bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Analysis of Traits Distinguishing Outcrossing and Self-Pollinating Forms of Currant Tomato, Lycopersicon pimpinellifolium (Jusl.) Mill.
Authors: Georgiady Michael S , Whitkus Richard W , Lord Elizabeth M 
Published: April 2021

Abstract
The evolution of inbreeding is common throughout the angiosperms, although little is known about the developmental and genetic processes involved. Lycopersicon pimpinellifolium (currant tomato) is a self-compatible species with variation in outcrossing rate correlated with floral morphology. Mature flowers from inbreeding and outcrossing populations differ greatly in characters affecting mating behavior (petal, anther, and style lengths); other flower parts (sepals, ovaries) show minimal differences. Analysis of genetic behavior, including quantitative trait locus (QTL) mapping, was performed on representative selfing and outcrossing plants derived from two contrasting natural populations. Six morphological traits were analyzed: flowers per inflorescence; petal, anther, and style lengths; and lengths of the fertile and sterile portions of anthers. All traits were smaller in the selfing parent and had continuous patterns of segregation in the F2. Phenotypic correlations among traits were all positive, but varied in strength. Quantitative trait locus mapping was done using 48 RFLP markers. Five QTL total were found involving four of the six traits: total anther length, anther sterile length, style length, and flowers per inflorescence. Each of these four traits had a QTL of major (&gt;25%) effect on phenotypic variance.
A Reaction-Diffusion Model for Interference in Meiotic Crossing Over
Authors: Fujitani Youhei , Mori Shintaro , Kobayashi Ichizo 
Published: April 2021

Abstract
One crossover point between a pair of homologous chromosomes in meiosis appears to interfere with occurrence of another in the neighborhood. It has been revealed that Drosophila and Neurospora, in spite of their large difference in the frequency of crossover points, show very similar plots of coincidence—a measure of the interference—against the genetic distance of the interval, defined as one-half the average number of crossover points within the interval. We here propose a simple reaction-diffusion model, where a “randomly walking” precursor becomes immobilized and matures into a crossover point. The interference is caused by pair-annihilation of the random walkers due to their collision and by annihilation of a random walker due to its collision with an immobilized point. This model has two parameters—the initial density of the random walkers and the rate of its processing into a crossover point. We show numerically that, as the former increases and/or the latter decreases, plotted curves of the coincidence vs. the genetic distance converge on a unique curve. Thus, our model explains the similarity between Drosophila and Neurospora without parameter values adjusted finely, although it is not a “genetic model” but is a “physical model,” specifying explicitly what happens physically.
A Neutral Model With Fluctuating Population Size and Its Effective Size
Authors: Iizuka Masaru , Tachida Hidenori , Matsuda Hirotsugu 
Published: April 2021

Abstract
We consider a diffusion model with neutral alleles whose population size is fluctuating randomly. For this model, the effects of fluctuation of population size on the effective size are investigated. The effective size defined by the equilibrium average heterozygosity is larger than the harmonic mean of population size but smaller than the arithmetic mean of population size. To see explicitly the effects of fluctuation of population size on the effective size, we investigate a special case where population size fluctuates between two distinct states. In some cases, the effective size is very different from the harmonic mean. For this concrete model, we also obtain the stationary distribution of the average heterozygosity. Asymptotic behavior of the effective size is obtained when the population size is large and/or autocorrelation of the fluctuation is weak or strong.
Population, Evolutionary and Genomic Consequences of Interference Selection
Authors: Comeron Josep M , Kreitman Martin 
Published: April 2021

