An Analysis of Polygenes Affecting Wing Shape on Chromosome 2 inDrosophila melanogaster

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1045-1057 ◽  
Author(s):  
Kenneth Weber ◽  
Robert Eisman ◽  
Shawn Higgins ◽  
Lisa Morey ◽  
April Patty ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
Genetic Effects ◽  
Wing Shape ◽  
Pleiotropic Effects ◽  
Phenotypic Variance ◽  
Chromosome 2 ◽  
Additive Effects ◽  
Chromosome Segments ◽  
Small Additive

AbstractGenetic effects on an index of wing shape on chromosome 2 of Drosophila melanogaster were mapped using isogenic recombinants with transposable element markers. At least 10 genes with small additive effects are dispersed evenly along the chromosome. Many interactions exist, with only small net effects in homozygous recombinants and little effect on phenotypic variance. Heterozygous chromosome segments show almost no dominance. Pleiotropic effects on leg shape are only minor. At first view, wing shape genes form a rather homogeneous class, but certain complexities remain unresolved.

scholarly journals An Analysis of Polygenes Affecting Wing Shape on Chromosome 3 in Drosophila melanogaster

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 773-786 ◽  
Author(s):  
Kenneth Weber ◽  
Robert Eisman ◽  
Lisa Morey ◽  
April Patty ◽  
Joshua Sparks ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Wing Shape ◽  
The Other ◽  
Chromosome 3 ◽  
Additive Effects ◽  
Data Set ◽  
The Third ◽  
Isogenic Lines ◽  
Negative Interactions

AbstractLoci on the third chromosome of Drosophila melanogaster that affect an index of wing shape were mapped, using recombinant isogenic lines, with transposable elements as markers. Many genes with small subequal effects are dispersed along the whole chromosome. Their alleles act nearly additively in heterozygotes. They have small correlated effects on leg shape, but no detectable effects on halteres. Small negative net interactions occur over most of the chromosome. The data set of 519 recombinant isogenic lines can be explained reasonably well by two models. One model posits an indefinitely large number of loci with no interactions. The other model posits 11 loci with additive effects whose sum equals the total phenotypic range and with large positive and negative interactions that nearly cancel each other.

scholarly journals Using the P{wHy} Hybrid Transposable Element to Disrupt Genes in Region 54D-55B in Drosophila melanogaster

Genetics ◽  
2002 ◽  
Vol 162 (1) ◽  
pp. 165-176 ◽  
Author(s):  
Stephanie E Mohr ◽  
William M Gelbart
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
Model Organism ◽  
Drosophila Genome ◽  
Chromosome 2 ◽  
Lethal Mutations ◽  
F Region ◽  
Nested Sets ◽  
Mutant Phenotypes ◽  
Improved Methods

Abstract Understanding the function of each gene in the genome of a model organism such as Drosophila melanogaster is an important goal. The development of improved methods for uncovering the mutant phenotypes of specific genes can accelerate achievement of this goal. The P{wHy} hybrid transposable element can be used to generate nested sets of precisely mapped deletions in a given region of the Drosophila genome. Here we use the P{wHy} method to generate overlapping, molecularly defined deletions from a set of three P{wHy} insertions in the 54E-F region of chromosome 2. Deletions that span a total of 0.5 Mb were identified and molecularly mapped precisely. Using overlapping deletions, the mutant phenotypes of nine previously uncharacterized genes in a 101-kb region were determined, including identification of new loci required for viability and female fertility. In addition, the deletions were used to molecularly map previously isolated lethal mutations. Thus, the P{wHy} method provides an efficient method for systematically determining the phenotypes of genes in a given region of the fly genome.

scholarly journals Somatic reversion of P transposable element insertion mutations in the singed locus of Drosophila melanogaster requiring specific P insertions and a trans- acting factor

1989 ◽  
Vol 54 (2) ◽  
pp. 101-112 ◽  
Author(s):  
John F. Y. Brookfield ◽  
Alan P. Lewis
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
Maternal Effect ◽  
P Element ◽  
Chromosome 2 ◽  
Restriction Maps ◽  
Element Insertion ◽  
Somatic Reversion ◽  
P Transposable Element ◽  
Insertion Mutations

SummaryDestabilization in somatic cells of P-element insertions in the X-linked singed gene of Drosophila melanogaster has been studied. We have shown that some but not all unstable P-element insertions in singed can form mosaics. The cause of this variation is not clear from studies of the restriction maps of the mutations tested. The transposable element movements occur early in development and require, in addition to an appropriate P-element insertion in singed, a trans-acting maternal effect component. Movements appear to occur preferentially in attached-X stocks. However, the maternal effect component maps to the central region of chromosome 2.

scholarly journals hobo enhancer trapping mutagenesis in Drosophila reveals an insertion specificity different from P elements.

