Molecular mapping of the centromeres of tomato chromosomes 7 and 9

The centromeres of two tomato chromosomes have been precisely localized on the molecular linkage map through dosage analysis of trisomic stocks. To map the centromeres of chromosomes 7 and 9, complementary telo-, secondary, and tertiary trisomic stocks were used to assign DNA markers to their respective chromosome arms and thus to localize the centromere at the junction of the short and long arms. It was found that both centromeres are situated within a cluster of cosegregating markers. In an attempt to order the markers within the centric clusters, genetic maps of the centromeric regions of chromosomes 7 and 9 were constructed from F₂ populations of 1620Lycopersicon esculentum × L. pennellii (E × P) plants and 1640L. esculentum × L. pimpinellifolium (E × PM) plants. Despite the large number of plants analyzed, very few recombination events were detected in the centric regions, indicating a significant suppression of recombination at this region of the chromosome. The fact that recombination suppression is equally strong in crosses between closely related (E × PM) and remotely related (E × P) parents suggests that centromeric suppression is not due to DNA sequence mismatches but to some other mechanism. The greatest number of centromeric markers was resolved in theL. esculentum × L. pennellii F₂ population. The centromere of chromosome 7 is surrounded by eight cosegregating markers: three on the short arm, five on the long arm. Similarly, the centric region of chromosome 9 contains ten cosegregating markers including one short arm marker and nine long arm markers. The localization of centromeres to precise intervals on the molecular linkage map represents the first step towards the characterization and ultimate isolation of tomato centromeres.     

Investigation of crossover interference in barley ( Hordeum vulgare L.) using the coefficient of coincidence

Interference, the interaction between recombination events, was analysed in seven mapping populations of barley (Hordeum vulgare L.). The coefficient of coincidence was applied to investigate the type and position of interference within the genome. Interference was analysed with respect to dependence on the recombination fraction, and simulations were used to obtain test statistics which consider the small sample size of 71-150 double haploid lines. In addition to positive interference in intermediate intervals, strong negative interference, i.e. encouraged double recombination, was found in short intervals. The relationship between recombination fraction and interference could not be described with a uniform function, neither for the entire genome nor for individual chromosomes. The analysis of the position of interference within the genome revealed that interference does not act in the same way in the whole genome. Intervals spanning the centromere exhibited significantly higher means for the coefficient of coincidence than intervals within the chromosome arms, especially with regard to small intervals. In general, positive interference was found in the chromosome arms and no or negative interference in the genetically small but physically large centromeric region.     

The interchromosomal effect of inversions in maize

Summary The interchromosomal effect of inversions in maize along the short arm of chromosome 9 yields results which are distinctly different from those which are reported with Drosophila melanogaster. Recombination was increased in the c ₁-sh₁ region of chromosome 9 while the sh ₁-wx region was unaffected. This increased frequency of recombination appears to be due to an increase in single exchange events as multiple events were unchanged. Increases in recombination were accompanied by either an increase in chromosome interference or normal interference levels. The magnitude of increase in recombination was much smaller than that seen in interchromosomal effects in Drosophila and is consistent with other observations made in maize. When two inversions were present in the same nucleus simultaneously, the effect on recombination was of the same magnitude as the effect of a single inversion. All inversions tested, regardless of size or position with respect to the centromere showed the same magnitude of increase.     

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.     

The extent and position of homoeologous recombination in a distant hybrid of Alstroemeria: a molecular cytogenetic assessment of first generation backcross progenies