Abstract
Weakly selected mutations are most likely to be physically clustered across genomes and, when sufficiently linked, they alter each others’ fixation probability, a process we call interference selection (IS). Here we study population genetics and evolutionary consequences of IS on the selected mutations themselves and on adjacent selectively neutral variation. We show that IS reduces levels of polymorphism and increases low-frequency variants and linkage disequilibrium, in both selected and adjacent neutral mutations. IS can account for several well-documented patterns of variation and composition in genomic regions with low rates of crossing over in Drosophila. IS cannot be described simply as a reduction in the efficacy of selection and effective population size in standard models of selection and drift. Rather, IS can be better understood with models that incorporate a constant “traffic” of competing alleles. Our simulations also allow us to make genome-wide predictions that are specific to IS. We show that IS will be more severe at sites in the center of a region containing weakly selected mutations than at sites located close to the edge of the region. Drosophila melanogaster genomic data strongly support this prediction, with genes without introns showing significantly reduced codon bias in the center of coding regions. As expected, if introns relieve IS, genes with centrally located introns do not show reduced codon bias in the center of the coding region. We also show that reasonably small differences in the length of intermediate “neutral” sequences embedded in a region under selection increase the effectiveness of selection on the adjacent selected sequences. Hence, the presence and length of sequences such as introns or intergenic regions can be a trait subject to selection in recombining genomes. In support of this prediction, intron presence is positively correlated with a gene’s codon bias in D. melanogaster. Finally, the study of temporal dynamics of IS after a change of recombination rate shows that nonequilibrium codon usage may be the norm rather than the exception.
Pleiotropic Model of Maintenance of Quantitative Genetic Variation at Mutation-Selection Balance
Authors: Zhang Xu-Sheng , Wang Jinliang , Hill William G 
Published: April 2021

Abstract
A pleiotropic model of maintenance of quantitative genetic variation at mutation-selection balance is investigated. Mutations have effects on a metric trait and deleterious effects on fitness, for which a bivariate gamma distribution is assumed. Equations for calculating the strength of apparent stabilizing selection (Vs) and the genetic variance maintained in segregating populations (VG) were derived. A large population can hold a high genetic variance but the apparent stabilizing selection may or may not be relatively strong, depending on other properties such as the distribution of mutation effects. If the distribution of mutation effects on fitness is continuous such that there are few nearly neutral mutants, or a minimum fitness effect is assumed if most mutations are nearly neutral, VG increases to an asymptote as the population size increases. Both VG and Vs are strongly affected by the shape of the distribution of mutation effects. Compared with mutants of equal effect, allowing their effects on fitness to vary across loci can produce a much higher VG but also a high Vs (Vs in phenotypic standard deviation units, which is always larger than the ratio VP/Vm), implying weak apparent stabilizing selection. If the mutational variance Vm is ∼10-3 Ve (Ve, environmental variance), the model can explain typical values of heritability and also apparent stabilizing selection, provided the latter is quite weak as suggested by a recent review.
Frequentist Estimation of Coalescence Times From Nucleotide Sequence Data Using a Tree-Based Partition
Authors: Tang Hua , Siegmund David O , Shen Peidong , Oefner Peter J , Feldman Marcus W 
Published: April 2021

Abstract
This article proposes a method of estimating the time to the most recent common ancestor (TMRCA) of a sample of DNA sequences. The method is based on the molecular clock hypothesis, but avoids assumptions about population structure. Simulations show that in a wide range of situations, the point estimate has small bias and the confidence interval has at least the nominal coverage probability. We discuss conditions that can lead to biased estimates. Performance of this estimator is compared with existing methods based on the coalescence theory. The method is applied to sequences of Y chromosomes and mtDNAs to estimate the coalescent times of human male and female populations.
Levels of DNA Polymorphism Vary With Mating System in the Nematode Genus Caenorhabditis
Authors: Graustein Andrew , Gaspar John M , Walters James R , Palopoli Michael F 
Published: April 2021

Abstract
Self-fertilizing species often harbor less genetic variation than cross-fertilizing species, and at least four different models have been proposed to explain this trend. To investigate further the relationship between mating system and genetic variation, levels of DNA sequence polymorphism were compared among three closely related species in the genus Caenorhabditis: two self-fertilizing species, Caenorhabditis elegans and C. briggsae, and one cross-fertilizing species, C. remanei. As expected, estimates of silent site nucleotide diversity were lower in the two self-fertilizing species. For the mitochondrial genome, diversity in the selfing species averaged 42% of diversity in C. remanei. Interestingly, the reduction in genetic variation was much greater for the nuclear than for the mitochondrial genome. For two nuclear genes, diversity in the selfing species averaged 6 and 13% of diversity in C. remanei. We argue that either population bottlenecks or the repeated action of natural selection, coupled with high levels of selfing, are likely to explain the observed reductions in species-wide genetic diversity.
Characterization of Essential Genes by Parasexual Genetics in the Human Fungal Pathogen Aspergillus fumigatus: Impact of Genomic Rearrangements Associated With Electroporation of DNA
Authors: Firon Arnaud , Beauvais Anne , Latgé Jean-Paul , Couvé Elisabeth , Grosjean-Cournoyer Marie-Claire , d'Enfert Christophe 
Published: April 2021

