The Occurrence of Double Strand DNA Breaks is not the Sole Condition for Meiotic Crossing over in Drosophila Melanogaster

Analysis of the interchromosomal effects of In(2L+2R)Cy, In(3L+3R)LVMand their joint effect on the frequencies of single and double crossovers in the cv-v-fregion of the X chromosome as well as interference showed that both inversions, occurring separately, increased the frequency of single as well as double crossovers and the coefficient of coincidence. However, when the inversions occurred together the frequencies of single crossovers no longer increased, but the frequency of double crossovers, as well as the coefficient of coincidence did increase. These results indicate firstly that the interchromosomal effects influence some precondition of exchange, but that this precondition is not an occurrence of double strand DNA breaks. Thus, the occurrence of double strand DNA breaks is not the sole condition for crossing over in Drosophila melanogaster.     

A Comparison of Heat and Interchromosomal Effects on Recombination and Interference in DROSOPHILA MELANOGASTER

Heat and interchromosomal effects on recombination have been compared for 23 regions comprising the predominantly euchromatic portions of the five arms of the Drosophila genome. Patterns of response are strikingly similar, with both modifiers causing proximal and distal increases and minimal effects in the middle of the arms. Changes in interference for the same regions in the presence of the two modifiers reveal little similarity, except for the X chromosome. The question of independent control of interference and recombination, as well as alternatives for their temporal sequence, is discussed. Recombination response to the two modifiers in the centric heterochromatin of chromosoaime 2 is markedly different from that found in euchromatin. The interchromosomal effect is absent here, whereas heat induces an increase roughly an order of magnitude greater than that found in euchromatin and totally unlike the lack of response in the proximal heterochromatin of the X chromosome. It is proposed that the sequestering of DNA satellite I (thermal dissociation 9–20° lower than that of the other major satellites) in the centromeric heterochromatin of chromosome 2 (but not in X or 3) may account for the increase.     

On intra- and interchromosomal associations in Drosophila ananassae

In Drosophila ananassae, three cosmopolitan inversions are very common in natural populations. Chromosomal polymorphism due to these inversions often persists when strains are maintained in the laboratory. A chromosomal analysis of a number of strains was made. Data on the frequencies of different gene sequences will be described separately. During the present investigation the same data have been analyzed in order to test the intra- and interchromosomal interactions in D. ananassae. The results reveal that interchromosomal interactions do not occur with respect to viability as unlinked inversions are associated randomly. However, the linked inversions of the third chromosome show non-random associations maintained by epistatic gene interaction and suppression of crossing over.     

Interchromosomal effects of inversions on crossover rate in maize

Summary The influence of heterozygous inversions on heterologous chromosome recombination has been studied in maize.Inv 2a causes an increase in crossing-over rate ofYg-Sh region of chromosome9: the reverse is true for the more proximal regionBz-Wx. The coincidence indexes for the traitYg-Sh-Bz is decreased, while the same index is increased for the regionSh-Bz-Wz. Inv 9a is accompanied by an high recombination rate in the distal region of chromsome2 Lg-Gl, while in the regionGl-V the effect is relatively less pronounced.The results seem to exclude mitotic recombination events, but are less suitable for supporting other specific interpretations. However, taking into considerationDrosophila experiments, our data are not conflicting with the physiological hypothesis proposed byRamel, which, at present, appears to explain most of the experimental results, although some difficulty arises in considering the cases of decreased recombination rate.The possibility of modifying, by genetical means, the recombination potential is of significance in some stage of plant breeding, at least in some species.With 2 Figures in the Text     

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.     

