bluuebunny/crossref_metadata_2025 huggingface dataset:
The effects of trinucleotide repeats found in human inherited disorders on palindrome inviability in Escherichia coli suggest hairpin folding preferences in vivo.
Authors: Darlow J M , Leach D R
Published: January 2021

Unusual DNA secondary structures have been implicated in the expansion of trinucleotide repeat tracts that are associated with several human inherited disorders. We present evidence consistent with the folding of these trinucleotide repeats into hairpin loops at the center of a long DNA palindrome in vivo. Our assay utilizes a palindrome in bacteriophage lambda, the center of which determines its ability to inhibit plaque formation in a manner that is consistent with folding into a hairpin or cruciform structure. We show that central inserts of even numbers of d(CAG).d(CTG) repeats inhibit plaque formation more than do odd numbers. Both d(CAG)2.d(CTG)2 and d(CGG)2.d(CCG)2 central sequences behave like DNA sequences known to form two-base loops in vitro, suggesting that they may also form compact and stable loops. By contrast, repeats of d(GAC).d(GTC) do not show any evidence consistent with unusual loop stability. These results agree with in vitro evidence that the unstable repeats can form hairpin secondary structures and suggest a favored position of folding. We discuss the potential roles of secondary structures, DNA replication and recombination in models of repeat tract expansion.
The size and continuity of DNA segments integrated in Bacillus transformation.
Authors: Zawadzki P , Cohan F M
Published: January 2021

We investigated the size and continuity of DNA segments integrated in Bacillus subtilis transformation. We transformed B. subtilis strain 1A2 toward rifampicin resistance (coded by rpoB) with genomic DNA and with a PCR-amplified 3.4-kb segment of the rpoB gene from several donors. Restriction analysis showed that smaller lengths of donor DNA integrated into the chromosome with transformation by PCR-amplified DNA than by genomic DNA. Nevertheless, integration of very short segments (< 2 kb) from large, genomic donor molecules was not a rare event. With PCR-amplified segments as donor DNA, smaller fragments were integrated when there was greater sequence divergence between donor and recipient. There was a large stochastic component to the pattern of recombination. We detected discontinuity in the integration of donor segments within the rpoB gene, probably due to multiple integration events involving a single donor molecule. The transfer of adaptations across Bacillus species may be facilitated by the small sizes of DNA segments integrated in transformation.
Recombination between chromosomal IS200 elements supports frequent duplication formation in Salmonella typhimurium.
Authors: Haack K R , Roth J R
Published: January 2021

Spontaneous tandem chromosomal duplications are common in populations of Escherichia coli and Salmonella typhimurium. They range in frequency for a given locus from 10(-2) to 10(-4) and probably form by RecA-dependent unequal sister strand exchanges between repetitive sequences in direct order. Certain duplications have been observed previously to confer a growth advantage under specific selective conditions. Tandem chromosomal duplications are unstable and are lost at high frequencies, representing a readily reversible source of genomic variation. Six copies of a small mobile genetic element IS200 are evenly distributed around the chromosome of S. typhimurium strain LT2. A survey of 120 independent chromosomal duplications (20 for each of six loci) revealed that recombination between IS200 elements accounted for the majority of the duplications isolated for three of the loci tested. Duplications of the his operon were almost exclusively due to recombination between repeated IS200 elements. These data add further support to the idea that mobile genetic elements provide sequence repeats that play an important role in recombinational chromosome rearrangements, which may contribute to adaptation of bacteria to stressful conditions.
Viable maternal-effect mutations that affect the development of the nematode Caenorhabditis elegans.
Authors: Hekimi S , Boutis P , Lakowski B
Published: January 2021

We carried out a genetic screen for viable maternal-effect mutants to identify genes with a critical function relatively early in development. This type of mutation would not have been identified readily in previous screens for viable mutants and therefore could define previously unidentified genes. We screened 30,000 genomes and identified 41 mutations falling into 24 complementation groups. We genetically mapped these 24 loci; only two of them appear to correspond to previously identified genes. We present a partial phenotypic characterization of the mutants and a quantitative analysis of the degree to which they can be maternally or zygotically rescued.
Comparative recombination distances among Zea mays L. inbreds, wide crosses and interspecific hybrids.
Authors: Williams C G , Goodman M M , Stuber C W
Published: January 2021

Recombination distances and linkage heterogeneity were compared among a wide range of maize inbreds, wide crosses and maize x teosinte hybrids. Twelve maize and four teosinte races were backcrossed to stocks fixed for rare marker alleles on chromosome arm 1L. Recombination fraction estimates were higher for exotic germplasm than for either U.S. maize or maize x teosinte crosses. Serrano, Tuxpeño and a US-adapted inbred line of tropical origin, NC300, exhibited enhanced recombination. Three of the four maize x teosinte hybrids had little or no recombination between two loci. The observed recombination "shrinkage" resulted from an apparent inversion in the vicinity of the Amp1 locus. Average recombination distances among common marker loci for composite maps were highly variable, even when map construction was restricted to maize germplasm of similar origins.
The pattern of neutral molecular variation under the background selection model.
Authors: Charlesworth D , Charlesworth B , Morgan M T
Published: January 2021

