The effect of abnormal chromosome 10 on transposition of modulator from the R locus in maize

Transposition of the non-specific repressor element, Modulator, from the R locus on chromosome 10 in maize, is enhanced by coupling with the K10 segment at a distance of at least 35 map units from R. There is no detectable interaction in the repulsion phase. The K10 effect appears to be relatively greater in the earlier somatic cell generations during ear development. The transposition rate also is affected by the direction of crosses, being somewhat higher on the ears of F₁ plants which received the compound mutable R allele from the pollen parent. The significance of the behavior of Modulator and other instability phenomena of higher plants is discussed in relation to chromosome organization.     

R-stippled maize as a transposable element system

The I-R element at the R locus destabilizes kernel pigmentation giving the variegated pattern known as stippled ( R-st). In trans linkage phase with R-st the element was shown to act as a modifier of stippled, intensifying seed spotting in parallel with effects of the dominant linked modifier M-st. Presence of I-R in the genome was, therefore, shown to be detectable as a modifier of R-st. When this test was used, new modifiers resembling M-st were often detected following mutations of R-st to the stable allele R-sc. Such mutations evidently occurred by transposition of I-R away from the R locus to a site where it was identifiable as a modifier. M-st may be such a transposed I-R. Analysis of mutations to R-sc during the second (sperm-forming) mitosis in pollen grains showed that some of the transposed I-R elements were linked with R, whereas others assorted independently. Their strengths varied from barely discernible to a level equal to M-st. Overreplication frequently accompanied transposition at the sperm-forming mitosis, leading to transposed I-R elements in both the mutant and nonmutant sperm.     

Segregation analysis and RFLP mapping of the R1 and R3 alleles conferring race-specific resistance to Phytophthora infestans in progeny of dihaploid potato parents

Phytophthora infestans (Mont.) de Bary is the most important fungal pathogen of the potato (Solanum tuberosum). The introduction of major genes for resistance from the wild species S. demissum into potato cultivars is the earliest example of breeding for resistance using wild germplasm in this crop. Eleven resistance alleles (R genes) are known, differing in the recognition of corresponding avirulence alleles of the fungus. The number of R loci, their positions on the genetic map and the allelic relationships between different R variants are not known, except that the R1 locus has been mapped to potato chromosome V The objective of this work was the further genetic analysis of different R alleles in potato. Tetraploid potato cultivars carrying R alleles were reduced to the diploid level by inducing haploid parthenogenetic development of 2n female gametes. Of the 157 isolated primary dihaploids, 7 set seeds and carried the resistance alleles R1, R3 and R10 either individually or in combinations. Independent segregation of the dominant R1 and R3 alleles was demonstrated in two F₁ populations of crosses among a dihaploid clone carrying R1 plus R3 and susceptible pollinators. Distorted segregation in favour of susceptibility was found for the R3 allele in 15 of 18 F₁ populations analysed, whereas the RI allele segregated with a 1:1 ratio as expected in five F₁ populations. The mode of inheritance of the R10 allele could not be deduced as only very few F₁ hybrids bearing R10 were obtained. Linkage analysis in two F₁ populations between R1, R3 and RFLP markers of known position on the potato RFLP maps confirmed the position of the R1 locus on chromosome V and localized the second locus, R3, to a distal position on chromdsome XI.     

A chromosome replication pattern deduced from pericarp phenotypes resulting from movements of the transposable element, modulator, in maize

Modulator (Mp) was mapped after it transposed from the P locus on chromosome 1 by studying 105 light variegated/red twin sectors on medium variegated pericarp ears. Sixty-one percent of the receptor sites were detectably linked to P, and these showed an asymmetry of distribution adjacent to P. No transpositions were mapped in the 4 map units proximal to P, whereas 23 cases mapped to the same length distal to P. The remaining transpositions of Mp on chromosome 1, both proximal and distal to P, were equally scattered. It has previously been shown that when Modulator transposes it replicates at the P locus and a second time at the receptor site. The pattern of transposition adjacent to P is consistent with a hypothesis that a replicon initiation site is situated proximal to P; that Modulator transposes at the time of replication; that it is not able to transpose into a replicated region but only into a replicating one. No difference in distribution of receptor sites was found when the Modulator was detected vs. not detected in the red co-twins by testing with a Dissociation element.     

