridge configurations in AI and AII indicated that of the two tandemly arranged copies of segments in rtds, the more distal inverted segments were more likely to cross over than the segments in their original orientations. These observations show that also in wheat, relative crossover frequencies along chromosome arms are predetermined and independent of the segment location. The segments normally not licensed to cross over do not do so even when placed in seemingly most favorable positions for it.     

Spatiotemporal Asymmetry of the Meiotic Program Underlies the Predominantly Distal Distribution of Meiotic Crossovers in Barley

Meiosis involves reciprocal exchange of genetic information between homologous chromosomes to generate new allelic combinations. In cereals, the distribution of genetic crossovers, cytologically visible as chiasmata, is skewed toward the distal regions of the chromosomes. However, many genes are known to lie within interstitial/proximal regions of low recombination, creating a limitation for breeders. We investigated the factors underlying the pattern of chiasma formation in barley (Hordeum vulgare) and show that chiasma distribution reflects polarization in the spatiotemporal initiation of recombination, chromosome pairing, and synapsis. Consequently, meiotic progression in distal chromosomal regions occurs in coordination with the chromatin cycles that are a conserved feature of the meiotic program. Recombination initiation in interstitial and proximal regions occurs later than distal events, is not coordinated with the cycles, and rarely progresses to form chiasmata. Early recombination initiation is spatially associated with early replicating, euchromatic DNA, which is predominately found in distal regions. We demonstrate that a modest temperature shift is sufficient to alter meiotic progression in relation to the chromosome cycles. The polarization of the meiotic processes is reduced and is accompanied by a shift in chiasma distribution with an increase in interstitial and proximal chiasmata, suggesting a potential route to modify recombination in cereals.     

Synapsis in Robertsonian heterozygotes and homozygotes of Dichroplus pratensis (Melanoplinae, Acrididae) and its relationship with chiasma patterns

Dichroplus pratensis has a complex system of Robertsonian rearrangements with central-marginal distribution; marginal populations are standard telocentric. Standard bivalents show a proximal-distal chiasma pattern in both sexes. In Robertsonian individuals a redistribution of chiasmata occurs: proximal chiasmata are suppressed in fusion trivalents and bivalents which usually display a single distal chiasma per chromosome arm. In this paper we studied the synaptic patterns of homologous chromosomes at prophase I of different Robertsonian status in order to find a mechanistic explanation for the observed phenomenon of redistribution of chiasmata. Synaptonemal complexes of males with different karyotypes were analysed by transmission electron microscopy in surface-spread preparations. The study of zygotene and early pachytene nuclei revealed that in the former, pericentromeric regions are the last to synapse in Robertsonian trivalents and bivalents and normally remain asynaptic at pachytene in the case of trivalents, but complete pairing in bivalents. Telocentric (standard) bivalents usually show complete synapsis at pachytene, but different degrees of interstitial asynapsis during zygotene, suggesting that synapsis starts in opposite (centromeric and distal) ends. The sequential nature of synapsis in the three types of configuration is directly related to their patterns of chiasma localisation at diplotene-metaphase I, and strongly supports our previous idea that Rb fusions instantly produce a redistribution of chiasmata towards chromosome ends by reducing the early pairing regions (which pair first, remain paired longer and thus would have a higher probability of forming chiasmata) from four to two (independently of the heterozygous or homozygous status of the fusion). Pericentromeric regions would pair the last, thus chiasma formation is strongly reduced in these areas contrary to what occurs in telocentric bivalents.     

Quantitative analysis of diploid translocation heterozygotes: test of models and equations

