Physical distribution of translocation breakpoints in homoeologous recombinants induced by the absence of the Ph1 gene in wheat and triticale

The physical distribution of translocation breakpoints was analyzed in homoeologous recombinants involving chromosomes 1A, 1B, 1D of wheat and 1R of rye, and the long arms of chromosome 7S of Aegilops speltoides and 7A of wheat. Recombination between homoeologues was induced by removal of the Ph1 gene. In all instances, translocation breakpoints were concentrated in the distal ends of the chromosome arms and were absent in the proximal halves of the arms. The relationship between the relative distance from the centromere and the relative homoeologous recombination frequency was best explained by the function f(x)=0.0091e^0.0592x. The pattern of recombination in homoeologous chromosomes was essentially the same as in homologues except that there were practically no double exchanges. Among 313 recombinant chromosomes, only one resulted from a double crossing-over. The distribution of translocation breakpoints in translocated arms indicated that positive chiasma interference operated in homoeologous recombination. This implies that the reduction of the length of alien chromosome segments present in translocations with wheat chromosomes may be more difficult than the production of the original recombinants.     

Mathematics of chromosome pairing

Analysis of frequencies of chromosome configurations in wheat-related species hybrids is extended to include cases involving homoeologous groups of size six. Further, the expected frequencies of the various configurations emanating from homologous and homoeologous pairing events have been determined for groups consisting of two and three homoeologous pairs of homologous chromosomes. Analysis of configuration frequencies of nullisomic 5B of wheat, in which both homologous and homoeologous pairing occurs, led to estimation of the relative frequencies of homologous and homoeologous pairing events as 17.9:1. In the samples analyzed, slightly less than one homoeologous exchange occurred per gamete.     

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.     

Homoeologous recombination in the presence of <Emphasis Type="Italic">Ph1</Emphasis> gene in wheat

A crossover (CO) and its cytological signature, the chiasma, are major features of eukaryotic meiosis. The formation of at least one CO/chiasma between homologous chromosome pairs is essential for accurate chromosome segregation at the first meiotic division and genetic recombination. Polyploid organisms with multiple sets of homoeologous chromosomes have evolved additional mechanisms for the regulation of CO/chiasma. In hexaploid wheat (2n = 6× = 42), this is accomplished by pairing homoeologous (Ph) genes, with Ph1 having the strongest effect on suppressing homoeologous recombination and homoeologous COs. In this study, we observed homoeologous COs between chromosome 5M^g of Aegilops geniculata and 5D of wheat in plants where Ph1 was fully active, indicating that chromosome 5M^g harbors a homoeologous recombination promoter factor(s). Further cytogenetic analysis, with different 5M^g/5D recombinants, showed that the homoeologous recombination promoting factor(s) may be located in proximal regions of 5M^g. In addition, we observed a higher frequency of homoeologous COs in the pericentromeric region between chromosome combination of rec5M^g#2S·5M^g#2L and 5D compared to 5M^g#1/5D, which may be caused by a small terminal region of 5DL homology present in chromosome rec5M^g#2. The genetic stocks reported here will be useful for analyzing the mechanism of Ph1 action and the nature of homoeologous COs.     

Induction of recombination between rye chromosome 1RL and wheat chromosomes

Summary The ph1b mutant in bread wheat has been used to induce homoeologous pairing and recombination between chromosome arm 1RL of cereal rye and wheat chromosome/s. A figure of 2.87% was estimated for the maximal frequency of recombination between a rye glutelin locus tightly linked to the centromere and the heterochromatic telomere on the long arm of rye chromosome 1R in the progeny of ph1b homozygotes. This equates to a gametic recombination frequency of 1.44%. This is the first substantiated genetic evidence for homoeologous recombination between wheat and rye chromosomes. No recombinants were confirmed in control populations heterozygous for ph1b. The ph1b mutant was also observed to generate recombination between wheat homoeologues.     