Stochastic simulations of the infinite sites model were used to study the behavior of genetic diversity at a neutral locus in a genomic region without recombination, but subject to selection against deleterious alleles maintained by recurrent mutation (background selection). In large populations, the effect of background selection on the number of segregating sites approaches the effect on nucleotide site diversity, i.e., the reduction in genetic variability caused by background selection resembles that caused by a simple reduction in effective population size. We examined, by coalescence-based methods, the power of several tests for the departure from neutral expectation of the frequency spectra of alleles in samples from randomly mating populations (Tajima's, Fu and Li's, and Watterson's tests). All of the tests have low power unless the selection against mutant alleles is extremely weak. In Drosophila, significant Tajima's tests are usually not obtained with empirical data sets from loci in genomic regions with restricted recombination frequencies and that exhibit low genetic diversity. This is consistent with the operation of background selection as opposed to selective sweeps. It remains to be decided whether background selection is sufficient to explain the observed extent of reduction in diversity in regions of restricted recombination.
Linkage analysis with an alternative formulation for the mixed model of inheritance: the finite polygenic mixed model.
Authors: Stricker C , Fernando R L , Elston R C
Published: January 2021

This paper presents an extension of the finite polygenic mixed model of Fernando et al. (1994) to linkage analysis. The finite polygenic mixed model, extended for linkage analysis, leads to a likelihood that can be calculated using efficient algorithms developed for oligogenic models. For comparison, linkage analysis of 5 simulated 4021-member pedigrees was performed using the usual mixed model of inheritance, approximated by Hasstedt (1982), and the finite polygenic mixed model extended for linkage analysis presented here. Maximum likelihood estimates of the finite polygenic mixed model could be inferred to be closer to the simulated values in these pedigrees.
pag-3, a Caenorhabditis elegans Gene Involved in Touch Neuron Gene Expression and Coordinated Movement
Authors: Jia Yiwen , Xie Guofeng , Aamodt Eric
Published: January 2021

Mutations in a newly identified gene, pag-3, cause ectopic expression of touch neuron genes mec-7, mec-7lacZ and mec-4lacZ in the lineal sisters of the ALM touch neurons, the BDU neurons. pag-3 mutants also show a reverse kinker uncoordinated phenotype. The first pag-3 allele was isolated in a screen for mutants with altered immunofluorescence staining patterns. Two additional pag-3 alleles were identified in a noncomplementation screen of 38,000 haploid genomes. All of the pag-3 alleles were recessive to wild type and cause the same phenotypes. Two-factor crosses, deficiency mapping and three-factor crosses located pag-3 to the right arm of the X chromosome between unc-3 and unc-7. Because recessive mutations in pag-3 result in expression of several touch cell specific genes in the BDU neurons, pag-3(+) must directly or indirectly suppress expression of these genes in the BDU neurons. Although pag-3 mutants did not show mec-3lacZ expression in their BDU neurons, expression of mec-7lacZ and mec-4lacZ in the BDU neurons of pag-3 mutants required mec-3(+).
Germline Transformation of Drosophila virilis Mediated by the Transposable Element hobo
Authors: Lozovskaya Elena R , Nurminsky Dmitry I , Hartl Daniel L , Sullivan David T
Published: January 2021

A laboratory strain of Drosophila virilis was genetically transformed with a hobo vector carrying the miniwhite cassette using a helper plasmid with an hsp70-driven hobo transposase-coding sequence. The rate of transformation was 0.5% per fertile G0 animal. Three transgenic insertions were cloned and characterized and found to be authentic hobo insertions. These results, together with the known widespread distribution of hobo in diverse insect species, suggest that hobo and related transposable elements may be of considerable utility in the germline transformation of insects other than D. melanogaster.
Mutation of the Axonal Transport Motor Kinesin Enhances paralytic and Suppresses Shaker in Drosophila
Authors: Hurd Daryl D , Stern Michael , Saxton William M
Published: January 2021

To investigate the possibility that kinesin transports vesicles bearing proteins essential for ion channel activity, the effects of kinesin (Khc) and ion channel mutations were compared in Drosophila using established tests. Our results show that Khc mutations produce defects and genetic interactions characteristic of paralytic (para) and maleless (mle) mutations that cause reduced expression or function of the alpha-subunit of voltage-gated sodium channels. Like para and mle mutations, Khc mutations cause temperature-sensitive (TS) paralysis. When combined with para or mle mutations, Khc mutations cause synthetic lethality and a synergistic enhancement of TS-paralysis. Furthermore, Khc mutations suppress Shaker and ether-a-go-go mutations that disrupt potassium channel activity. In light of previous physiological tests that show that Khc mutations inhibit compound action potential propagation in segmental nerves, these data indicate that kinesin activity is required for normal inward sodium currents during neuronal action potentials. Tests for phenotypic similarities and genetic interactions between kinesin and sodium/potassium ATPase mutations suggest that impaired kinesin function does not affect the driving force on sodium ions. We hypothesize that a loss of kinesin function inhibits the anterograde axonal transport of vesicles bearing sodium channels.
Adjacent Sequences Influence DNA Repair Accompanying Transposon Excision in Maize
Authors: Scott LuAnn , LaFoe Daniel , Weil Clifford F
Published: January 2021

