bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative Genetics of Sperm Precedence in Drosophila melanogaster
Authors: Hughes Kimberly A
Published: January 2021

To assess the genetic basis of sperm competition under conditions in which it occurs, I estimated additive, dominance, homozygous and environmental variance components, the effects of inbreeding, and the weighted average dominance of segregating alleles for two measures of sperm precedence in a large, outbred laboratory population. Both first and second male precedence show significant decline on inbreeding. Second male precedence demonstrates significant dominance variance and homozygous genetic variance, but the additive variance is low and not significantly different from zero. For first male precedence, the variance among homozygous lines is again significant, and dominance variance is larger than the additive variance, but is not statistically significant. In contrast, male mating success and other fitness components in Drosophila generally exhibit significant additive variance and little or no dominance variance. Other recent experiments have shown significant genotypic variation for sperm precedence and have associated it with allelic variants of accessory-gland proteins. The contrast between sperm precedence and other male fitness traits in the structure of quantitative genetic variation suggests that different mechanisms maybe responsible for the maintenance of variation in these traits. The pattern of genetic variation and inbreeding decline shown in this experiment suggests that one or a few genes with major effects on sperm precedence may be segregating in this population.
A Salmonella Phage-P22 Mutant Defective in Abortive Transduction
Authors: Benson Nicholas R , Roth John
Published: January 2021

In the course of a lytic infection the Salmonella phage P22 occasionally encapsulates bacterial DNA instead of phage DNA. Thus, phage lysates include two classes of viral particles. Phage particles carrying bacterial DNA are referred to as transducing particles and deliver this DNA to a host as efficiently as particles carrying phage DNA. Once injected, the transduced DNA can either recombine with the recipient chromosome to form a “complete” transductant, or it can establish itself as an expressible, nonreplicating genetic element and form an “abortive” transductant. In this work, we describe a P22-phage mutant with reduced ability to form abortive transductants. The mutation responsible for this phenotype, called tdx-1, was found as one of two mutations contributing to the high-transducing phenotype of the P22-mutant HT12/4. In addition, the tdx-1 mutation is lethal when combined with an erf-am mutation. The tdx-1 mutation has been mapped to a region of the P22 genome that encodes several injected proteins and may involve more than one mutant locus. The phenotypes of the tdx-1 mutation suggest that the Tdx protein(s) normally assist in the circularization of the P22 genome and also contribute to the formation of DNA circles thought to be required for abortive transduction.
The Mutation masculinizer (man) Defines a Sex-Determining Gene With Maternal and Zygotic Functions in Musca domestica L.
Authors: Schmidt R , Hediger M , Nöthiger R , Dübendorfer A
Published: January 2021

In Musca domestica, the primary signal for sex determination is the dominant factor M, which is assumed to regulate a postulated female-determining gene F. Presence of M prevents expression of F so that male development ensues. In the absence of M, F can become active, which dictates the female pathway. The existence of F is inferred from FD, a dominant factor that is epistatic to M. We describe a new mutation masculinizer, which has all the properties expected for a null or strongly hypomorphic allele of F: (1) it maps to the same chromosomal location as FD, (2) homozygous man/man animals develop as males, (3) homozygous man/man clones generated in man/+ female larvae differentiate male structures, (4) man has a sex-determining maternal effect. About a third of the morphological males synthesize yolk proteins, which indicates that they are intersexual in internal structures. The maternal effect of man is complete in offspring that derive from homozygous man/man pole cells transplanted into female hosts. In this case, all man/+ progeny become fertile males that do not produce yolk proteins. A sex-determining maternal effect has previously been demonstrated for FD. Like F, maternal man  + is needed for zygotic man  + to become active, providing further evidence that man is a loss-of-function allele of F.
The Evolution of Mammalian Olfactory Receptor Genes
Authors: Issel-Tarver Laurie , Rine Jasper
Published: January 2021

We performed a comparative study of four subfamilies of olfactory receptor genes first identified in the dog to assess changes in the gene family during mammalian evolution, and to begin linking the dog genetic map to that of humans. The human subfamilies were localized to chromosomes 7, 11, and 19. The two subfamilies that were tightly linked in the dog genome were also tightly linked in the human genome. The four subfamilies were compared in human (primate), horse (perissodactyl), and a variety of artiodactyls and carnivores. Some changes in gene number were detected, but overall subfamily size appeared to have been established before the divergence of these mammals 60–100 million years ago.
Microsatellite Genetic Distances With Range Constraints: Analytic Description and Problems of Estimation
Authors: Feldman Marcus W , Bergman Aviv , Pollock David D , Goldstein David B
Published: January 2021

Statistical properties of the symmetric stepwise-mutation model for microsatellite evolution are studied under the assumption that the number of repeats is strictly bounded above and below. An exact analytic expression is found for the expected products of the frequencies of alleles separated by k repeats. This permits characterization of the asymptotic behavior of our distances D1 and (δμ)2 under range constraints. Based on this characterization we develop transformations that partially restore linearity when allele size is restricted. We show that the appropriate transformation cannot be applied in the case of varying mutation rates (β) and range constraints (R) because of statistical difficulties. In the special case of no variation in β and R across loci, however, the transformation simplifies to a usable form and results in a distance much more linear with time than distances developed for an infinite range. Although analytically incorrect in the case of variation in β and R, the simpler transformation is surprisingly insensitive to variation in these parameters, suggesting that it may have considerable utility in phylogenetic studies.
Highly Mismatched Molecules Resembling Recombination Intermediates Efficiently Transform Mismatch Repair Proficient Escherichia coli
Authors: Westmoreland James , Porter Gregory , Radman Miroslav , Resnick Michael A
Published: January 2021

