Recombination and chiasmata: few but intriguing discrepancies.

The paradigm that meiotic recombination and chiasmata have the same basis has been challenged, primarily for plants. High resolution genetic mapping frequently results in maps with lengths far exceeding those based on chiasma counts. In addition, recombination between specific homoeologous chromosomes derived from interspecific hybrids is sometimes much higher than can be explained by meiotic chiasma frequencies. However, almost the entire discrepancy disappears when proper care is taken of map inflation resulting from the shortcomings of the mapping algorithm and classification errors, the use of dissimilar material, and the difficulty of accurately counting chiasmata. Still, some exchanges, especially of short interstitial segments, cannot readily be explained by normal meiotic behaviour. Aberrant meiotic processes involving segment replacement or insertion can probably be excluded. Some cases of unusual recombination are somatic, possibly premeiotic exchange. For other cases, local relaxation of chiasma interference caused by small interruptions of homology disturbing synaptonemal complex formation is proposed as the cause. It would be accompanied by a preference for compensating exchanges (negative chromatid interference) resulting from asymmetry of the pairing chromatid pairs, so that one side of each pair preferentially participates in pairing. Over longer distances, the pairing face may switch, causing the normal random chromatid participation in double exchanges and the relatively low frequency of short interstitial exchanges. Key words : recombination frequency, map length, chiasmata, discrepancy, chromatid interference.     

Son-sire-regression based heritability estimates of chiasma frequency, using T70H mouse translocation heterozygotes, and the relation between univalence, chiasma frequency and sperm production.

T(1;13)70H/+ translocation heretozygous mice were used for assessing heritability values for chiasma frequencies and the epididymal sperm count. The chiasma frequency estimates were based on 15 son-sire pairs, the translocation heterozygotes being maintained in a Swiss random-bred genetic background. The chiasma frequencies were scored separately for the T70H/+ derived multivalent, specific pairing segments within the multivalent and the remaining bivalents. Chiasma counts within these specified parts of the genome were positively correlated. The heritability estimates, significantly greater than zero, ranged from 0.78-0.98, depending on the chromosome segments included. These results indicate a strong genetic control on a cellular basis for the formation of chiasmata in the mouse. Despite significantly positive correlations and regressions between the various chiasma frequencies and the sperm count (for which 29 pairs of observations were available), no significant heritability estimate for the sperm count was obtained. The relation between the chiasma frequency and the sperm count was weakest when the chiasma count was confined to a region of the translocation-caused multivalent in which the absence of a chiasma almost always resulted in the production of an univalent. This indicates that in the translocation heterozygotes used, the overall chiasma frequency has a greater predictive value for the sperm count than autosomal univalence alone.     

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 pattern of pairing that is effective for crossing over in complex B-A chromosome rearrangements in maize

The study of the mechanism of meiotic homolog pairing, approached by comparing chiasma frequencies in rearranged segments that differ in relative length and intrachromosomal location, is substantially extended here. For the first time, two kinds of evidence were found that centers specialized for alignment pairing may exist in maize chromosomes: (1) for two segments, higher than average crossover frequency per unit length was maintained when these were located in several different chromosomal positions with respect to centromere and telomere, and in fact apart from their own normal centromeres and telomeres. High crossover frequencies in these segments regardless of position are considered to reflect innate capacity for alignment pairing due to relatively strong pairing center content. (2) For a short rearranged segment, chiasma frequency was drastically reduced, and evidence suggests that all of the chiasmata found there depended upon juxtaposition made possible by the completion of the zip-up pairing process in the other arms of the translocation configuration. This short segment is thought to be essentially devoid of pairing center content. It seems possible that crossover frequency depression in short rearranged segments may usually not be due, as commonly supposed, to mechanical difficulties inherent in formation of contorted configurations, but rather to absence of pairing centers within them and the relative rarity (compared to the normal sequence situation) of enabling zip-up pairing. Evidence also indicates that pairing which leads to crossing over must frequently occur between internal translocated segments and their normal sequence counterparts in a way which cannot be dependent upon zipping-up of two-by-two pairing initiated at or near telomeres. Pairing centers in maize are probably numerous and widely dispersed, since coarse direct proportionality is found when chiasma frequency is compared for an array of segment lengths.     

