Low Levels Of Recombination Research Articles

The evolution and population genetics of the ALDH2 locus: random genetic drift, selection, and low levels of recombination.

The catalytic deficiency of human aldehyde dehydrogenase 2 (ALDH2) is caused by a nucleotide substitution (G1510A; Glu487Lys) in exon 12 of the ALDH2 locus. This SNP, and four non-coding SNPs, including one in the promoter, span 40 kb of ALDH2; these and one downstream STRP have been tested in 37 worldwide populations. Only four major SNP-defined haplotypes account for almost all chromosomes in all populations. A fifth haplotype harbours the functional variant and is only found in East Asians. Though the SNPs showed virtually no historic recombination, LD values are quite variable because of varying haplotype frequencies, demonstrating that LD is a statistical abstraction and not a fundamental aspect of the genome, and is not a function solely of recombination. Among populations, different sets of tagging SNPs, sometimes not overlapping, can be required to identify the common haplotypes. Thus, solely because haplotype frequencies vary, there is no common minimum set of tagging SNPs globally applicable. The Fst values of the promoter region SNP and the functional SNP were about two S.D. above the mean for a reference distribution of 117 autosomal biallelic markers. These high Fst values may indicate selection has operated at these or very tightly linked sites.

The nature of introns 4-7 largely reflects the lineage specificity of HLA-A alleles.

For most HLA-A alleles the phylogeny of the 3' non-coding regions has not yet been studied systematically. In this study, we have determined the sequences of introns 4-7 in 50 HLA-A variants, and have computed nucleotide substitution rates and phylogenetic relationships. The A2/A28, A9, and A10 groups were characterized by clear lineage specificity. For the A19 group, lineage specificity was weaker. A*3001 clustered together with the alleles of the A1/A3/A11/A36 serological family, but not with the A19 group alleles. Reduced lineage specificity was also observed for the alleles of the A1/A3/A11/A36groups. The 3' intron sequences of A*8001 were clearly distinct from all other alleles studied. In several cases two allelic groups shared identical intron sequences, whereby the patterns varied with the introns. A similar situation has been previously described for the 5' introns. Since recombination is the major mechanism of HLA diversification, the intronic lineage specificity corresponds to the comparatively lower recombination rate of the HLA-A 3' exons. The low level of recombination within the 3' region of HLA-A is supported by the low CpG content with a maximum of 3.0% in this region compared with up to 10.7% in the 5' region. Apart from phylogenetic studies of HLA diversity and diversification, the sequence data obtained in our study may prove valuable for the development of a haplotype-specific sequencing strategy for the HLA-A3' exons and for the explanation of recombination events in newly described HLA class I alleles.

AFLP maps of Petunia hybrida: building maps when markers cluster.

AFLP mapping in Petunia hybrida was undertaken with the intention of building a high-density genetic map suitable for applications such as map-based gene cloning. In total five maps were constructed from two mapping populations, with placement of more than 800 markers. Despite the large number of markers the resulting map is roughly ten-fold smaller than those of other plant species, including the closely related tomato. Low levels of recombination are reflected in clusters of tightly linked markers, both AFLPs and RFLPs, in all the maps. Clustering patterns vary between mapping populations, however, such that loci tightly linked in one population may be separable in another. Combined with earlier reports of aberrant meiotic pairing and recombination, our results suggest that, for species like petunia, map-based cloning may be more complex than in model species such as arabidopsis and tomato.

Osmoregulation of dimer resolution at the plasmid pJHCMW1 mwr locus by Escherichia coli XerCD recombination.

Xer-mediated dimer resolution at the mwr site of plasmid pJHCMW1 is osmoregulated in Escherichia coli. Whereas under low-salt conditions, the site-specific recombination reaction is efficient, under high-salt conditions, it proceeds inefficiently. Regulation of dimer resolution is independent of H-NS and is mediated by changes in osmolarity rather than ionic effects. The low level of recombination at high salt concentrations can be overcome by high levels of PepA or by mutating the ARG box to a sequence closer to the E. coli ARG box consensus. The central region of the mwr core recombination site plays a role in regulation of site-specific recombination by the osmotic pressure of the medium.