Summary Equations have been derived for two different models of chromosome pairing and chiasmata distribution. The first model represents the normal condition and assumes complete synapsis of homologous bivalents and the arms of interchange quadrivalents. This is followed by a nonrandom distribution of chiasmata among bivalents and multivalents such that each bivalent or bivalent-equivalent always has at least one chiasma. Univalents occur only as part of a III, I configuration at diakinesis or metaphase I. The second model assumes that a hologenomic mutation is present in which all chromosomes of a genome are equally affected. Two different assumptions can be made for such a mutation, and both give the same results: (1) homologous or homoeologous chromosome arms may be randomly paired or unpaired, but synapsis always leads to a crossover; (2) homologous or homoeologous arms always pair, but chiasmata are randomly distributed among the arms. The meiotic configurations at diakinesis or metaphase I are the same for both assumptions. Meiotic configurations of normal diploid interchange heterozygotes show good agreement with numbers predicted by the equations for nonrandom chiasmata distribution among configurations. Inter-specific hybrids with supernumerary chromosomes produced meiotic configurations frequencies in agreement with predictions of equations for random chiasmata distribution, but a hybrid without supernumeraries fitted the nonrandom expectations.     

The quantitative analysis of chromosome pairing and chiasma formation based on the relative frequencies of M I configurations

In autotetraploids, chromosome pairing may be in the form of quadrivalents or bivalent pairs. Whether or not the quadrivalents are maintained until first meiotic metaphase depends on the formation of chiasmata. The relative frequencies of M I configurations thus contain information both on pairing and on chiasma formation. With distal chiasma localisation six configurations can be recognised and their relative frequencies determined: ring quadrivalents, chain quadrivalents, trivalents (with univalent), ring bivalents, open (rod) bivalents, univalent pairs. These represent five degrees of freedom permitting five parameters to be estimated: the frequency (f) of quadrivalent pairing; the frequencies of chiasmate association of the two ends (arms in metacentrics), a′, b′, after quadrivalent pairing, and a, b after bivalent pairing. — The appropriate formulae have been derived and applied to observations on Tradescantia virginiana (4n=24) which has pronounced distal chiasma localisation. Slight modifications make the model applicable to autotetraploids with interstitial in addition to distal chiasmata. In T. virginiana, chromosome pairing appeared to be random between homologues (65.8% quadrivalent pairing; 55.4% observed at M I). After quadrivalent pairing chiasmate association is frequent in the “average long” arm (95.0%) and much less so in the other arm (60.5%). This is attributed to partner exchange. After bivalent pairing chiasma frequencies are still different for the two arms (93.8% and 83.5% association respectively) but much less pronounced. Various complications are discussed.     

Meiotic behaviour of chromosomes 1R, 2R and 5R in autotetraploid rye

The meiotic behaviour of chromosomes 1R, 2R and 5R was studied in C-banded preparations of autotetraploid rye. Analysis of pairing and chiasma formation was based on metaphase I configurations, using the model designed by Sybenga, with slight modifications. Frequencies of two modes of pairing (one quadrivalent or two bivalents) differed from those expected for random pairing. Although preferential pairing for some arm pairs of chromosome 2R was detected, this did not seem to be the cause of the increased bivalent pairing. This increase was attributed to either the spatial separation of the four homologous chromosomes in some premeiotic cells into two groups of two, or a correction of the synaptonemal complex, or both. The number of chiasmate associations showed variation between chromosomes and between arms within the same chromosome. It was closely related to arm length, but different after quadrivalent and bivalent pairing. This is suggested to be a consequence of partner exchange interfering with pairing and, consequently, with chiasma formation, and a different chiasma distribution after quadrivalent pairing. Variation between chromosomes in the frequencies of alternate and adjacent co-orientation in metaphase I quadrivalents without interstitial chiasmata suggests that the relative positions of the centromeres in the quadrivalent influence their co-orientation.     

On the influence of decreased chiasma frequency on preferential MI pairing behaviour of rye chromosomes in wheat-rye derivatives

Meiotic behaviour of identical and homologous rye chromosomes was investigated in colchicine-induced duplicated meiocytes obtained from different wheat-rye derivatives. A great reduction in the amount of metaphase I (MI) associations accompanied by a strong tendency for identical over homologous nonidentical preferential MI pairing was found in all of the four rye chromosome arms analysed. Both of these features appear to be associated with a more distal chiasma localization where the presence of an interstitial C-band has allowed two distinct regions within the same chromosome arm to be studied separately. On the other hand, the MI pairing failure observed for the rye chromosomes under analysis does not seem to be an effect of telomeric or interstitial C-heterochromatin.by P.B. Moens     