Simultaneous negative and positive chiasma interference across the break point in interchange heterozygotes

The impossibility to obtain real roots from equations published earlier for estimating chiasma frequencies in the two translocated segments from configuration frequencies in interchange heterozygotes, was shown to be a result of lack of independence of chiasma formation. This is interpreted as negative interference. Similarly, negative interference could be shown to operate between the two interstitial segments. In all cases where a sufficient number of bivalents was formed by the interchange complex, chiasma frequency in the interstitial segments was strikingly higher in bivalents (having no chiasmata in the translocated segments) than in multivalents (with chiasmata in one or both translocated segments). This indicates strong positive interference between the interstitial and translocated segments.Negative interference between opposite-and positive interference between adjacent segments across the break point of the interchange occurred simultaneously in the cell populations. The phenomenon was attributed to complications in effective chromosome pairing at the point of partner exchange which in interchanges is determined by the breakpoint.The material was Secale cereale where five interchanges were analysed in a total of 12000 PMC's from 14 plants.     

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.     

Chiasma frequency and position in male and female mice of chromosomes involved in homozygous and heterozygous translocations and tertiary trisomy

Chiasma frequency and position were analyzed at a predominantly late diplotene-diakinesis stage of the first meiotic division in oocytes and spermatocytes from T(1;13)70H homozygotes and heterozygotes, T(2;8)26H heterozygotes and from Ts(I¹³)70H tertiary trisomics of the mouse, Mus musculus. For T70H/T70H, the 13¹ long marker bivalent was studied and for the other karyotypes, analysis was confined to the multivalent configurations adopted by the rearranged chromosomes and their homologues. For the 13¹ bivalent, the chiasma frequency tended to be increased in the female. For the T26H and the T70H multivalents, the chiasma frequencies were higher in the female, largely due to the much higher values in the short interstitial segments. This observed enhancement has been attributed to pairing differences rather than to differences in chiasma forming capability. Both in the telomeric region of the 13¹ bivalent and in the short translocated segments of the reciprocal translocation and tertiary trisomic multivalents, females showed fewer chiasmata than males. The determinations of chiasma position in the 13¹ bivalent indicated chiasma interference with respect to position, leading to clustering of chiasmata somewhat beyond the centromere and towards the telomere of this chromosome.     

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.     

Meiotic behaviour of single-arm tetrasomic combinations of isochromosomes,telocentrics and normal chromosomes in rye (Secale cereale L.)

The isochromosome studied was derived from the short arm of the satellite chromosome of rye (Secale cereale, 2n=14); the telocentrics represent both the short and long arms of the same chromosome. Three different combinations, tetrasomic for the short arm, have been composed and studied: I: 2 isochromosomes (short arm) + 2 telocentrics (long arm) + 6 normal pairs. II: 1 isochromosome + 2 telocentrics (short arm) + 2 telocentrics (long arm) + 6 normal pairs. III: 1 isochromosome + 1 telocentric (short arm) + 1 normal satellite chromosome + 1 telocentric (long arm) + 6 normal pairs. — Over 20,000 cells were analysed. Simple mathematical models describing the frequencies of the different types of MI configurations in terms of frequency of chiasmata in the different pairing combinations of the polysomic arms, and of the frequency of multivalent pairing of this arm, were developed. They were used to derive estimates for chiasma frequencies and multivalent pairing frequencies in the different chromosome constitutions from the observations on configuration frequencies. Variation between plants and within plants was studied, and it was concluded that much of the within plant heterogeneity was due to regulatory variation expressed independently in different chromosomal segments. There was also a significant genetic component. Analysis of the reasons for the models to fail under certain conditions led to suggestions for extension of the models.     