A Trans-Acting Protein Effect Causes Severe Eye Malformation in the Mp Mouse

Mp is an irradiation-induced mouse mutation associated with microphthalmia, micropinna and hind limb syndactyly. We show that Mp is caused by a 660 kb balanced inversion on chromosome 18 producing reciprocal 3-prime gene fusion events involving Fbn2 and Isoc1. The Isoc1-Fbn2 fusion gene (Isoc1^Mp) mRNA has a frameshift and early stop codon resulting in nonsense mediated decay. Homozygous deletions of Isoc1 do not support a significant developmental role for this gene. The Fbn2-Isoc1 fusion gene (Fbn2 ^Mp) predicted protein consists of the N-terminal Fibrillin-2 (amino acids 1–2646, exons 1–62) lacking the C-terminal furin-cleavage site with a short out-of-frame extension encoded by the final exon of Isoc1. The Mp limb phenotype is consistent with that reported in Fbn2 null embryos. However, severe eye malformations, a defining feature of Mp, are not seen in Fbn2 null animals. Fibrillin-2^Mp forms large fibrillar structures within the rough endoplasmic reticulum (rER) associated with an unfolded protein response and quantitative mass spectrometry shows a generalised defect in protein secretion in conditioned media from mutant cells. In the embryonic eye Fbn2 is expressed within the peripheral ciliary margin (CM). Mp embryos show reduced canonical Wnt-signalling in the CM – known to be essential for ciliary body development - and show subsequent aplasia of CM-derived structures. We propose that the Mp “worse-than-null” eye phenotype plausibly results from a failure in normal trafficking of proteins that are co-expressed with Fbn2 within the CM. The prediction of similar trans-acting protein effects will be an important challenge in the medical interpretation of human mutations from whole exome sequencing.     

Do the BEAF insulator proteins regulate genes involved in cell polarity and neoplastic growth?

It was reported that a chromosome with the BEAF^NP6377 (NP6377) allele leads to a loss of cell polarity and neoplastic growth in Drosophila melanogaster when homozygous ( Gurudatta et al., 2012). We had previously generated the BEAF^AB-KO (AB-KO) allele by homologous recombination and did not note these phenotypes ( Roy et al., 2007). Both alleles are null mutations. It was unclear why two null alleles of the same gene would give different phenotypes. To resolve this, we performed genetic tests to explore the possibility that the chromosome with the NP6377 allele contained other, second site mutations that might account for the different phenotypes. We found that the chromosome with NP6377 has at least two additional mutations. At least one of these, possibly in combination with the NP6377 allele, is presumably responsible for the reported effects on gene expression, cell polarity and neoplastic growth.     

Associations of Alleles of the Esterase-1 Locus with Gene Arrangements of the Left Arm of the Second Chromosome in DROSOPHILA ROBUSTA

Evidence of strong associations of Est-1 alleles with the 2L, 2L1 and 2L3 gene arrangements of the left arm of the second chromosome in D. robusta is presented. Each gene arrangement is polymorphic for three to four Est-1 alleles. The allele frequencies differ in the 2L3 and 2L arrangements; the allele Est-1^.92 is 8% in the 2L3 arrangement (n=203)—this allele is 82% in the 2L arrangement (n=203); the allele Est-1^1.0 is 66% and 14.8% in the 2L3 and 2L arrangements, respectively. There are no differences in allele frequencies in 2L3 arrangements from any of the widely separated seven different populations; similarly the allele frequencies in the 2L arrangement are alike in all five widely separated populations studied. The allele frequencies in the 2L1 arrangement are intermediate to those observed in the 2L3 and the 2L arrangements and show north-south clinal change. These associations between Est-1 alleles and gene arrangements of the left arm of the second chromosome are due to natural selection favoring different allele frequencies in different gene arrangements, as a result of epistatic interactions between the Est-1 locus and the loci on the gene arrangements. As expected, we observe that the proportion of heterozygotes is greater in the inversion heterokaryotypes than in the homokaryotypes.     