Genetics ◽  
1993 ◽  
Vol 135 (4) ◽  
pp. 1063-1076 ◽  
Author(s):  
D Smith ◽  
J Wohlgemuth ◽  
B R Calvi ◽  
I Franklin ◽  
W M Gelbart
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
Enhancer Trap ◽  
P Element ◽  
Present Evidence ◽  
P Elements ◽  
Element Insertion ◽  
Enhancer Trapping ◽  
Indispensable Tool

Abstract P element enhancer trapping has become an indispensable tool in the analysis of the Drosophila melanogaster genome. However, there is great variation in the mutability of loci by these elements such that some loci are relatively refractory to insertion. We have developed the hobo transposable element for use in enhancer trapping and we describe the results of a hobo enhancer trap screen. In addition, we present evidence that a hobo enhancer trap element has a pattern of insertion into the genome that is different from the distribution of P elements in the available database. Hence, hobo insertion may facilitate access to genes resistant to P element insertion.

scholarly journals Genomic prediction with non-additive effects in beef cattle: stability of variance component and genetic effect estimates against population size

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Akio Onogi ◽  
Toshio Watanabe ◽  
Atsushi Ogino ◽  
Kazuhito Kurogi ◽  
Kenji Togashi
Keyword(s):  
Population Size ◽  
Genomic Prediction ◽  
Variance Components ◽  
Variance Component ◽  
Predictive Accuracy ◽  
Genetic Effect ◽  
Genetic Effects ◽  
Additive Effects ◽  
Additive Variance ◽  
Additive Genetic Effects

Abstract Background Genomic prediction is now an essential technology for genetic improvement in animal and plant breeding. Whereas emphasis has been placed on predicting the breeding values, the prediction of non-additive genetic effects has also been of interest. In this study, we assessed the potential of genomic prediction using non-additive effects for phenotypic prediction in Japanese Black, a beef cattle breed. In addition, we examined the stability of variance component and genetic effect estimates against population size by subsampling with different sample sizes. Results Records of six carcass traits, namely, carcass weight, rib eye area, rib thickness, subcutaneous fat thickness, yield rate and beef marbling score, for 9850 animals were used for analyses. As the non-additive genetic effects, dominance, additive-by-additive, additive-by-dominance and dominance-by-dominance effects were considered. The covariance structures of these genetic effects were defined using genome-wide SNPs. Using single-trait animal models with different combinations of genetic effects, it was found that 12.6–19.5 % of phenotypic variance were occupied by the additive-by-additive variance, whereas little dominance variance was observed. In cross-validation, adding the additive-by-additive effects had little influence on predictive accuracy and bias. Subsampling analyses showed that estimation of the additive-by-additive effects was highly variable when phenotypes were not available. On the other hand, the estimates of the additive-by-additive variance components were less affected by reduction of the population size. Conclusions The six carcass traits of Japanese Black cattle showed moderate or relatively high levels of additive-by-additive variance components, although incorporating the additive-by-additive effects did not improve the predictive accuracy. Subsampling analysis suggested that estimation of the additive-by-additive effects was highly reliant on the phenotypic values of the animals to be estimated, as supported by low off-diagonal values of the relationship matrix. On the other hand, estimates of the additive-by-additive variance components were relatively stable against reduction of the population size compared with the estimates of the corresponding genetic effects.

scholarly journals A NOTE ON THE MATERNAL EFFECT MUTANTS DAUGHTERLESS AND ABNORMAL OOCYTE IN DROSOPHILA MELANOGASTER

Genetics ◽  
1973 ◽  
Vol 73 (1) ◽  
pp. 73-86
Author(s):  
Arthur P Mange ◽  
L Sandler
Keyword(s):  
Drosophila Melanogaster ◽  
Maternal Effect ◽  
Sex Chromosome ◽  
Chromosome 2 ◽  
Dominant Marker ◽  
Enhancing Effect ◽  
X Irradiation ◽  
The Right ◽  
Chromosome Breakpoint ◽  
Special Region