Abstract
We have evaluated the usefulness of parasexual genetics in the identification of genes essential for the growth of the human fungal pathogen Aspergillus fumigatus. First, essentiality of the A. fumigatus AfFKS1 gene, encoding the catalytic subunit of the β-(1,3)-glucan synthase complex, was assessed by inactivating one allele of AfFKS1 in a diploid strain of A. fumigatus obtained using adequate selectable markers in spore color and nitrate utilization pathways and by performing haploidization under conditions that select for the occurrence of the disrupted allele. Haploid progeny could not be obtained, demonstrating that AfFKS1 and, hence, β-(1,3)-glucan synthesis are essential in A. fumigatus. Second, random heterozygous insertional mutants were generated by electroporation of diploid conidia with a heterologous plasmid. A total of 4.5% of the transformants failed to produce haploid progeny on selective medium. Genomic analysis of these heterozygous diploids led in particular to the identification of an essential A. fumigatus gene encoding an SMC-like protein resembling one in Schizosacccharomyces pombe involved in chromosome condensation and cohesion. However, significant plasmid and genomic DNA rearrangements were observed at many of the identified genomic loci where plasmid integration had occurred, thus suggesting that the use of electroporation to build libraries of A. fumigatus insertional mutants has relatively limited value and cannot be used in an exhaustive search of essential genes.
Dominant Alleles of the Basic Helix-Loop-Helix Transcription Factor ATR2 Activate Stress-Responsive Genes in Arabidopsis
Authors: Smolen Gromoslaw A , Pawlowski Laura , Wilensky Sharon E , Bender Judith 
Published: April 2021

AbstractMembers of the R/B basic helix-loop-helix (bHLH) family of plant transcription factors are involved in a variety of growth and differentiation processes. We isolated a dominant mutation in an R/B-related bHLH transcription factor in the course of studying Arabidopsis tryptophan pathway regulation. This mutant, atr2D, displayed increased expression of several tryptophan genes as well as a subset of other stress-responsive genes. The atr2D mutation creates an aspartate to asparagine change at a position that is highly conserved in R/B factors. Substitutions of other residues with uncharged side chains at this position also conferred dominant phenotypes. Moreover, overexpression of mutant atr2D, but not wild-type ATR2, conferred pleiotropic effects, including reduced size, dark pigmentation, and sterility. Therefore, atr2D is likely to be an altered-function allele that identifies a key regulatory site in the R/B factor coding sequence. Double-mutant analysis with atr1D, an overexpression allele of the ATR1 Myb factor previously isolated in tryptophan regulation screens, showed that atr2D and atr1D have additive effects on tryptophan regulation and are likely to act through distinct mechanisms to activate tryptophan genes. The dominant atr mutations thus provide tools for altering tryptophan metabolism in plants.
Two O-Linked N-Acetylglucosamine Transferase Genes of Arabidopsis thaliana L. Heynh. Have Overlapping Functions Necessary for Gamete and Seed Development
Authors: Hartweck Lynn M , Scott Cheryl L , Olszewski Neil E 
Published: April 2021

Abstract
The Arabidopsis SECRET AGENT (SEC) and SPINDLY (SPY) proteins are similar to animal O-linked N-acetylglucosamine transferases (OGTs). OGTs catalyze the transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to Ser/Thr residues of proteins. In animals, O-GlcNAcylation has been shown to affect protein activity, stability, and/or localization. SEC protein expressed in Escherichia coli had autocatalytic OGT activity. To determine the function of SEC in plants, two tDNA insertional mutants were identified and analyzed. Although sec mutant plants did not exhibit obvious phenotypes, sec and spy mutations had a synthetic lethal interaction. This lethality was incompletely penetrant in gametes and completely penetrant postfertilization. The rate of both female and male sec spy gamete transmission was higher in plants heterozygous for both mutations than in plants heterozygous for sec and homozygous for spy. Double-mutant embryos aborted at various stages of development and no double-mutant seedlings were obtained. These results indicate that OGT activity is required during gametogenesis and embryogenesis with lethality occurring when parentally derived SEC, SPY, and/or O-GlcNAcylated proteins become limiting.
A Combined Amplified Fragment Length Polymorphism and Randomly Amplified Polymorphism DNA Genetic Linkage Map of Mycosphaerella graminicola, the Septoria Tritici Leaf Blotch Pathogen of Wheat
Authors: Kema Gert H J , Goodwin Stephen B , Hamza Sonia , Verstappen Els C P , Cavaletto Jessica R , Van der Lee Theo A J , de Weerdt Marjanne , Bonants Peter J M , Waalwijk Cees 
Published: April 2021