Most of the homoeologous pairing at metaphase I in wheat-rye hybrids is not chiasmatic

The use of telomeric C-bands in wheat-rye hybrids has made it possible to distinguish three types of wheat-wheat (1B^L) and wheat-rye associations (a, end-to-end extremely distal; b, end-to-ed distal; and c, interstitial) between homoeologous chromosomes at different metaphase I stages (early, middle and late) and also to estimate the actual recombination frequencies for such associations at anaphase I. There was a decrease of the a and b association frequencies during the different metaphase I stages, whereas the c type remained without variation in all stages. A good fit between the frequencies of c associations at metaphase I and the number of recombinant chromosomes at anaphase I, assuming a maximum of one chiasma per bond, was found; however, there was no correspondence between metaphase I and anaphase I data when all associations (a + b + c) were considered. In addition, rye-rye homologous pairing was observed at metaphase I, but no evidence for rye-rye recombination was found at anaphase I. The results indicate that most of end-to-end (a and b) homoeologous and nonhomologous associations are actually nonchiasmatic and are a remnant of prophase pairing.     

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.     

Development of a wheat single gene FISH map for analyzing homoeologous relationship and chromosomal rearrangements within the Triticeae

Key message

A cytogenetic map of wheat was constructed using FISH with cDNA probes. FISH markers detected homoeology and chromosomal rearrangements of wild relatives, an important source of genes for wheat improvement.

Abstract

To transfer agronomically important genes from wild relatives to bread wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) by induced homoeologous recombination, it is important to know the chromosomal relationships of the species involved. Fluorescence in situ hybridization (FISH) can be used to study chromosome structure. The genomes of allohexaploid bread wheat and other species from the Triticeae tribe are colinear to some extent, i.e., composed of homoeoloci at similar positions along the chromosomes, and with genic regions being highly conserved. To develop cytogenetic markers specific for genic regions of wheat homoeologs, we selected more than 60 full-length wheat cDNAs using BLAST against mapped expressed sequence tags and used them as FISH probes. Most probes produced signals on all three homoeologous chromosomes at the expected positions. We developed a wheat physical map with several cDNA markers located on each of the 14 homoeologous chromosome arms. The FISH markers confirmed chromosome rearrangements within wheat genomes and were successfully used to study chromosome structure and homoeology in wild Triticeae species. FISH analysis detected 1U-6U chromosome translocation in the genome of Aegilops umbellulata, showed colinearity between chromosome A of Ae. caudata and group-1 wheat chromosomes, and between chromosome arm 7S#3L of Thinopyrum intermedium and the long arm of the group-7 wheat chromosomes.     

Chromosome distribution and catenation in Rhoeo spathacea var. concolor

The twelve chromosomes of Rhoeo spathacea variety concolor are arranged in a definite sequence in a ring at meiosis. Identification of all the 12 chromosomes was possible in 119 diakinesis and metaphase I cells. — Pollen viability was measured to be 36.54% by cotton blue staining procedure. Forty five of 56 metaphase I cells (80.36%) had adjacent distribution. Each of the 12 chromosomes was equally likely to be involved in adjacent distribution regardless of their sizes and heterobrachialness. Adjacent distribution occurred randomly at each arm-position in the ring regardless of the lengths of the arm-pairs. — The most frequent chromosome configuration at diakinesis and metaphase I was a chain-of-12 chromosomes (41.18%). Cells with 1 to 4 chains of chromosomes were observed. The observed frequencies of various configurations were in good agreement with the calculated frequencies. The mean number of chiasmata was 10.90 per cell and 0.908 per pair of chromosome arms. The 131 chiasma failures were distributed at random among the 12 arm-positions. Since the lengths of arm-pairs in the ring vary, the randomness may mean that chiasma formation was limited to short terminal segments on all chromosomes.     