ABSTRACT Two deficiencies for, and a dominant enhancer of, the second chromosome maternal effect mutant, "daughterless" (da), were induced with X-irradiation. Their properties were studied with respect to both da and the linked maternal effect mutant, "abnormal oocyte" (abo), with the following conclusions. (1) The most probable map positions of da and abo are: J–½–da–2½–abo, where J is a dominant marker located at 41 on the standard map. (2) The da locus is in bands 31CD-F on the polytene chromosome map; abo is to the right of 32A. (3) Because homozygous da individuals survive while individuals carrying da and a deficiency for da are lethal, it is concluded that da is hypomorphic. (4) From a weak da-like maternal effect in heterozygous da females induced by an "Enhancer of da," we have confirmed a previous report that (a) the amount of sex chromosome heterochromatin contributed by the father can influence the severity of the da maternal effect, and (b) the sex chromosome heterochromatin which influences the da effect is different from that which influences the abo effect. (5) The possibility that da and abo are in a special region of chromosome 2 concerned with the regulation of sex chromosome heterochromatin is strengthened by the observation that the Enhancer of da appears to rescue abnormal eggs produced by homozygous abo mothers. (6) The Enhancer of da is a translocation between chromosomes 2 and 3 with the second chromosome breakpoint in the basal heterochromatin; because the enhancing effect maps in this region of chromosome 2, it is possible that autosomal, as well as sex chromosomal, heterochromatin interacts with da and abo.

scholarly journals Recombinogenic Effects of Suppressors of Position-Effect Variegation in Drosophila

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 609-621
Author(s):  
Thomas Westphal ◽  
Gunter Reuter
Keyword(s):  
Chromatin Structure ◽  
Position Effect ◽  
Heterochromatic Region ◽  
Crossing Over ◽  
Position Effect Variegation ◽  
Chromosome 2 ◽  
Additive Effects ◽  
Suppressor Mutations ◽  
Effect Variegation ◽  
Meiotic Nondisjunction

Abstract Compact chromatin structure, induction of gene silencing in position-effect variegation (PEV), and crossing-over suppression are typical features of heterochromatin. To identify genes affecting crossing-over suppression by heterochromatin we tested PEV suppressor mutations for their effects on crossing over in pericentromeric regions of Drosophila autosomes. From the 46 mutations (28 loci) studied, 16 Su(var) mutations of the nine genes Su(var)2-1, Su(var)2-2, Su(var)2-5, Su(var)2-10, Su(var)2-14, Su(var) 2-15, Su(var)3-3, Su(var)3-7, and Su(var)3-9 significantly increase in heterozygotes or by additive effects in double and triple heterozygotes crossing over in the ri-pp region of chromosome 3. Su(var)2-201 and Su(var) 2-1401 display the strongest recombinogenic effects and were also shown to enhance recombination within the light-rolled heterochromatic region of chromosome 2. The dominant recombinogenic effects of Su(var) mutations are most pronounced in proximal euchromatin and are accompanied with significant reduction of meiotic nondisjunction. Our data suggest that crossing-over suppression by heterochromatin is controlled at chromatin structure as well as illustrate the possible effects of heterochromatin on total crossing-over frequencies in the genome.

SOME EFFECTS ON FRUIT SIZE OF CHROMOSOME 2 OF THE TOMATO

1965 ◽  
Vol 43 (1) ◽  
pp. 137-146
Author(s):  
L. Butler
Keyword(s):  
Linkage Map ◽  
Fruit Size ◽  
Cell Number ◽  
Major Effect ◽  
Fruit Weight ◽  
Pleiotropic Effects ◽  
Chromosome 2 ◽  
Small Fruit ◽  
Number Of Cells

Fruit weights taken from two F2's of 1500 plants indicated that the genes d p o s Lc dil and suf all affect fruit weight. The recessive alleles, except suf and Lc, were associated with small fruit size. The data were analyzed to determine whether this association was the result of linkage or pleiotropic effects. The major effect occurred in the o region, which is some 44 units from the centromere of chromosome 2. The o gene makes the genes oval or pear-shaped instead of spherical, and it is shown that when the locule wall of a spherical fruit and an oval fruit are composed of the same number of cells, the spherical fruit is always heavier. Since cell number is the inherited unit of fruit size, then o is always associated with small size. A gene controlling number of locules, which affects fruit size, is also located in this section of the chromosome. The genes d and s, which are at opposite ends of the present linkage map, both appear to be linked with fruit size genes. It is suggested that these size genes lie in the hetero-chromatin which is adjacent to both ends of the linkage map. The genes dil and suf, which were produced by radiation of the same variety, appear to have pleiotropic effects on fruit size; suf increasing, and dil decreasing fruit size.