Mobile elements transposing via DNA intermediates often leave small rearrangements, or “transposon footprints,” at sites where they excise. Each excision event leaves its own footprint and, at any given site, these vary in size and sequence. Footprint formation involves DNA repair of sequences flanking the element. We have analyzed the footprints formed by a 2-kb Ds element excising from six different sites in exons of the maize waxy (Wx) gene. We find that groups of footprints left at individual sites are surprisingly nonrandom; different excision products predominate consistently at each site. Less frequent footprints left by each insertion appear related to the predominant type. The data suggest that flanking sequences affect the DNA repair processes associated with element excision. Two models have been proposed to explain footprint formation, one featuring a 5′ exonuclease and the other featuring hairpin loop formation and an endonuclease. Our data have interesting implications for both these models. Evidence is also presented to support the presence of a separate excision mechanism that can remove Ac/Ds elements without leaving any footprint and that operates in parallel with the footprint-forming mechanism.
Genome-Wide High-Resolution Mapping by Recurrent Intermating Using Arabidopsis thaliana as a Model
Authors: Liu Sin-Chieh , Kowalski Stanley P , Lan Tien-Hung , Feldmann Kenneth A , Paterson Andrew H
Published: January 2021

We demonstrate a method for developing populations suitable for genome-wide high-resolution genetic linkage mapping, by recurrent intermating among F2 individuals derived from crosses between homozygous parents. Comparison of intermated progenies to F2 and “recombinant inbred” (RI) populations from the same pedigree corroborate theoretical expectations that progenies intermated for four generations harbor about threefold more information for estimating recombination fraction between closely linked markers than either RI-selfed or F2 individuals (which are, in fact, equivalent in this regard). Although intermated populations are heterozygous, homozygous “intermated recombinant inbred” (IRI) populations can readily be generated, combining additional information afforded by intermating with the permanence of RI populations. Intermated populations permit fine-mapping of genetic markers throughout a genome, helping to bridge the gap between genetic map resolution and the DNA-carrying capacity of modern cloning vectors, thus facilitating merger of genetic and physical maps. Intermating can also facilitate high-resolution mapping of genes and QTLs, accelerating map-based cloning. Finally, intermated populations will facilitate investigation of other fundamental genetic questions requiring a genome-wide high-resolution analysis, such as comparative mapping of distantly related species, and the genetic basis of heterosis.
Transcription of gypsy Elements in a Y-Chromosome Male Fertility Gene of Drosqbhila hydei
Authors: Hochstenbach Ron , Harhangi Harry , Schouren Karin , Bindels Petra , Suijkerbuijk Ron , Hennig Wolfgang
Published: January 2021

We have found that defective gypsy retrotransposons are a major constituent of the lampbrush loop pair Nooses in the short arm of the Y chromosome of Drosophila hydei. The loop pair is formed by male fertility gene Q during the primary spermatocyte stage of spermatogenesis, each loop being a single transcription unit with an estimated length of 260 kb. Using fluorescent in situ hybridization, we show that throughout the loop transcripts gypsy elements are interspersed with blocks of a tandemly repetitive Y-specific DNA sequence, ay1. Nooses transcripts containing both sequence types show a wide size range on Northern blots, do not migrate to the cytoplasm, and are degraded just before the first meiotic division. Only one strand of ay1 and only the coding strand of gypsy can be detected in the loop transcripts. However, as cloned genomic DNA fragments also display opposite orientations of ay1 and gypsy, such DNA sections cannot be part of the Nooses. Hence, they are most likely derived from the flanking heterochromatin. The direction of transcription of ayl and gypsy thus appears to be of a functional significance.
Rearrangements Involving Repeated Sequences Within a P Element Preferentially Occur Between Units Close to the Transposon Extremities
Authors: Pâques Frédéric , Bucheton Bruno , Wegnez Maurice
Published: January 2021

In a previous report we described rearrangements occurring at a high rate (30% of the progeny of dysgenic flies) within a cluster of 5S genes internal to a P element. These events were characterized as precise amplifications and deletions of 5S units. Here we analyze recombination events within P elements containing two repeated arrays of 5S genes flanking a central white gene. Deletions (50%) and duplications (3%) of the white gene together with various amounts of flanking 5S genes were observed. These recombinations occur preferentially between the most external 5S units of P transposons. Such rearrangements could be favored by interactions between the proteins bound to the P terminal sequences.
Estimating Long-Term Mating Systems Using DNA Sequences
Authors: Milligan Brook G
Published: January 2021

Plant mating systems often involve a mixture of self fertilizations and outcross fertilizations. The degree of selfing has a large impact on the genetic composition of natural populations and on the evolution of the mating system itself in response to such factors as inbreeding depression. This paper describes a means of estimating the long-term rate of self-fertilization from samples of alleles taken from individuals in a population. Use is made of the genealogy of pairs of alleles at a locus within individuals and pairs between individuals. The degree of selfing is closely related to the extent to which the number of nucleotide sites differing within an individual is reduced relative to the number differing between individuals. Importantly, the estimate of long-term selfing is largely independent of population size and is not affected by historical fluctuations in population size; instead it responds directly to the mating system itself. The approach outlined here is most appropriate to evolutionary problems in which the long-term nature of the mating system is of interest, such as to determine the relationship between prior inbreeding and inbreeding depression.
Synonymous Nucleotide Divergence: What Is “Saturation”?
Authors: Smith J Maynard , Smith N H
Published: January 2021