To estimate the extent and position of homoeologous recombination during meiosis in an interspecific hybrid between two distantly related Alstroemeria species, the chromosome constitution of six first generation backcross (BC₁) plants was analysed using sequential fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH) analysis. Four different probes were used for the FISH analysis: two species-specific and two rDNA probes. The six BC₁ plants were obtained from crosses between the hybrid A. aurea×A. inodora with its parent A. inodora. GISH clearly identified all chromosomes of both parental genomes as well as recombinant chromosomes. The sequential GISH and FISH analysis enabled the accurate identification of all individual chromosomes in the BC₁ plants, resulting in the construction of detailed karyotypes of the plants. The identification of the recombinant chromosomes provided evidence which chromosomes of the two species are homoeologous. Two of the BC₁ plants were aneuploid (2n=2x+1=17) and four triploid (2n=3x=24), indicating that both n and 2n gametes were functional in the F₁ hybrid. Using GISH, it was possible to estimate homeologous recombination in two different types of gametes in the F₁ hyrid. The positions of the crossover points ranged from highly proximal to distal and the maximum number of crossover points per chromosome arm was three. Compared with the aneuploid plants, the triploid plants (which received 2n gametes) clearly possessed fewer crossovers per chromosome, indicating reduced chromosome pairing/recombination prior to the formation of the 2n gametes. Besides homeologous recombination, evidence was found for the presence of structural rearrangements (inversion and translocation) between the chromosomes of the parental species. The presence of the ancient translocation was confirmed through FISH analysis of mitotic and meiotic chromosomes. Received: 7 October 1998; in revised form: 4 December 1998 / Accepted: 10 December 1998     

Recombination suppression in heterozygotes for a pericentric inversion induces the interchromosomal effect on crossovers in Arabidopsis

During meiosis, recombination ensures allelic exchanges through crossovers (COs) between the homologous chromosomes. Advances in our understanding of the rules of COs have come from studies of mutations including structural chromosomal rearrangements that, when heterozygous, are known to impair COs in various organisms. In this work, we investigate the effect of a large heterozygous pericentric inversion on male and female recombination in Arabidopsis. The inversion was discovered in the Atmcc1 mutant background and was characterized through genetic and next‐generation sequencing analysis. Reciprocal backcross populations, each consisting of over 400 individuals, obtained from the mutant and the wild type, both crossed with Landsberg erecta, were analyzed genome‐wide by 143 single‐nucleotide polymorphisms. The negative impact of inversion became evident in terms of CO loss in the rearranged chromosome in both male and female meiosis. No single‐CO event was detected within the inversion, consistent with a post‐meiotic selection operating against unbalanced gametes. Cytological analysis of chiasmata in F₁ plants confirmed that COs were reduced in male meiosis in the chromosome with inversion. Crossover suppression on the rearranged chromosome is associated with a significant increase of COs in the other chromosomes, thereby maintaining unchanged the number of COs per cell. The CO pattern observed in our study is consistent with the interchromosomal (IC) effect as first described in Drosophila. In contrast to male meiosis, in female meiosis no IC effect is visible. This may be related to the greater strength of interference that constrains the CO number in excess of the minimum value imposed by CO assurance in Arabidopsis female meiosis.     

Genome-wide reduction in recombination of backcross progeny derived from male versus female gametes in an interspecific cross of tomato

Summary We have determined that meiotic recombination differs between male and female gametes derived from the same plant. A single F₁ plant was backcrossed to each of the parents, Lycopersicon esculentum and L pennellii, as the male (BCE) and female (BCP) parent, respectively. A total of 85 RFLP markers, covering more than 75% of the tomato genome, was used to construct a genetic map for both populations. Since both recurrent parents were homozygous, recombination measured in each population reflects crossing-over rates leading to male (BCE) and female (BCP) gametes. Comparisons were made by interval (genetic distance between two adjacent markers), by chromosome, and for the total length of the genome. Significantly less recombination was observed for male gametes at all levels. No significant relationship was found between areas of reduced recombination and approximate location to the centromere. That selection plays some role could not be eliminated, but no clear evidence was observed for single-locus selection as a major factor in the general reduction of crossing-overs in male gametes.     

