bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dominance is the major genetic basis of heterosis in rice as revealed by QTL analysis using molecular markers.
Authors: Xiao J , Li J , Yuan L , Tanksley S D 
Published: January 2021

Abstract
A set of 194 F7 lines derived from a subspecific rice cross showing strong F1 heterosis was backcrossed to the two parents. The materials (388 BC1F7 lines, 194 F8 lines, two parents, F1) were phenotyped for 12 quantitative traits. A total of 37 significant QTLs (LOD &gt; or = 2.0) was detected through 141 RFLP markers in the BC1F7 populations. Twenty-seven (73%) quantitative trait loci (QTLs) were detected in only one of the BC1F7 populations. In 82% of these cases, the heterozygotes were superior to the respective homozygotes. The remaining 10 (27%) QTLs were detected in both BC1F7 populations, and the heterozygote had a phenotype falling between those of the two homozygotes and in no instances were the heterozygotes found to be superior to both homozygotes. These results suggest that dominance complementation is the major genetic basis of heterosis in rice. This conclusion was strengthened by the finding that there was no correlation between most traits and overall genome heterozygosity and that there were some recombinant inbred lines in the F8 population having phenotypic values superior to the F1 for all of the traits evaluated--a result not expected if overdominance was a major contributor to heterosis. Digenic epistasis was not evident.
Analysis of DNA diversity by spatial autocorrelation.
Authors: Bertorelle G , Barbujani G 
Published: January 2021

Abstract
Two statistics are proposed for summarizing spatial patterns of DNA diversity. These autocorrelation indices for DNA analysis, or AIDAs, can be applied to RFLP and sequence data; the resulting set of autocorrelation coefficients, or correlogram, measures whether, and to what extent, individual DNA sequences or haplotypes resemble the haplotypes sampled at arbitrarily chosen spatial distances. Analyses of computer-generated sets of data, and of RFLP data from two natural populations, show that AIDAs allow one to objectively and simply identify basic patterns in the spatial distribution of haplotypes. These statistics, therefore, seem to be a useful tool both to explore the genetic structure of a population and to suggest hypotheses on the evolutionary processes that shaped the observed patterns.
Transcription termination signals in the nin region of bacteriophage lambda: identification of Rho-dependent termination regions.
Authors: Cheng S W , Court D L , Friedman D I 
Published: January 2021

Abstract
The approximately 3-kb nin region of bacteriophage lambda, located between genes P and Q contains transcription termination signals as well as 10 open reading frames. Deletions in the nin region frees phage growth from dependence on the lambda-encoded N-transcription antitermination system, conferring a Nin phenotype (N-independence). A subregion of nin, roc, is defined by a 1.9-kb deletion (delta roc) which partially frees lambda growth from the requirement for N antitermination. The roc region has strong transcription termination activity as assayed by a plasmid-based terminator testing system. We report the following features of the roc region: the biologically significant terminators in the roc region are Rho dependent, deletion analysis located the biologically significant termination signals to a 1.2 kb-segment of roc, and analysis of other deletions and point mutations in the roc region suggested at least two biologically significant regions of termination, tR3 (extending from bp 42020 to 42231) and tR4 (extending from bp 42630 to 42825).
Molecular analysis of lambda bio transducing phage produced by oxolinic acid-induced illegitimate recombination in vivo.
Authors: Shimizu H , Yamaguchi H , Ikeda H 
Published: January 2021

