Reassessment of the evolution of wheat chromosomes 4A, 5A,and 7B

Key message

Comparison of genome sequences of wild emmer wheat and Aegilops tauschii suggests a novel scenario of the evolution of rearranged wheat chromosomes 4A, 5A, and 7B.

Abstract

Past research suggested that wheat chromosome 4A was subjected to a reciprocal translocation T(4AL;5AL)1 that occurred in the diploid progenitor of the wheat A subgenome and to three major rearrangements that occurred in polyploid wheat: pericentric inversion Inv(4AS;4AL)1, paracentric inversion Inv(4AL;4AL)1, and reciprocal translocation T(4AL;7BS)1. Gene collinearity along the pseudomolecules of tetraploid wild emmer wheat (Triticum turgidum ssp. dicoccoides, subgenomes AABB) and diploid Aegilops tauschii (genomes DD) was employed to confirm these rearrangements and to analyze the breakpoints. The exchange of distal regions of chromosome arms 4AS and 4AL due to pericentric inversion Inv(4AS;4AL)1 was detected, and breakpoints were validated with an optical Bionano genome map. Both breakpoints contained satellite DNA. The breakpoints of reciprocal translocation T(4AL;7BS)1 were also found. However, the breakpoints that generated paracentric inversion Inv(4AL;4AL)1 appeared to be collocated with the 4AL breakpoints that had produced Inv(4AS;4AL)1 and T(4AL;7BS)1. Inv(4AS;4AL)1, Inv(4AL;4AL)1, and T(4AL;7BS)1 either originated sequentially, and Inv(4AL;4AL)1 was produced by recurrent chromosome breaks at the same breakpoints that generated Inv(4AS;4AL)1 and T(4AL;7BS)1, or Inv(4AS;4AL)1, Inv(4AL;4AL)1, and T(4AL;7BS)1 originated simultaneously. We prefer the latter hypothesis since it makes fewer assumptions about the sequence of events that produced these chromosome rearrangements.

     

Presence of an extra chromosome alters meiotic double-stranded break repair dynamics and MLH1 foci distribution in human oocytes

Studies performed on human trisomic 21 oocytes have revealed that during meiosis, the three homologues 21 synapse and, in some cases, achieve what looks like a trivalent. This implies that meiotic recombination takes place among the three homologous chromosomes 21, and to some extent, crossovers form between them. To see how meiotic recombination is in the presence of an extra chromosome 21, we analyzed the distribution of three recombination markers (γH2AX, RPA, and MLH1) on trisomic 21 oocytes at pachynema and, in particular, on chromosomes 21. Results clearly show how the presence of an extra chromosome 21 alters meiotic recombination progression, leading to the presence of a higher number of early recombination markers at pachynema. Moreover, the distribution on these chromosomes 21 of some of these markers is different in aneuploid oocytes. Finally, there is a substantial increase in the number of MLH1 foci, a marker of most crossovers in mammals, which is related to the number of synapsed chromosomes in pachynema. Thus, bivalents 21 had fewer MLH1 foci than partial or total trivalents, suggesting a close relationship between synapsis and crossover designation. All of the data presented suggest that the presence of an extra chromosome alters meiotic recombination globally in aneuploid human oocytes.     

Distribution of crossing over on mouse synaptonemal complexes using immunofluorescent localization of MLH1 protein

We have used immunofluorescent localization to examine the distribution of MLH1 (MutL homolog) foci on synaptonemal complexes (SCs) from juvenile male mice. MLH1 is a mismatch repair protein necessary for meiotic recombination in mice, and MLH1 foci have been proposed to mark crossover sites. We present evidence that the number and distribution of MLH1 foci on SCs closely correspond to the number and distribution of chiasmata on diplotene-metaphase I chromosomes. MLH1 foci were typically excluded from SC in centromeric heterochromatin. For SCs with one MLH1 focus, most foci were located near the middle of long SCs, but near the distal end of short SCs. For SCs with two MLH1 foci, the distribution of foci was bimodal regardless of SC length, with most foci located near the proximal and distal ends. The distribution of MLH1 foci indicated interference between foci. We observed a consistent relative distance (percent of SC length in euchromatin) between two foci on SCs of different lengths, suggesting that positive interference between MLH1 foci is a function of relative SC length. The extended length of pachytene SCs, as compared to more condensed diplotene-metaphase I bivalents, makes mapping crossover events and interference distances using MLH1 foci more accurate than using chiasmata.     