Serum esterase genetics in rabbits. IV. The prealbumin and β-globulin systems

Discontinuous starch gel electrophoresis revealed a fourth allele of rabbit prealbumin serum esterase at locus Est-2. This allele is designated Est-2 ^f and appears to be silent. In addition to the prealbumin serum esterases, another serum esterase system was studied in rabbits. This system is localized in the β-globulin region. Genetic analysis indicated that one locus with two codominant alleles controls the variation in this region. Linkage of this system with Est-1 and Est-2 of the prealbumin serum esterases was demonstrated. Comparison of the arrangement of these esterase loci on linkage group VI with the esterase loci on chromosome 8 of the mouse gives additional support for the theory of evolutionary conservation of chromosomal segments coding for mammalian esterases.     

Preferential transposition of aDrosophila P element to the corresponding region of the homologous chromosome

Genetic and physical analyses have demonstrated an intimate interaction or pairing of homologous chromosomes in the nuclei of manyDrosophila cell types. Experiments were performed to determine whether P elements transposing from a given chromosome to its homolog would preferentially insert in the region corresponding to the donor site, perhaps due to such a proximity. AP[lacZ;ry ⁺] element at thecactus locus (35F) on the second chromosome was mobilized and 96 insertions on the homolog were recovered. The distribution of these new insertions was determined by recombination mapping and molecular analysis, and compared with a control set of 93 second-chromosome insertions originating from theX chromosome. A nearly threefold preference was observed for re-insertion in a region of two to three number divisions aroundcactus on the homolog. However, none of these “local” insertions was actually within ～ 50 kb of the site atcactus corresponding to the starting site. This is in marked contrast to the previously described phenomenon of intrachromosomal local transposition, where the majority of local transpositions are within 10 kb. The data suggest that the mechanisms for intrachromosomal and interchromosomal local transposition are distinct, and are consistent with a model for interchromosomal local transposition involving proximity of homologous chromosomal regions in the nuclei of the germline cells.     

High chlorpyrifos resistance in Culex pipiens mosquitoes: strong synergy between resistance genes

We investigated the genetic determinism of high chlorpyrifos resistance (HCR), a phenotype first described in 1999 in Culex pipiens mosquitoes surviving chlorpyrifos doses ⩾1 mg l⁻¹ and more recently found in field samples from Tunisia, Israel or Indian Ocean islands. Through chlorpyrifos selection, we selected several HCR strains that displayed over 10 000-fold resistance. All strains were homozygous for resistant alleles at two main loci: the ace-1 gene, with the resistant ace-1^R allele expressing the insensitive G119S acetylcholinesterase, and a resistant allele of an unknown gene (named T) linked to the sex and ace-2 genes. We constructed a strain carrying only the T-resistant allele and studied its resistance characteristics. By crossing this strain with strains harboring different alleles at the ace-1 locus, we showed that the resistant ace-1^R and the T alleles act in strong synergy, as they elicited a resistance 100 times higher than expected from a simple multiplicative effect. This effect was specific to chlorpyrifos and parathion and was not affected by synergists. We also examined how HCR was expressed in strains carrying other ace-1-resistant alleles, such as ace-1^V or the duplicated ace-1^D allele, currently spreading worldwide. We identified two major parameters that influenced the level of resistance: the number and the nature of the ace-1-resistant alleles and the number of T alleles. Our data fit a model that predicts that the T allele acts by decreasing chlorpyrifos concentration in the compartment targeted in insects.     

Genetic Dissection of Segregation Distortion. I. Suicide Combinations of SD Genes

Two major loci in the Tft–cn region of an SD chromosome have been separated by recombination and identified. The allele at the left-hand locus on an SD chromosome is called Sd; the allele at the right-hand locus is called Rsp. Both Sd and Rsp are necessary to bring about a distortion of the segregation ratio in heterozygous SD males, although the particular degree of distortion exhibited by an SD chromosome is influenced by the constellation of polygenic modifiers of SD in the genome. The coupling phase of the alleles, Sd Rsp/Sd⁺Rsp⁺, produces about 89-90% of Sd Resp-bearing progeny. The repulsion phase, Sd Rsp⁺/Sd⁺ Rsp, produces 10-20% of Sd Rsp⁺-bearing progeny. No coupling-repulsion effects between Sd and Rsp are apparent.     