scholarly journals Genome-wide single nucleotide polymorphism heritability of nicotine dependence as a multidimensional phenotype

2016 ◽  
Vol 46 (10) ◽  
pp. 2059-2069 ◽  
Author(s):  
L. C. Bidwell ◽  
R. H. C. Palmer ◽  
L. Brick ◽  
J. E. McGeary ◽  
V. S. Knopik
Keyword(s):  
Nicotine Dependence ◽  
Twin Studies ◽  
Factor Models ◽  
Genetic Effects ◽  
European Ancestry ◽  
Relationship Matrix ◽  
Phenotypic Variance ◽  
Single Nucleotide ◽  
Common Genetic Variants ◽  
Dsm Iv

BackgroundHeritability estimates from twin studies of the multi-faceted phenotype of nicotine dependence (ND) range from moderate to high (31–60%), but vary substantially based on the specific ND-related construct examined. The current study estimated the aggregate role of common genetic variants on key ND constructs.MethodGenomic-relationship-matrix restricted maximum likelihood (GREML) was used to decompose phenotypic variance across multiple ND indices using 796 125 polymorphisms from 2346 unrelated ‘lifetime ever smokers’ of European ancestry. Measures included DSM-IV ND and Fagerström Test for Nicotine Dependence (FTND) summary measures and constituent constructs (e.g. withdrawal severity, tolerance, heaviness of smoking and time spent smoking). Exploratory and confirmatory factor models were used to describe the covariance structure across ND measures; resulting factor(s) were the subject(s) of GREML analyses.ResultsFactor models indicated highly correlated DSM-IV and FTND factors for ND (0.545, 95% confidence interval 0.50–0.60) that could be represented as a higher-order factor (NIC DEP). Additive genetic influence on NIC DEP was 33% (s.e. = 0.14, p = 0.009). Post-hoc analyses indicated moderate genetic effects on the DSM-IV (34%, s.e. = 0.14, p = 0.008) and FTND (26%, s.e. = 0.14, p = 0.032) factors, both of which were influenced by the same genetic effects (rG-SNP = 1.00, s.e. = 0.09, p < 0.00001).ConclusionsOverall, common single nucleotide polymorphisms accounted for a large proportion of the genetic influences on ND-related phenotypes that have been observed in twin studies. Genetic contributions across distinct ND scales were largely influenced by shared genetic factors.

A cDNA from Drosophila melanogaster encodes a lamin C-like intermediate filament protein

1993 ◽  
Vol 104 (4) ◽  
pp. 1263-1272 ◽  
Author(s):  
C.A. Bossie ◽  
M.M. Sanders
Keyword(s):  
Drosophila Melanogaster ◽  
Intermediate Filament ◽  
Blot Analysis ◽  
Polytene Chromosomes ◽  
Intermediate Filament Protein ◽  
Chromosome 2 ◽  
Cross Hybridization ◽  
Intermediate Filament Proteins ◽  
Nuclear Lamins ◽  
Filament Protein

A novel intermediate filament cDNA, pG-IF, has been isolated from a Drosophila melanogaster embryonic expression library screened with a polyclonal antiserum produced against a 46 kDa cytoskeletal protein isolated from Kc cells. This 46 kDa protein is known to be immunologically related to vertebrate intermediate filament proteins. The screen resulted in the isolation of four different cDNA groups. Of these, one has been identified as the previously characterized Drosophila nuclear lamin cDNA, Dm0, and a second, pG-IF, demonstrates homology to Dm0 by cross hybridization on Southern blots. DNA sequence analysis reveals that pG-IF encodes a newly identified intermediate filament protein in Drosophila. Its nucleotide sequence is highly homologous to nuclear lamins with lower homology to cytoplasmic intermediate filament proteins. pG-IF predicts a protein of 621 amino acids with a predicted molecular mass of 69,855 daltons. In vitro transcription and translation of pG-IF yielded a protein with a SDS-PAGE estimated molecular weight of approximately 70 kDa. It contains sequence principles characteristic of class V intermediate filament proteins. Its near neutral pI (6.83) and the lack of a terminal CaaX motif suggests that it may represent a lamin C subtype in Drosophila. In situ hybridization to polytene chromosomes detects one band of hybridization on the right arm of chromosome 2 at or near 51A. This in conjunction with Southern blot analysis of various genomic digests suggests one or more closely placed genes while Northern blot analysis detects two messages in Kc cells.

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