Genetic linkage and molecular evolution

The different models make similar predictions which makes it difficult to ascribe an observation to just one process. Are there any observations that allow one to identify which process is operating? It turns out that the distribution of frequencies of neu-tral variants in a sample of sequences (the frequency spectrum) is model-dependent. A large distortion of the frequency spectrum towards rare variants is more likely with selective sweeps (Fig. 1Fig. 1). And when there is some recombination, so that initially rare variants are not necessarily swept to complete fixation, a transient sig-nature of a sweep is provided by the occurrence of an excess of ‘derived’ variants at a high frequency within a sample. (One can infer if a variant is derived or ancestral from the sequence of a closely related species.) Other features of genetic variation, such as patterns of linkage disequilibrium, may also be useful in testing alternative models. Perhaps the best way to quantify the relative importance of these processes is to get solid estimates of the rate at which deleterious mutations occur, and of the distribution of their effects on fitness. Although this is a simple question to ask, it is hard to answer. But given such information, and using the increasing amount of information on DNA sequence variation and evolution, one can perhaps try to answer an even harder question: what is the rate at which advantageous mutations occur, and what are their effects on fitness?Key references

A Novel Host Cell Reactivation Assay to Assess Homologous Recombination Capacity in Human Cancer Cell Lines

Repair of DNA double-strand breaks (DSB) is essential for cell viability and genome stability. Homologous recombination repair plays an important role in DSB repair and impairment of this repair mechanism may lead to loss of genomic integrity, which is one of the hallmarks of cancer. Recent research has shown that the tumor suppressor genes p53 and BRCA1 and -2 are involved in the proper control of homologous recombination, suggesting a role of this type of repair in human cancer. We developed a novel assay based on recombination between two Green Fluorescent Protein (GFP) sequences in transiently transfected plasmid DNA. The plasmid construct contains an intact, emission-shifted, “blue” variant of GFP (BFP), with a 300 nucleotide stretch of homology to a nonfunctional copy of GFP. In the absence of homologous recombination only BFP is present, but homologous recombination can create a functional GFP. The homologous regions in the plasmid were constructed in both the direct and the inverted orientation of transcription to detect possible differences in the recombination mechanisms involved. A panel of human tumor cell lines was chosen on the basis of genetic background and chromosome integrity and tested for homologous recombination using this assay. The panel included cell lines with varying levels of karyotypic abnormalities, isogenic cell lines with normal and mutant p53, isogenic cell lines with or without DNA mismatch repair, BRCA1 and -2 mutant cell lines, and the lymphoma cell line DT40. With this assay, the observed differences between cell lines with the lowest and highest levels of recombination were about 100-fold. Increased levels of recombination were associated with mutant p53, whereas a low level of recombination was found in the BRCA1 mutant cell line. In the cell line HT1080TG, a mutagenized derivative of HT1080 with two mutant alleles of p53, high levels of recombination were found with the direct orientation but not with the inverted orientation plasmid. No difference in recombination was detected between two isogenic cell lines that only differed in DNA mismatch repair capability. We conclude that this assay can detect differences in homologous recombination capacity in cultured cell lines and that these differences follow the patterns that would be expected from the different genotypes of these cell lines. Future application in normal cells may be useful to identify genetic determinants controlling genomic integrity or to detect differences in DNA repair capacity in individuals.

The Complete Sequence of a Heterochromatic Island from a Higher Eukaryote

Heterochromatin, constitutively condensed chromosomal material, is widespread among eukaryotes but incompletely characterized at the nucleotide level. We have sequenced and analyzed 2.1 megabases (Mb) of Arabidopsis thaliana chromosome 4 that includes 0.5–0.7 Mb of isolated heterochromatin that resembles the chromosomal knobs described by Barbara McClintock in maize. This isolated region has a low density of expressed genes, low levels of recombination and a low incidence of genetrap insertion. Satellite repeats were absent, but tandem arrays of long repeats and many transposons were found. Methylation of these sequences was dependent on chromatin remodeling. Clustered repeats were associated with condensed chromosomal domains elsewhere. The complete sequence of a heterochromatic island provides an opportunity to study sequence determinants of chromosome condensation.