VE161小麦促进部分同源染色体配对的遗传

ＶＥ１６１小麦包括具有一对长穗偃麦草染色体的雄性不育代换系、可育附加系和杂育系,杂育系由其代换系×附加系产生。ＶＥ１６１小麦在与其它小麦品系的杂交Ｆ１中,具有促进部分同源染色体配对的作用,但其本身部分同源配对频率较低。研究结果表明,ＶＥ１６１小麦本身部分同源染色体配对水平较低,是因其小麦染色体组中存在有一对纯合隐性上位基因,它能够抑制Ｅ染色体（Ｅｐｈ基因）,促进部分同源染色体配对作用的表达,而一般小麦品系中具有该基因的相对显性基因。同时,在促进小麦部分同源染色体配对作用上,Ｅ染色体（Ｅｐｈ基因）具有剂量效应     

Meiotic homoeologous recombination-based mapping of wheat chromosome 2B and its homoeologues in <Emphasis Type="Italic">Aegilops speltoides</Emphasis> and <Emphasis Type="Italic">Thinopyrum elongatum</Emphasis>

Key message

We physically dissected and mapped wheat chromosome 2B and its homoeologues in Aegilops speltoides and Thinopyrum elongatum based on meiotic homoeologous recombination, providing a unique physical framework for genome studies.

Abstract

Common wheat has a large and complex genome with narrow genetic diversity and various degrees of recombination between the A, B, and D subgenomes. This has limited the homologous recombination-based genome studies in wheat. Here, we exploited meiotic homoeologous recombination for molecular mapping of wheat chromosome 2B and its homoeologue 2S from Aegilops speltoides and 2E from Thinopyrum elongatum. The 2B–2S and 2B–2E recombination was induced by the ph1b mutant, and recovered using molecular markers and fluorescent genomic in situ hybridization (FGISH). A total of 112 2B–2S and 87 2B–2E recombinants involving different chromosome regions were developed and physically delineated by FGISH. The 2B–2S and 2B–2E recombination hotspots mapped to the subterminal regions on both arms. Recombination hotspots with the highest recombination rates mapped to the short arms. Eighty-three 2B–2S and 67 2B–2E recombinants were genotyped using the wheat 90 K SNP arrays. Based on the genotyping results and FGISH patterns of the recombinants, chromosomes 2B, 2S, and 2E were partitioned into 93, 66, and 46 bins, respectively. In total, 1037 SNPs physically mapped onto distinct bins of these three homoeologous chromosomes. A homoeologous recombination-based bin map was constructed for chromosome 2B, providing a unique physical framework for genome studies in wheat and its relatives. Meiotic homoeologous recombination also facilitates gene introgression to diversify the wheat genome for germplasm development. Therefore, homoeologous recombination-based studies enhance understanding of the wheat genome and its homoeologous counterparts from wild grasses, and expand the genetic variability of the wheat genome.

     

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.     

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.     

The Rad50 genes of diploid and polyploid wheat species. Analysis of homologue and homoeologue expression and interactions with Mre11

The MRN complex plays a central role in the DNA repair pathways of eukaryotic cells and takes part in many other processes, including cell cycle checkpoint signalling, meiosis, DNA replication and telomere maintenance. This complex is formed by the interaction of the products of the Mre11, Rad50 and Nbs1 genes. This paper reports the molecular characterization, expression and interactions of the Rad50 gene in several wheat species with different levels of ploidy. The homoeologous Rad50 wheat genes were found to show a high level of conservation. Most of the RAD50 domains and motifs previously described in other species were also present in wheat RAD50; these proteins are therefore likely to have similar functions. Interactions between the RAD50 wheat proteins and their MRE11 counterparts in the MRN complex were observed. The level of expression of Rad50 in each of the species examined was determined and compared with those previously reported for the Mre11 genes. In some cases similar levels of expression were seen, as expected. The expression of the RAD50 homoeologous genes was assessed in two polyploid wheat species using quantitative PCR. In both cases, an overexpression of the Rad50B gene was detected. Although the results indicate the maintenance of function of these species?? three homoeologous Rad50 genes, the biased expression of Rad50B might indicate ongoing silencing of one or both other homoeologues in polyploid wheat. To assess the consequences of such silencing on the formation of the MRN complex, the interactions between individual homoeologues of Rad50 and their genomic counterpart Mre11 genes were examined. The results indicate the inexistence of genomic specificity in the interactions between these genes. This would guarantee the formation of an MRN complex in wheat.     