The ability of related DNAs to undergo recombination decreases with increased sequence divergence. Mismatch repair has been proposed to be a key factor in preventing homeologous recombination; however, the contribution of mismatch repair is not universal. Although mismatch repair has been proposed to act by preventing strand exchange and/or inactivating multiply mismatched heteroduplexes, there has been no systematic study to determine at what step(s) in recombination mismatch repair acts in vivo. Since heteroduplex is a commonly proposed intermediate in many models of recombination, we have investigated the consequences of mismatch repair on plasmids that are multiply mismatched in heteroduplex structures that are similar to those that might arise during recombination. Plasmids containing multiply mismatched regions were transformed into wild-type and Mut–  Eschericia coli mutants. There was only a 30–40% reduction in transformation of Mut+ as compared to mutS and mutL strains for DNAs containing an 18% mismatched heteroduplex. The products obtained from mutS hosts differed from those obtained from Mut+ hosts in that there were many more colonies containing mixtures of two plasmids, due to survival of both strands of the heteroduplex. There were nearly 10 times more recombinants obtained from the mutS as compared to the wild-type host. Based on these results and those from other studies with E. coli and yeast, we propose that the prevention of recombination between highly diverged DNAs may be at a step earlier than heteroduplex formation.
RAD9, RAD17, and RAD24 Are Required for S Phase Regulation in Saccharomyces cerevisiae in Response to DNA Damage
Authors: Paulovich A G , Margulies R U , Garvik B M , Hartwell L H
Published: January 2021

We have previously shown that a checkpoint dependent on MEC1 and RAD53 slows the rate of S phase progression in Saccharomyces cerevisiae in response to alkylation damage. Whereas wild-type cells exhibit a slow S phase in response to damage, mec1-1 and rad53 mutants replicate rapidly in the presence or absence of DNA damage. In this report, we show that other genes (RAD9, RAD17, RAD24) involved in the DNA damage checkpoint pathway also play a role in regulating S phase in response to DNA damage. Furthermore, RAD9, RAD17, and RAD24 fall into two groups with respect to both sensitivity to alkylation and regulation of S phase. We also demonstrate that the more dramatic defect in S phase regulation in the mec1-1 and rad53 mutants is epistatic to a less severe defect seen in rad9Δ, rad17Δ, and rad24Δ. Furthermore, the triple rad9Δ rad17Δ rad24Δ mutant also has a less severe defect than mec1-1 or rad53 mutants. Finally, we demonstrate the specificity of this phenotype by showing that the DNA repair and/or checkpoint mutants mgt1Δ, mag1Δ, apn1Δ, rev3Δ, rad18Δ, rad16Δ, dun1-Δ100, sad4-1, tel1Δ, rad26Δ, rad51Δ, rad52-1, rad54Δ, rad14Δ, rad1Δ, pol30–46, pol30–52, mad3Δ, pds1Δ/esp2Δ, pms1Δ, mlh1Δ, and msh2Δ are all proficient at S phase regulation, even though some of these mutations confer sensitivity to alkylation.
Proteolytic Activation of Rim1p, a Positive Regulator of Yeast Sporulation and Invasive Growth
Authors: Li Weishi , Mitchell Aaron P
Published: January 2021

In the yeast Saccharomyces cerevisiae, rim1, 8, 9, or 13 mutations cause four phenotypes: poor growth at low temperature, altered colony morphology, inefficient sporulation due to reduced expression of the meiotic activator IME1, and, as shown here, defective invasive growth. In this report, we have determined the relationship between RIM1 and the other genes, RIM8, 9, and 13, in this group. We have analyzed production of epitope-tagged Rim1p derivatives with HA epitopes at the N-terminus or in the middle of the protein. These Rim1p derivatives exist primarily as a small form (90 kD for Rim1-HA2p) in wild-type cells and as a large form (98 kD for Rim1-HA2p) in rim8, 9, and 13 mutants. We have also analyzed production of β-galactosidase in strains that express a RIM1-lacZ fusion gene. β-galactosidase exists primarily as a ∼130 kD form in wild-type cells and as a ∼190 kD form in rim9 mutants. These results indicate that Rim1p undergoes C-terminal proteolytic cleavage, and that rim8, 9, and 13 mutations block cleavage. Expression of a Rim1p C-terminal deletion derivative suppresses rim8, 9, and 13 mutations. Thus the phenotypes of rim8, 9, and 13 mutants arise from the defect in Rim1p C-terminal cleavage. Cleavage of Rim1p, like that of its Aspergillus nidulans homologue PacC, is stimulated under alkaline growth conditions. Therefore, Rim1p, PacC and their respective processing pathways may represent a conserved signal transduction pathway.
Nucleotide Variation and Conservation at the dpp Locus, a Gene Controlling Early Development in Drosophila
Authors: Richter Brent , Long Manyuan , Lewontin R C , Nitasaka Eiji
Published: January 2021