Non-homologous chromosome pairing and crossover formation in haploid rice meiosis

While many studies have provided significant insight into homolog pairing during meiosis, information on non-homologous pairing is much less abundant. In the present study, fluorescence in situ hybridization (FISH) was used to investigate non-homologous pairing in haploid rice during meiosis. At pachytene, non-homologous chromosomes paired and formed synaptonemal complexes. FISH analysis data indicated that chromosome pairing could be grouped into three major types: (1) single chromosome paired fold-back as the univalent structure, (2) two non-homologous chromosomes paired as the bivalent structure, and (3) three or more non-homologous chromosomes paired as the multivalent structure. In the survey of 70 cells, 65 contained univalents, 45 contained bivalents, and 49 contained multivalent. Moreover, chromosomes 9 and 10 as well as chromosomes 11 and 12 formed non-homologous bivalents at a higher frequency than the other chromosomes. However, chiasma was always detected in the bivalent only between chromosomes 11 and 12 at diakinesis or metaphase I, indicating the pairing between these two chromosomes leads non-homologous recombination during meiosis. The synaptonemal complex formation between non-homologs was further proved by immunodetection of RCE8, PAIR2, and ZEP1. Especially, ZEP1 only loaded onto the paired chromosomes other than the un-paired chromosomes at pachytene in haploid.     

Discrete chiasma formation models and their associated high order interference

. We introduce some special chiasma formation processes. First a family of discrete chiasma formation processes is introduced and we determine the nature of higher order interference associated with those processes. Secondly we consider a two-stage chiasma formation process, where the associated recombination frequency between two markers depends not only on their map distance but also on their location along the chromosomes. We characterise under this process, in some cases, the nature of interference between two segments. Received: 22 January 1996 / Revised version: 17 September 1997     

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.     

Unexpected behavior of an inverted rye chromosome arm in wheat

Distal location of chiasmata in chromosome arms is thought to be a consequence of the distal initiation of synapsis. Observations of meiotic behavior of a rye chromosome with an inverted arm show that patterns of chiasma distribution and frequency are also inverted; therefore, the patterns of synapsis and chiasma distribution are independent, and recombination frequency along a chromosome is position-independent and segment-specific. Since cases of random distribution of chiasmata and recombination are known in rye, a genetic mechanism must be present that licenses specific chromosome regions for recombination. Large differences in the metaphase I pairing of the inversion in various combinations of two armed and telocentric chromosomes confirm the major role of the telomere bouquet in early homologue recognition. However, occasional synapsis and chiasmate pairing of the distal regions of normal arms with the proximal regions of the inversion suggest that an alternative mechanism for juxtaposing of homologues must also be present. Synapsis in inversion heterozygotes was mostly complete but in the antiparallel orientation, hence defying homology, but non-homologues never synapsed. Instances of synapsis strictly limited to the chiasma-capable segments of the arm suggest that, in rye, both recombination-dependent and recombination-independent mechanisms for homologue recognition must be present.     

Chromosome pairing in tetraploid hybrids between Lolium perenne and L. multiflorum

Summary Chromosome association at first meiotic metaphase in tetraploid hybrids between Lolium perenne and L. multiflorum was compared with that in autotetraploid L. perenne. The hybrids were found to have significantly higher levels of bivalent frequency, and lower levels of multivalent and chiasma frequency. A significant increase in multivalent frequency with increasing chiasma formation was found in both groups, but the increase was much less in the hybrids. These differences in chromosome associations between the two groups must therefore reflect differences in chiasma distribution and it is suggested that the results indicate a significant degree of preferential bivalent pairing in the hybrids.     

Heterosynapsis and suppression of chiasmata within heterozygous pericentric inversions of the Sitka deer mouse

The patterns of chromosomal pairing and chiasma distribution were analyzed in male Sitka deer mice (Peromyscus sitkensis) polymorphic for terminally positioned pericentric inversions of chromosomes 6 and 7. Gand C-banding of somatic metaphases indicated that the inversions involved 30% and 40% of chromosomes 6 and 7, respectively. Analysis of silver-stained synaptonemal complexes in surface-spread zygotene and pachytene nuclei from heterozygous individuals revealed that inversion loops were not formed. The inverted segments proceeded directly to heterosynapsis without an intervening homosynaptic phase, and the heteromorphic bivalents remained straight-paired throughout pachynema. C-banded pachytene nuclei corroborated the occurrence of heterosynapsis, as the heteromorphic bivalents exhibited nonaligned centromeres. Analysis of diplonema and diakinesis indicated that crossing over had not occurred within the heterosynapsed inverted segments. The observation of chiasma suppression within the inversions indicates that pericentric inversion heterozygosity does not lead to the production of unbalanced gametes. Heterosynapsis of the inverted segments during zygonema and pachynema and the resulting chiasma suppression therefore represent a meiotic mechanism for the maintenance of pericentric inversion polymorphisms in this population of P. sitkensis.     