A dominant, recombination-defective allele of Dmc1 causing male-specific sterility

DMC1 is a meiosis-specific homolog of bacterial RecA and eukaryotic RAD51 that can catalyze homologous DNA strand invasion and D-loop formation in vitro. DMC1-deficient mice and yeast are sterile due to defective meiotic recombination and chromosome synapsis. The authors identified a male dominant sterile allele of Dmc1, Dmc1^Mei11, encoding a missense mutation in the L2 DNA binding domain that abolishes strand invasion activity. Meiosis in male heterozygotes arrests in pachynema, characterized by incomplete chromosome synapsis and no crossing-over. Young heterozygous females have normal litter sizes despite having a decreased oocyte pool, a high incidence of meiosis I abnormalities, and susceptibility to premature ovarian failure. Dmc1^Mei11 exposes a sex difference in recombination in that a significant portion of female oocytes can compensate for DMC1 deficiency to undergo crossing-over and complete gametogenesis. Importantly, these data demonstrate that dominant alleles of meiosis genes can arise and propagate in populations, causing infertility and other reproductive consequences due to meiotic prophase I defects.     

Allelic exclusion of the immunoglobulin heavy chain locus is independent of its nuclear localization in mature B cells

In developing B cells, the immunoglobulin heavy chain (IgH) locus is thought to move from repressive to permissive chromatin compartments to facilitate its scheduled rearrangement. In mature B cells, maintenance of allelic exclusion has been proposed to involve recruitment of the non-productive IgH allele to pericentromeric heterochromatin. Here, we used an allele-specific chromosome conformation capture combined with sequencing (4C-seq) approach to unambigously follow the individual IgH alleles in mature B lymphocytes. Despite their physical and functional difference, productive and non-productive IgH alleles in B cells and unrearranged IgH alleles in T cells share many chromosomal contacts and largely reside in active chromatin. In brain, however, the locus resides in a different repressive environment. We conclude that IgH adopts a lymphoid-specific nuclear location that is, however, unrelated to maintenance of allelic exclusion. We additionally find that in mature B cells—but not in T cells—the distal V_H regions of both IgH alleles position themselves away from active chromatin. This, we speculate, may help to restrict enhancer activity to the productively rearranged V_H promoter element.     

Genetic Change in Mutations at the T/t-Locus in the Mouse

Recessive lethal or semilethal alleles at the T/t locus in the mouse generate new t-variants, with characteristics different from the parent allele at a rate of about 10^-3. Almost invariably the variant chromosome carries marker genes derived from the opposite parental chromosome. New t-mutations obtained in this way are sometimes recessive lethals that are indistinguishable from those in already known complementation groups. Most derived t-mutations are viable, however. This paper summarizes data on the rate and types of variants produced by members of each of the six lethal complementation groups, and by semilethal alleles. It appears that particular complementation groups preferentially generate certain types of variants, and that in general, the pattern of variant production runs "uphill," that is, to less abnormal states. The data are compatible with the hypothesis that t-mutations represent some extent of altered chromosome and that variants are produced by loss of abnormal material.     

A quantitative trait locus involved in maize yield is tightly associated to the r1 gene on the long arm of chromosome 10

We produced and studied for 3?years two synthetic populations of maize differing in their constitution only for the selected alleles present at the red color 1 (r1) locus (R-sc vs. r?Cr). r1 is a regulatory gene conferring anthocyanin pigmentation in different tissues: the R-sc allele confers pigmentation only in the aleurone seed layer, while the r?Cr allele confers pigmentation in several tissues such as root, silk and anther but the seed is colourless. The colourless population (r?Cr/r?Cr) was characterized by improved agronomic features, such as ear weight and plant height, compared with the R-sc/R-sc coloured population. This finding was confirmed by studying single F4 R/r families where the presence of the r?Cr allele conferred positive features, acting as a dominant trait. Quantitative trait locus (QTL) analysis performed using molecular markers on the long arm of chromosome 10 (bin 10.06), where the r1 gene maps, identified a QTL map position for plant height tightly associated to the r1 gene. Thus the r1 gene may represent a major QTL or it could be closely linked to another gene involved in the agronomic performance of the two populations studied.     