Immunofluorescent synaptonemal complex analysis in azoospermic men

The molecular cause of germ cell meiotic defects in azoospermic men is rarely known. During meiotic prophase I, a proteinaceous structure called the synaptonemal complex (SC) appears along the pairing axis of homologous chromosomes and meiotic recombination takes place. Newly-developed immunofluorescence techniques for SC proteins (SCP1 and SCP3) and for a DNA mismatch repair protein (MLH1) present in late recombination nodules allow simultaneous analysis of synapsis, and of meiotic recombination, during the first meiotic prophase in spermatocytes. This immunofluorescent SC analysis enables accurate meiotic prophase substaging and the identification of asynaptic pachytene spermatocytes. Spermatogenic defects were examined in azoospermic men using immunofluorescent SC and MLH1 analysis. Five males with obstructive azoospermia, 18 males with nonobstructive azoospermia and 11 control males with normal spermatogenesis were recruited for the study. In males with obstructive azoospermia, the fidelity of chromosome pairing (determined by the percentage of cells with gaps [discontinuities]/splits [unpaired chromosome regions] in the SCs, and nonexchange SCs [bivalents with 0 MLH1 foci]) was similar to those in normal males. The recombination frequencies (determined by the mean number of MLH1 foci per cell at the pachytene stage) were significantly reduced in obstructive azoospermia compared to that in controls. In men with nonobstructive azoospermia, a marked heterogeneity in spermatogenesis was found: 45% had a complete absence of meiotic cells; 5% had germ cells arrested at the zygotene stage of meiotic prophase; the rest had impaired fidelity of chromosome synapsis and significantly reduced recombination in pachytene. In addition, significantly more cells were in the leptotene and zygotene meiotic prophase stages in nonobstructive azoospermic patients, compared to controls. Defects in chromosome pairing and decreased recombination during meiotic prophase may have led to spermatogenesis arrest and contributed in part to this unexplained infertility.     

MSH4 acts in conjunction with MLH1 during mammalian meiosis.

MSH4 is a meiosis-specific MutS homolog. In yeast, it is required for reciprocal recombination and proper segregation of homologous chromosomes at meiosis I. MLH1 (MutL homolog 1) facilitates both mismatch repair and crossing over during meiosis in yeast. Germ-line mutations in the MLH1 human gene are responsible for hereditary nonpolyposis cancer, but the analysis of MLH1-deficient mice has revealed that MLH1 is also required for reciprocal recombination in mammals. Here we show that hMSH4 interacts with hMLH1. The two proteins are coimmunoprecipitated regardless of the presence of DNA or ATP, suggesting that the interaction does not require the binding of MSH4 to DNA. The domain of hMSH4 responsible for the interaction is in the amino-terminal part of the protein whereas the region that contains the ATP binding site and helix-turn-helix motif does not bind to hMLH1. Immunolocalization analysis shows that MSH4 is present at sites along the synaptonemal complex as soon as homologous chromosomes synapse. The number of MSH4 foci decreases gradually as pachynema progresses. During this transition, MLH1 foci begin to appear and colocalize with MSH4. These results suggest that MSH4 is first required for chromosome synapsis and that this MutS homologue is involved later with MLH1 in meiotic reciprocal recombination.     

Discontinuities and unsynapsed regions in meiotic chromosomes have a trans effect on meiotic recombination of some chromosomes in human males