Spontaneous chromosome inversions of guatemalan teosintes (Zea mexicana)

Two paracentric inversions,In3 andIn9, were found in the F1 hybrids of maize and Florida teosinte and these inversions were contributed by the teosinte parent. The length ofIn3 was equivalent to about 35 percent of the length of the long arm of chromosome 3, while that ofIn9, about 60 percent of the length of the short arm of chromosome 9.There were also two paracentric inversions,In1 andIn9, in the F1 hybrids of maize and Jutiapa teosinte and these inversions were inherited from the teosinte parent. The length of theIn1 occupied 22 percent of the total length of the long arm of chromosome 1, while that ofIn9, 60 percent of the total length of the short arm of chromosome 9.Only one paracentric inversion,In9, was identified in the F1 hybrids of maize and Lake Retana teosinte, and this inversion was also from the teosinte parent. As length and location are considered, thisIn9 is the same as theIn9's of Florida teosinte and Jutiapa teosinte.At anaphases I and II of the microsporocyte divisions of the F1 hybrids, evidences of crossovers within the inverted segments, such as bridges and fragments, were obtained for all of these inversions. The interchromosome effect ofIn3 of Florida teosinte, and that ofIn1 of Jutiapa teosinte on the frequency of crossovers within the inverted segment ofIn9's are discussed.Chromosome inversions have probably accompanied the divergence of geographical races of teosinte. This might also be true for the race diversities of maize. The absence ofIn9 in certain teosinte races of southern Mexico and northern Guatemala is accounted for by the substitution of maize chromosome for this inversion.     

Recombination and selection in the maintenance of the adaptive value of inversions

A huge amount of data seem to confirm the adaptive value of inversions in Drosophila. The inhibition of recombination in heterokaryotypes mediated by inversions seems fundamental in maintaining their adaptive role. This study shows that recombination is highly suppressed in Drosophila subobscura because of chromosomal inversions, not only inside the inversions but also outside them. It seems that the region outside the inversion where recombination is inhibited is asymmetrical and independent of the inversion length. Despite the difficulty of crossovers taking place near inversion breakpoints, the only two recombination events detected inside inversions were located close to the breakpoint. Thus, selection could be largely responsible for the recombination reduction maintaining sets of adaptive alleles inside the inverted region. Heterokaryotype descendants were always in higher frequency than inbred or outbred homokaryotypes, regardless of the geographical origin of the chromosome, suggesting that chromosomes carrying the same arrangement, although with a different set of alleles for neutral markers, could be submitted to the same selection processes.     

Further studies on the interchromosomal effect on crossing over in Drosophila melanogaster affecting the preconditions of exchange

The second chromosome inversion In (2L+2R) Cy in a heterozygous condition was studied for its effect on frequency and interference of crossing over in three different regions of the X chromosome of Drosophila melanogaster. A significant increase in crossing over frequency was observed in the proximal and distal regioins of the X chromosome while in the middle of the chromosome crossing over frequency remained unaltered. The effect on interference remained unaltered at both ends of the X chromosome while a significant decrease was observed in the middle of the chromosome. These results suggest that the interchromosomal effect on crossing over affects the preconditions of exchange differently in different regions of the X chromosome, and possibly the duration of chromosome pairing.     

Intra-and interchromosomal effects of heterozygous inversions on recombination in the third chromosome of Drosophila ananassae

In order to study intra-and interchromosomal effects of heterozygous inversions on recombination in the third chromosome of D.ananassae, experiments were conducted using Stw-pr marker stock and five wild stocks with known karyotypes. The stocks used were homozygous for standard or inverted gene sequence in 2L, 3L, and 3R. Recombination was investigated in both sexes. There was complete absence of crossing-over in males in all the experiments which appeared to be the characteristic of marker stock as spontaneous male crossing-over was reported earlier with the same wild stocks when the second chromosome markers were used. Based on the data of karyotypically homozygous F1 females, the map distance between stw-pr was 36.55 map units. The heterozygosity due to a lengthy inversion in 2L increased the level of crossing-over between stw-pr genes of the third chromosome indicating interchromosomal effect. There was a considerable reduction in the rate of recombination between the same markers due to inversion heterozygosity in 3R indicating intrachromosomal effect. However, 3L inversion heterozygosity had no effect on crossover rate. These results provide evidence for intra-and interchromosomal effects of inversions on crossing-over in the third chromosome of D. ananassae.     