Abstract
To study the mechanism of DNA gyrase-mediated illegitimate recombination in Escherichia coli, we examined the formation of lambda Spi- phage during prophage induction. The frequency of Spi- phage was two to three orders of magnitude higher in the presence of oxolinic acid, an inhibitor of DNA gyrase A subunit, than in the absence of the drug, while it was very low in nalAr bacteria with the drug. RecA function is not required for the formation of these phages, indicating that this enhancement is not caused by the expression of SOS-controlled genes. Analyses of att region and recombination junctions of Spi- phages revealed that they have essentially the same structures as lambda bio transducing phages but are classified into two groups with respect to recombination sites. In the majority class of the transducing phages, there were not more than 3-bp homologies between the parental E. coli bio and lambda recombination sites. In the minority class of the transducing phages, on the other hand, 9-10-bp homologies were found between the parental recombination sites. These results suggested that oxolinic acid-induced illegitimate recombination takes place by two variants of a DNA gyrase-dependent mechanism.
Integrated maps of the chromosomes in Dictyostelium discoideum.
Authors: Loomis W F , Welker D , Hughes J , Maghakian D , Kuspa A 
Published: January 2021

Abstract
Detailed maps of the six chromosomes that carry the genes of Dictyostelium discoideum were constructed by correlating physically mapped regions with parasexually determined linkage groups. Chromosomally assigned regions were ordered and positioned by the pattern of altered fragment sizes seen in a set of restriction enzyme mediated integration-restriction fragment length polymorphism (REMI-RFLP) strains each harboring an inserted plasmid that carries sites recognized by NotI, SstI, SmaI, BglI and ApaI. These restriction enzymes were used to digest high molecular weight DNA prepared from more than 100 REMI-RFLP strains and the resulting fragments were separated and sized by pulsed-field gels. More than 150 gene probes were hybridized to blots of these gels and used to map the insertion sites relative to flanking restriction sites. In this way, we have been able to restriction map the 35 mb genome as well as determine the map position of more than 150 genes to with approximately 40 kb resolution. These maps provide a framework for subsequent refinement.
Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans.
Authors: Barnes T M , Kohara Y , Coulson A , Hekimi S 
Published: January 2021

Abstract
The genetic map of each Caenorhabditis elegans chromosome has a central gene cluster (less pronounced on the X chromosome) that contains most of the mutationally defined genes. Many linkage group termini also have clusters, though involving fewer loci. We examine the factors shaping the genetic map by analyzing the rate of recombination and gene density across the genome using the positions of cloned genes and random cDNA clones from the physical map. Each chromosome has a central gene-dense region (more diffuse on the X) with discrete boundaries, flanked by gene-poor regions. Only autosomes have reduced rates of recombination in these gene-dense regions. Cluster boundaries appear discrete also by recombination rate, and the boundaries defined by recombination rate and gene density mostly, but not always, coincide. Terminal clusters have greater gene densities than the adjoining arm but similar recombination rates. Thus, unlike in other species, most exchange in C. elegans occurs in gene-poor regions. The recombination rate across each cluster is constant and similar; and cluster size and gene number per chromosome are independent of the physical size of chromosomes. We propose a model of how this genome organization arose.
Developmental analysis of the ovarian tumor gene during Drosophila oogenesis.
Authors: Rodesch C , Geyer P K , Patton J S , Bae E , Nagoshi R N 
Published: January 2021

Abstract
Severe alleles of the ovarian tumor (otu) and ovo genes result in female sterility in Drosophila melanogaster, producing adult ovaries that completely lack egg chambers. We examined the developmental stage in which the agametic phenotype first becomes apparent. Germ cell development in embryos was studied using a strategy that allowed simultaneous labeling of pole cells with the determination of embryonic genotype. We found that ovo- or otu- XX embryonic germ cells were indistinguishable in number and morphology from those present in wild-type siblings. The effects of the mutations were not consistently manifested in the female germline until pupariation, and there was no evidence that either gene was required for germ cell viability at earlier stages of development. The requirement for otu function in the pupal and adult ovary is supported by temperature-shift experiments using a heat-inducible otu gene construct. We demonstrate that otu activity limited to prepupal stages was not sufficient to support oogenesis, while induction during the pupal and adult periods caused suppression of the otu mutant phenotype.
Mutations of zeste that mediate transvection are recessive enhancers of position-effect variegation in Drosophila melanogaster.
Authors: Judd B H 
Published: January 2021