A study of polymorphism and species divergence of the dpp gene of Drosophila has been made. Eighteen lines from a population of D. melanogaster were sequenced for 5200 bp of the Hin region of the gene, coding for the dpp polypeptide. A comparison was made with sequence from D. simulans. Ninety-six silent polymorphisms and three amino acid replacement polymorphisms were found. The overall silent polymorphism (0.0247) is low, but haplotype diversity (0.0066 for effectively silent sites and 0.0054 for all sites) is in the range found for enzyme loci. Amino acid variation is absent in the N-terminal signal peptide, the C-terminal TGF-β peptide and in the N-terminal half of the pro-protein region. At the nucleotide level there is strong conservation in the middle half of the large intron and in the 3′ untranslated sequence of the last exon. The 3′ untranslated conservation, which is perfect for 110 bp among all the divergent species, is unexplained. There is strong positive linkage disequilibrium among polymorphic sites, with stretches of apparent gene conversion among originally divergent sequences. The population apparently is a migration mixture of divergent clades.
Suppression of pdc2 Regulating Pyruvate Decarboxylase Synthesis in Yeast
Authors: Velmurugan Soundarapandian , Lobo Zita , Maitra Pabitra K
Published: January 2021

Mutants lacking pyruvate decarboxylase cannot grow on glucose. We have isolated three different complementation groups of extragenic suppressors that suppress mutations in pdc2, a regulatory locus required for the synthesis of the glycolytic enzyme pyruvate decarboxylase. The most frequent of these is a recessive mutation in the structural gene PFK1 of the soluble phosphofructokinase. The other class XSP18 (extragenic suppressor of pdc2) is a dominant temperature-sensitive suppressor that allows the cells to grow on glucose only at 30° but not at 36°. It also affects the normal induction of the glucose-inducible enolase 2, which can be rescued by providing a copy of wild-type xsp18 in trans-heterozygotes. The pyruvate decarboxylase activity in the triple mutant pdc2 pfk1 XSP18 is nearly equal to the sum of the activities in the two double mutants pdc2 pfk1 and pdc2 XSP18, respectively. This implies that the two suppressors act through independent pathways or that there is no cooperativity between them. In the pdc2 pfk1 XSP18 strain, pfk1 suppresses the loss of induction of glucose-inducible enolase 2 brought about by XSP18, but fails to rescue temperature sensitivity. The third class (xsp37) supports the growth of the pdc2 mutant on glucose but fails to support growth on gluconeogenic carbon sources. All the three suppressors suppress pdc2Δ as well and act on PDC1 at the level of transcription.
The Evolution of Ribosomal DNA Divergent Paralogues and Phylogenetic Implications
Authors: Buckler Edward S , Ippolito Anthony , Holtsford Timothy P
Published: January 2021

Although nuclear ribosomal DNA (rDNA) repeats evolve together through concerted evolution, some genomes contain a considerable diversity of paralogous rDNA. This diversity includes not only multiple functional loci but also putative pseudogenes and recombinants. We examined the occurrence of divergent paralogues and recombinants in Gossypium, Nicotiana, Tripsacum, Winteraceae, and Zea ribosomal internal transcribed spacer (ITS) sequences. Some of the divergent paralogues are probably rDNA pseudogenes, since they have low predicted secondary structure stability, high substitution rates, and many deamination-driven substitutions at methylation sites. Under standard PCR conditions, the low stability paralogues amplified well, while many high-stability paralogues amplified poorly. Under highly denaturing PCR conditions (i.e., with dimethylsulfoxide), both low- and high-stability paralogues amplified well. We also found recombination between divergent paralogues. For phylogenetics, divergent ribosomal paralogues can aid in reconstructing ancestral states and thus serveas good outgroups. Divergent paralogues can also provide companion rDNA phylogenies. However, phylogeneticists must discriminate among families of divergent paralogues and recombinants or suffer from muddled and inaccurate organismal phylogenies.
Secondary Tetrasomic Segregation of MDH-B and Preferential Pairing of Homeologues in Rainbow Trout
Authors: Allendorf Fred W , Danzmann Roy G
Published: January 2021

We examined the inheritance of allelic variation at an isozyme locus, MDH-B, duplicated by ancestral polyploidy in salmonid fishes. We detected only disomic segregation in females. Segregation ratios in males were best explained by a mixture of disomic and tetrasomic inheritance. We propose a two-stage model of pairing in male meiosis in which, first, homologous chromosomes pair and recombine in the proximal region of the chromosome. Next, homeologous chromosomes pair and recombine distally. We suggest that this type of tetrasomic inheritance in which centromeres segregate disomically should be referred to as “secondary tetrasomy” to distinguish it from tetrasomy involving entire chromosomes (i.e., “primary tetrasomy”). Differences in segregation ratios between males indicate differences between individuals in the amount of recombination between homeologous chromosomes. We also consider the implication of these results for estimation of allele frequencies at duplicated loci in salmonid populations.
The Location of Genes Governing Long First Internode of Corn
Authors: Troyer A Forrest
Published: January 2021