The nucleotide divergence at synonymous third sites between two lineages will increase with time since the latest common ancestor, up to some saturation level. The “null-hypothesis divergence” is defined as the percentage of difference predicted at synonymous third sites, allowing for amino acid composition and codon bias, but assuming that codon bias is the same at all sites occupied by a given amino acid, when equilibrium has been reached between forward and backward substitutions. For two highly expressed genes, gapA and ompA, in the enterobacteria, the estimated values of the null-hypothesis divergence are 39.3 and 38.15%, respectively, compared to estimated values of saturation divergence of 19.0 and 25.4%. A possible explanation for this discrepancy is that different codons for a given amino acid are favored at different sites in the same gene.
Genetic Requirements for the Single-Strand Annealing Pathway of Double-Strand Break Repair in Saccharomyces cerevisiae
Authors: Ivanov Evgeny L , Sugawara Neal , Fishman-Lobell Jacqueline , Haber James E
Published: January 2021

HO endonuclease-induced double-strand breaks (DSBs) within a direct duplication of Escherichia coli lacZ genes are repaired either by gene conversion or by single-strand annealing (SSA), with >80% being SSA. Previously it was demonstrated that the RAD52 gene is required for DSB-induced SSA. In the present study, the effects of other genes belonging to the RAD52 epistasis group were analyzed. We show that RAD51, RAD54, RAD55, and RAD57 genes are not required for SSA irrespective of whether recombination occurred in plasmid or chromosomal DNA. In both plasmid and chromosomal constructs with homologous sequences in direct orientation, the proportion of SSA events over gene conversion was significantly elevated in the mutant strains. However, gene conversion was not affected when the two lacZ sequences were in inverted orientation. These results suggest that there is a competition between SSA and gene conversion processes that favors SSA in the absence of RAD51, RAD54, RAD55 and RAD57. Mutations in RAD50 and XRS2 genes do not prevent the completion, but markedly retard the kinetics, of DSB repair by both mechanisms in the lacZ direct repeat plasmid, a result resembling the effects of these genes during mating-type (MAT) switching.
A Genome-Wide Survey of Hybrid Incompatibility Factors by the Introgression of Marked Segments of Drosophila mauritiana Chromosomes into Drosophila simulans
Authors: True John R , Weir Bruce S , Laurie Cathy C
Published: January 2021

In hybrids between Drosophila simulans and D. mauritiana, males are sterile and females are fertile, in compliance with Haldane's rule. The genetic basis of this phenomenon was investigated by introgression of segments of the mauritiana genome into a simulans background. A total of 87 positions throughout the mauritiana genome were marked with P-element insertions and replicate introgressions were made by repeated backcrossing to simulans for 15 generations. The fraction of hemizgyous X chromosomal introgressions that are male sterile is ~50% greater than the fraction of homozygous autosomal segments. This result suggests that male sterility factors have evolved at a higher rate on the X, but chromosomal differences in segment length cannot be ruled out. The fraction of homozygous autosomal introgressions that are male sterile is several times greater than the fraction that are either female sterile or inviable. This observation strongly indicates that male sterility factors have evolved more rapidly than either female sterility or inviability factors. These results, combined with previous work on these and other species, suggest that Haldane> 's rule has at least two causes: recessivity of incompatibility factors and differential accumulation of sterility factors affecting males and females.
The Drosophila engrailed and invected Genes: Partners in Regulation, Expression and Function
Authors: Gustavson Elizabeth , Goldsborough Andrew S , Ali Zehra , Kornberg Thomas B
Published: January 2021

We isolated and characterized numerous engrailed and invected alleles. Among the deficiencies we isolated, a mutant lacking invected sequences was viable and phenotypically normal, a mutant lacking engrailed was an embryo lethal and had slight segmentation defects, and a mutant lacking both engrailed and invected was most severely affected. In seven engrailed alleles, mutations caused translation to terminate prematurely in the central or C-terminal portion of the coding sequence, resulting in embryonic lethality and segmentation defects. Both engrailed and invected expression declined prematurely in these mutant embryos. In wild-type embryos, engrailed and invected are juxtaposed and are expressed in essentially identical patterns. A breakpoint mutant that separates the mgrailed and invected transcription units parceled different aspects of the expression pattern to engrailed or invected. We also found that both genes cause similar defects when expressed ectopically and that the protein products of both genes act to repress transcription in cultured cells. We propose that the varied phenotypes of the engrailed alleles can be explained by the differential effects these mutants have on the combination of engrailed and invected activities, that engrailed and invected share a regulatory region, and that they encode redundant functions.
Hermes, a Functional Non-Drosophilid Insect Gene Vector From Musca domestica
Authors: O'Brochta David A , Warren William D , Saville Kenneth J , Atkinson Peter W
Published: January 2021