Time of Recombination in the DROSOPHILA MELANOGASTER Oocyte. III. Selection and Characterization of Temperature-Sensitive and -Insensitive, Recombination-Deficient Alleles in Drosophila

The procedure for the selection of a temperature-sensitive recombination mutant in Drosophila is described. Use of this procedure has led to the recovery of three alleles at a new recombination locus called rec-1, located within the region of chromosome 3 circumscribed by Deficiency (3R)sbd¹⁰⁵. One allele, rec-1²⁶, is temperature sensitive, and the other two alleles, rec-1⁶ and rec-1¹⁶, are temperature insensitive. Gene dosage studies reveal rec-1²⁶ to be a leaky mutant with greater recombination activity in two doses than in one. The other two alleles show no dose response, implying that they may be null mutants. The temperature response curves of rec-1²⁶ as a homozygote and in heteroallelic combination with rec-1¹⁶ suggest that the sharp decrease in recombination between 28° and 31° indicates temperature denaturation of an enzyme or other protein specified by the mutant and associated with the recombination process. The ability of small changes in temperature to reverse or abolish polarity in recombination along the X chromosome arm in rec-1 ²⁶/rec-1¹⁶ females brings into question the use of the "polarity" criterion to partition mutants into two functional types, i.e., precondition mutants that display polarity and exchange mutants that do not. Evidence that rec-1 may be part of a complex locus residing in a chromosome segment harboring a variety of recombination-related genes is presented.     

Genetics of the St Serotype System in TETRAHYMENA PYRIFORMIS, Syngen 1

Genetic analyses using lines of Tetrahymena pyroformis manifesting different serotypes indicate that the St serotypes are governed by alleles at a single genetic locus. These alleles are termed St^A and St^C. The St locus is not closely linked to any of the other well-studied loci examined. Differentiation in St^A/St^C heterozygotes follows a pattern very similar to that observed with lines heterozygous at the other loci. Initially both alleles are expressed, but as the synclone divides, lines develop that manifest one allele or the other but not both. The time of differentiation is very early in the clonal life cycle, and the output ratio is eccentric. The pattern of development of the St locus places it in a category with the mating type and H serotype loci.     

Sure facts, speculations, and open questions about the evolution of transposable element copy number

Transposable elements (TEs) are sequences capable of multiplying in their host's genome. They survive by increasing copy numbers due to transpositions, and natural selection washes them out because hosts with heavier loads of TEs have lower fitness. The available phylogenetic evidence supports the view that TEs have existed in living organisms for hundreds of millions of years. A fundamental question facing the field is how can an equilibrium be attained between transposition and selection which allows these parasitic genetic elements to persist for such a long time period? To answer this question, it is necessary to understand how the rate of TE transposition is controlled and to describe the mechanisms with which natural selection opposes TE accumulation. Perhaps the best models for such a study are copia and gypsy retrotransposons in Drosophila. Their average rate of transposition in nature is between 10^?5 ? 10^?4 transpositions per copy per generation. Unlike nature, transposition rates vary widely, from zero to 10^?2, between laboratory lines. This variability in transposition rate is controlled by host genes. It is probable that in nature TE site heterogeneity is caused by frequent transpositions in rare flies with permissive alleles, and no transpositions happen in the rest of flies. The average rate of TE transposition in nature may thus depend on the frequency of permissive alleles, which is a function of the rate of mutation from restrictive to permissive alleles, the mechanism and the strength of selection opposing TE multiplication, and population size. Thus, evolution of the frequency of permissive alleles of genes controlling transposition must be accounted for to understand evolution of TE copy numbers.     

Second Locus of Bacteriophage P22 Necessary for the Maintenance of Lysogeny

A temperature-sensitive allele of a locus of phage P22, known to be involved in establishment of lysogeny, has been isolated. This mutant, P22 ts mnt, forms stable lysogens at 30 C which are induced by heating to 43 C. This shows that this locus is involved in the maintenance of lysogeny. The ts mnt locus is about 18 recombination units away from the c region. The wild allele, mnt⁺, is dominant over mnt and is responsible for a cytoplasmically diffusible product.