Abstract
Evidence is presented demonstrating that mutations of zeste, particularly the null state, are strong recessive enhancers of position-effect variegation (PEV) for the white, roughest and Notch loci. The zeste locus encodes a DNA-binding protein that acts as a transcription factor and mediates transvection phenomena at several loci. Its involvement with these seemingly diverse phenomena suggests that the normal zeste product functions in the decondensation of chromatin. A model is presented proposing that zeste is important for opening and stabilizing domains of chromatin, a step in gene determination and the establishment of cell memory. It postulates that chromatin domains that have been structurally modified by chromosomal rearrangement or by insertion of transposable elements are particularly sensitive to the absence or modification of the zeste protein. Such a view unifies the role of zeste in transcription, transvection and PEV.
The tolkin gene is a tolloid/BMP-1 homologue that is essential for Drosophila development.
Authors: Finelli A L , Xie T , Bossie C A , Blackman R K , Padgett R W 
Published: January 2021

Abstract
The Drosophila decapentaplegic (dpp) gene, a member of the transforming growth factor beta superfamily of growth factors, is critical for specification of the embryonic dorsal-ventral axis, for proper formation of the midgut, and for formation of Drosophila adult structures. The Drosophila tolloid gene has been shown to genetically interact with dpp. The genetic interactions between tolloid and dpp suggests a model in which the tolloid protein participates in a complex containing the DPP ligand, its protease serving to activate DPP, either directly or indirectly. We report here the identification and cloning of another Drosophila member of the tolloid/bone morphogenic protein (BMP) 1 family, tolkin, which is located 700 bp 5' to tolloid. Its overall structure is like tolloid, with an N-terminal metalloprotease domain, five complement subcomponents C1r/C1s, Uegf, and Bmp1 (CUB) repeats and two epidermal growth factor (EGF) repeats. Its expression pattern overlaps that of tolloid and dpp in early embryos and diverges in later stages. In larval tissues, both tolloid and tolkin are expressed uniformly in the imaginal disks. In the brain, both tolloid and tolkin are expressed in the outer proliferation center, whereas tolkin has another stripe of expression near the outer proliferation center. Analysis of lethal mutations in tolkin indicate it is vital during larval and pupal stages. Analysis of its mutant phenotypes and expression patterns suggests that its functions may be mostly independent of tolloid and dpp.
Molecular organization and germinal instability of R-stippled maize.
Authors: Eggleston W B , Alleman M , Kermicle J L 
Published: January 2021

Abstract
The spotted seed allele R-stippled (R-st) is comprised of the following genetic components: strong seed color (Sc), inhibitor-of-R (I-R) and near-colorless seed (Nc). I-R is a mobile element that represses (Sc) expression irregularly. Germinal I-R losses produce progeny with fully colored seed. Southern blot analysis revealed four r-hybridizing segments in R-st and three, two or one in two sets of unequal crossover deletion products. By comparison to published reports of r gene structure, we maintain that each segment contains at least one r gene. The proximal r gene, Sc, confers strong seed color; the three distal r genes together produce near-colorless seed. R-st's seed spotting phenotype is correlated with the presence of a 3.3-kb insert in Sc identified as I-R. The level of the near-colorless phenotype is inversely correlated with the number of r genes present, suggesting involvement of a multiple copy silencing mechanism in their regulation. Phenotypic changes in R-st occurred primarily by unequal exchange between r genes. The locations of exchange positions showed a strong polarity, nearly all occurring in the 3' portions of the identified r genes.
Distribution of unlinked transpositions of a Ds element from a T-DNA locus on tomato chromosome 4.
Authors: Bríza J , Carroll B J , Klimyuk V I , Thomas C M , Jones D A , Jones J D 
Published: January 2021