Hermes is a short inverted repeat-type transposable element from the house fly, Musca domestica. Using an extra-chromosomal transpositional recombination assay, we show that Hermes elements can accurately transpose in M. domestica embryos. To test the ability of Hermes to function in species distantly related to M. domestica we used a nonautonomous Hermes element containing the Drosophila melanogaster white (w  +) gene and created D. melanogaster germline transformants. Transgenic G1, insects were recovered from 34.6% of the fertile Go adults developing from microinjected w  − embryos. This transformation rate is comparable with that observed using P or hobo vectors in D. melanogaster, however, many instances of multiple-element insertions and large clusters were observed. Genetic mapping, Southern blotting, polytene chromosome in situ hybridization and DNA sequence analyses confirmed that Hermes elements were chromosomally integrated in transgenic insects. Our data demonstrate that Hermes elements transpose at high rates in D. melanogaster and may be an effective gene vector and gene-tagging agent in this species and distantly related species of medical and agricultural importance.
Multiple Pathways for Steel Regulation Suggested by Genomic and Sequence Analysis of the Murine Steel Gene
Authors: Bedell Mary A , Copeland Neal G , Jenkins Nancy A
Published: January 2021

The Steel (Sl) locus encodes mast cell growth factor (Mgf) that is required for the development of germ cells, hematopoietic cells and melanocytes. Although the expression patterns of the Mgf gene are well characterized, little is known of the factors which regulate its expression. Here, we describe the cloning and sequence of the full-length transcription unit and the 5′ flanking region of the murine Mgf gene. The full-length Mgf mRNA consists of a short 5′ untranslated region (UTR), a 0.8-kb ORF and a long 3′ UTR. A single transcription initiation site is used in a number of mouse tissues and is located just downstream of binding sites for several known transcription factors. In the 5′ UTR, two ATGs were found upstream of the initiator methionine and are conserved among different species, suggesting that Mgf may be translationally regulated. At least two Mgf mRNAs are produced by alternative use of polyadenylation sites, but numerous other potential polyadenylation sites were found in the 3′ UTR. In addition, the 3′ UTR contains numerous sequence motifs that may regulate Mgf mRNA stability. These studies suggest multiple ways in which expression of Mgf may be regulated.
A Genetic Map of Gibberella fujikuroi Mating Population A (Fusarium moniliforme)
Authors: Xu Jin-rong , Leslie John F
Published: January 2021

We constructed a recombination-based map of the fungal plant pathogen Gibberella fujikuroi mating population A (asexual stage Fusarium moniliforme). The map is based on the segregation of 142 restriction fragment length polymorphism (RFLP) markers, two auxotrophic genes (arg1, nic1), mating type (matA+ / matA−), female sterility (ste1), spore-killer (Sk), and a gene governing the production of the mycotoxin fumonisin B1 (fum1) among 121 random ascospore progeny from a single cross. We identified 12 linkage groups corresponding to the 12 chromosome-sized DNAs previously observed in contour-clamped homogeneous electric field (CHEF) gels. Linkage groups and chromosomes were correlated via Southern blots between appropriate RFLP markers and the CHEF gels. Eleven of the 12 chromosomes are meiotically stable, but the 12th (and smallest) is subject to deletions in 3% (4/121) of the progeny. Positive chiasma interference occurred on five of the 12 chromosomes, and nine of the 12 chromosomes averaged more than one crossover per chromosome. The average kb/cM ratio in this cross is ~32.
Suppressors of the unc-73 Gene of Caenorhabditis elegans
Authors: Run Jin-Quan , Steven Robert , Hung Ming-shiu , van Weeghel Rob , Culotti Joseph G , Way Jeffrey C
Published: January 2021

The unc-73 gene of Caenorhabditis elegans is necessary for proper axon guidance. Animals mutant in this gene are severely uncoordinated and also exhibit defects in cell migration and cell lineages. We have isolated coordinated revertants of unc-73(e936). These fall into three classes: intragenic revertants, extragenic dominant suppressors (sup-39), and a single apparently intragenic mutation that is a dominant suppressor with a linked recessive lethal phenotype. sup-39 mutations cause early embryonic lethality, but escapers have a wild-type movement phenotype as larvae and adults. Gonads of sup-39 mutant animals show a novel defect: normal gonads have a single row of oocytes, but sup-39 gonads often have two rows of oocytes. This result suggests that the mutant gonad is defective in choosing on its surface only a single site from which nuclei will emerge to form oocytes. These results are interpreted in terms of an effect of unc-73 on determination of cell polarity.
Effects of Single P-Element Insertions on Bristle Number and Viability in Drosophila melanogaster
Authors: Lyman Richard F , Lawrence Faye , Nuzhdin Sergey V , Mackay Trudy F C
Published: January 2021