During meiosis, homologous chromosome pairing and synapsis are essential for subsequent meiotic recombination (crossing-over). Discontinuous regions (gaps) and unsynapsed regions (splits) were most frequently observed in the heterochromatic regions of bivalent synaptonemal complex (SC) 9, and we have previously demonstrated that gaps and splits significantly altered the distribution of MLH1 recombination foci on SC 9. Here, immunofluorescence techniques (using antibodies against SC proteins and the crossover-associated MLH1 protein) were combined with a centromere-specific fluorescence in situ hybridization technique that allows identification of every individual chromosome. The effect of gaps/splits on meiotic recombination patterns in autosomes other than chromosome 9 during the pachytene stage of meiotic prophase was then examined in 6,026 bivalents from 262 pachytene cells from three human males. In 64 analyzed cells with a gapped SC 9, the frequency of MLH1 foci in SCs 5 and 10 and in SC arms 10q, 11p and 16q was decreased compared to 168 analyzed cells with a normally-synapsed SC 9 (controls). In 24 analyzed cells with splits in SC 9, there was a significant reduction in MLH1 focus frequency for SC 5q and the whole SC5 bivalent. The positioning of MLH1 foci on other SCs in cells with gapped/split SC 9 was not altered. These studies suggest that gaps and splits not only have a cis effect, but may also have a trans effect on meiotic recombination in humans.     

Recombination map of the common shrew, Sorex araneus (Eulipotyphla, Mammalia)

The Eurasian common shrew (Sorex araneus L.) is characterized by spectacular chromosomal variation, both autosomal variation of the Robertsonian type and an XX/XY(1)Y(2) system of sex determination. It is an important mammalian model of chromosomal and genome evolution as it is one of the few species with a complete genome sequence. Here we generate a high-precision cytological recombination map for the species, the third such map produced in mammals, following those for humans and house mice. We prepared synaptonemal complex (SC) spreads of meiotic chromosomes from 638 spermatocytes of 22 males of nine different Robertsonian karyotypes, identifying each autosome arm by differential DAPI staining. Altogether we mapped 13,983 recombination sites along 7095 individual autosomes, using immunolocalization of MLH1, a mismatch repair protein marking recombination sites. We estimated the total recombination length of the shrew genome as 1145 cM. The majority of bivalents showed a high recombination frequency near the telomeres and a low frequency near the centromeres. The distances between MLH1 foci were consistent with crossover interference both within chromosome arms and across the centromere in metacentric bivalents. The pattern of recombination along a chromosome arm was a function of its length, interference, and centromere and telomere effects. The specific DNA sequence must also be important because chromosome arms of the same length differed substantially in their recombination pattern. These features of recombination show great similarity with humans and mice and suggest generality among mammals. However, contrary to a widespread perception, the metacentric bivalent tu usually lacked an MLH1 focus on one of its chromosome arms, arguing against a minimum requirement of one chiasma per chromosome arm for correct segregation. With regard to autosomal chromosomal variation, the chromosomes showing Robertsonian polymorphism display MLH1 foci that become increasingly distal when comparing acrocentric homozygotes, heterozygotes, and metacentric homozygotes. Within the sex trivalent XY(1)Y(2), the autosomal part of the complex behaves similarly to other autosomes.     

Mouse HFM1/Mer3 Is Required for Crossover Formation and Complete Synapsis of Homologous Chromosomes during Meiosis

Faithful chromosome segregation during meiosis requires that homologous chromosomes associate and recombine. Chiasmata, the cytological manifestation of recombination, provide the physical link that holds the homologs together as a pair, facilitating their orientation on the spindle at meiosis I. Formation of most crossover (CO) events requires the assistance of a group of proteins collectively known as ZMM. HFM1/Mer3 is in this group of proteins and is required for normal progression of homologous recombination and proper synapsis between homologous chromosomes in a number of model organisms. Our work is the first study in mammals showing the in vivo function of mouse HFM1. Cytological observations suggest that initial steps of recombination are largely normal in a majority of Hfm1^−/− spermatocytes. Intermediate and late stages of recombination appear aberrant, as chromosomal localization of MSH4 is altered and formation of MLH1foci is drastically reduced. In agreement, chiasma formation is reduced, and cells arrest with subsequent apoptosis at diakinesis. Our results indicate that deletion of Hfm1 leads to the elimination of a major fraction but not all COs. Formation of chromosome axial elements and homologous pairing is apparently normal, and Hfm1^−/− spermatocytes progress to the end of prophase I without apparent developmental delay or apoptosis. However, synapsis is altered with components of the central region of the synaptonemal complex frequently failing to extend the full length of the chromosome axes. We propose that initial steps of recombination are sufficient to support homology recognition, pairing, and initial chromosome synapsis and that HFM1 is required to form normal numbers of COs and to complete synapsis.     