Abstract
In maize, receptor sites for unlinked transpositions of Activator (Ac) elements are not distributed randomly. To test whether the same is true in tomato, the receptor sites for a Dissociation (Ds) element derived from Ac, were mapped for 26 transpositions unlinked to a donor T-DNA locus on chromosome 4. Four independent transposed Dss mapped to sites on chromosome 4 genetically unlinked to the donor T-DNA, consistent with a preference for transposition to unlinked sites on the same chromosome as opposed to sites on other chromosomes. There was little preference among the nondonor chromosomes, except perhaps for chromosome 2, which carried seven transposed Dss, but these could not be proven to be independent. However, these data, when combined with those from other studies in tomato examining the distribution of transposed Acs or Dss among nondonor chromosomes, suggest there may be absolute preferences for transposition irrespective of the chromosomal location of the donor site. If true, transposition to nondonor chromosomes in tomato would differ from that in maize, where the preference seems to be determined by the spatial arrangement of chromosomes in the interphase nucleus. The tomato lines carrying Ds elements at known locations are available for targeted transposon tagging experiments.
Enhancers of glp-1, a gene required for cell-signaling in Caenorhabditis elegans, define a set of genes required for germline development.
Authors: Qiao L , Lissemore J L , Shu P , Smardon A , Gelber M B , Maine E M 
Published: January 2021

Abstract
The distal tip cell (DTC) regulates the proliferation or differentiation choice in the Caenorhabditis elegans germline by an inductive mechanism. Cell signaling requires a putative receptor in the germline, encoded b y the glp-1 gene, and a putative signal from the DTC, encoded by the lag-2 gene. Both glp-1 and lag-2 belong to multigene gene families whose members are essential for cell signaling during development of various tissues in insects and vertebrates as well as C. elegans. Relatively little is known about how these pathways regulate cell fate choice. To identify additional genes involved in the glp-1 signaling pathway, we carried out screens for genetic enhancers of glp-1. We recovered mutations in five new genes, named ego (enhancer of glp-1), and two previously identified genes, lag-1 and glp-4, that strongly enhance a weak glp-1 loss-of-function phenotype in the germline. Ego mutations cause multiple phenotypes consistent with the idea that gene activity is required for more than one aspect of germline and, in some cases, somatic development. Based on genetic experiments, glp-1 appears to act upstream of ego-1 and ego-3. We discuss the possible functional relationships among these genes in light of their phenotypes and interactions with glp-1.
Evidence for an inducible repair-recombination system in the female germ line of Drosophila melanogaster. II. Differential sensitivity to gamma rays.
Authors: Laurençon A , Bregliano J C 
Published: January 2021

Abstract
In a previous paper, we reported that the reactivity level, which regulates the frequency of transposition of I factor, a LINE element-like retrotransposon, is enhanced by the same agents that induce the SOS response in Escherichia coli. In this report, we describe experimental evidence that, for identical genotypes, the reactivity levels correlate with the sensitivity of oogenesis to gamma rays, measured by the number of eggs laid and by frequency of dominant lethals. This strongly supports the hypothesis that the reactivity level is one manifestation of an inducible DNA repair system taking place in the female germ line of Drosophila melanogaster. The implications of this finding for the understanding of the regulation of I factor are discussed and some other possible biological roles of this system are outlined.
Molecular analysis of scabrous mutant alleles from Drosophila melanogaster indicates a secreted protein with two functional domains.
Authors: Hu X , Lee E C , Baker N E 
Published: January 2021

Abstract
Mutations at the scabrous locus (sca) affect cell-cell signaling during neural development. Twenty-one mutant alleles of scabrous have been analyzed. Many synthesize no sca protein. In others, a defective protein is arrested intracellularly. Two mutants in which protein is not arrested must affect sca protein function outside the cell. Both affect the fibrinogen related domain (FReD), a 200-amino acid segment conserved in fibrinogen, tenascins, and other proteins. In fibrinogen, this region is involved in protein interactions and is altered in human mutations affecting blood clotting. In sca(UM2), an invariant Asp residue is replaced by Asn. In sca(MSKF) allele has dominant negative properties, indicating that the truncated amino-terminal portion interferes with the function of so me other gene product. These mutations show that the conserved FReD is essential for wild-type sca function, but suggest that the amino-terminal domain also interacts with other proteins, but other neural mutations were without effect. Models for the role of a two-domain protein in neural development are discussed.
Molecular mapping of wheat: major genes and rearrangements in homoeologous groups 4, 5, and 7.
Authors: Nelson J C , Sorrells M E , Van Deynze A E , Lu Y H , Atkinson M , Bernard M , Leroy P , Faris J D , Anderson J A 
Published: January 2021