Single P-element mutagenesis was used to construct 1094 lines with P[lArB] inserts on all three major chromosomes in an isogenic background previously free of P elements. The effects of insertions on bristle number and on viability were assessed by comparison to 392 control lines. The variance and effects of P-element inserts on bristle number and viability were larger than those inferred from spontaneous mutations. The distributions of effects on bristle number were symmetrical and highly leptokurtic, such that a few inserts with large effects caused most of the increase in variance. The distribution of effects on viability were negatively skewed and platykurtic. On average, the effects of P-element insertions on bristle number were partly recessive and on viability were completely recessive. P-element inserts with large effects on bristle number tended to have reduced viability, but the correlation between the absolute value of the effects on bristle number and on viability was not strong. Fifty P-element inserts tagging quantitative trait loci (QTLs) with large effects on bristle number were mapped cytogenetically. Two P-element-induced scabrous alleles and five extramacrochaetae alleles were generated. Single P-element mutagenesis is a powerful method for identifylng QTLs at the level of genetic locus.
Courtship Anomalies Caused by doublesex Mutations in Drosophila melanogaster
Authors: Villella Adriana , Hall Jeffrey C
Published: January 2021

The role played by the sex-deterrnining gene doublesex (dsx) and its influence on Drosophila courtship were examined. Against a background of subnormal male-like behavior that is reported to be an attribute of haplo-X flies homozygous for the original dsx mutation, and given that a sex-specific muscle is unaffected by genetic variation at this locus, analyses of several reproductive behaviors and control for genetic background effects indicated that XY dsx mutants are impaired in their willingness to court females. When they did court, certain behavioral actions were normal, including components of courtship song. However, these mutants never produced courtship humming sounds. Mature XY dsx flies elicited anomalously high levels of courtship; that this occurs merely because of a delay in imaginal development was experimentally discounted. The current analysis reconciled two ostensibly conflicting reports involving the courtship-stimulating qualities of this mutant type. Such experiments also uncovered a new behavioral anomaly: dsx mutations caused chromosomal males to court other males at abnormally high levels. These results are discussed from the perspective of doublesex's influence on internal tissues of adult Drosophila involved in the triggering and neural control of male- and female-like elements of courtship, reproductive pheromone production, or a combination of such factors.
The yl Gene of Maize Codes for Phytoene Synthase
Authors: Buckner Brent , Miguel Phillip San , Janick-Buckner Diane , Bennetzen Jeffrey L
Published: January 2021

The cloned yl locus of maize was sequenced and found to encode phytoene synthase. Different “wild-type” alleles of the locus were found to differ by the insertion of transposable elements in their promoter and polyA addition regions, and by the length of a CCA tandem repeat series, without any obvious effect on function of the gene. A dominant Yl (“wild-type”) allele was observed to be expressed at highest levels in the seedling but also in the embryo and endosperm. The Mu3 transposable element insertion responsible for a pastel allele of yl, which gives lowered levels of carotenoids in the endosperm of kernels and seedlings grown at high temperatures, was located in the 5′ end of the gene. Although the size of the transcript from this yl mutation suggests that the Mu3 element provides the promoter for this allele, leaf tissue in this mutant line contained approximately normal amounts of yl mRNA. A recessive allele of yl, which conditions normal levels of carotenoids in the embryo and seedling, but almost no carotenoids in the endosperm, was found to accumulate normal amounts of yl mRNA in the seedling and embryo, while yl transcripts were not detected in the endosperm.
A Generalization of the Mixture Model in the Mapping of Quantitative Trait Loci for Progeny From a Biparental Cross of Inbred Lines
Authors: Fisch R D , Ragot M , Gay G
Published: January 2021

The recent advent of molecular markers has created a great potential for the understanding of quantitative inheritance. In parallel to rapid developments and improvements in molecular marker technologies, biometrical models have been constructed, refined and generalized for the mapping of quantitative trait loci (QTL). However, current models present restricitions in terms of breeding designs to which they apply. In this paper, we develop an approach for the generalization of the mixture model for progeny from a single bi-parental cross of inbred lines. Detailed derivations are given for genetic designs involving populations developed by selfing, i.e., where marker genotypes are obtained from Fx (x ≤ 2) individuals and where phenotypes are measured on Fy (y ≥ x) individuals or families. Extensions to designs involving doubled-haploids, backcrossderived individuals and random matings are outlined. The derivations presented here can easily be combined with current QTL mapping approaches.
Establishing Genetic Interactions by a Synthetic Dosage Lethality Phenotype
Authors: Kroll Eugene S , Hyland Katherine M , Hieter Philip , Li Joachim J
Published: January 2021

We have devised a genetic screen, termed synthetic dosage lethality, in which a cloned “reference” gene is inducibly overexpressed in a set of mutant strains carrying potential “target” mutations. To test the specificity of the method, two reference genes, CTF13, encoding a centromere binding protein, and ORC6, encoding a subunit of the origin of replication binding complex, were overexpressed in a large collection of mutants defective in either chromosome segregation or replication. CTF13 overexpression caused synthetic dosage lethality in combination with ctf14-42 (cbf2, ndc10), ctf17-61 (ch14), ctf19-58 and ctf19-26. ORC6 overexpression caused synthetic dosage lethality in combination with cdc2-1, cdc6-l, cdc14-1, cdcl6-1 and cdc46-1. These relationships reflect specific interactions, as overexpression of CTF13 caused lethality in kinetochore mutants and overexpression of ORC6 caused lethality in replication mutants. In contrast, only one case of dosage suppression was observed. We suggest that synthetic dosage lethality identifies a broad spectrum of interacting mutations and is of general utility in detecting specific genetic interactions using a cloned wild-type gene as a starting point. Furthermore, synthetic dosage lethality is easily adapted to the study of cloned genes in other organisms.
Suppression Analysis Reveals a Functional Difference Between the Serines in Positions Two and Five in the Consensus Sequence of the C-Terminal Domain of Yeast RNA Polymerase II
Authors: Yuryev Anton , Corden Jeffry L
Published: January 2021