Chromosomal control of chiasma distribution in house mice. Analysis of chiasma distribution in homo- and heterozygotes by inversion in chromosome 1

Examination of chiasma distribution in the chromosome 1 in male mice homo- and heterozygous for distal inversion In(1)12Rk and in normal mice was carried out. No differences in chiasma distribution was found between homozygotes for the inversion and homozygotes for normal chromosome 1. A drastic change in this trait was revealed in heterozygous animals. In heterozygotes, the telomeric segments of SC were asynapsed and unavailable for recombination. This leads to significant decrease in the frequency of bivalents bearing chiasmata in pretelomeric region. In turn, it produced chiasma redistribution in proximal noninverted portion of the bivalent 1. These results could be interpreted as evidence for chromosomal control of chiasma distribution pattern: the distance of certain part of the chromosome from telomere and interference (which also operates at the chromosomal level) are more important for determination of the chiasmata frequency in the given region, than its genetic content.     

The coupling of crossing over and homologous synapsis in maize inversions

Because fresh initiations of synapsis must occur for homologous synapsis of internal heterozygously inverted chromosome segments, attention has been directed at homologous synapsis and crossing over in overlapping paracentric inversions in the long arm of chromosome 1 of maize. In an earlier study with a relatively short inversion (where double crossovers within the inversion were rare), a recombination nodule (RN) was generally found at pachytene in reverse paired (homologously synapsed) inverted regions. Crossover frequency within the inversion, which could be independently estimated from analysis of bridge and fragment frequency at anaphase I and II, closely corresponded to crossover frequency estimated from observed RN frequency in pachytene inversion loops. These findings were consistent with the interpretation that establishment of homologous synapsis in this case is generally coupled to crossing over. This coupling suggests that there is very early commitment to the form of resolution of recombination intermediates that results in reciprocal recombination events instead of conversion only or other noncrossover events. This study examines another, larger paracentric inversion in the long arm of chromosome 1 that completely overlaps the first inversion. It is sufficiently longer than the first inversion that double crossover events are found within it with substantial frequency and interference considerations are feasible. This study confers additional insight into the interrelationships of synapsis and crossing over and the probable sequence in which the various involved processes usually occur. It raises the strong possibility that crossovers can be initiated during the alignment phase that precedes synapsis.     

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.     

Pairing competition between identical and homologous chromosomes in autotetraploid rye heterozygous for interstitial C-bands

Pairing competition between identical and homologous non-identical chromosomes is analysed in autotetraploid metaphase I cells of rye where one pair of identical partners bears an interstitial C-band in the long arm of chromosome 6R whereas the other pair of identical partners lacks such a C-band. This makes it possible to study pairing preferences in two distinct regions of the same chromosome arm. A significant excess of associations involving homologous partners is always observed in the proximal segment (from the centromere to the C-band), whereas a good fit with the expected random ratio, or else identical pairing preferences, is found in the distal segment (from the C-band to the telomere). Differences in the processes of pairing and chiasma formation in 6RL, and/or a readjustment in the pattern of chiasma distribution due to heterozygosity for the interstitial C-band as a result of homologous nonidentical pairing, may be responsible for the different behaviour detected in the two regions of the marked arm.     

Genetic and physical mapping of homoeologous recombination points involving wheat chromosome 2B and rye chromosome 2R.