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.     

Induced suppression of genetic recombination in females of the Mediterranean fruit fly,Ceratitis capitata (Wied.), by translocation heterozygosity

Chromosomal recombination suppressors (RS) were induced and studied as part of a programme to induce and isolate temperature-sensitive recessive lethal factors, for subsequent use in genetic sexing mechanisms in the medfly, Ceratitis capitata (Wied.).The presence of induced RS factors was identified through the complete linkage of two morphologicla markers, ap and dc, located 18.25 recombination units apart. Adult +dc males were irradiated one day after emergence with 50 Gy in a cobalt-60 source. The irradiated males were mated to marked ap + females and the F1 females were crossed to ap dc males. A total of 5 heterozygous RS factors was isolated from 570 irradiated and screened chromosomes. Suppression of female recombination in the heterozygous lines ranged from 77.6% in RS 19 to 99.1% in RS 30B. Chromosomal analysis showed all RS lines to contain a single reciprocal translocation involving in all cases chromosome 3 and one other autosome. It appears that recombination between the two morphological markers is suppressed either through lethality conferred upon the gametes, which results from recombinant events taking place in the interstitial segment between the centromere and the translocation breakpoints, or through interference by the translocation heterozygote with the initiation or maintenance of cross-over synapsis thus preventing the appearance of cross-over products.All 5 translocations involved chromosome 3 and one of the other autosomes, providing the first evidence for a correlation between the ap-dc linkage group and chromosome 3.This work forms part of a joint FAO/IAEA research programme for the development of genetic sexing mechanisms for the Mediterranean fruit fly, Ceratitis capitata (Wied.).     

The mismatch repair protein MLH1 marks a subset of strongly interfering crossovers in tomato

In most eukaryotes, the prospective chromosomal positions of meiotic crossovers are marked during meiotic prophase by protein complexes called late recombination nodules (LNs). In tomato (Solanum lycopersicum), a cytological recombination map has been constructed based on LN positions. We demonstrate that the mismatch repair protein MLH1 occurs in LNs. We determined the positions of MLH1 foci along the 12 tomato chromosome pairs (bivalents) during meiotic prophase and compared the map of MLH1 focus positions with that of LN positions. On all 12 bivalents, the number of MLH1 foci was approximately 70% of the number of LNs. Bivalents with zero MLH1 foci were rare, which argues against random failure of detecting MLH1 in the LNs. We inferred that there are two types of LNs, MLH1-positive and MLH1-negative LNs, and that each bivalent gets an obligate MLH1-positive LN. The two LN types are differently distributed along the bivalents. Furthermore, cytological interference among MLH1 foci was much stronger than interference among LNs, implying that MLH1 marks the positions of a subset of strongly interfering crossovers. Based on the distances between MLH1 foci or LNs, we propose that MLH1-positive and MLH1-negative LNs stem from the same population of weakly interfering precursors.     

The Effects of Translocations on Recombination Frequency in Caenorhabditis Elegans

In the nematode Caenorhabditis elegans, recombination suppression in translocation heterozygotes is severe and extensive. We have examined the meiotic properties of two translocations involving chromosome I, szT1(I;X) and hT1(I;V). No recombination was observed in either of these translocation heterozygotes along the left (let-362-unc-13) 17 map units of chromosome I. Using half-translocations as free duplications, we mapped the breakpoints of szT1 and hT1. The boundaries of crossover suppression coincided with the physical breakpoints. We propose that DNA sequences at the right end of chromosome I facilitate pairing and recombination. We use the data from translocations of other chromosomes to map the location of pairing sites on four other chromosomes. hT1 and szT1 differed markedly in their effect on recombination adjacent to the crossover suppressed region. hT1 had no effect on recombination in the adjacent interval. In contrast, the 0.8 map unit interval immediately adjacent to the szT1(I;X) breakpoint on chromosome I increased to 2.5 map units in translocation heterozygotes. This increase occurs in a chromosomal interval which can be expanded by treatment with radiation. These results are consistent with the suggestion that the szT1(I) breakpoint is in a region of DNA in which meiotic recombination is suppressed relative to the genomic average. We propose that DNA sequences disrupted by the szT1 translocation are responsible for determining the frequency of meiotic recombination in the vicinity of the breakpoint.     