The largest subunit of RNA polymerase II contains a repetitive C-terminal domain (CTD) consisting of tandem repeats of the consensus sequence TyrlSer2Pro3Thr4Ser5Pro6Ser7. Substitution of nonphosphe rylatable amino acids at positions two or five of the Saccharomyces cerevisiae CTD is lethal. We developed a selection ssytem for isolating suppressors of this lethal phenotype and cloned a gene, SCA1 (suppressor of CTD alanine), which complements recessive suppressors of lethal multiple-substitution mutations. A partial deletion of SCA1 (sca1Δ::hisG) suppresses alanine or glutamate substitutions at position two of the consensus CTD sequence, and a lethal CTD truncation mutation, but SCA1 deletion does not suppress alanine or glutamate substitutions at position five. SCA1 is identical to SRB9, a suppressor of a cold-sensitive CTD truncation mutation. Strains carrying dominant SRB mutations have the same suppression properties as a sca1Δ::hisG strain. These results reveal a functional difference between positions two and five of the consensus CTD heptapeptide repeat. The ability of SCA1 and SRB mutant alleles to suppress CTD truncation mutations suggest that substitutions at position two, but not at position five, cause a defect in RNA polymerase II function similar to that introduced by CTD truncation.
Meiotic Recombination Initiated by a Double-Strand Break in rad50Δ Yeast Cells Otherwise Unable to Initiate Meiotic Recombination
Authors: Malkova A , Ross L , Dawson D , Hoekstra Merl F , Haber J E
Published: January 2021

Meiotic recombination in Saccharomyces cerevisiae is initiated by double-strand breaks (DSBs). We have developed a system to compare the properties of meiotic DSBs with those created by the site-specific HO endonuclease. HO endonuclease was expressed under the control of the meiotic-specific SPO13 promoter, creating a DSB at a single site on one of yeast's 16 chromosomes. In Rad+ strains the times of appearance of the HO-induced DSBs and of subsequent recombinants are coincident with those induced by normal meiotic DSBs. Physical monitoring of DNA showed that SPO13::HO induced gene conversions both in Rad+ and in rad50Δ cells that cannot initiate normal meiotic DSBs. We find that the RAD50 gene is important, but not essential, for recombination even after a DSB has been created in a meiotic cell. In rad50Δ cells, some DSBs are not repaired until a broken chromosome has been packaged into a spore and is subsequently germinated. This suggests that a broken chromosome does not signal an arrest of progression through meiosis. The recombination defect in rad50Δ diploids is not, however, meiotic specific, as mitotic rad50 diploids, experiencing an HO-induced DSB, exhibit similar departures from wild-type recombination.
DLH1 is a Functional Candida albicans Homologue of the Meiosis-Specific Gene DMC1
Authors: Diener Andrew C , Fink Gerald R
Published: January 2021

DMC1/LIM15 homologue 1 (DLH1), a gene related to meiosis-specific genes, has been isolated from Candida albicans, a fungus thought not to undergo meiosis. The deduced protein sequence of DLH1 contains 74% amino acid identity with Dmclp from Saccharomyces cermisiae and 63% with Liml5p from the plant Lilium long)lmm, meiosisspecific homologues of Escherichia coli RecA. Candida DLH1 complements a dmcl/dmcl null mutant in S. cermisiae: High copy expression of DLH1 restores both sporulation and meiotic recombination to a Saccharomyces dmclΔ/dmclΔ strain. Unlike the DMCl gene, which is transcribed only in meiotic cells, the heterologous Candida DLH1 gene is transcribed in both vegetative and meiotic cells of S. cermisiae. Transcription of DLH1 is not detected or induced in C. albicans under conditions that induce DMC1 and meiosis in S. cermisiae. The presence of an intact homologue of a meiosis-specific gene in C. albicans raises the possibility that this organism has a cryptic meiotic pathway.
Genetic Map of Diploid Wheat, Triticum monococcum L., and Its Comparison With Maps of Hordeum vulgare L.
Authors: Dubcovsky Jorge , Luo Ming-Cheng , Zhong Gan-Yuan , Bransteitter Ronda , Desai Amrita , Kilian Andrzej , Kleinhofs Andris , Dvořák Jan
Published: January 2021