Abstract
An F1 mapping population of the septoria tritici blotch pathogen of wheat, Mycosphaerella graminicola, was generated by crossing the two Dutch field isolates IPO323 and IPO94269. AFLP and RAPD marker data sets were combined to produce a high-density genetic linkage map. The final map contained 223 AFLP and 57 RAPD markers, plus the biological traits mating type and avirulence, in 23 linkage groups spanning 1216 cM. Many AFLPs and some RAPD markers were clustered. When markers were reduced to 1 per cluster, 229 unique positions were mapped, with an average distance of 5.3 cM between markers. Because M. graminicola probably has 17 or 18 chromosomes, at least 5 of the 23 linkage groups probably will need to be combined with others once additional markers are added to the map. This was confirmed by pulsed-field gel analysis; probes derived from 2 of the smallest linkage groups hybridized to two of the largest chromosome-sized bands, revealing a discrepancy between physical and genetic distance. The utility of the map was demonstrated by identifying molecular markers tightly linked to two genes of biological interest, mating type and avirulence. Bulked segregant analysis was used to identify additional molecular markers closely linked to these traits. This is the first genetic linkage map for any species in the genus Mycosphaerella or the family Mycosphaerellaceae.
The bantam Gene Regulates Drosophila Growth
Authors: Hipfner David R , Weigmann Katrin , Cohen Stephen M 
Published: April 2021

Abstract
We report here the consequences of mutations of a novel locus, named bantam, whose product is involved in the regulation of growth in Drosophila. bantam mutant animals are smaller than wild type, due to a reduction in cell number but not cell size, and do not have significant disruptions in patterning. Conversely, overexpression of the bantam product using the EP element EP(3)3622 causes overgrowth of wing and eye tissue. Overexpression in clones of cells results in an increased rate of cell proliferation and a matched increase in cellular growth rate, such that the resulting tissue is composed of more cells of a size comparable to wild type. These effects are strikingly similar to those associated with alterations in the activity of the cyclinD-cdk4 complex. However, epistasis and genetic interaction analyses indicate that bantam and cyclinD-cdk4 operate independently. Thus, the bantam locus represents a novel regulator of tissue growth.
A Targeted RNAi Screen for Genes Involved in Chromosome Morphogenesis and Nuclear Organization in the Caenorhabditis elegans Germline
Authors: Colaiácovo M P , Stanfield G M , Reddy K C , Reinke V , Kim S K , Villeneuve A M 
Published: April 2021

Abstract
We have implemented a functional genomics strategy to identify genes involved in chromosome morphogenesis and nuclear organization during meiotic prophase in the Caenorhabditis elegans germline. This approach took advantage of a gene-expression survey that used DNA microarray technology to identify genes preferentially expressed in the germline. We defined a subset of 192 germline-enriched genes whose expression profiles were similar to those of previously identified meiosis genes and designed a screen to identify genes for which inhibition by RNA interference (RNAi) elicited defects in function or development of the germline. We obtained strong germline phenotypes for 27% of the genes tested, indicating that this targeted approach greatly enriched for genes that function in the germline. In addition to genes involved in key meiotic prophase events, we identified genes involved in meiotic progression, germline proliferation, and chromosome organization and/or segregation during mitotic growth.
Courtship and Other Behaviors Affected by a Heat-Sensitive, Molecularly Novel Mutation in the cacophony Calcium-Channel Gene of Drosophila
Authors: Chan Betty , Villella Adriana , Funes Pablo , Hall Jeffrey C 
Published: April 2021