Knowing breeding behavior and cytological location of traits helps breeders. My objective was to locate dominant genes for long first internode of corn (Zea mays L.). I determined that Hopi Indian corn PI213733 (variety Komona) displayed the trait and grew well in the U.S. Corn Belt. I crossed PI213733 to 26 translocation tester stocks in Minnesota inbred A188 background, backcrossed semi-sterile plants carrying the translocation to A188 the next generation, and grew the segregating generation planted in trenches 15 cm deep with ridges of dirt 10 cm high one year, in trenches 25 cm deep the other year and also at normal (6 cm) depth. Emerged plants were classified for semi-sterility or for normal pollen. I concluded from multiple testers for each chromosome arm that dominant genes for long first internode are located (chromosome and region) on 3S, on 6 near the centromere, and on 9S; spurious associations occurred for two testers. Measurement of cell lengths indicated that PI213733 had more cells than A188 both in upper and in lower mesocotyl sections and that lower, older cells elongated sooner. I found a normal-sized kernel with twin embryos that developed two long first internode seedlings indicating that the amount of endosperm did not limit mesocotyl growth.
Fine-Scale Mapping of Quantitative Trait Loci Using Historical Recombinations
Authors: Xiong Momiao , Guo Sun-Wei
Published: January 2021

With increasing popularity of QTL mapping in economically important animals and experimental species, the need for statistical methodology for fine-scale QTL mapping becomes increasingly urgent. The ability to disentangle several linked QTL depends on the number of recombination events. An obvious approach to increase the recombination events is to increase sample size, but this approach is often constrained by resources. Moreover, increasing the sample size beyond a certain point will not further reduce the length of confidence interval for QTL map locations. The alternative approach is to use historical recombinations. We use analytical methods to examine the properties of fine QTL mapping using historical recombinations that are accumulated through repeated intercrossing from an F2 population. We demonstrate that, using the historical recombinations, both simple and multiple regression models can reduce significantly the lengths of support intervals for estimated QTL map locations and the variances of estimated QTL map locations. We also demonstrate that, while the simple regression model using historical recombinations does not reduce the variances of the estimated additive and dominant effects, the multiple regression model does. We further determine the power and threshold values for both the simple and multiple regression models. In addition, we calculate the Kullback-Leibler distance and Fisher information for the simple regression model, in the hope to further understand the advantages and disadvantages of using historical recombinations relative to F2 data.
A Dominant Mutation in the Chlamydomonas reinhardtii Nuclear Gene SIM30 Suppresses Translational Defects Caused by Initiation Codon Mutations in Chloroplast Genes
Authors: Chen Xuemei , Simpson Clare L , Kindle Karen L , Stern David B
Published: January 2021

A suppressor of a translation initiation defect caused by an AUG to AUU mutation in the Chlamydomonas reinhardtii chloroplast petD gene was isolated, defining a nuclear locus that we have named SIM30. A dominant mutant allele at this locus, sim30-1d, was found to increase the translation initiation rate of the mutant petD mRNA. sim30-1d was also able to suppress the translational defect caused by an AUG to AUC mutation in the petD gene, and an AUG to AUU mutation in the chloroplast petA gene. We therefore suggest that the SIM30 gene may encode a general chloroplast translation factor. The ability of sim30-1d to suppress the petD AUG to AUU mutation is diminished in the presence of one or more antibiotic resistance markers located within the 16S and 23S rRNAs, suggesting that the activity of the sim30-1d gene product in translation initiation may involve interaction with ribosomal subunits.
Selective Introgression of Paracentric Inversions Between Two Sibling Species of the Anopheles gambiae Complex
Authors: della Torre A , Merzagora L , Powell J R , Coluzzi M
Published: January 2021

The Anopheles gambiae complex includes the major vectors of malaria in sub-Saharan Africa where >80% of all world-wide cases occur. These mosquitoes are characterized by chromosomal inversions associated to the speciation process and to intraspecific ecological and behavioral flexibility. It has been postulated that introgressive hybridization has selectively transferred inversions on the second chromosome between A. gambiae and A. arabiensis, the two most important vectors of malaria. Here we directly test this hypothesis with laboratory experiments in which hybrid populations were established and the fate of chromosomal inversions were followed. Consistent with the hypothesis, “foreign” X chromosomes were eliminated within two generations, while some “foreign” second chromosomes persisted for the duration of the experiments and, judging from the excess of heterozygotes, established stable heterotic polymorphisms. Only those second chromosome inversions found naturally in the species could be introgressed.
Isolation of Mutations in the Drosophila Homologues of the Human Neurofibromatosis 2 and Yeast CDC42 Genes Using a Simple and Efficient Reverse-Genetic Method
Authors: Fehon Richard G , Oren Tal , LaJeunesse Dennis R , Melby Thomas E , McCartney Brooke M
Published: January 2021