The Size Distribution of Homozygous Segments in the Human Genome

In the field of population genetics, there is a rich history of advancements made by noting discrepancies between models and theory. If observed segments of autozygosity differ in size from model predictions, we can begin to identify several possible reasons. First, natural selection will remove from the population those individuals who are autozygous for very deleterious alleles, leaving a smaller-than-expected block size. We do not tend to keep track of consanguinity if the potential common ancestor is more than four or so generations back, but having common ancestors five, 10, or even 20 generations ago is far from being “outbred” in the context of tracking homozygous segments in entire genomes. Very large segments can remain intact for long periods (fig. 1afig. 1a). There will be large sampling problems to face, and the identification of homozygous blocks will depend on marker density and heterozygosity, as Broman and Weber (1999xLong homozygous chromosomal segments in the CEPH families. Broman, KW and Weber, JL. Am J Hum Genet. 1999; 65: 1493–1500Abstract | Full Text | Full Text PDF | PubMed | Scopus (121)See all References1999 [in this issue]) illustrate. Population growth will also distort the distribution of times back to common ancestry (Bertorelle and Slatkin 1995xThe number of segregating sites in expanding human populations, with implications for estimates of demographic parameters. Bertorelle, G and Slatkin, M. Mol Biol Evol. 1995; 12: 887–892PubMedSee all References1995), and this may be especially evident in distributions of homozygous segments. Regions of the genome with low levels of recombination per megabase are expected to have larger segments of homozygosity. Observation of unexpectedly large homozygous blocks may also have a genetic cause, such as uniparental disomy (Smith et al. 1994xFamilial unbalanced translocation t(8;15)(p23.3;q11) with uniparental disomy in Angelman syndrome. Smith, A, Deng, ZM, Beran, R, Woodage, T, and Trent, RJ. Hum Genet. 1994; 93: 471–473Crossref | PubMed | Scopus (25)See all References1994; Martin et al. 1999xMaternal uniparental disomy of chromosome 14 confined to an interstitial segment (14q23-14q24.2). Martin, RA, Sabol, DW, and Rogan, PK. J Med Genet. 1999; 36: 633–636PubMedSee all References1999; Uehara et al. 1999xComplete androgen insensitivity in a 47,XXY patient with uniparental disomy for the X chromosome. Uehara, S, Tamura, M, Nata, M, Kanetake, J, Hashiyada, M, Terada, Y, Yaegashi, N et al. Am J Med Genet. 1999; 86: 107–111Crossref | PubMed | Scopus (9)See all References1999). Our ascertainment for uniparental disomy is through clinical cases, and, if some uniparental disomy for some chromosomes is asymptomatic, this phenomenon may well be more common than currently thought.Coalescence approaches will allow us to take the exciting step of turning these problems around, making inferences, and estimating population parameters from observed distributions of homozygous segment lengths. Although classical population-genetics theory tells us that one can have the same net inbreeding coefficient either with one short path of common ancestry or with several longer paths, the consequences will be very different for the distribution of blocks of homozygosity. The complete genome sequence of an individual will give the complete distribution of homozygous segments, and this distribution will allow unprecedented resolution for inferences about the number and depth of common ancestors. Many interesting inferential challenges will arise when we consider the population genetics of whole genomes.

Reduced sequence variability on the Neo-Y chromosome of Drosophila americana americana.