A genetic map of diploid wheat, Triticum monococcum L., involving 335 markers, including RFLP DNA markers, isozymes, seed storage proteins, rRNA, and morphological loci, is reported. T. monococcum and barley linkage groups are remarkably conserved. They differ by a reciprocal translocation involving the long arms of chromosomes 4 and 5, and paracentric inversions in the long arm of chromosomes 1 and 4; the latter is in a segment of chromosome arm 4L translocated to 5L in T. monococcum. The order of the markers in the inverted segments in the T. monococcum genome is the same as in the B and D genomes of T. aestivum L. The T. monococcum map differs from the barley maps in the distribution of recombination within chromosomes. The major 5s rRNA loci were mapped on the short arms of T. monococcum chromosomes 1 and 5 and the long arms of barley chromosomes 2 and 3. Since these chromosome arms are colinear, the major 5s rRNA loci must be subjected to positional changes in the evolving Triticeae genome that do not perturb chromosome colinearity. The positional changes of the major 5s rRNA loci in Triticeae genomes are analogous to those of the 18S5.8S26S rRNA loci.
A Genetic Analysis of pannier, a Gene Necessary for Viability of Dorsal Tissues and Bristle Positioning in Drosophila
Authors: Heitzler Pascal , Haenlin Marc , Ramain Philippe , Calleja Manuel , Simpson Pat
Published: January 2021

A genetic and phenotypic analysis of the gene pannier is described. Animals mutant for strong alleles die as embryos in which the cells of the amnioserosa are prematurely lost. This leads to a dorsal cuticular hole. The dorsal-most cells of the imagos are also affected: viable mutants exhibit a cleft along the dorsal midline. pannier mRNA accumulates specifically in the dorsal-most regions of the embryo and the imaginal discs. Viable mutants and mutant combinations also affect the thoracic and head bristle patterns in a complex fashion. Only those bristles within the area of expression of pannier are affected. A large number of alleles have been studied and reveal that pannier may have opposing effects on the expression of achaete and scute leading to a loss or a gain of bristles.
The Broom of the Sorcerer's Apprentice: The Fine Structure of a Chromosomal Region Causing Reproductive Isolation Between Two Sibling Species of Drosophila
Authors: Davis Andrew W , Wu Chug-I
Published: January 2021

How many genes contribute to reproductive isolation between closely related species? We determined the number of genes located in the 9D-12B region of the Drosophila mauritiana X chromosome that cause hybrid male sterility in a D. simulans background. Previous low resolution studies suggested that a single hybrid sterility factor was associated with this region. In this study, by taking advantage of a cluster of visible and DNA markers, we identified three D. mauritiana factors in this region and then subjected one of them to detailed analysis. This factor again turned out to be comprised of three factors; one of which, mapped to within 200 kb, may in fact be two factors. The title refers to this exercise of splitting sterile introgressions into ever smaller ones, each of which retains partial or full sterility effects. In a region representing a mere 3% of the Drosophila genome, no fewer than six loci of hybrid sterility were identified between two sibling species that have not shown clear divergence at the molecular level. These results suggest that levels of genetic divergence between closely related species may be quite high for functionally important traits even when the opposite is true for randomly chosen loci.
Speciation by Reinforcement: A Model Derived from Studies of Drosophila
Authors: Kelly John K , Noor Mohamed A F
Published: January 2021

Reinforcement is an increase in premating reproductive isolation between taxa resulting from selection against hybrids. We present a model of reinforcement with a novel type of selection on female mating behavior. Previous models of reinforcement have focused on the divergence of female mating preferences between nascent species. We suggest that an increase in the level of female mating discrimination can yield reinforcement without further divergence of either male characters or female preferences. This model indicates that selection on mating discrimination is a viable mechanism for reinforcement and may allow speciation under less stringent conditions than selection on female preference. This model also incorporates empirical results from genetic studies of hybrid fitness determination in Drosophila species. We find that the details of inheritance, which include sex-linked transmission, sex-limited fertility reduction, and X-autosome epistasis, have important effects on the likelihood of reinforcement. In particular, X-autosome epistasis for hybrid fitness determination facilitates reinforcement when hybrid fertility reduction occurs in males, but hinders the process when it occurs in females. Haldane's rule indicates that hybrid sterility will generally evolve in males prior to females within nascent species. Thus, Haldane's rule and X-autosome epistasis provide conditions that are surprisingly favorable for reinforcement in Drosophila.
Repair of Double-Strand Breaks in Bacteriophage T4 by a Mechanism That Involves Extensive DNA Replication
Authors: George James W , Kreuzer Kenneth N
Published: January 2021

We investigated double-strand break (dsb) repair in bacteriophage T4 using a physical assay that involves a plasmid substrate with two inverted DNA segments. A dsb introduced into one repeat during a T4 infection induces efficient dsb repair using the second repeat as a template. This reaction is characterized by the following interesting features. First, the dsb induces a repair reaction that is directly coupled to extensive plasmid replication; the repaired/replicated product is in the form of long plasmid concatemers. Second, repair of the dsb site is frequently associated with exchange of flanking DNA. Third, the repair reaction is absolutely dependent on the products of genes uvsX, uusY, 32, 46, and 59, which are also required for phage genomic recombination-dependent DNA replication. Fourth, the coupled repair/replication reaction is only partly dependent on endonuclease VII (gp49), suggesting that either another Holliday-junction-cleaving activity or an alternate resolution pathway is active during T4 infections. Because this repair reaction is directly coupled to extensive replication, it cannot be explained by the Szostak  et al. model. We present and discuss a model for the coupled repair/replication reaction, called the extensive chromosome replication model for dsb repair.