Reverse genetic analysis in Drosophila has been greatly aided by a growing collection of lethal P transposable element insertions that provide molecular tags for the identification of essential genetic loci. However, because the screens performed to date primarily have generated autosomal P-element insertions, this collection has not been as useful for performing reverse genetic analysis of X-linked genes. We have designed a reverse genetic screen that takes advantage of the hemizygosity of the X chromosome in males together with a cosmid-based transgene that serves as an autosomally linked duplication of a small region of the X chromosome. The efficacy and efficiency of this method is demonstrated by the isolation of mutations in Drosophila homologues of two well-studied genes, the human Neurofibromatosis 2 tumor suppressor and the yeast CDC42 gene. The method we describe should be of general utility for the isolation of mutations in other X-linked genes, and should also provide an efficient method for the isolation of new alleles of existing X-linked or autosomal mutations in Drosophila.
Dominant Mutations of Drosophila MAP Kinase Kinase and Their Activities in Drosophila and Yeast MAP Kinase Cascades
Authors: Lim Young-Mi , Tsuda Leo , Inoue Yoshihiro H , Irie Kenji , Adachi-Yamada Takashi , Hata Mami , Nishi Yoshimi , Matsumoto Kunihiro , Nishida Yasuyoshi
Published: January 2021

Eight alleles of Dsor1 encoding a Drosophila homologue of mitogen-activated protein (MAP) kinase kinase were obtained as dominant suppressors of the MAP kinase kinase kinase D-raf. These Dsor1 alleles themselves showed no obvious phenotypic consequences nor any effect on the viability of the flies, although they were highly sensitive to upstream signals and strongly interacted with gain-of-function mutations of upstream factors. They suppressed mutations for receptor tyrosine kinases (RTKs); torso (tor), sevenless (sev) and to a lesser extent Drosophila EGF receptor (DER). Furthermore, the Dsor1 alleles showed no significant interaction with gain-of-function mutations of DER. The observed difference in activity of the Dsor1 alleles among the RTK pathways suggests Dsor1 is one of the components of the pathway that regulates signal specificity. Expression of Dsor1 in budding yeast demonstrated that Dsor1 can activate yeast MAP kinase homologues if a proper activator of Dsor1 is coexpressed. Nucleotide sequencing of the Dsor1 mutant genes revealed that most of the mutations are associated with amino acid changes at highly conserved residues in the kinase domain. The results suggest that they function as suppressors due to increased reactivity to upstream factors.
Fixation, Segregation and Linkage of Allozyme Loci in Inbred Families of the Pacific Oyster Crassostrea gigas (Thunberg): Implications for the Causes of Inbreeding Depression
Authors: McGoldrick Daniel J , Hedgecock Dennis
Published: January 2021

The effect that inbreeding has on the fixation and segregation of genes has rarely been confirmed by direct observation. Here, fixation, segregation, and linkage of allozymes is investigated in the progeny of self-fertilized hermaphrodites of the normally outcrossing Pacific oyster Crassostrea gigas. The estimate of fixation pooled over loci, individuals, and families, F = 0.462, is significantly lower than the expected value of 0.5. Log-likelihood ratios reveal significant heterogeneity in fixation among individuals, among families, and among loci. In addition, the grand pooled segregation ratio, 127:243:54, deviates significantly from 1:2:1, with a bias against homozygotes for alleles of lesser frequency in the natural population. Segregation ratios for 11 of 14 loci are significantly heterogeneous among families, and exact tests for segregation within families reveal 16 significant results out of 51 tests. Thus, fixation and segregation of allozyme markers in inbred oyster families deviates from the expectations of neutral inbreeding theory. Di-genic disequilibria are significant for four of 74 di-locus pairs revealing two linkage groups. Strong viability selection is apparently conditional on the genotype of the hermaphrodite-founders and is largely focused on these two linkage groups. These genetic effects are explained by interaction between cis-linked factors and polymorphic regulatory backgrounds.
Genetic Analysis of Default Mating Behavior in Saccharomyces cerevisiae
Authors: Dorer Russell , Boone Charles , Kimbrough Tyler , Kim Joshua , Hartwell Leland H
Published: January 2021

Haploid Saccharomyces cerevisiae cells find each other during conjugation by orienting their growth toward each other along pheromone gradients (chemotropism). However, when their receptors are saturated for pheromone binding, yeast cells must select a mate by executing a default pathway in which they choose a mating partner at random. We previously demonstrated that this default pathway requires the SPA2 gene. In this report we show that the default mating pathway also requires the AXL1, FUS1, FUS2, FUS3, PEAZ, RVS161, and BNI1 genes. These genes, including SPA2, are also important for efficient cell fusion during chemotropic mating. Cells containing null mutations in these genes display defects in cell fusion that subtly affect mating efficiency. In addition, we found that the defect in default mating caused by mutations in SPA2 is partially suppressed by multiple copies of two genes, FUS2 and MFA2. These findings uncover a molecular relationship between default mating and cell fusion. Moreover, because axl1 mutants secrete reduced levels of a-factor and are defective at both cell fusion and default mating, these results reveal an important role for a-factor in cell fusion and default mating. We suggest that default mating places a more stringent requirement on some aspects of cell fusion than does chemotropic mating.
rco-3, a Gene Involved in Glucose Transport and Conidiation in Neurospora crassa
Authors: Madi Lea , McBride Sheila A , Bailey Lori A , Ebbole Daniel J
Published: January 2021