Frequency and character of alternative somatic recombination fates of paralogous genes during T-DNA integration

A synthetic RBCSB gene cluster was transformed into Arabidopsis in order to simultaneously evaluate the frequency and character of somatic illegitimate recombination, homologous recombination, and targeted gene replacement events associated with T-DNA-mediated transformation. The most frequent type of recombination event observed was illegitimate integration of the T-DNA without activation of the silent ΔRBCS1B: LUC transgene. Sixteen luc⁺ (firefly luciferase positive) T1 plants were isolated. Six of these were due to illegitimate recombination events resulting in a gene trapping effect. Nine resulted from homologous recombination between paralogous RBCSB sequences associated with T-DNA integration. The frequency of somatic homologous recombination associated with T-DNA integration was almost 200 times higher than previously reported rates of meiotic homologous recombination with the same genes. The distribution of (somatic homologous) recombination resolution sites generally fits a fractional interval length model. However, a small region adjacent to an indel showed a significant over-representation of resolution sites, suggesting that DNA mismatch recognition may also play an important role in the positioning of somatic resolution sites. The frequency of somatic resolution within exon-2 was significantly different from that previously observed during meiotic recombination. Electronic Supplementary Material Supplementary material is available for this article at     

Transmission of 5R Chromosomes via Gametes and Its Influence on Spring Bread Wheat Somatic Embryoidogenesis in Vitro

Transmission of chromosomes 5R via gametes and its effect on somatic embryoidogenesis have been studied with the use of the model 5R(5A) substitution line L2837 = L503/Secale cereale L., cultivar Saratovskaya 5//L503, where L503 is a cultivar of spring bread wheat. It has been found that the frequencies of transmission of univalent chromosomes 5R and 5A determined in experiments on F₁ reciprocal hybrids with cultivar Saratovskaya 29 do not reflect their frequencies in the self-pollinated offspring of F₁ hybrids; the frequency of transmission of chromosomes 5R and 5A depends on the genotypes of both the recipient cultivar and the donor rye cultivar; and the 5R(5A) substitution in cultivar L503 significantly increases the parameters of somatic embryoidogenesis in vitro in explants from inflorescences.     

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.     

Detailed Recombination Studies Along Chromosome 3B Provide New Insights on Crossover Distribution in Wheat (Triticum aestivum L.)

In wheat (Triticum aestivum L.), the crossover (CO) frequency increases gradually from the centromeres to the telomeres. However, little is known about the factors affecting both the distribution and the intensity of recombination along this gradient. To investigate this, we studied in detail the pattern of CO along chromosome 3B of bread wheat. A dense reference genetic map comprising 102 markers homogeneously distributed along the chromosome was compared to a physical deletion map. Most of the COs (90%) occurred in the distal subtelomeric regions that represent 40% of the chromosome. About 27% of the proximal regions surrounding the centromere showed a very weak CO frequency with only three COs found in the 752 gametes studied. Moreover, we observed a clear decrease of CO frequency on the distal region of the short arm. Finally, the intensity of interference was assessed for the first time in wheat using a Gamma model. The results showed m values of 1.2 for male recombination and 3.5 for female recombination, suggesting positive interference along wheat chromosome 3B.     

Centromere mitotic recombination in mammalian cells

Centromeres are special structures of eukaryotic chromosomes that hold sister chromatid together and ensure proper chromosome segregation during cell division. Centromeres consist of repeated sequences, which have hindered the study of centromere mitotic recombination and its consequences for centromeric function. We use a chromosome orientation fluorescence in situ hybridization technique to visualize and quantify recombination events at mouse centromeres. We show that centromere mitotic recombination occurs in normal cells to a higher frequency than telomere recombination and to a much higher frequency than chromosome-arm recombination. Furthermore, we show that centromere mitotic recombination is increased in cells lacking the Dnmt3a and Dnmt3b DNA methyltransferases, suggesting that the epigenetic state of centromeric heterochromatin controls recombination events at these regions. Increased centromere recombination in Dnmt3a,3b-deficient cells is accompanied by changes in the length of centromere repeats, suggesting that prevention of illicit centromere recombination is important to maintain centromere integrity in the mouse.     