Chiasmata and variability in Lolium and Festuca populations

There are significant differences in mean pollen mother cell chiasma frequencies between populations within Lolium perenne, L. multiflorum and Festuca pratensis. The differences are genotypically controlled. With low chiasma frequencies the chiasmata are distally located. With increasing chiasma frequency the frequency of chiasmata in interstitial segments increases. Shorter lived populations have higher chiasma frequencies than the more perennial. — The higher the chiasma frequency of a population the lower the phenotypic and genetic variance for characters under polygenic control, such as flowering time, and the less effective also is the response to selection for such characters. These observations are interpreted on the premise that high chiasma frequencies are instrumental in the breaking up of supergene sequences in interstitial chromosome segments.     

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.     

Molecular cytogenetic characterization of Roegneria ciliaris chromosome additions in common wheat

The development of alien addition lines is important both for transferring useful genes from related species into common wheat and for studying the relationship between alien chromosomes and those of wheat. Roegneria ciliaris (2n=4x=28, S^cS^cY^cY^c) is reported to be a potential source of resistance to wheat scab, which may be useful in wheat improvement. The amphiploid common wheat-R. ciliaris and BC₁F₇ or BC₂F₆ derivatives were screened by C-banding, genomic in situ hybridization (GISH), fluorescent in situ hybridization (FISH) and restriction fragment length polymorphism (RFLP) for the presence of R. ciliaris chromatin introgressed into wheat. Six lines were identified as disomic chromosome additions (DA), one as a ditelosomic addition (Dt), two as double disomic additions (dDA) and one as a monosomic chromosome addition (MA). RFLP analysis using wheat homoeologous group-specific clones indicated that the R. ciliaris chromosomes involved in these lines belong to groups 1, 2, 3, 5 and 7. The genomic affinities of the added R. ciliaris chromosomes were determined by FISH analysis using the repetitive sequence pCbTaq4.14 as a probe. These data suggest that the R. ciliaris chromosomes in five lines belong to the S^c genome. Based on the molecular cytogenetic data, the lines are designated as DA2S^c#1, Dt2S^c#1L, DA3S^c#1, dDA1S^c#2+5Y^c#1, DA5Y^c#1, DA7S^c#1, DA7Y^c#1 and MA?Y^c#1. Based on the present and previous work, 8 of the 14 chromosomes of R. ciliaris have been transferred into wheat.     

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     

Cytogenetic relationship ofAegilops longissima chromosomes with common wheat chromosomes

The relationships of three wheat-Aegilops longissima chromosome addition lines A, C, and D with homoeologous wheat chromosomes were studied in PMC meiosis. Substitutions of alien chromosome A for wheat chromosome 6 B, chromosome C for 1 B and chromosome D for 4 B were obtained. The production of 4 BS/C and 7 BS/D chromosome translocations indicated cytogenetic relationships of C partially to homoeologous wheat chromosomes of group 1 and 4, and D partially to homoeologous wheat chromosomes of group 4 and 7.     

Comparative chiasma analysis using a computerised optical digitiser

A new computerised technique has been devised for measuring the distribution of chiasmata along diplotene bivalents. The method involves the introduction into the field of view of the microscope, of a fine light spot which can be accurately manipulated along the chromosomes of each bivalent. The data recorded include (a) the positions of the chiasmata along the bivalent in terms of their relative distances from the centromere and (b) the individual bivalent and cellular chiasma frequencies. — The method has been applied to the analysis of chiasma distribution patterns in the two known species of the genus Caledia, C. species nova 1 and C. captiva and in two chromosomal races of the latter. Statistical tests indicate that within bivalents at least 40% of the comparative distribution patterns of chiasmata between races and species are significantly different. Similar comparisons between populations within races reveal only 18% significant differences. — The observed distribution patterns of chiasmata in this genus suggest that chiasma formation is sequential from centromere to telomere. — The variation in the frequency and distribution of chiasmata between races and species suggests that the interference distances between successive chiasmata are, at least partially, independent of chiasma frequency and position. — The interracial and interspecific differences in chromosome structure are correlated with changes in chiasma pattern.