Macroconidiation in Neurospora crassa is influenced by a number of environmental cues, including the nutritional status of the growing organism. Conidia formation is normally observed when the fungus is exposed to air. However, carbon limitation can induce conidiation in mycelia submerged in an aerated liquid medium. A mutant was previously isolated that could conidiate in submerged culture without imposing nutrient limitation and the gene responsible for this phenotype (rco-3) has now been cloned. RCO3 exhibits sequence similarity to members of the sugar transporter gene superfamily, with greatest similarity to glucose transporters of yeast. Consistent with this structural similarity, we find that glucose transport activity is altered in the mutant. However, growth of the mutant in media containing alternate carbon sources does not suppress conidiation in submerged culture. The properties of the mutant suggest that RCO3 is required for expression of glucose transport activity, glucose regulation of gene expression, and general carbon repression of development.
Altering Developmental Trajectories in Mice by Restricted Index Selection
Authors: Atchley William R , Xu Shizhong , Cowley David E
Published: January 2021

A restricted index selection experiment on mice was carried out for 14 generations on rate of early postnatal development (growth rate from birth to 10 days of age) vs. rate of development much later in ontogeny (growth rate from 28 to 56 days of age). Early rate of development (E) approximates hyperplasia (changes in cell number) and later rate (L) reflects hypertropy (changes in cell size). The selection criteria were as follows: E+L0 was selected to increase early body weight gain while holding late body weight gain constant; E–L0 was selected to decrease early body gain while holding late gain constant; E0L+ was selected to increase late gain holding early gain constant; and E0L– was selected to decrease late gain holding early gain constant. After 14 generations of selection, significant divergence among lines has occurred and the changes in the growth trajectories are very close to expectation. The genetic and developmental bases of complex traits are discussed as well as the concept of developmental homoplasy.
Ancestral Polymorphism of Mhc Class II Genes in Mice: Implications for Balancing Selection and the Mammalian Molecular Clock
Authors: Edwards Scott V , Chesnut Kye , Satta Yoko , Wakeland Edward K
Published: January 2021

To investigate the evolutionary dynamics at Mhc class II DR genes of mice (genus Mus), we sequenced the peptide binding regions (PBRs) of 41 DRB (=Eβ) genes and eight DRA (=Eα) genes from 15 strains representing eight species. As expected trees of these PBR sequences imply extensive maintenance of ancestral DRB alleles across species. We use a coalescent simulation model to show that the number of interspecific coalescent events (c) observed on these trees was higher than the number expected for neutral genealogies and similar sample sizes and is more consistent with balancing selection than with neutrality. Patterns of ancestral polymorphism in mouse DRB alleles were also used to examine the tempo of synonymous substitution in the PBR of mouse class II genes. Both absolute and relative rate tests on DRA and DRB genes imply increased substitution rates at two- and fourfold degnerate sites of mice and rats relative to primates, and decreased rates for the DRB genes of primates relative to ungulate and carnivore relatives. Thus rates of synonymous substitution at Mhc DR genes in mammals appear to be subject to generation time effects in ways similar to those found at other mammalian genes.
The Probability of Fixation in Populations of Changing Size
Authors: Otto Sarah P , Whitlock Michael C
Published: January 2021

The rate of adaptive evolution of a population ultimately depends on the rate of incorporation of beneficial mutations. Even beneficial mutations may, however, be lost from a population since mutant individuals may, by chance, fail to reproduce. In this paper, we calculate the probability of fixation of beneficial mutations that occur in populations of changing size. We examine a number of demographic models, including a population whose size changes once, a population experiencing exponential growth or decline, one that is experiencing logistic growth or decline, and a population that fluctuates in size. The results are based on a branching process model but are shown to be approximate solutions to the diffusion equation describing changes in the probability of fixation over time. Using the diffusion equation, the probability of fixation of deleterious alleles can also be determined for populations that are changing in size. The results developed in this paper can be used to estimate the fixation flux, defined as the rate at which beneficial alleles fix within a population. The fixation flux measures the rate of adaptive evolution of a population and, as we shall see, depends strongly on changes that occur in population size.
Mapping-Linked Quantitative Trait Loci Using Bayesian Analysis and Markov Chain Monte Carlo Algorithms
Authors: Uimari Pekka , Hoeschele Ina
Published: January 2021

A Bayesian method for mapping linked quantitative trait loci (QTL) using multiple linked genetic markers is presented. Parameter estimation and hypothesis testing was implemented via Markov chain Monte Carlo (MCMC) algorithms. Parameters included were allele frequencies and substitution effects for two biallelic QTL, map positions of the QTL and markers, allele frequencies of the markers, and polygenic and residual variances. Missing data were polygenic effects and multi-locus marker-QTL genotypes. Three different MCMC schemes for testing the presence of a single or two linked QTL on the chromosome were compared. The first approach includes a model indicator variable representing two unlinked QTL affecting the trait, one linked and one unlinked QTL, or both QTL linked with the markers. The second approach incorporates an indicator variable for each QTL into the model for phenotype, allowing or not allowing for a substitution effect of a QTL on phenotype, and the third approach is based on model determination by reversible jump MCMC. Methods were evaluated empirically by analyzing simulated granddaughter designs. All methods identified correctly a second, linked QTL and did not reject the one-QTL model when there was only a single QTL and no additional or an unlinked QTL.
Evolution of Repeated Sequence Arrays in the D-Loop Region of Bat Mitochondrial DNA
Authors: Wilkinson Gerald S , Mayer Frieder , Kerth Gerald , Petri Barbara
Published: January 2021