Genetic positioning of centromeres using half-tetrad analysis in a 4x-2x cross population of potato

From biological and genetic standpoints, centromeres play an important role in the delivery of the chromosome complement to the daughter cells at cell division. The positions of the centromeres of potato were determined by half-tetrad analysis in a 4x-2x population where the male parent produced 2n pollen by first-division restitution (FDR). The genetic linkage groups and locations of 95 male parent-derived amplified fragment length polymorphism markers could be determined by comparing their position on a 2x-2x highly saturated linkage map of potato. Ten centromere positions were identified by 100% heterozygosity transmitted from the 2n heterozygous gametes of the paternal parent into the tetraploid offspring. The position of these centromeric marker loci was in accordance with those predicted by the saturated 2x-2x map using the level of marker clustering as a criterion. Two remaining centromere positions could be determined by extrapolation. The frequent observation of transmission of 100% heterozygosity proves that the meiotic restitution mechanism is exclusively based on FDR. Additional investigations on the position of recombination events of three chromosomes with sufficient numbers of markers showed that only one crossover occurred per chromosome arm, proving strong interference of recombination between centromere and telomere.     

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

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

DeepTetrad: high‐throughput image analysis of meiotic tetrads by deep learning in Arabidopsis thaliana

Meiotic crossovers facilitate chromosome segregation and create new combinations of alleles in gametes. Crossover frequency varies along chromosomes and crossover interference limits the coincidence of closely spaced crossovers. Crossovers can be measured by observing the inheritance of linked transgenes expressing different colors of fluorescent protein in Arabidopsis pollen tetrads. Here we establish DeepTetrad, a deep learning‐based image recognition package for pollen tetrad analysis that enables high‐throughput measurements of crossover frequency and interference in individual plants. DeepTetrad will accelerate the genetic dissection of mechanisms that control meiotic recombination.     

Mitotic Recombination in the Heterochromatin of the Sex Chromosomes of DROSOPHILA MELANOGASTER

The frequency of spontaneous and X-ray-induced mitotic recombination involving the Y chromosome has been studied in individuals with a marked Y chromosome arm and different XY compound chromosomes. The genotypes used include X chromosomes with different amounts of X heterochromatin and either or both arms of the Y chromosome attached to either side of the centromere. Individuals with two Y chromosomes have also been studied. The results show that the bulk of mitotic recombination takes place between homologous regions.     

The segregation pattern of a translocation quadrivalent

The segregation pattern of a translocation quadrivalent was studied in three hybrid families of the tetraploid (2n=28) oat, of the Avena strigosa polyploid complex. The rate of IV formation in F₁ was high and the fertility was normal. The adjacent-alternate orientation of this quadrivalent was very variable. Conspicuous variation in this frequency was found between anthers of the same floret and between florets. The alternate type was usually more common toward the end of MI. The adjacent-alternate ratio was found to be an unreliable measure for calculating the type of gametes produced by the F₁ and the F₂ plants derived from them. An attempt was made to determine the type of viable gametes produced on the F₁ and their frequency by examining the cytology of F₂ plants. The various combinations of the chromosomes of the translocation complex expected in the F₂ plants were derived and their expected frequencies calculated by taking into account chiasma formation at the chromosome ends and various restrictions of gamete viability. In none of the three hybrid families F₂ individuals were found to produce trivalents as the most complex chromosome configuration, indicating that one type of gamete derived from adjacent separation was not formed. The 11 ratio between F₂ plants having only bivalents (2II) and those with F ₁-like quadrivalent configuration R(c), expected when gametes resulting from alternate separation are fully functional, with the exclusion of other types, was not found. That ratio 2II/R(c), was 2-1/3 in the various families. The cytology of selected F₃ individuals basically followed the predictions based on chromosome association in the F₂.     