Wide hybrids have been used in generating genetic maps of many plant species. In this study, genetic and physical mapping was performed on ph1b-induced recombinants of rye chromosome 2R in wheat (Triticum aestivum L.). All recombinants were single breakpoint translocations. Recombination 2RS-2BS was absent from the terminal and the pericentric regions and was distributed randomly along an intercalary segment covering approximately 65% of the arm's length. Such a distribution probably resulted from structural differences at the telomeres of 2RS and wheat 2BS arm that disrupted telomeric initiation of pairing. Recombination 2RL-2BL was confined to the terminal 25% of the arm's length. A genetic map of homoeologous recombination 2R-2B was generated using relative recombination frequencies and aligned with maps of chromosomes 2B and 2R based on homologous recombination. The alignment of the short arms showed a shift of homoeologous recombination toward the centromere. On the long arms, the distribution of homoeologous recombination was the same as that of homologous recombination in the distal halves of the maps, but the absence of multiple crossovers in homoeologous recombination eliminated the proximal half of the map. The results confirm that homoeologous recombination in wheat is based on single exchanges per arm, indicate that the distribution of these single homoeologous exchanges is similar to the distribution of the first (distal) crossovers in homologues, and suggest that successive crossovers in an arm generate specific portions of genetic maps. A difference in the distribution of recombination between the short and long arms indicates that the distal crossover localization in wheat is not dictated by a restricted distribution of DNA sequences capable of recombination but by the pattern of pairing initiation, and that can be affected by structural differences. Restriction of homoeologous recombination to single crossovers in the distal part of the genetic map complicates chromosome engineering efforts targeting genes in the proximal map regions.     

Chiasma distribution in rye chromosomes of diploid rye and in wheat/rye addition lines in relation to C-heterochromatin

Summary In five genetically different inbred lines of rye and in the seven Chinese Spring/Imperial wheatrye addition lines, chiasma distribution in rye chromosomes was studied with respect to the amount and position of constitutive heterochromatin (Giemsa C-bands). In all inbred lines, rye chromosomes with one primary terminal band were more frequently found as univalents than those with primary bands on both telomeres. These chromosomes were most probably 5R and/or 6R. In the addition lines a highly significant reduction in the number of arms bound by chiasmata was found for rye chromosomes 5R and 6R. Because of the similar chiasma distribution in the inbred lines and in the rye chromosomes of the addition lines, no effect of the wheat genome on the number of chiasmata in the rye chromosomes can be ascertained. However, a relationship between chiasma frequency and chromosome arm length seems to exist, since under reduced chiasma conditions the two shortest arms of the rye complement, those of chromosomes 5R and 6R, frequently fail to form a chiasma. No effect of the large blocks of constitutive heterochromatin in the telomeres of the rye chromosomes on the position of chiasmata within a bivalent could be established.This study was financially supported by the Deutsche Forschungsgemeinschaft     

Correlation between Pairing Initiation Sites, Recombination Nodules and Meiotic Recombination in Sordaria Macrospora

The decrease of meiotic exchanges (crossing over and conversion) in two mutants of Sordaria macrospora correlated strongly with a reduction of chiasmata and of both types of "recombination nodules." Serial section reconstruction electron microscopy was used to compare the synapsis pattern of meiotic prophase I in wild type and mutants. First, synapsis occurred but the number of synaptonemal complex initiation sites was reduced in both mutants. Second, this reduction was accompanied by, or resulted in, modifications of the pattern of synapsis. Genetic and synaptonemal complex maps were compared in three regions along one chromosome arm divided into well marked intervals. Reciprocal exchange frequencies and number of recombination nodules correlated in wild type in the three analyzed intervals, but disparity was found between the location of recombination nodules and exchanges in the mutants. Despite the twofold exchange decrease, sections of the genome such as the short arm of chromosome 2 and telomere regions were sheltered from nodule decrease and from pairing modifications. This indicated a certain amount of diversity in the control of these features and suggested that exchange frequency was dependent not only on the amount of effective pairing but also on the localization of the pairing sites, as revealed by the synaptonemal complex progression in the mutants.     

Chiasmata and chromosome breakages are related to crossing over in Drosophila ananassae males.

A cytogenetic analysis of male crossing over in Drosophila ananassae revealed that cytological exchanges resulted in genetic crossing over, and that chiasma frequency and the genetic recombination correlated positively in chromosomes 2 and 3. Furthermore, the frequency of chromosome breakages correlated positively with chiasma frequency. Paracentric inversion heterozygosity had no detectable influence on the chromosome pairing or exchange events within the inversion loop at meiosis. Scoring of the chiasma demonstrated that males homozygous for the previously mapped enhancers of male crossing over had low frequencies of chiasmata, whereas higher frequencies of chiasmata were observed in males heterozygous for enhancers. The results presented here indicate that the genetic factors controlling male crossing over are involved in the origin of chromosome breakages and in exchange events.     