Recombination between heterozygous inversions in Drosophila ananassae

The rate of recombination between linked inversions of the third chromosome of Drosophila ananassae has been investigated by means of the salivary gland smear technique. Different homozygous strains of the species were utilised during the present investigation. The data show that the crossover rate between heterozygous inversions of the third chromosome of D. ananassae varies among different strains. This suggests that recombination between heterozygous inversions is influenced by genic (strain) factors.     

Double crossing over: elementary events and the sequence of their occurrence

Analysis of the crossing over increment in the structurally normal chromosome of Drosophila caused by a rearrangement in nonhomologous chromosome (interchromosomal effect on crossing over, IEC) was carried out based on the author's personal and literature data. The IEC in the left arm of chromosome 2 caused by inversions in chromosomes X and 3, as well as the IEC in X chromosome caused by inversions in chromosomes 2 and 3, were examined. The IEC-induced increment of crossing over results from the increase of the number of double exchanges under the constant or reduced number of single exchanges. Tetrad analysis showed that the given alternation of the crossing over processes could occur only in the case of conversion of the tetrads with single exchanges into the tetrads with double exchanges. In other words, the events leading to the formation of double exchanges occur consecutively. The borders of the IEC-induced double exchanges can be seen all over the chromosome body. However, the IEC-induced increase of chromosome recombination length occurs only in the proximal region (in rare cases, in proximal and distal regions) of the chromosome arm. This means that a double exchange is formed when the first event with predominant location in the middle of the arm is supplemented with the second event predominantly localized at the arm T end, most frequently in the proximal region. The pattern of the IEC-induced double exchange formation can be satisfactorily described in terms of the contact model of the crossing over. According to the model, an elementary crossing-over event is the local contact between the homologues. Neither single exchange nor a double-stranded DNA break can serve as an elementary event in the process of any multiple exchange formation.     

Analysis of male recombination in third chromosomes of Drosophila melanogaster

Data on male recombination in twenty third-chromosomal lines of Drosophila melanogaster are presented. Frequencies of female and male recombination have been calculated in seven intervals along the third chromosome. The influence on male recombination (M.R.) exercised by different factors such as population origin (cellar, vineyard), the presence of heterozygous inversions and recessive lethal chromosomes, is analyzed. The results obtained lead to the main conclusion that M.R. is not affected by the presence of heterozygous inversions which reduce female recombination in the same lines. In the light of this effect, the possible mechanism operating on male recombination is discussed. Lethal chromosomes reduce significantly the number of male recombination events as compared with wild chromosomes. We have not obtained significant differences in male recombination frequencies between the cellar and the vineyard lines.     

Repeatability and heritability of divergent recombination frequencies in the Iowa Stiff Stalk Synthetic (Zea mays L.)

Variability in recombination frequency was reported in the Iowa Stiff Stalk Synthetic. The objectives of the present research were to verify the differences in recombination frequency among individuals in the Iowa Stiff Stalk Synthetic maize population and to determine if the recombination frequency differences persisted among the S₁ progeny. Testcrosses to measure male recombination frequency on three chromosomes (4, su1-c2; 5, a2-bt1-pr1; 9, sh1-bz1-wx1) were repeated for eight S₀ individuals. Recombination frequencies were repeatably divergent among those individuals which were selected based on high or low recombination frequencies on specific chromosomes. Individuals which had been selected for long and short total map distances across the three chromosome regions produced repeatably divergent recombination frequencies only at the su1-c2 region. The recombination frequencies of the S₁ lines, derived from the S₀ individuals which had the most divergent recombination frequencies on a single chromosome, were significantly different. The broadsense heritability estimates derived from the regression of six S₁ lines on six S₀ individuals ranged from 0.69 to 0.20 for the five chromosome regions. We conclude that genetic differences for recombination frequency exist in this population and that modification by selection should be possible.     