Abstract
The cacophony (cac) locus of Drosophila melanogaster, which encodes a calcium-channel subunit, has been mutated to cause courtship-song defects or abnormal responses to visual stimuli. However, the most recently isolated cac mutant was identified as an enhancer of a comatose mutation’s effects on general locomotion. We analyzed the cacTS2 mutation in terms of its intragenic molecular change and its effects on behaviors more complex than the fly’s elementary ability to move. The molecular etiology of this mutation is a nucleotide substitution that causes a proline-to-serine change in a region of the polypeptide near its EF hand. Given that this motif is involved in channel inactivation, it was intriguing that cacTS2 males generate song pulses containing larger-than-normal numbers of cycles—provided that such males are exposed to an elevated temperature. Similar treatments caused only mild visual-response abnormalities and generic locomotor sluggishness. These results are discussed in the context of calcium-channel functions that subserve certain behaviors and of defects exhibited by the original cacophony mutant. Despite its different kind of amino-acid substitution, compared with that of cacTS2, cacS males sing abnormally in a manner that mimics the new mutant’s heat-sensitive song anomaly.
Genetic Interaction Between Integrins and moleskin, a Gene Encoding a Drosophila Homolog of Importin-7
Authors: Baker Scott E , Lorenzen James A , Miller Steven W , Bunch Thomas A , Jannuzi Alison L , Ginsberg Mark H , Perkins Lizabeth A , Brower Danny L 
Published: April 2021

Abstract
The Drosophila PS1 and PS2 integrins are required to maintain the connection between the dorsal and ventral wing epithelia. If αPS subunits are inappropriately expressed during early pupariation, the epithelia separate, causing a wing blister. Two lines of evidence indicate that this apparent loss-of-function phenotype is not a dominant negative effect, but is due to inappropriate expression of functional integrins: wing blisters are not generated efficiently by misexpression of loss-of-function αPS2 subunits with mutations that inhibit ligand binding, and gain-of-function, hyperactivated mutant αPS2 proteins cause blistering at expression levels well below those required by wild-type proteins. A genetic screen for dominant suppressors of wing blisters generated null alleles of a gene named moleskin, which encodes the protein DIM-7. DIM-7, a Drosophila homolog of vertebrate importin-7, has recently been shown to bind the SHP-2 tyrosine phosphatase homolog Corkscrew and to be important in the nuclear translocation of activated D-ERK. Consistent with this latter finding, homozygous mutant clones of moleskin fail to grow in the wing. Genetic tests suggest that the moleskin suppression of wing blisters is not directly related to inhibition of D-ERK nuclear import. These data are discussed with respect to the possible regulation of integrin function by cytoplasmic ERK.
Comparative Sequencing in the Genus Lycopersicon: Implications for the Evolution of Fruit Size in the Domestication of Cultivated Tomatoes
Authors: Nesbitt T Clint , Tanksley Steven D 
Published: April 2021

Abstract
Sequence variation was sampled in cultivated and related wild forms of tomato at fw2.2—a fruit weight QTL key to the evolution of domesticated tomatoes. Variation at fw2.2 was contrasted with variation at four other loci not involved in fruit weight determination. Several conclusions could be reached: (1) Fruit weight variation attributable to fw2.2 is not caused by variation in the FW2.2 protein sequence; more likely, it is due to transcriptional variation associated with one or more of eight nucleotide changes unique to the promoter of large-fruit alleles; (2) fw2.2 and loci not involved in fruit weight have not evolved at distinguishably different rates in cultivated and wild tomatoes, despite the fact that fw2.2 was likely a target of selection during domestication; (3) molecular-clock-based estimates suggest that the large-fruit allele of fw2.2, now fixed in most cultivated tomatoes, arose in tomato germplasm long before domestication; (4) extant accessions of L. esculentum var. cerasiforme, the subspecies thought to be the most likely wild ancestor of domesticated tomatoes, appear to be an admixture of wild and cultivated tomatoes rather than a transitional step from wild to domesticated tomatoes; and (5) despite the fact that cerasiforme accessions are polymorphic for large- and small-fruit alleles at fw2.2, no significant association was detected between fruit size and fw2.2 genotypes in the subspecies—as tested by association genetic studies in the relatively small sample studied—suggesting the role of other fruit weight QTL in fruit weight variation in cerasiforme.