A paracentric inversion suppresses genetic recombination at the <Emphasis Type="Italic">FON3</Emphasis> locus with breakpoints corresponding to sequence gaps on rice chromosome 11L

Paracentric inversion is known to inhibit genetic recombination between normal and inverted chromosomal segments in heterozygous arrangements. Insect inversion polymorphisms have been studied to reveal adaptive processes for maintaining genetic variation. We report the first paracentric inversion in rice (Oryza sativa), which was discovered in our effort to clone the floral organ number gene FON3. Recombination at the FON3 locus on the long arm of chromosome 11 was severely suppressed over a distance of more than 36 cM. An extensive screening among 8,242 F₂ progeny failed to detect any recombinants. Cytological analysis revealed a loop-like structure on pachytene chromosomes, whereas FISH analysis showed the migration of a BAC clone from a distal location to a position closer to the centromere. Interestingly, the locations where the genetic recombination suppression began were coincided with the positions of two physical gaps on the chromosome 11, suggesting a correlation between the physical gaps, the inversion breakpoints. Transposons and retrotransposons, and tandemly arranged members of gene families were among the sequences immediately flanking the gaps. Taken together, we propose that the genetic suppression at the FON3 locus was caused by a paracentric inversion. The possible genetic mechanism causing such a spontaneous inversion was proposed.     

High recombination between the breakpoint of a reciprocal translocation in rye (Secale cereale L.) and an interstitially located gene

Summary The recombination fraction between the interstitially located gene an and interchange 303 of rye was found to be 0.244±0.038 in a test cross using the translocation as the male parent. In first metaphase translocation configurations in pollen mother cells of the same plant, the chiasma frequency between an and the translocation breakpoint was found to be significantly more than twice the recombination fraction. Recombination was concluded to be masked by a difference in the alternate frequency between configurations without interstitial chiasmata and configurations with interstitial chiasmata, the effect of the first type being of major importance. Random centromere orientation of translocation multivalents with interstitial chiasmata was concluded to be a realistic assumption. The exceptionally high recombination between an and translocation 303 is discussed. Consideration is also given to the use of interchanges in the establishment of a marker's chromosomal position, and to the use of translocation chromosomes in balanced systems for hybrid breeding purposes.     

The modification of crossing over in maize by extraneous chromosomal elements

Summary Five regions of the maize genome were tested for their response to endogenous factors influencing recombination. These included heterochromatic B chromosomes and abnormal chromosome 10 as well as the sex in which recombination occurred.The frequency of recombination in the proximal A ₂-Bt and Bt-Pr segments of chromosome 5 was increased in the presence of B chromosomes, with the male meiocytes showing a greater response than the female meiocytes. In addition, experiments involving 0, 1, 2 and 4 B's revealed a dosage effect of B chromosomes on crossing over in chromosome 5. Recombination in the proximal Wx-Gl ₁₅ interval of chromosome 9 was found to be slightly higher than normal in male flowers when two B chromosomes were present. This increase was accompanied by a decrease in the adjacent Sh-Wx segment. Crossing over in the distal C-Sh segment and in the C-Sh-Wx-Gl ₁₅ regions of female flowers was unaffected by B's.Comparisons of plants heterozygous for abnormal chromosome 10 (K10 k10) and homozygous for the standard chromosome 10 (k10 k10) showed that abnormal 10 greatly enhances crossing over in the A ₂-Bt and Bt-Pr segments of chromosome 5. In contrast to the finding with B's, the effect is greater in female than in male sporocytes. K10 showed no significant effect on recombination in the C-Sh-Wx-Gl ₁₅ region of chromosome 9 except in male sporocytes, where there was a slight increase in the Sh-Wx region of 0 B K10 k10 plants and a possible interaction with B chromosomes to raise the level of recombination between Wx and Gl ₁₅. The fact that the regions adjacent to the centromere of chromosome 9 show little or no response to the presence of K10 indicates that the proximal heterochromatin of this chromosome differs qualitatively from that of other maize chromosomes. This conclusion is supported by a comparison of the effects of B chromosomes, K10 and sex on crossing over in chromosomes 5 and 9.Dedicated to Dr. M. M. Rhoades on the occasion of his seventieth birthday.