The Nature of Genetic Recombination near the Third Chromosome Centromere of DROSOPHILA MELANOGASTER

Previous studies have indicated that recombination near the third chromosome centromere is associated with negative chromosome interference, a phenomenon for which Green (1975) and Sinclair (1975) suggested gene conversion as a possible mechanism. In this report, we demonstrate that negative chromosome interference is still observed when deficiencies or translocation breakpoints are scored as the middle markers in recombination experiments and the rate of recombination is increased by interchromosomal effect. We argue that these chromosomal rearrangement breakpoints are not subject to conversion. Since neither successive premeiotic and meiotic exchanges, nor negative chromatid interference, can by themselves account for the negative chromosome interference, we conclude that a greater than expected frequency of multiple exchanges actually occurs. We further suggest that negative chromosome interference may be characteristic of all chromosomal regions normally showing very little exchange in relation to physical length.     

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.     

Meiosis and apoptosis in germ cells of X-autosome translocation carrier boars

Meiotic features and fate of germ cells were studied using electron microscopy on surface spread spermatocytes and in situ tests for apoptosis on testicular tissues of normal boars and X-autosome translocation (X-AT) carrier boars. Histological sections of the translocation t(Xp+; 14q-) carrier boars showed accumulation of degenerating germ cells including binucleate and multinucleate cells, as well as pyknosis and nuclear fragmentation characteristic of apoptosis. Synaptonemal complex analysis of X-AT carrier boars revealed 19 bivalents including a large complex made up of the altered X (Xp+) and normal chromosome 14, and a smaller element representing the Y chromosome in synapsis with the derived chromosome 14 (14q-) in most (89.3%) of the germ cells. In situ tests for apoptotic DNA fragmentation revealed positive signals exclusively among early spermatocytes and degenerating germ cells. These findings and the absence of stages beyond pachytene suggest that the meiocytes are arrested at pachytene and eliminated through apoptotic process in spite of the complete synapsis displayed by the chromosomes involved in this translocation. Failure of meiotic progress in our X-AT carriers would appear to be the result of the disruption of gene sequence (or function) caused by the involvement of the X chromosome in this rearrangement, rather than the deleterious consequences of abnormal segregation anticipated in reciprocal translocation carriers. We hypothesize that this disruption could have affected the induction of stage-specific gene products in meiosis such as heat shock proteins and caused the excessive release of endonucleases normally produced by early prophase meiocytes, leading to their apoptosis in our X-autosome translocation carrier boars.     

Common sequence motifs at the rearrangement sites of a constitutional X/autosome translocation and associated deletion.

Reciprocal chromosome translocations are common de novo rearrangements that occur randomly throughout the human genome. To learn about causative mechanisms, we have cloned and sequenced the breakpoints of a cytologically balanced constitutional reciprocal translocation, t(X;4)(p21.2;q31.22), present in a girl with Duchenne muscular dystrophy (DMD). Physical mapping of the derivative chromosomes, after their separation in somatic cell hybrids, reveals that the translocation disrupts the DMD gene in Xp21 within the 18-kb intron 16. Restriction mapping and sequencing of clones that span both translocation breakpoints as well as the corresponding normal regions indicate the loss of approximately 5 kb in the formation of the derivative X chromosome, with 4-6 bp deleted from chromosome 4. RFLP and Southern analyses indicate that the de novo translocation is a paternal origin and that the father's X chromosome contains the DNA that is deleted in the derivative X. Most likely, deletion and translation arose simultaneously from a complex rearrangement event that involves three chromosomal breakpoints. Short regions of sequence homology were present at the three sites. A 5-bp sequence, GGAAT, found exactly at the translocation breakpoints on both normal chromosomes X and 4, has been preserved only on the der(4) chromosome. It is likely that the X-derived sequence GGAATCA has been lost in the formation of the der(X) chromosome, as it matches an inverted GAATCA sequence present on the opposite strand exactly at the other end of the deleted 5-kb fragment. These findings suggest a possible mechanism which may have juxtaposed the three sites and mediated sequence-specific breakage and recombination between nonhomologous chromosomes in male meiosis.     

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.