Estimation of Fine-Scale Recombination Intensity Variation in the <Emphasis Type="Italic">white–echinus</Emphasis> Interval of <Emphasis Type="Italic">D. melanogaster</Emphasis>

Accurate assessment of local recombination rate variation is crucial for understanding the recombination process and for determining the impact of natural selection on linked sites. In Drosophila, local recombination intensity has been estimated primarily by statistical approaches, by estimating the local slope of the relationship between the physical and genetic maps. However, these estimates are limited in resolution and, as a result, the physical scale at which recombination intensity varies in Drosophila is largely unknown. Although there is some evidence suggesting as much as a 40-fold variation in crossover rate at a local scale in D. pseudoobscura, little is known about the fine-scale structure of recombination rate variation in D. melanogaster. Here we experimentally examine the fine-scale distribution of crossover events in a 1.2-Mb region on the D. melanogaster X chromosome using a classic genetic mapping approach. Our results show that crossover frequency is significantly heterogeneous within this region, varying approximately 3.5-fold. Simulations suggest that this degree of heterogeneity is sufficient to affect levels of standing nucleotide diversity, although the magnitude of this effect is small. We recover no statistical association between empirical estimates of nucleotide diversity and recombination intensity, which is likely due to the limited number of loci sampled in our population genetic data set. However, codon bias is significantly negatively correlated with fine-scale recombination intensity estimates, as expected. Our results shed light on the relevant physical scale to consider in evolutionary analyses relating to recombination rate and highlight the motivations to increase the resolution of the recombination map in Drosophila.     

Allozyme divergence between different gene arrangements in Drosophila subobscura

Allozyme and chromosomal polymorphism were analysed simultaneously in three population samples of Drosophila subobscura from Scotland, Germany and Italy. The study revealed significant genic divergence between the various chromosomal gene arrangements for the loci Acph, Lap and Pep, which are located inside inversions. No difference was found with the loci Me and Odh, which are both on the same chromosome but proximal to the structurally polymorphic region. Samples of a given gene arrangement taken from the different localities are genetically uniform. The data indicate that the observed non-random associations between enzyme genes and chromosomal inversions are the result of inhibited recombination in heterokaryotypes and gradual differentiation of the separated gene pools, rather than selection and coadaptation.     

Variability of recombination frequencies in the Iowa Stiff Stalk Synthetic (Zea mays L.)

Variability in recombination frequency has been reported in several plant populations. The objectives of the present research were to establish the range in variability in recombination among genotypes in the important corn population Iowa Stiff Stalk Synthetic and to identify individual genotypes which produced increased or decreased recombination frequencies. Approximately 150 individual S₀ plants were testcrossed to measure male recombination frequency on three chromosomes: 4, sul-c2; 5, a2-btl-pr1; and 9, sh1-bz1-wx1. Although the variance component for individuals accounted for only 20–33% of the total variation, highly significant variability among individuals was present at all chromosome regions. Thus the environmental effects did not prevent measurement of differences between S₀ individuals. At each chromosome region, individual genotypes with recombination frequencies at least two standard deviations above or below the population mean were isolated. Reports in the literature suggest that the variability reported here for the BSSS population should be representative of that present in other corn breeding populations. Recombination frequencies were positively correlated between adjacent regions of chromosome 9 and also between adjacent regions of chromosome 5. Recombination frequencies were positively correlated between both regions on chromosome 5 with the su1-c2 region of chromosome 4. Negative correlations were observed between chromosome 9 recombination and recombination in each region of chromosomes 4 and 5. Thus rankings of S₀ individual recombination frequencies were not consistent for all three chromosomes.     

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.     