Analysis of mitochondrial DNA control region sequences from 41 species of bats representing 11 families revealed that repeated sequence arrays near the tRNA-Pro gene are present in all vespertilionine bats. Across 18 species tandem repeats varied in size from 78 to 85 bp and contained two to nine repeats. Heteroplasmy ranged from 15% to 63%. Fewer repeats among heteroplasmic than homoplasmic individuals in a species with up to nine repeats indicates selection may act against long arrays. A lower limit of two repeats and more repeats among heteroplasmic than homoplasmic individuals in two species with few repeats suggests length mutations are biased. Significant regressions of heteroplasmy, θ and π, on repeat number further suggest that repeat duplication rate increases with repeat number. Comparison of vespertilionine bat consensus repeats to mammal control region sequences revealed that tandem repeats of similar size, sequence and number also occur in shrews, cats and bighorn sheep. The presence of two conserved protein-binding sequences in all repeat units indicates that convergent evolution has occurred by duplication of functional units. We speculate that D-loop region tandem repeats may provide signal redundancy and a primitive repair mechanism in the event of somatic mutations to these binding sites.
The New RGA Locus Encodes a Negative Regulator of Gibberellin Response in Arabidopsis thaliana
Authors: Silverstone Aron L , Mak Pui Ying Annie , Martinez Eva Casamitjana , Sun Tai-ping
Published: January 2021

We have identified a new locus involved in gibberellin (GA) signal transduction by screening for suppressors of the Arabidopsis thaliana GA biosynthetic mutant ga1-3. The locus is named RGA for repressor of ga1-3. Based on the recessive phenotype of the digenic rga/ga1-3 mutant, the wild-type gene product of RGA is probably a negative regulator of GA responses. Our screen for suppressors of ga1-3 identified 17 mutant alleles of RGA as well as 10 new mutant alleles at the previously identified SPY locus. The digenic (double homozygous) rga/ga1-3 mutants are able to partially repress several defects of ga1-3 including stem growth, leaf abaxial trichome initiation, flowering time, and apical dominance. The phenotype of the trigenic mutant (triple homozygous) rga/spy/ga1-3 shows that rga and spy have additive effects regulating flowering time, abaxial leaf trichome initiation and apical dominance. This trigenic mutant is similar to wild type with respect to each of these developmental events. Because rga/spy/ga1-3 is almost insensitive to GA for hypocotyl growth and its bolting stem is taller than the wild-type plant, the combined effects of the rga and spy mutations appear to allow GA-independent stem growth. Our studies indicate that RGA lies on a separate branch of the GA signal transduction pathway from SPY, which leads us to propose a modified model of the GA response pathway.
Region-Specific Cis- and Trans-Acting Factors Contribute to Genetic Variability in Meiotic Recombination in Maize
Authors: Timmermans Marja C P , Das O Prem , Bradeen James M , Messing Joachim
Published: January 2021

Understanding the genetic basis for variability in recombination rates is important for general genetic studies and plant-breeding efforts. Earlier studies had suggested increased recombination frequencies in particular F2 populations derived from the maize inbred A188. A detailed phenotypic and molecular analysis was undertaken to extend these observations and dissect the responsible factors. A heritable increase in recombination in the sh1-bz1 interval was observed in these populations. A factor causing an approximate twofold increase mapped to the A188 Sh1-Bz1 region, behaved as a dominant, cis-acting factor, affected recombination equally in male and female sporogenesis and did not reduce the well-studied complete interference in the adjacent bz1-wx interval. This factor also did not increase recombination frequencies in the c1-sh1 and bz1-wx intervals, demonstrating independent control of recombination in adjacent intervals. Additional phenotypic analysis of recombination in the c1-sh1 and bz1-wx intervals and RFLP analysis of recombination along chromosomes 7 and 5 suggested that heritable factors controlling recombination in these intervals act largely independently and in trans. Our results show that recombination in these populations, and possibly maize in general, is controlled by both cis- and trans-acting factors that affect specific chromosomal regions.
Comparison of Flowering Time Genes in Brassica rapa, B. napus and Arabidopsis thaliana
Authors: Osborn T C , Kole C , Parkin I A P , Sharpe A G , Kuiper M , Lydiate D J , Trick M
Published: January 2021

The major difference between annual and biennial cultivars of oilseed Brassica napus and B. rapa is conferred by genes controlling vernalization-responsive flowering time. These genes were compared between the species by aligning the map positions of flowering time quantitative trait loci (QTLs) detected in a segregating population of each species. The results suggest that two major QTLs identified in B. rapa correspond to two major QTLs identified in B. napus. Since B. rapa is one of the hypothesized diploid parents of the amphidiploid B. napus, the vernalization requirement of B. napus probably originated from B. rapa. Brassica genes also were compared to flowering time genes in Arabidopsis thaliana by mapping RFLP loci with the same probes in both B. napus and Arabidopsis. The region containing one pair of Brassica QTLs was collinear with the top of chromosome 5 in A. thaliana where flowering time genes FLC, FY and CO are located. The region containing the second pair of QTLs showed fractured collinearity with several regions of the Arabidopsis genome, including the top of chromosome 4 where FRI is located. Thus, these Brassica genes may correspond to two genes (FLC and FRI) that regulate flowering time in the latest flowering ecotypes of Arabidopsis.
The Maize Transposable Element Ac Induces Recombination Between the Donor Site and an Homologous Ectopic Sequence
Authors: Shalev Gil , Levy Avraham A
Published: January 2021