Differing requirements for RAD51 and DMC1 in meiotic pairing of centromeres and chromosome arms in Arabidopsis thaliana

During meiosis homologous chromosomes pair, recombine, and synapse, thus ensuring accurate chromosome segregation and the halving of ploidy necessary for gametogenesis. The processes permitting a chromosome to pair only with its homologue are not fully understood, but successful pairing of homologous chromosomes is tightly linked to recombination. In Arabidopsis thaliana, meiotic prophase of rad51, xrcc3, and rad51C mutants appears normal up to the zygotene/pachytene stage, after which the genome fragments, leading to sterility. To better understand the relationship between recombination and chromosome pairing, we have analysed meiotic chromosome pairing in these and in dmc1 mutant lines. Our data show a differing requirement for these proteins in pairing of centromeric regions and chromosome arms. No homologous pairing of mid-arm or distal regions was observed in rad51, xrcc3, and rad51C mutants. However, homologous centromeres do pair in these mutants and we show that this does depend upon recombination, principally on DMC1. This centromere pairing extends well beyond the heterochromatic centromere region and, surprisingly, does not require XRCC3 and RAD51C. In addition to clarifying and bringing the roles of centromeres in meiotic synapsis to the fore, this analysis thus separates the roles in meiotic synapsis of DMC1 and RAD51 and the meiotic RAD51 paralogs, XRCC3 and RAD51C, with respect to different chromosome domains.     

A comparison of physical distribution of recombination in chromosome 1R in diploid rye and in hexaploid triticale

Summary Polymorphism for six C-bands on chromosome 1R was used to study the frequency and distribution of recombination along the chromosome in a diploid rye (Secale cereale L.) and in a hexaploid triticale (X Triticosecale Wittmack) derived from it. In rye, the total recombination frequency in five segments of chromosome 1R was 93.7%. Recombination was concentrated in the distal regions of both chromosome arms and was infrequent in the proximal regions. In hexaploid triticale the total recombination frequency in the same chromosome was reduced to 51.7%. In both backgrounds the distal half of the long arm showed similar recombination frequencies, 51.4% and 45.7% for rye and triticale, respectively. The remaining about two-thirds of the chromosome length showed 42.3% recombination in rye but only 6% recombination in triticale. The results demonstrate that the genetic background in which mapping is performed not only affects the total amount of recombination, but also its distribution along the chromosome length.     

Physical distribution of recombination in B-genome chromosomes of tetraploid wheat

Summary Several studies have indicated a noncorrespondence between genetic and physical distances in wheat chromosomes. To study the physical distribution of recombination, polymorphism for C-banding patterns was used to monitor recombination in 67 segments in 11 B-genome chromosome arms of Triticum turgidum. Recombination was absent in proximal regions of all chromosome arms; its frequency increased exponentially with distance from the centromere. A significant difference was observed between the distribution of recombination in physically short and physically long arms. In physically short arms, recombination was almost exclusively concentrated in distal segments and only those regions were represented in their genetic maps. In physically long arms, while a majority of the genetic distance was again based upon recombination in distal chromosome segments, some interstitial recombination was observed. Consequently, these regions also contributed to the genetic maps. Such a pattern of recombination, skewed toward terminal segments of chromosomes, is probably a result of telomeric pairing initiation and strong positive chiasma interference. Interference averaged 0.81 in 35 pairs of adjacent segments and 0.57 across the entire recombining portions of chromosome arms. The total genetic map lengths of the arms corresponded closely to those expected on the basis of their metaphase-I chiasma frequencies. As a consequence of this uneven distribution of recombination there can be a 153-fold difference (or more) in the number of DNA base pairs per unit (centiMorgan) of genetic length.     

Near-normal chiasma formation and maintenance in a short distal translocated segment in maize

Study of successful crossover pairing and chiasma formation is informatively extended to a very short translocated segment. Contrary to previous suggestion it now seems likely that the extreme distal region of the long arm of maize chromosome 1 is not deficient in intrinsic capacity for the initiation of crossover pairing. In addition, chiasmata formed in this short region appear to be efficiently maintained.