Sex chromosomes are generally morphologically and functionally distinct, but the evolutionary forces that cause this differentiation are poorly understood. Drosophila americana americana was used in this study to examine one aspect of sex chromosome evolution, the degeneration of nonrecombining Y chromosomes. The primary X chromosome of D. a. americana is fused with a chromosomal element that was ancestrally an autosome, causing this homologous chromosomal pair to segregate with the sex chromosomes. Sequence variation at the Alcohol Dehydrogenase (Adh) gene was used to determine the pattern of nucleotide variation on the neo-sex chromosomes in natural populations. Sequences of Adh were obtained for neo-X and neo-Y chromosomes of D. a. americana, and for Adh of D. a. texana, in which it is autosomal. No significant sequence differentiation is present between the neo-X and neo-Y chromosomes of D. a. americana or the autosomes of D. a. texana. There is a significantly lower level of sequence diversity on the neo-Y chromosome relative to the neo-X in D. a. americana. This reduction in variability on the neo-Y does not appear to have resulted from a selective sweep. Coalescent simulations of the evolutionary transition of an autosome into a Y chromosome indicate there may be a low level of recombination between the neo-X and neo-Y alleles of Adh and that the effective population size of this chromosome may have been reduced below the expected value of 25% of the autosomal effective size, possibly because of the effects of background selection or sexual selection.

A global survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus.

A four-site haplotype system at the dopamine D2 receptor locus (DRD2) has been studied in a global sample of 28 distinct populations. The haplotype system spans about 25 kb, encompassing the coding region of the gene. The four individual markers include three TaqI restriction site polymorphisms (RSPs) -- TaqI "A", "B", and "D" sites -- and one dinucleotide short tandem repeat polymorphism (STRP). All four of the marker systems are polymorphic in all regions of the world and in most individual populations. The haplotype system shows the highest average heterozygosity in Africa, a slightly lower average heterozygosity in Europe, and the lowest average heterozygosities in East Asia and the Americas. Across all populations, 20 of the 48 possible haplotypes reached a frequency of at least 5% in at least one population sample. However, no single population had more than six haplotypes reaching that frequency. In general, African populations had more haplotypes present in each population and more haplotypes occurring at a frequency of at least 5% in that population. Permutation tests for significance of overall disequilibrium (all sites considered simultaneously) were highly significant (P<0.001) in all 28 populations. Except for three African samples, the pairwise disequilibrium between the outermost RSP markers, TaqI "B" and "A", was highly significant with D' values greater than 0.8; in two of those exceptions the RSP marker was not polymorphic. Except for those same two African populations, the 16-repeat allele at the STRP also showed highly significant disequilibrium with the TaqI "B" site in all populations, with D' values usually greater than 0.7. Only four haplotypes account for more than 70% of all chromosomes in virtually all non-African populations, and two of those haplotypes account for more than 70% of all chromosomes in most East Asian and Amerindian populations. A new measure of the amount of overall disequilibrium shows least disequilibrium in African populations, somewhat more in European populations, and the greatest amount in East Asian and Amerindian populations. This pattern seems best explained by random genetic drift with low levels of recombination, a low mutation rate at the STRP, and essentially no recurrent mutation at the RSP sites, all in conjunction with an "Out of Africa" model for recent human evolution.

Association of leaf rust and powdery mildew resistance in a recombinant derived from a Hordeum vulgare × Hordeum bulbosum hybrid

AbstractWhile studying powdery mildew resistance in a recombinant line (code 81882) derived from a Hordeum vulgare (cv. ‘Vada’) ×Hordeum bulbosum hybrid, a low infection type of resistance to leaf rust was observed. To determine the mode of inheritance of the leaf rust resistance and whether there was linkage between the two resistances, F2 and F3 progenies from crosses between 81882 and ‘Vada’ were inoculated with the leaf rust and powdery mildew pathogens. Southern blots were prepared using restricted DNA extracted from leaves of 82 F2 plants and four chromosome 2HS sequences were hybridized with the blots to define the length of the introgression. The leaf rust resistance appears to be inherited as a single dominant gene on chromosome 2HS, which co‐segregates with the powdery mildew resistance. There was an almost complete association between the resistances and the respective molecular markers, but it is likely that the strong linkage results from the frequent inheritance of the introgressed H. bulbosum DNA as an intact segment of chromatin with only low levels of recombination within the segment.