The prominent repair mechanism of DNA double-strand breaks formed upon excision of the maize Ac transposable element is via nonhomologous end joining. In this work we have studied the role of homologous recombination as an additional repair pathway. To this end, we developed an assay whereby β-Glucuronidase (GUS) activity is restored upon recombination between two homologous ectopic (nonallelic) sequences in transgenic tobacco plants. One of the recombination partners carried a deletion at the 5′ end of GUS and an Ac or a Ds element inserted at the deletion site. The other partner carried an intact 5′ end of the GUS open reading frame and had a deletion at the 3′ end of the gene. Based on GUS reactivation data, we found that the excision of Ac induced recombination between ectopic sequences by at least two orders of magnitude. Recombination events, visualized by blue staining, were detected in seedlings, in pollen and in protoplasts. DNA fragments corresponding to recombination events were recovered exclusively in crosses with Ac-carrying plants, providing physical evidence for Ac-induced ectopic recombination. The occurrence of ectopic recombination following double-strand breaks is a potentially important factor in plant genome evolution.
Isolation of COM1, a New Gene Required to Complete Meiotic Double-Strand Break-Induced Recombination in Saccharomyces cerevisiae
Authors: Prinz Susanne , Amon Angelika , Klein Franz
Published: January 2021

We have designed a screen to isolate mutants defective during a specific part of meiotic prophase I of the yeast Saccharomyces cerevisiae. Genes required for the repair of meiotic double-strand breaks or for the separation of recombined chromosomes are targets of this mutant hunt. The specificity is achieved by selecting for mutants that produce viable spores when recombination and reductional segregation are prevented by mutations in SPO11 and SP013 genes, but fail to yield viable spores during a normal Rec+ meiosis. We have identified and characterized a mutation com1-1, which blocks processing of meiotic double-strand breaks and which interferes with synaptonemal complex formation, homologous pairing and, as a consequence, spore viability after induction of meiotic recombination. The COM1/SAE2 gene was cloned by complementation, and the deletion mutant has a phenotype similar to com1-1. com1/sae2 mutants closely resemble the phenotype of rad50S, as assayed by phase-contrast microscopy for spore formation, physical and genetic analysis of recombination, fluorescence in situ hybridization to quantify homologous pairing and immunofluorescence and electron microscopy to determine the capability to synapse axial elements.
A 140-bp-Long Palindromic Sequence Induces Double-Strand Breaks During Meiosis in the Yeast Saccharomyces cerevisiae
Authors: Nag Dilip K , Kurst Alicia
Published: January 2021

Palindromic sequences have the potential to form hairpin or cruciform structures, which are putative substrates for several nucleases and mismatch repair enzymes. A genetic method was developed to detect such structures in vivo in the yeast Saccharomyces cerevisiae. Using this method we previously showed that short hairpin structures are poorly repaired by the mismatch repair system in S. cerevisiae. We show here that mismatches, when present in the stem of the hairpin structure, are not processed by the repair machinery, suggesting that they are treated differently than those in the interstrand base-paired duplex DNA. A 140-bp-long palindromic sequence, on the contrary, acts as a meiotic recombination hotspot by generating a site for a double-strand break, an initiator of meiotic recombination. We suggest that long palindromic sequences undergo cruciform extrusion more readily than short ones. This cruciform structure then acts as a substrate for structure-specific nucleases resulting in the formation of a double-strand break during meiosis in yeast. In addition, we show that residual repair of the short hairpin structure occurs in an MSH2-independent pathway.
Saccharomyces cerevisiae PAC2 Functions With CIN1, 2 and 4 in a Pathway Leading to Normal Microtubule Stability
Authors: Hoyt M Andrew , Macke Jennifer P , Roberts B Tibor , Geiser John R
Published: January 2021

The products of the Saccharomyces cerevisiae CIN1, CIN2 and CIN4 genes participate in a nonessential pathway required for normal microtubule function. In this article, we demonstrate that the product of PAC2 also functions in this pathway. PAC2 deletion mutants displayed phenotypes and genetic interactions similar to those caused by cin1Δ, cin2Δ and cin4Δ. These include cold-sensitive microtubule structures and sensitivity to the microtubule depolymerizing agent benomyl. Involvement in a common functional pathway is indicated by the observation that all double mutant combinations are viable and no more affected than any single mutant. In addition, extra copies of CIN1 were found to suppress the benomyl sensitivity of pac2Δ, cin2Δ and cin4Δ, but not that caused by other mutations that affect microtubule function. Cin1p and Pac2p were found to be related in sequence to mammalian proteins that aid in the folding of β-tubulin into an assembly-competent state. Alleles of CIN1 were identified that could suppress the benomyl sensitivity of cin4-4 in a highly specific fashion. Our findings suggest that the guanine nucleotide-binding Cin4p interacts with Cin1p and regulates its tubulin folding activity.