Abstract
A molecular-marker linkage map of hexaploid wheat (Triticum aestivum L. em. Thell) provides a framework for integration with teh classical genetic map and a record of the chromosomal rearrangements involved in the evolution of this crop species. We have constructed restriction fragment length polymorphism (RFLP) maps of the A-, B-, and D-genome chromosomes of homoeologous groups 4, 5, and 7 of wheat using 114 F7 lines from a synthetic X cultivated wheat cross and clones from 10 DNA libraries. Chromosomal breakpoints for known ancestral reciprocal translocations involving these chromosomes and for a known pericentric inversion on chromosome 4A were localized by linkage and aneuploid analysis. Known genes mapped include the major vernalization genes Vrn1 and Vrn3 on chromosome arms 5AL and 5DL, the red-coleoptile gene Rc1 on 7AS, and presumptively the leaf-rust (Puccinia recondita f.sp. tritici) resistance gene Lr34 on 7DS and the kernel-hardness gene Ha on 5DS. RFLP markers previously obtained for powdery-mildew (Blumeria graminis f.sp. tritici) resistance genes Pm2 and Pm1 were localized on chromosome arms 5DS and 7AL.
Methodology and accuracy of estimation of quantitative trait loci parameters in a half-sib design using maximum likelihood.
Authors: Mackinnon M J , Weller J I 
Published: January 2021

Abstract
Maximum likelihood methods were developed for estimation of the six parameters relating to a marker-linked quantitative trait locus (QTL) segregating in a half-sib design, namely the QTL additive effect, the QTL dominance effect, the population mean, recombination between the marker and the QTL, the population frequency of the QTL alleles, and the within-family residual variance. The method was tested on simulated stochastic data with various family structures under two genetic models. A method for predicting the expected value of the likelihood was also derived and used to predict the lower bound sampling errors of the parameter estimates and the correlations between them. It was found that standard errors and confidence intervals were smallest for the population mean and variance, intermediate for QTL effects and allele frequency, and highest for recombination rate. Correlations among standard errors of the parameter estimates were generally low except for a strong negative correlation (r = -0.9) between the QTL's dominance effect and the population mean, and medium positive and negative correlations between the QTL's additive effect and, respectively, recombination rate (r = 0.5) and residual variance (r = -0.6). The implications for experimental design and method of analysis on power and accuracy of marker-QTL linkage experiments were discussed.
The ecdysone-inducible Broad-complex and E74 early genes interact to regulate target gene transcription and Drosophila metamorphosis.
Authors: Fletcher J C , Thummel C S 
Published: January 2021

Abstract
Pulses of the steroid hormone ecdysone initiate Drosophila metamorphosis by inducing widespread changes in gene expression. The Broad-Complex (BR-C) and E74 are induced directly by ecdysone and encode families of transcription factors that regulate ecdysone primary- and secondary-response genes. Genetic analyses have revealed that mutations in the BR-C and E74 are lethal during metamorphosis and that these mutations cause some similar lethal phenotypes and alterations in secondary-response gene transcription. To examine whether the BR-C and E74 function together during development, we have combined representative alleles from each BR-C and E74 complementation group. Analysis of the morphological and molecular phenotypes of the double-mutant animals reveals that BR-C and E74 alleles act together to produce both novel and synergistic effects. We find that the BR-C and E74 share functions in puparium formation, pupation and early gene induction. In addition, our evidence suggests that the BR-C and E74 transcription factors may directly interact to regulate the expression of salivary gland glue and late genes. This data is consistent with current models which propose that combinations of ecdysone primary-response genes regulate common morphogenetic pathways during insect metamorphosis.