Isolation and cytogenetic analyses of genetic sexing strains for the medfly, Ceratitis capitata

Over the last 10 years, several genetic sexing strains have been isolated for the Mediterranean fruit fly, Ceratitis capitata, with the aim of improving the Sterile Insect Technique. However, a major problem with the currently used genetic sexing system, which is based on translocations, is their potential genetic instability. Therefore, careful monitoring and chromosome analyses are necessary when new genetic sexing strains are developed. Instability of a genetic sexing strain can be the consequence of recombination or the survival of aneuploid individuals occurring as a consequence of adjacent-1 segregation in the meiosis of males with Y-autosome translocations. Recently, genetic sexing strains have been isolated that show only low levels of recombination. However, many aneuploid flies are produced by these strains. Therefore, we have made an attempt to isolate new genetic sexing strains that show a low percentage of recombination and no survival of aneuploid individuals. We report their genetic behaviour and the polytene chromosome structure of these new strains.

RFLP markers associated with Sr22 and recombination between chromosome 7A of bread wheat and the diploid species Triticum boeoticum

Analysis of the bread wheat variety Schomburgk, and related lines in its pedigree, identified RFLP markers associated with the segment of chromosome 7A carrying the Sr22 gene derived from the diploid species T. boeoticum. The distribution of the RFLP markers indicated that at least 50% of 7AS and 80% of 7AL in Schomburgk is of T. boeoticum origin. Evaluation of five sets of nearisogenic lines, backcross lines in 20 different genetic backgrounds and an F2 population segregating for Sr22 demonstrated a very low level of recombination between the 7A chromosomes of T. boeoticum and T. aestivum. Several recombinants carrying Sr22 but with a much reduced segment of T. boeoticum were identified and these may prove useful in the breeding of further varieties with Sr22.

Genetic and cytogenetic analysis of Y-autosome translocations in the Mediterranean fruit fly, Ceratitis capitata

Radiation-induced translocations in the Mediterranean fruit fly, Ceratitis capitata, linking the Y chromosome to either autosome 3 or 4 produced pseudolinkage between sex and the mutations dark pupa (dp) and apricot eye (ap), respectively. The genetic behaviour of six new strains is described and the structural basis of five of them is determined through analysis of polytene and mitotic chromosomes. Five strains exhibited low levels of recombination; however, one strain produced a larger number than expected of aberrant, wild-type females. We provide evidence that this is the consequence of the survival of adjacent-1 segregation products until adulthood.Key words: medfly, mass rearing, genetic sexing, recombination, segregation.

The TSM1 gene of Saccharomyces cerevisiae overlaps the MAT locus

We have cloned the region from MAT to THR4 on chromosome III of Saccharomyces cerevisiae. Although the region is only 15 kb, the two loci are genetically separated by 22 cM. This is in sharp contrast to the very low level of recombination (2 cM in 22 kb) that is observed in the adjacent CRY1-MAT interval, and suggests that there may be a "hot spot" for recombination in the MAT-THR4 region. The DNA sequence of the first 4.4 kb distal to MAT reveals an open reading frame that we have identified as the essential gene, TSM1. Surprisingly, the TSM1 open reading frame of 1,410 amino acids extends into the MAT locus, such that the 3'-end of the MAT alpha 1 transcript ends 15 bp from the 3'-end of the TSM1 open reading frame.

Extensive linkage disequilibrium in the achaete-scute complex of Drosophila melanogaster.

We have analyzed the level of gametic association between restriction map variants in a sample of 44 X chromosomes from a natural population of Drosophila melanogaster. Of 21 pairwise tests involving 7 restriction map polymorphisms in the yellow-achaete-scute complex, 17 were found to be significant, including some between restriction sites over 80 kb apart. Three-way linkage disequilibria and their variances were also estimated for all 35 three-way comparisons between these loci. Twelve such tests were found to be significant, again spanning distances of up to 80 kb on the restriction map. Only 9 of a possible 128 haplotypes were represented in the sample and 8 of these could be linked together by changes at a single site. The strength of these associations at y-ac-sc is unusual by comparison with studies on other regions of the genome of D. melanogaster, and is consistent with the very low level of recombination which has been reported for the complex. However, our estimate of nucleotide diversity in the region is not significantly different from those made for some other loci in this species.

Genetic control of RNA polymerase I-stimulated recombination in yeast.