Architecture of the X Chromosome,Expression of LIM Kinase 1, and Recombination in the agnostic Mutants of Drosophila: A Model for Human Williams Syndrome

As the Human Genome and Drosophila Genome Projects were completed, it became clear that functions of human disease-associated genes may be elucidated by studying the phenotypic expression of mutations affecting their structural or functional homologs in Drosophila.Genomic diseases were identified as a new class of human disorders. Their cause is recombination, which takes place at gene-flanking duplicons to generate chromosome aberrations such as deletions, duplications, inversions, and translocations. The resulting imbalance of the dosage of developmentally important genes arises at a frequency of 10^-3 (higher than the mutation rate of individual genes) and leads to syndromes with multiple manifestations, including cognitive defects. Genomic DNA fragments were cloned from the Drosophila melanogaster agnostic locus, whose mutations impair learning ability and memory. As a result, the locus was exactly localized in X-chromosome region 11AB containing the LIM kinase 1 (LIMK1) gene (CG1848), which is conserved among many species. Hemizygosity for the LIMK1 gene, which is caused by recombination at neighboring extended repeats, underlies cognitive disorders in human Williams syndrome. LIMK1 is a component of the integrin signaling cascade, which regulates the functions of the actin cytoskeleton, synaptogenesis, and morphogenesis in the developing brain. Immunofluorescence analysis revealed LIMK1 in all subdomains of the central complex and the visual system of Drosophila melanogaster.Like in the human genome, theD. melanogaster region is flanked by numerous repeats, which were detected by molecular genetic methods and analysis of ectopic chromosome pairing. The repeats determined a higher rate of spontaneous and induced recombination, including unequal crossing over, in theagnostic gene region. Hence, the agnostic locus was considered as the first D. melanogaster model suitable for studying the genetic defect associated with Williams syndrome in human.     

Chromosome Rearrangement by Ectopic Recombination in Drosophila Melanogaster: Genome Structure and Evolution

Ectopic recombination between interspersed repeat sequences generates chromosomal rearrangements that have a major impact on genome structure. A survey of ectopic recombination in the region flanking the white locus of Drosophila melanogaster identified 25 transposon-mediated rearrangements from four parallel experiments. Eighteen of the 25 were generated from females carrying X chromosomes heterozygous for interspersed repeat sequences. The cytogenetic and molecular analyses of the rearrangements and the parental chromosomes show: (1) interchromosomal and intrachromosomal recombinants are generated in about equal numbers; (2) ectopic recombination appears to be a meiotic process that is stimulated by the interchromosomal effect to about the same degree as regular crossing over; (3) copies of the retrotransposon roo were involved in all of the interchromosomal exchanges; some copies were involved much more frequently than others in the target region; (4) homozygosis for interspersed repeat sequences and other sequence variations significantly reduced ectopic recombination.     

Estimation of gametic frequencies from F2 populations using the EM algorithm and its application in the analysis of crossover interference in rice

The gametes produced in meiosis provide information on the frequency of recombination and also on the interdependence of recombination events, i.e. interference. Using F₂ individuals, it is not possible in all cases to derive the gametes, which have fused, and which provide the information about interference unequivocally when three or more segregating markers are considered simultaneously. Therefore, a method was developed to estimate the gametic frequencies using a maximum likelihood approach together with the expectation maximisation algorithm. This estimation procedure was applied to F₂ mapping data from rice (Oryza sativa L.) to carry out a genome-wide analysis of crossover interference. The distribution of the coefficient of coincidence in dependence on the recombination fraction revealed for all chromosomes increasing positive interference with decreasing interval size. For some chromosomes this mutual inhibition of recombination was not so strong in small intervals. The centromere had a significant effect on interference. The positive interference found in the chromosome arms were reduced significantly when the intervals considered spanned the centromere. Two chromosomes even demonstrated independent recombination and slightly negative interference for small intervals including the centromere. Different marker densities had no effect on the results. In general, interference depended on the frequency of recombination events in relation to the physical length. The strength of the centromere effect on interference seemed to depend on the strength of recombination suppression around the centromere.Electronic Supplementary Material Supplementary material is available for this article at