Synaptonemal complex spreading in Allium cepa and A. fistulosum

The general features and fine structure of homologous chromosome alignment and pairing have been investigated in two species of Allium (A. fistulosum and A. cepa), which have similar karyotypes but very different patterns of chiasma distribution. Although there is no support for the occurrence of a general pre-meiotic alignment of homologous chromosomes, both species show some alignment of homologues as an immediate prelude to synaptonemal complex (SC) formation. In both species pairing usually commences at sub-terminal sites and is succeeded by numerous separate intercalary initiations of pairing in interstitial and distal regions and then in proximal regions. The last parts to pair, in both species, are pericentromeric and telomeric regions. There is, therefore, no evident relationship between the sequence of pairing and chiasma distribution in these species. Regularly alternating convergences and divergences of aligned axial cores (ACs), termed multiple association sites, are frequently observed. It is proposed that these represent potential pairing initiation sites and from observations on their spatial distribution it is argued that they may be evenly distributed through most of the genome. Small spherical or ellipsoid nodules are found at association sites and between closely aligned ACs which persist in the SC segments present during zygotene, but most of them disappear abruptly at the end of zygotene. These are termed zygotene nodules (ZN) and it is proposed that they are involved in matching corresponding sites on homologous chromosomes as well as possibly having a recombinational role. Their composition, structure, mode of action and relationship to pachytene recombination nodules are at present unknown.     

Chiasma interference and centromere co-orientation in a spontaneous translocation heterozygote of Euchorthippus pulvinatus gallicus (Acrididae; Orthoptera)

The meiosis of an individual of the species Euchorthippus pulvinatus gallicus heterozygous for a reciprocal translocation involving chromosomes 3 and 6 has been analysed using the Giemsa C-banding technique. It is concluded that: (i) Chiasma interference in the quadrivalent seems to act only at the arm level. There is no interference across the translocation break point. No interchromosomal chiasma interference could be demonstrated, (ii) The results concerning the co-orientation of the quadrivalent suggest that the length of the chromosomal segments between two adjacent centromeres at metaphase I is related with their orientation behaviour.     

Chromosome pairing in a Lolium temulentum X Lolium perenne diploid hybrid with a low chiasma frequency

Summary Despite an average difference of about 50% in DNA amount, homoeologous chromosomes pair effectively at first metaphase in the diploid interspecific hybrid between Lolium temulentum and Lolium perenne. However, in the presence of accessory B chromosomes and diploidising genes pairing at metaphase I is severely reduced. Reconstruction of serial electron micrographs through pollen mother cell nuclei show that synaptonemal complexes are formed at pachytene between not only homoeologous but also non-homologous chromosome segments resulting in multivalent formation. These associations are largely ineffective in terms of chiasma formation and degenerate at late pachytene. It is highly probable that the pairing determinants exercise their control on chromosome pairing largely by prohibiting the siting of crossovers in homoeologously paired chromosome segments.     

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).     

Meiotic chromosome interactions in inbred autotetraploid rye (Secale cereale).

Electron microscopy of whole-mount surface-spread synaptonemal complex complements and conventional light microscopy of chromosomes at first metaphase of meiosis were used to compare the relative frequencies of pairing configurations at the two stages in inbred autotetraploid rye (Secale cereale L.). Statistical tests showed significantly fewer multivalents at first metaphase than expectations based on random initiation of synapsis at each telomeric site within each group of four homologues. Direct observations of synaptic behaviour of chromosomes showed that this deviation is due primarily to a preponderance of bivalents during zygotene and pachytene. It is also the result of a significant drop in multivalent frequency from meiotic prophase to metaphase I, which is attributable both to a lack of chiasmata with which to consolidate multivalents and inhibition of chiasma formation in synaptonemal complex segments of multivalents that are nonhomologous.