We examined the genetic control of the activity of HOT1, a cis-acting recombination-stimulatory sequence of Saccharomyces cerevisiae. Mutations in RAD1 and RAD52 decrease the ability of HOT1 to stimulate intrachromosomal recombination while mutations in RAD4 and RAD50 do not affect HOT1 activity. In rad1 delta strains, the stimulation of excisive recombination by HOT1 is decreased while the rate of gene replacement is not affected. In rad52-8 strains the ability of HOT1 to stimulate both excisive recombination and gene replacement is decreased. All of the recombinants in the rad52-8 strains that would be categorized as gene replacements based on their phenotype are diploids apparently derived by endomitosis and excisive recombination. Studies on rad1 delta rad52-8 strains show that these mutations interact synergistically in the presence or absence of HOT1, resulting in low levels of recombination. The rate of gene replacement but not excisive recombination is stimulated by HOT1 in rad1 delta rad52-8 strains. Taken together, the results show that HOT1 stimulates exchange using multiple recombination pathways. Some of the activity of HOT1 is RAD1-dependent, some is RAD52-dependent, and some requires either RAD1 or RAD52 as suggested by the synergistic interaction found in double mutant strains. There is also a component of HOT1 activity that is independent of both RAD1 and RAD52.

Inheritance of restriction fragment length polymorphisms in Agaricus brunnescens.

The cultivated mushroom, Agaricus brunnescens, is secondarily homothallic; most basidia produce only two basidiospores, each of which receives two of the four post meiotic nuclei. The segregation of restriction fragment length polymorphisms (RFLPs) detected by four plasmid probes carrying single-copy nuclear DNA of Agaricus was followed in seven parental strains including commercial, wild-collected, and artificially synthesized heterokaryons. Of a total of 367 single-spore progeny examined, 351 (95.6%) were heteroallelic at all RFLP loci heteroallelic in the respective parents. Of the 16 segregant isolates, ten (2.7% of the total) were homoallelic at all segregating loci assayed, suggesting that these isolates were most probably derived from rare spores that had received only a single postmeiotic nucleus. Some of these ten isolates had recombinant genotypes. Only five isolates (1.4% of the total) showed homoallelism at one of the loci heteroallelic in the parent, while remaining heteroallelic at other loci. These five genotypes suggest that a crossover had occurred between a marker locus and its respective centromere. Taken together, the results suggest that meiosis in A. brunnescens is accompanied by low levels of recombination and that nonsister nuclei are preferentially incorporated into basidiospores after meiosis II.

Plasmid-to-chromosome gene transfer in Haemophilus influenza during growth.

A low level of recombination between homologous regions of plasmids and the host chromosome occurred during cell growth. The plasmids contained antibiotic resistance markers on the homologous regions which were only expressed when they were integrated into the chromosome. Such recombination took place in Rec+ rec-2 mutants but not in rec-1 mutants.

THE CYTOGENETIC LOCALIZATION OF THE ALCOHOL DEHYDROGENASE-1 LOCUS IN MAIZE

The alcohol dehydrogenase-1 (Adh) locus in maize has been positioned relative to thirteen reciprocal translocations that have breakpoints in the long arm of chromosome 1(1L). The methods of Gopinath and Burnham (1956) to produce interstitial segmental trisomy with overlapping translocations and of Rakha and Robertson (1970) to produce compound B-A translocations were coupled with the co-dominant nature of the ADH isozymes to allow the cytological placement. The results of several crosses are consistent with Adh being in the region of 0.80-0.90 of 1L.--The duplication that results from the overlap of translocations 1-3(5267) and 1-3(5242) and that includes Adh was studied with respect to meiotic segregation and pollen transmission. When heterozygous with normal chromosomes, a low level of recombination within the duplicated regions is detectable and the duplication and normals are recovered with equal frequencies through the female. In the pollen, the hyperploid grains cannot compete equally with the euploids in achieving fertilization.--The use of co-dominant heteromultimeric isozymes as genetic markers for the development of a series of interstitial segmental trisomics in maize is discussed.